园艺-分子生物合辑Horticulture — Genetics

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Domestication and breeding changed tomato fruit transcriptome

LIU Dan, YANG Liang, ZHANG Jin-zhe, ZHU Guang-tao, Lü Hong-jun, Lü Ya-qing, WANG Yan-ling, CAO Xue, SUN Tian-shu, HUANG San-wen, WU Yao-yao

2020, 19 (1): 120-132. DOI: 10.1016/S2095-3119(19)62824-8

Abstract （192） PDF in ScienceDirect

Tomato (Solanum lycopersicum) stress resistance and fruit total soluble solid (TSS) content have changed dramatically during selective breeding, and transcriptome variation has played a critical role in this rewiring. However, the single tomato reference genome impedes characterization of whole-transcriptome variation during domestication and breeding at the population level. Here, we constructed a pan-transcriptome of orange-stage tomato fruit, and investigated global expression presence/absence variation (ePAV) and differentially expressed genes (DEGs) based on RNA sequencing (RNA-seq) data from 399 tomato accessions. A total of 7 181 genes absent from the reference genome were identified, 6 122 of which were ePAV genes during tomato domestication and breeding including resistance genes such as late blight resistance gene PIM_DN29746_c0_g3_i1 and peroxidase P7-like gene PIM_DN30274_c0_g2_i1. In addition, 3 629 genes were significantly differentially expressed during tomato selection, among which 19 genes were associated with the reduced fruit TSS content of modern tomato cultivars, including LIN5, TIV1, and seven novel sugar transporter genes. Our results indicate that natural and artificial selection greatly shaped the tomato transcriptome, thereby altering the fruit TSS content and resistance to abiotic and biotic stresses.

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The MADS-box transcription factor CmAGL11 modulates somatic embryogenesis in Chinese chestnut (Castanea mollissima Blume)

GAO Yue-rong, SUN Jia-chen, SUN Zhi-lin, XING Yu, ZHANG Qing, FANG Ke-feng, CAO Qing-qin, QIN Ling

2020, 19 (4): 1033-1043. DOI: 10.1016/S2095-3119(20)63157-4

Abstract （93） PDF in ScienceDirect

Somatic embryogenesis (SE) is an effective approach of in vitro regeneration that depends on plant cell totipotency. However, largely unknown of molecular mechanisms of SE in woody plants such as Chinese chestnut (Castanea mollissima Blume), limits the development of the woody plant industry. Here, we report the MADS-box transcription factor CmAGL11 in Chinese chestnut. CmAGL11 transcripts specifically accumulated in the globular embryo. Overexpression of CmAGL11 in chestnut callus enhanced its SE capacity, and the development of somatic embryos occurred significantly faster than in the control. RNA-seq results showed that CmAGL11 affects the expression of several genes related to the gibberellin, auxin, and ethylene pathways. Moreover, the analysis of DNA methylation status indicated that the promoter methylation plays a role in regulation of CmAGL11 expression during SE. Our results demonstrated that CmAGL11 plays an important role in the SE process in Chinese chestnut, possibly by regulating gibberellin, auxin, and ethylene pathways. It will help establish an efficient platform to accelerate genetic improvement and germplasm innovation in Chinese chestnut.

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Genome-wide identification and expression analysis of anthocyanin biosynthetic genes in Brassica juncea

ZHANG Da-wei, LIU Li-li, ZHOU Ding-gang, LIU Xian-jun, LIU Zhong-song, YAN Ming-li

2020, 19 (5): 1250-1260. DOI: 10.1016/S2095-3119(20)63172-0

Abstract （91） PDF in ScienceDirect

Anthocyanins confer the wide range of colors for plants and also play beneficial health roles as potentially protective factors against heart disease and cancer. Brassica juncea is cultivated as an edible oil resource and vegetable crop worldwide, thus elucidating the anthocyanin biosynthetic pathway would be helpful to improve the nutritional quality of Brassica juncea through the breeding and cultivating of high anthocyanin content varieties. Herein, 129 genes in B. juncea were identified as orthologs of 41 anthocyanin biosynthetic genes (ABGs) in Arabidopsis thaliana by comparative genomic analyses. The B. juncea ABGs have expanded by whole genome triplication and subsequent allopolyploidizatoin, but lost mainly during the whole genome triplication between B. rapa/B. nigra and A. thaliana, rather than the allopolyploidization process between B. juncea and B. rapa/B. nigra, leading to different copy numbers retention of A. thaliana homologous genes. Although the overall expansion levels ABGs were similar to the whole genome, more negative regulatory genes were retained in the anthocyanin biosynthesis regulatory system. Transcriptional analysis of B. juncea with different anthocyanin accumulation showed that BjDFR, BjTT19, BjTT8 are significantly up-regulated in plants with purple leaves as compared with green leaves. The overexpression of BjTT8 and these target genes which were involved in late anthocyanin biosynthesis and transport might account for increasing levels of anthocyanin accumulation in purple leaves. Our results could promote the understanding of the genetic mechanism of anthocyanin biosynthesis in B. juncea.

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Genome-wide identification and expression analysis of asparagine synthetase family in apple

YUAN Xi-sen, YU Zi-peng, LIU Lin, XU Yang, ZHANG Lei, HAN De-guo, ZHANG Shi-zhong

2020, 19 (5): 1261-1273. DOI: 10.1016/S2095-3119(20)63171-9

Abstract （73） PDF in ScienceDirect

Asparagine is an efficient nitrogen transport and storage carrier. Asparagine synthesis occurs by the amination of aspartate which is catalyzed by asparagine synthetase (ASN) in plants. Complete genome-wide analysis and classifications of the ASN gene family have recently been reported in different plants. However, systematic analysis and expression profiles of these genes have not been performed in apple (Malus domestica). Here, a comprehensive bioinformatics approach was applied to identify MdASNs in apple. Then, plant phylogenetic tree, chromosome location, conserved protein motif, gene structure, and expression pattern of MdASNs were analyzed. Five members were identified and distributed on 4 chromosomes with conserved GATase-7 and ASN domains. Expression analysis indicated that all MdASNs mRNA accumulated at the highest level in reproductive organs, namely flowers or fruits, which may be associated with the redistribution of free amino acids in plant metabolic organs and reservoirs. Additionally, most of MdASNs were dramatically up-regulated under various nitrogen supplies, especially in the aboveground part. Taken together, MdASNs may be assigned to be responsible for the nitrogen metabolism and asparagine synthesis in apple.

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Genome-wide identification and expression analysis of StPP2C gene family in response to multiple stresses in potato (Solanum tuberosum L.)

WANG Yi-fan, LIAO Yu-qiu, WANG Ya-peng, YANG Jiang-wei, ZHANG Ning, SI Huai-jun

2020, 19 (6): 1609-1624. DOI: 10.1016/S2095-3119(20)63181-1

Abstract （115） PDF in ScienceDirect

The plant protein phosphatase 2Cs (PP2Cs) play an essential role in response to stress and abscisic acid (ABA) signaling pathway. However, to date, no systemic characterization of the PP2Cs has yet been conducted in potato (Solanum tuberosum L.). In the study, a comprehensive research was performed on genome-wide identification and expression analysis of StPP2C genes in potato. A total of 78 potato StPP2C genes were identified based on specific structure of PP2C domain, which were distributed across 11 out of 12 potato chromosomes and divided into 12 (A–L) phylogenetic branches. The result from gene duplication analysis showed that 14 StPP2Cs were involved in gene tandem duplication and 8 genes formed fragment duplication events, which indicated that both tandem and fragment duplication contributed to the expansion of the gene family in evolution. Exon–intron structural analysis showed that they had a wide range of exon numbers. Analysis of protein conservative motif demonstrated that StPP2Cs contained more similar motif structures in the same phylogenetic branches. The cis-elements in StPP2C gene promoter regions were mainly responded to light, phytohormone and abiotic stress. Most of them exhibited tissue-specific expression patterns, and some members could differentially express under abiotic stress. The evidence suggested that StPP2C genes may contribute to different functions in several physiological stress and environmental stress conditions. This study could provide new insights to further investigate StPP2C functional characteristics responding to various stresses in potato.

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What are the differences in yield formation among two cucumber (Cucumis sativus L.) cultivars and their F₁ hybrid?

WANG Xiu-juan, KANG Meng-zhen, FAN Xing-rong, YANG Li-li, ZHANG Bao-gui, HUANG San-wen, Philippe DE REFFYE, WANG Fei-yue

2020, 19 (7): 1789-1801. DOI: 10.1016/S2095-3119(20)63218-X

Abstract （92） PDF in ScienceDirect

To elucidate the mechanisms underlying the differences in yield formation among two parents (P₁ and P₂) and their F₁ hybrid of cucumber, biomass production and whole source–sink dynamics were analyzed using a functional–structural plant model (FSPM) that simulates both the number and size of individual organs. Observations of plant development and organ biomass were recorded throughout the growth periods of the plants. The GreenLab Model was used to analyze the differences in fruit setting, organ expansion, biomass production and biomass allocation. The source–sink parameters were estimated from the experimental measurements. Moreover, a particle swarm optimization algorithm (PSO) was applied to analyze whether the fruit setting is related to the source–sink ratio. The results showed that the internal source–sink ratio increased in the vegetative stage and reached a peak until the first fruit setting. The high yield of hybrid F₁ is the compound result of both fruit setting and the internal source–sink ratio. The optimization results also revealed that the incremental changes in fruit weight result from the increases in sink strength and proportion of plant biomass allocation for fruits. The model-aided analysis revealed that heterosis is a result of a delicate compromise between fruit setting and fruit sink strength. The organ-level model may provide a computational approach to define the target of breeding by combination with a genetic model.

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Induction and characterization of polyploids from seeds of Rhododendron fortunei Lindl.

MO Lan, CHEN Jun-hao, CHEN Fei, XU Qiang-wei, TONG Zai-kang, HUANG Hua-hong, DONG Ren-hui, LOU Xiong-zhen, LIN Er-pei

2020, 19 (8): 2016-2026. DOI: 10.1016/S2095-3119(20)63210-5

Abstract （107） PDF in ScienceDirect

Most Rhododendron species are ornamental flowering species widely distributed in Asia, North America, and West Europe. Rhododendron fortunei, one of the endemic Rhododendron species in China, has beautiful flowers with bright colors and is being exploited to meet the needs of the flower market. Polyploid plants usually show superiority in growth, disease resistance, and adaption over their diploid relatives. Here, we report the first case of polyploid induction in R. fortunei. In order to induce polyploidy in R. fortunei, germinating seeds were treated with different concentrations of oryzalin for 16 h. By evaluating ploidy level with flow cytometry, a total of 34 polyploid R. fortunei lines, including 27 tetraploid lines and seven octoploid lines, were obtained. A comparison of treatments indicated that 7.5 mg L^–1 oryzalin was the optimal concentration for polyploid induction in seeds of R. fortunei. Compared with diploid plants, tetraploid and octoploid plants exhibited slower growth rates and had thicker and rounder curled leaves with more leaf epidermal hairs. Moreover, larger stomata at lower density were also observed in the leaves of polyploid plants. Chlorophyll contents were also significantly increased in polyploid plants, which leads to a darker green leaf color. Both small and large individuals exhibiting the same characteristics were observed among the obtained tetraploid plants. Overall, our study establishes a feasible method for polyploid induction in R. fortunei, thus providing a basis for breeding new R. fortunei varieties.

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Overexpression of StCYS1 gene enhances tolerance to salt stress in the transgenic potato (Solanum tuberosum L.) plant

LIU Min-min, LI Ya-lun, LI Guang-cun, DONG Tian-tian, LIU Shi-yang, LIU Pei, WANG Qing-guo

2020, 19 (9): 2239-2246. DOI: 10.1016/S2095-3119(20)63262-2

Abstract （89） PDF in ScienceDirect

Salt stress seriously restricts the growth and yield of potatoes. Plant cystatins are vital players in biotic stress and development, however, their roles in salt stress resistance remain elusive. Here, we report that StCYS1 positively regulates salt tolerance in potato plants. An in vitro biochemical test demonstrated that StCYS1 is a bona fide cystatin. Overexpression of StCYS1 in both Escherichia coli and potato plants significantly increased their resistance to high salinity. Further analysis revealed that the transgenic plants accumulated more proline and chlorophyll under salt stress conditions. Moreover, the transgenic plants displayed higher H₂O₂ scavenging capability and cell membrane integrity compared with wild-type potato. These results demonstrate that StCYS1 is closely correlated with salt stress and its overaccumulation can substantially enhance salt stress resistance.

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Endogenous phytohormones and the expression of flowering genes synergistically induce flowering in loquat

CHI Zhuo-heng, WANG Yong-qing, DENG Qun-xian, ZHANG Hui, PAN Cui-ping, YANG Zhi-wu

2020, 19 (9): 2247-2256. DOI: 10.1016/S2095-3119(20)63246-4

Abstract （80） PDF in ScienceDirect

Flowering is an important process for the reproduction of higher plants. Up to this point, the studies on flowering have mostly focused on the model plant Arabidopsis thaliana, and the flowering mechanism of fruit trees remains mostly unknown. The diversity of the flowering time of loquat (Eriobotrya japonica Lindl.) makes it an ideal material to study the regulation of flowering. In this study, we first observed the inflorescence bud differentiation in two varieties of loquat that had different blooming times (cv. Dawuxing (E. japonica), that blooms in the fall and cv. Chunhua (E. japonica×Eriobotrya bengalensis Hook. f.) that blooms in the spring) and found that the starting time of inflorescence bud differentiation and the speed of inflorescence development were responsible for the difference in blooming times. The determination of endogenous phytohormones by high performance liquid chromatography (HPLC) indicated that abscisic acid (ABA), zeatin (ZT), and gibberellin (GA₃) promoted flowering in loquat, while indole-3-acetic acid (IAA) was mainly involved in inflorescence bud differentiation in Chunhua. A transcription level analysis illustrated that multiple flowering-related genes could respond to different signals, integrate to the TFL1, AP1 and FT genes, and then synergistically regulate flowering in loquat. Thus, this study provides a new insight into flowering regulation mechanisms in loquat.

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Silencing the SLB3 transcription factor gene decreases drought stress tolerance in tomato

WANG Zi-yu, bAO Yu-fang, PEI Tong, WU Tai-ru, DU Xu, HE Meng-xi, WANG Yue, LIU Qi-feng, YANG Huan-huan, JIANG Jing-bin, ZHANG He, LI Jing-fu, ZHAO Ting-ting, XU Xiang-yang

2020, 19 (11): 2699-2708. DOI: 10.1016/S2095-3119(20)63350-0

Abstract （97） PDF in ScienceDirect

BRI1-EMS-SUPPRESSOR 1 (BES1) transcription factor is closely associated with the brassinosteroid (BR) signaling pathway and plays an important role in plant growth and development. SLB3 is a member of BES1 transcription factor family and its expression was previously shown to increase significantly in tomato seedlings under drought stress. In the present study,we used virus-induced gene silencing (VIGS) technology to downregulate SLB3 expression to reveal the function of the SLB3 gene under drought stress further. The downregulated expression of SLB3 weakened the drought tolerance of the plants appeared earlier wilting and higher accumulation of H₂O₂ and O₂^–·, decreased superoxide dismutase (SOD) activity, and increased proline (PRO) and malondialdehyde (MDA) contents and peroxidase (POD) activity. Quantitative real-time PCR (qRT-PCR) analysis of BR-related genes revealed that the expression of SlCPD, SlDWARF and BIN2-related genes was significantly upregulated in SLB3-silenced seedlings under drought stress, but that the expression of TCH4-related genes was downregulated. These results showed that silencing the SLB3 gene reduced the drought resistance of tomato plants and had an impact on the BR signaling transduction which may be probably responsible for the variation in drought resistance of the tomato plants.

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Genome-wide identification and expression profiling of MYB transcription factor genes in radish (Raphanus sativus L.)

Everlyne M’mbone MULEKE, WANG Yan, ZHANG Wan-ting, XU Liang, YING Jia-li, Bernard K. KARANJA, ZHU Xian-wen, FAN Lian-xue, Zarwali AHMADZAI, LIU Li-wang

2021, 20 (1): 120-131. DOI: 10.1016/S2095-3119(20)63308-1

Abstract （136） PDF in ScienceDirect

Radish (Raphanus sativus L.), an important root vegetable crop of the Brassicaceae family, has a high level of anthocyanin accumulation in its pigment root tissues. It was reported that MYB transcription factors (TFs) play vital roles in plant development and anthocyanin metabolism, and the PAP1/2 could promote expression of anthocyanin biosynthesis genes. In this study, a total of 187 radish MYB genes (RsMYBs) were identified in the radish genome and clustered into 32 subfamilies. Among them, 159 RsMYBs were localized on nine radish chromosomes. Interestingly, 14 RsMYBs exhibited differential expression profiles in different taproot developmental stages among four differently colored radish lines. A number of RsMYBs were highly expressed in the pigmented root tissues at the maturity stage, several genes including RsMYB41, RsMYB117, and RsMYB132 being homologous to PAP1/2, showed high expression levels in the red skin of NAU-YH (red skin-white flesh) taproot, while RsMYB65 and RsMYB159 were highly expressed in the purple root skin of NAU-YZH (purple skin-red flesh), indicating that these RsMYBs might positively regulate the process of anthocyanin accumulation in radish taproot. These results would provide valuable information for further functional characterization of RsMYBs, and facilitate clarifying the molecular mechanism underlying anthocyanin biosynthesis in radish.

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Integrative analysis of the metabolome and transcriptome reveals seed germination mechanism in Punica granatum L.

FU Fang-fang, PENG Ying-shu, WANG Gui-bin, Yousry A. EL-KASSABY, CAO Fu-liang

2021, 20 (1): 132-146. DOI: 10.1016/S2095-3119(20)63399-8

Abstract （95） PDF in ScienceDirect

We conducted an integrative system biology of metabolome and transcriptome profile analyses during pomegranate (Punica granatum L.) seed germination and utilized a weighted gene co-expression network analysis (WGCNA) to describe the functionality and complexity of the physiological and morphogenetic processes as well as gene expression and metabolic differences during seed germination stages. In total, 489 metabolites were detected, including 40 differentially accumulated metabolites. The transcriptomic analysis showed the expression of 6 984 genes changed significantly throughout the whole germination process. Using WGCNA, we identified modules related to the various seed germination stages and hub genes. In the initial imbibition stage (stage 1), the pivotal genes involved in RNA transduction and the glycolytic pathway were most active, while in the sprouting stage (stage 4), the pivotal genes were involved in multiple metabolic pathways. In terms of secondary metabolic pathways, we found flavonoid 4-reductase genes of anthocyanin biosynthesis pathway are most significantly affected during pomegranate seed germination, while the flavonol synthase gene was mainly involved in the regulation of isoflavonoid biosynthesis.

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Transcriptomic insights into growth promotion effect of Trichoderma afroharzianum TM2-4 microbial agent on tomato plants

ZHAO Juan, LIU Ting, LIU Wei-cheng, ZHANG Dian-peng, DONG Dan, WU Hui-ling, ZHANG Tao-tao, LIU De-wen

2021, 20 (5): 1266-1276. DOI: 10.1016/S2095-3119(20)63415-3

Abstract （100） PDF in ScienceDirect

Plant growth promoting fungi are receiving increased attention as valuable beneficial microorganisms in crop cultivation due to their capacity to produce bioactive substances, promote plant growth and enhance immune defense functions. In this study, a novel Trichoderma isolate, designated as TM2-4, was screened from healthy tomato rhizosphere soil and identified as Trichoderma afroharzianum. Culture filtrate of the isolate TM2-4 displayed obvious bioactive substance production and an evident effect in promoting tomato seed germination, with hypocotyl length, radical length and vigor index increased by 28.7, 19.4 and 62.1%, respectively, after a 100-fold dilution treatment. To assess the promotion effect and related mechanism of isolate TM2-4, the plant biological indexes and gene expression profiles of tomato plants treated with or without T. afroharzianum TM2-4 microbial agent were investigated by greenhouse pot experiment and RNA sequencing. The results demonstrated that T. afroharzianum TM2-4 significantly promoted tomato plant growth in terms of plant height, dry weight, number of leaves per plant and root activity, through efficient colonization in the rhizosphere and root system of the plants. Transcriptome analyses identified a total of 984 differentially expressed genes in T. afroharzianum microbial agent inoculated tomato roots, which were mainly engaged in the biological process of phytohormone homeostasis, antioxidant activity, as well as metabolic pathways including phenylpropanoid biosynthesis and glutathione metabolism. These findings provide useful information for understanding the mechanism of isolate TM2-4 for tomato plant growth promotion, which would facilitate further development of T. afroharzianum TM2-4 microbial agent for use in vegetable crop production.

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Fingerprinting 146 Chinese chestnut (Castanea mollissima Blume) accessions and selecting a core collection using SSR markers

NIE Xing-hua, WANG Ze-hua, LIU Ning-wei, SONG Li, YAN Bo-qian, XING Yu, ZHANG Qing, FANG Ke-feng, ZHAO Yong-lian, CHEN Xin, WANG Guang-peng, QIN Ling, CAO Qing-qin

2021, 20 (5): 1277-1286. DOI: 10.1016/S2095-3119(20)63400-1

Abstract （117） PDF in ScienceDirect

Chinese chestnut is an important nut tree around the world. Although the types of Chinese chestnut resources are abundant, resource utilization and protection of chestnut accessions are still very limited. Here, we fingerprinted and determined the genetic relationships and core collections of Chinese chestnuts using 18 fluorescently labeled SSR markers generated from 146 chestnut accessions. Our analyses showed that these markers from the tested accessions are highly polymorphic, with an average allele number (N_a) and polymorphic information content (PIC) of 8.100 and 0.622 per locus, respectively. Using these strongly distinguishing markers, we successfully constructed unique fingerprints for 146 chestnut accessions and selected seven of the SSR markers as core markers to rapidly distinguish different accessions. Our exploration of the genetic relationships among the five cultivar groups indicated that Chinese chestnut accessions are divided into three regional type groups: group I (North China (NC) and Northwest China (NWC) cultivar groups), group II (middle and lower reaches of the Yangtze River (MLY) cultivar group) and group III (Southeast China (SEC) and Southwest China (SWC) cultivar groups). Finally, we selected 45 core collection members which represent the most genetic diversity of Chinese chestnut accessions. This study provides valuable information for identifying chestnut accessions and understanding the phylogenetic relationships among cultivar groups, which can serve as the basis for efficient breeding in the future.

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High density genetic map and quantitative trait loci (QTLs) associated with petal number and flower diameter identified in tetraploid rose

YU Chao, WAN Hui-hua, Peter M. BOURKE, CHENG Bi-xuan, LUO Le, PAN Hui-tang, ZHANG Qi-xiang

2021, 20 (5): 1287-1301. DOI: 10.1016/S2095-3119(20)63416-5

Abstract （107） PDF in ScienceDirect

Rose is one of the most important ornamental and economic plants in the world. Modern rose cultivars are primarily tetraploid, and during meiosis, they may exhibit double reduction or preferential chromosome pairing. Therefore, the construction of a high density genetic map of tetraploid rose is both challenging and instructive. In this study, a tetraploid rose population was used to conduct a genetic analysis using genome sequencing. A total of 17 382 single nucleotide polymorphism (SNP) markers were selected from 2 308 042 detected SNPs. Combined with 440 previously developed simple sequence repeats (SSR) and amplified fragment length polymorphism (AFLP) markers, a marker dosage of 6 885 high quality markers was successfully assigned by GATK software in the tetraploid model. These markers were used in the construction of a high density genetic map, containing the expected seven linkage groups with 6 842 markers, a total map length of 1 158.9 cM, and an average inter-marker distance of 0.18 cM. Quantitative trait locus (QTL) analysis was subsequently performed to characterize the genetic architecture of petal number and flower diameter. One major QTL (qpnum-3-1) was detected for petal number in three consecutive years, which explained 20.18–22.11% of the variation in petal number. Four QTLs were detected for flower diameter; the main locus, qfdia-2-2, was identified in two consecutive years. Our results will benefit the molecular marker-assisted breeding of modern rose cultivars. In addition, this study provides a guide for the genetic and QTL analysis of autotetraploid plants using sequencing-based genotyping methods.

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Functional analysis of the nitrogen metabolism-related gene CsGS1 in cucumber

XIN Ming, QIN Zhi-wei, YANG Jing, ZHOU Xiu-yan, WANG Lei

2021, 20 (6): 1515-1524. DOI: 10.1016/S2095-3119(20)63305-6

Abstract （91） PDF in ScienceDirect

Glutamine synthetase (GS) plays an important role in nitrogen (N) metabolism in cucumber. In this study, we cloned and sequenced the CsGS1 gene, and analyzed the expression patterns and subcellular localization of the GS1 protein in response to different N conditions in order to determine its role in low-nitrogen (LN) tolerance. CsGS1 was abundantly expressed in the leaves of the low N-requiring cultivar D0328, while the high N-requiring cultivar D0422 showed similar expression levels across different tissues including leaves, shoots and roots. Furthermore, the GS1 protein was primarily localized in the cytoplasm of plant cells. Both cultivars were then transformed with the CsGS1 coding sequence or antisense sequence via Agrobacterium tumefaciens in order to overexpress and silence GS1 expression, respectively. Overexpression of CsGS1 significantly improved LN tolerance and photosynthetic parameters, and increased chlorophyll b content, biomass, plant height, root length, N accumulation and GS activity under LN condition compared to the control. CsGS1 silencing on the other hand significantly reduced the above indices. Taken together, CsGS1 is crucial for maintaining N metabolism in cucumber plants during N deprivation, and is a promising target for generating novel transgenic breeds with increasing nitrogen utilization efficiency.

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Differences of aroma development and metabolic pathway gene expression between Kyoho and 87-1 grapes

JI Xiao-hao, WANG Bao-liang, WANG Xiao-di, WANG Xiao-long, LIU Feng-zhi, WANG Hai-bo

2021, 20 (6): 1525-1539. DOI: 10.1016/S2095-3119(20)63481-5

Abstract （122） PDF in ScienceDirect

Aroma is an important quality trait of grapes and often the focus of consumers, viticulturists and grapevine breeders. Kyoho is a hybrid between Vitis vinifera and Vitis labrusca with a strawberry-like scent, while 87-1 is an early-ripening mutant of Muscat hamburg, belonging to Vitis vinifera, with a rose scent. In this study, we compared their aroma compositions and concentrations during berry development by headspace-SPME combined with gas chromatography-mass spectrometry (GC-MS), and analyzed the expression differences of enzyme-encoding genes in the LOX-HPL, MEP and MVA metabolic pathways by qRT-PCR. Twelve esters were detected in Kyoho during the whole berry development and they were abundant after veraison, but no esters were detected in 87-1 berries. Linalool was the dominant terpene among the 14 terpenes detected in 87-1 berries, while limited amounts of terpenes were detected in Kyoho berries. qRT-PCR analysis indicated that the low expression of VvAAT might explain the low content of ester volatiles in 87-1 berries, and the low expression of coding genes in the MEP pathway, especially VvPNLinNer1, might be the reason for the low content of volatile terpenes in Kyoho berries. The results from this work will promote our understanding of aroma metabolic mechanisms of grapes, and offer some suggestions for grape aromatic quality improvement.

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The transcriptional landscape of cultivated strawberry (Fragaria×ananassa) and its diploid ancestor (Fragaria vesca) during fruit development

LI Yong-ping, LIU Tian-jia, LUO Hui-feng, LIU Sheng-cai

2021, 20 (6): 1540-1553. DOI: 10.1016/S2095-3119(20)63376-7

Abstract （83） PDF in ScienceDirect

Cultivated strawberry (Fragaria×ananassa) originated from four diploid ancestors: F. vesca, F. viridis, F. iinumae and F. nipponica. Among them, F. vesca is the dominant subgenome for cultivated strawberry. It is not well understood how differences in gene expression between diploid and octoploid strawberry contribute to differences during fruit development. In this study, we used comprehensive transcriptomic analyses of F. vesca and F.×ananassa to investigate gene expression at the different stages of fruit development. In total, we obtained 3 508 (turning stage) and 3 958 (red stage) differentially expressed genes with pairwise comparisons between diploid and octoploid. The genes involved in flavonoid biosynthesis were almost upregulated in the turning stages of octoploid, and we also discovered a ripe fruit-specific module associated with several flavonoid biosynthetic genes, including FveMYB10, FveMYB9/11, and FveRAP, using weighted gene coexpression network analysis (WGCNA). Furthermore, we identified the species-specific regulated networks in the octoploid and diploid fruit. Notably, we found that the WAK and F-box genes were enriched in the octoploid and diploid fruits, respectively. This study elucidates new findings on flavonoid biosynthesis and fruit size of strawberry with important implications for future molecular breeding in cultivated strawberry.

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Integration of the metabolome and transcriptome reveals the metabolites and genes related to nutritional and medicinal value in Coriandrum sativum

WU Tong, FENG Shu-yan, YANG Qi-hang, Preetida J BHETARIYA, GONG Ke, CUI Chun-lin, SONG Jie, PING Xiao-rui, PEI Qiao-ying, YU Tong, SONG Xiao-ming

2021, 20 (7): 1807-1818. DOI: 10.1016/S2095-3119(20)63358-5

Abstract （97） PDF in ScienceDirect

Coriandrum sativum (Coriander) or Chinese parsley is a culinary herb with multiple medicinal effects, which is widely used in cooking and traditional medicine. It is enriched with essential oils and anti-oxidant compounds with unknown significance. To explore the untapped reservoir of Coriander, we studied the transcriptome and metabolic profiles from three developmental stages. Here, we identified 10 tyrosine metabolic pathway-related genes (TMPRGs), six porphyrins and chlorophyll metabolic pathway-related genes (PCMPRGs), and five Vitamin E metabolic pathway-related genes (VEMPRGs). These genes were associated with the early development of Coriander. Our analysis suggests that these pathways are involved in the production of critical phenolic metabolites. Furthermore, we constructed the interaction network between these pathway-related genes and transcription factors (TFs), which supported the regulatory pathways for phenolic metabolites. Interestingly, we identified several nutritional or medicinally relevant metabolites, including 59 phenols, two polyamines, 12 alkaloids, and one terpenoid. The higher concentrations of metabolites were from caffeic acid, agmatine, and its derivatives. We found higher levels of caffeic acid and agmatine at 30 days compared to 60 or 90 days. This study provides evidence to stimulate further investigation of the role of these metabolites in medicinal and nutritional research.

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Transcriptome analysis for understanding the mechanism of dark septate endophyte S16 in promoting the growth and nitrate uptake of sweet cherry

WU Fan-lin, QU De-hui, TIAN Wei, WANG Meng-yun, CHEN Fei-yan, LI Ke-ke, SUN Ya-dong, SU Ying-hua, YANG Li-na, SU Hong-yan, WANG Lei

2021, 20 (7): 1819-1831. DOI: 10.1016/S2095-3119(20)63355-X

Abstract （112） PDF in ScienceDirect

Sweet cherry is one of the most popular fresh fruits in the world. Previously, we isolated a soilborne dark septate endophyte (DSE) strain, S16, which promoted the growth of Gisela 5 sweet cherry rootstock. However, little is known about the molecular mechanism of the effect of S16 on the growth of sweet cherry. In this study, the physiological parameters and transcript profiles of sweet cherry roots were analyzed under S16 treatment compared with a control to elucidate the molecular mechanisms of the effect of this strain on sweet cherry growth. After inoculation with S16, sweet cherry seedlings exhibited more vigorous growth. Moreover, we identified 4 249 differentially expressed genes (DEGs) between S16-treated plants and the control. Many of the DEGs are involved in pathways related to plant growth, such as cellular metabolic and plant hormone pathways. Additionally, some genes involved in nitrate regulation were also enriched; and these genes may be involved in the regulation of nitrate uptake in plants. Physiological index detection demonstrated that S16 could improve the nitrate assimilation of sweet cherry via NO₃^– transporters. This RNA-seq dataset provides comprehensive insight into the transcriptomic landscape to reveal the molecular mechanisms whereby the DSE influences the growth of sweet cherry.

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Development and application of microsatellite markers within transcription factors in flare tree peony (Paeonia rockii) based on next-generation and single-molecule long-read RNA-seq

LIU Na, CHENG Fang-yun, GUO Xin, ZHONG Yuan

2021, 20 (7): 1832-1848. DOI: 10.1016/S2095-3119(20)63402-5

Abstract （77） PDF in ScienceDirect

Tree peonies native to China are a precious crop with ornamental, medicinal and edible oil properties, of which flare tree peony (Paeonia rockii) is one of the most significant germplasms in Paeonia. The development and application of expressed sequence tag-simple sequence repeat (EST-SSR) markers are very valuable for genetic and breeding applications, but EST-SSR resources for the genus Paeonia are still limited. In this study, we first reported the development of SSRs within transcription factors (TFs) in P. rockii based on next-generation sequencing (NGS) and single-molecule long-read sequencing (SMLRS). A total of 166 EST-SSRs containing six nucleotide repeat types were identified from 959 candidate TFs associated with yield, with an average of one SSR per 5.83 unigenes. In total, 102 (61.45%) pairs of primers produced amplification products in the two RNA-seq cultivars. Among them, 58 (56.86%) pairs of primers from 18 gene families (AP2, bHLH, HSF, etc.) were identified to be polymorphic both in the parents of a linkage mapping population and in eight randomly selected accessions of P. rockii. Further, the 58 EST-SSRs indicated a high level of informativeness with PIC values ranging from 0.32 to 0.91 (mean 0.70) after assessment in 37 tree peony accessions. Transferability studies indicated that the amplification ratio of the 58 pairs of primers ranged from 89.66 to 100% across seven species of Paeonia. In addition, a genetic relationship study was performed in 62 accessions. Cluster analysis using the neighbour-joining (NJ) tree demonstrated that major clusters corresponded to the known pedigree trees. Taken together, these newly developed EST-SSRs have a potential use in the conservation of tree peony germplasm and marker-assisted selection (MAS) breeding.

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Mapping and predicting a candidate gene for flesh color in watermelon

WANG Chao-nan, LUAN Fei-shi, LIU Hong-yu, Angela R. DAVIS, ZHANG Qi-an, DAI Zu-yun, LIU Shi

2021, 20 (8): 2100-2111. DOI: 10.1016/S2095-3119(20)63487-6

Abstract （126） PDF in ScienceDirect

The color of watermelon flesh is an important trait determined by a series of carotenoids. Herein, we used Cream of Saskatchewan (pale yellow flesh) and PI 186490 (white flesh) as parental materials for an F₂segregation and initial mapping using the bulked segregant analysis sequencing (BSA-seq) strategy. The BSA results revealed a flesh color-related QTL that spans approximately 2.45 Mb on chromosome 6. This region was preliminarily positioned in a 382-kb segment, and then narrowed down into a 66.8-kb segment with 1 260 F₂ individuals. A total of nine candidate genes were in the fine mapping interval, but only Cla007528 (encoding chlorophyllase) had non-synonymous mutations and was significantly expressed between the parental materials throughout flesh development. We also checked the expression patterns of the carotenoid metabolic pathway genes based on RNA-seq data and qRT-PCR validation. Three genes in the xanthophyll cycle (ClCHYB, ClNCED-1 and ClNCED-7) exhibited differential expression patterns between the two parental lines at different flesh color formation stages. ClPSY1, ClPDS, ClZDS, ClCHXE, ClCRTISO and ClLCYB also exhibited clearly different expression patterns accompanied by carotenoid accumulation.

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Genome-wide identification, molecular evolution, and expression divergence of the hexokinase gene family in apple

ZHU Ling-cheng, SU Jing, JIN Yu-ru, ZHAO Hai-yan, TIAN Xiao-cheng, ZHANG Chen, MA Feng-wang, LI Ming-jun, MA Bai-quan

2021, 20 (8): 2112-2125. DOI: 10.1016/S2095-3119(20)63562-6

Abstract （107） PDF in ScienceDirect

Hexokinase (HXK) is the first irreversible catalytic enzyme in the glycolytic pathway, which not only provides energy for plant growth and development but also serves as a signaling molecule in response to environmental changes. However, the evolutionary pattern of the HXK gene family in apple remains unknown. In this study, a total of nine HXK genes were identified in the Malus×domestica genome GDDH13 v1.1. The physiological and biochemical properties, exon-intron structures, conserved motifs, and cis-elements of the MdHXK genes were determined. Predicted subcellular localization indicated that the MdHXK genes were mainly distributed in the mitochondria, cytoplasm, and nucleus. Gene duplication revealed that whole-genome duplication (WGD) and segmental duplication played vital roles in MdHXK gene family expansion. The ω values of pairwise MdHXK genes indicated that this family was subjected to strong purifying selection during apple domestication. Additionally, five subfamilies were classified, and recent/old duplication events were identified based on phylogenetic tree analysis. Different evolutionary rates were estimated among the various HXK subfamilies. Moreover, divergent expression patterns of the MdHXK genes in four source-sink tissues and at five different apple fruit developmental stages indicated that they play vital roles in apple fruit development and sugar accumulation. Our study provides a theoretical basis for future elucidation of the biological functions of the MdHXK genes during apple fruit development.

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Preharvest application of melatonin induces anthocyanin accumulation and related gene upregulation in red pear (Pyrus ussuriensis)

SUN Hui-li, WANG Xin-yue, SHANG Ye, WANG Xiao-qian, DU Guo-dong, LÜ De-guo

2021, 20 (8): 2126-2137. DOI: 10.1016/S2095-3119(20)63312-3

Abstract （137） PDF in ScienceDirect

Anthocyanins are important components in the peel of red pears and contribute to the appearance of the fruit. Melatonin application is known to affect anthocyanin biosynthesis, but the effect of preharvest melatonin application on fruit coloration remains largely unknown. The objective of this study was to determine the effects of preharvest melatonin application on pigmentation, phenolic compounds, and the expression of related genes in Nanhong pear (Pyrus ussuriensis). The applications were performed during the pre-color-change period by spraying 50 or 200 μmol L^–1 of melatonin on fruits. We found that treatment with melatonin had a significant effect on color development. The concentrations of anthocyanins and favonols were enhanced by melatonin treatment, whereas hydroxycinnamate and favanol concentrations were reduced. Quantitative real-time PCR analyses indicated that the transcription levels for most anthocyanin biosynthetic genes and anthocyanin-related transcription factors were induced by melatonin. Melatonin application also stimulated the expression of melatonin biosynthesis-related genes and consequently caused an increase in endogenous melatonin concentration. These results provide insights into melatonin-induced fruit coloration and will facilitate the application of exogenous melatonin in agriculture.

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Genome-wide identification and expression analysis of Argonaute gene family from longan embryogenic callus

CHEN Rong-zhu, SHEN Xu, ZHANG Shu-ting, ZHAO Hua, CHEN Xiao-hui, XU Xiao-ping, HUO Wen, ZHANG Zi-hao, LIN Yu-ling, LAI Zhong-xiong

2021, 20 (8): 2138-2155. DOI: 10.1016/S2095-3119(20)63313-5

Abstract （87） PDF in ScienceDirect

Argonaute (AGO) proteins are the core of the RNA-induced gene silencing complex which regulate a wide variety of processes in plants, from organ development to abiotic stress responses. They have been identified in many plants, but little is known in longan (Dimocarpus longan Lour.), and how AGO functions in the signaling pathways in plant embryos in response to changing environmental stimuli remains unclear. In the present research, a genome-wide analysis of the AGO gene family members and their roles in somatic embryogenesis (SE), zygotic embryogenesis (ZE), tissue developmental processes, and responses to hormones, light and abiotic stress in longan were conducted. Ten longan AGO genes were identified genome-wide and divided into four clades. They were distributed on chromosomes 1, 4, 8, 10, 12, 13, 14, and 15, and had 2–23 introns. The expression profiling implied that DlAGOs regulated early and middle embryogenesis, as well as developmental processes of seed, flower, and stem in longan. In addition, the transcript levels of DlAGOs in response to exogenous hormones, light and abiotic stress showed differences in expression patterns. These results provide the useful information for further elucidation of RNAi-mediated gene silencing in longan embryogenic callus (EC).

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Identification and expression analysis of the PbrMLO gene family in pear, and functional verification of PbrMLO23

GUO Bing-bing, LI Jia-ming, LIU Xing, QIAO Xin, Musana Rwalinda FABRICE, WANG Peng, ZHANG Shao-ling, WU Ju-you

2021, 20 (9): 2410-2423. DOI: 10.1016/S2095-3119(20)63558-4

Abstract （114） PDF in ScienceDirect

Mildew resistance locus O (MLO) is a plant-specific gene family that plays an important role in the growth and development of plants and their interactions with the environment. However, the available information on this gene family in pear is limited. Here, 24 PbrMLO genes were identified and divided into five subfamilies (I, II, III, IV and V). Whole-genome duplication (WGD) and dispersed duplication contributed to the expansion of the PbrMLO family. In addition, gene expression analysis revealed that PbrMLO genes were distributed in various pear tissues, suggesting their diverse functions. We selected PbrMLO23 for further functional analysis. Expression profile analysis by qRT-PCR showed that PbrMLO23 was highly expressed in pollen. Subcellular localization analysis showed that PbrMLO23 was located on the plasma membrane. When the expression level of PbrMLO23 was knocked down by using antisense oligonucleotides, pollen tube lengths increased, indicating that PbrMLO23 plays a functional role in inhibiting pollen tube growth. In summary, these results provide evolutionary insight into PbrMLO and its functional characteristics and lay a foundation for further analysis of the functions of PbrMLO members in pear.

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Transcriptional profiles underlying the effects of salicylic acid on fruit ripening and senescence in pear (Pyrus pyrifolia Nakai)

SHI Hai-yan, CAO Li-wen, XU Yue, YANG Xiong, LIU Shui-lin, LIANG Zhong-shuo, LI Guo-ce, YANG Yu-peng, ZHANG Yu-xing, CHEN Liang

2021, 20 (9): 2424-2437. DOI: 10.1016/S2095-3119(20)63568-7

Abstract （119） PDF in ScienceDirect

Salicylic acid (SA) plays a pivotal role in delaying fruit ripening and senescence. However, little is known about its underlying mechanism of action. In this study, RNA sequencing was conducted to analyze and compare the transcriptome profiles of SA-treated and control pear fruits. We found a total of 159 and 419 genes differentially expressed between the SA-treated and control pear fruits after 12 and 24 h of treatment, respectively. Among these differentially expressed genes (DEGs), 125 genes were continuously differentially expressed at both treatment times, and they were identified as candidate genes that might be associated with SA-regulated fruit ripening and senescence. Bioinformatics analysis results showed that 125 DEGs were mainly associated with plant hormone biosynthesis and metabolism, cell wall metabolism and modification, antioxidant systems, and senescence-associated transcription factors. Additionally, the expression of several candidate DEGs in ripening and senescent pear fruits after SA treatments were further validated by quantitative real-time PCR (qRT-PCR). This study provides valuable information and enhances the understanding of the comprehensive mechanisms of SA-meditated pear fruit ripening and senescence.

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Genome-wide analysis of the invertase genes in strawberry (Fragaria×ananassa)

YUAN Hua-zhao, PANG Fu-hua, CAI Wei-jian, CHEN Xiao-dong, ZHAO Mi-zhen, YU Hong-mei

2021, 20 (10): 2652-2665. DOI: 10.1016/S2095-3119(20)63381-0

Abstract （91） PDF in ScienceDirect

Sugar is an important material basis in fruit development, and strawberry fruit flavour and sweetness largely depend on the sugar content and variety. Invertases (INVs) play an important role in the regulation of sugar accumulation because they irreversibly catalyse the hydrolysis of sucrose into the corresponding nucleoside diphosphate-glucose, glucose or fructose in fruit. In this work, we provided a comprehensive analysis of the INV gene family in octoploid strawberry (Fragaria×ananassa), including the gene structure, chromosomal locations, conserved domains, and gene evolution and expression profiles during strawberry fruit development. Our study revealed that polyploid events resulted in the abundant amplification (almost three- or four-fold) of the INV gene in the F.×ananassa genome, and these amplified INV genes showed dominant expression in strawberry fruit. More than half of the FaINVs transcripts with low expression had incomplete coding sequences by alternative splicing. Previous studies have shown that cell wall invertases (CWINV) are involved in the regulation of phloem unloading and sink strength establishment. The expression of FaCWINV1 was markedly upregulated during fruit development and strongly expressed in ripe fruit. Moreover, a significant correlation was observed between the total sugar content and the FaCWINV1 expression level. These findings suggest that FaCWINV1 may be involved in sugar accumulation in strawberry fruit. Taken together, the results of our study will be beneficial for further research into the functions of INVs in the regulation of fruit ripening.

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Genome-wide analysis of the SCPL gene family in grape (Vitis vinifera L.)

WANG Xi-cheng, WU Wei-min, ZHOU Bei-bei, WANG Zhuang-wei, QIAN Ya-ming, WANG Bo, YAN Li-chun

2021, 20 (10): 2666-2679. DOI: 10.1016/S2095-3119(20)63587-0

Abstract （178） PDF in ScienceDirect

Serine carboxypeptidase-like (SCPL) proteins are a group of acyltransferase enzymes that have important roles in plant growth, development, and stress responses. Although SCPL proteins have been studied in many plants, the biological functions of SCPL genes in grape are still unknown. In this study, 59 putative SCPL proteins were identified from the grape genome. A bioinformatics analysis, including chromosomal locations, exon/intron structures, phylogeny, cis-elements, and conserved motifs, was performed for the gene family. The phylogenetic analysis revealed that VvSCPL proteins could be classified into three groups, with the gene motifs in each group showing high similarity levels. The number of exons in the VvSCPL genes ranged from 1 to 19, suggesting significant variations among grape SCPL genes. The expression of the VvSCPL genes, as assessed by RNA sequencing (RNA-seq) and quantitative real-time PCR, showed that most VvSCPL genes responded to drought- and waterlogging-stress treatments, which indicated their roles in abiotic stress responses. The results provide useful information for further study of SCPL genes in grape.

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Construction of high-density SNP genetic maps and QTL mapping for dwarf-related traits in Litchi chinensis Sonn

HU Fu-chu, CHEN Zhe, WANG Xiang-he, WANG Jia-bao, FAN Hong-yan, QIN Yong-hua, ZHAO Jietang, HU Gui-bing

2021, 20 (11): 2900-2913. DOI: 10.1016/S2095-3119(20)63387-1

Abstract （159） PDF in ScienceDirect

Litchi chinensis Sonn is widely cultivated in subtropical regions and has an important economic value. A high-density genetic map is a valuable tool for mapping quantitative trait loci (QTL) and marker-assisted breeding programs. In this study, a single nucleotide polymorphism (SNP)-based high-density linkage map was constructed by a genotyping-by-sequencing (GBS) protocol using an F1 population of 178 progenies between two commercial litchi cultivars, ‘Ziniangxi’ (dwarf) and ‘Feizixiao’ (vigorous). The genetic map consisted of 3 027 SNP markers with a total length of 1 711.97 cM in 15 linkage groups (LGs) and an average marker distance of 0.57 cM. Based on this high-density linkage map and three years of phenotyping, a total of 37 QTLs were detected for eight dwarf-related traits, including length of new branch (LNB), diameter of new branch (DNB), length of common petiole (LCP), diameter of common petiole (DCP), length of internode (LI), length of single leaf (LSL), width of single leaf (WSL), and plant height (PH). These QTLs could explain 8.0 to 14.7% (mean=9.7%) of the phenotypic variation. Among them, several QTL clusters were observed, particularly on LG04 and LG11, which might show enrichment for genes regulating the dwarf-related traits in litchi. There were 126 candidate genes identified within the QTL regions, 55 of which are differentially expressed genes by RNA-seq analysis between ‘Ziniangxi’ and ‘Feizixiao’. These DEGs were found to participate in the regulation of cell development, material transportation, signal transduction, and plant morphogenesis, so they might play important roles in regulating plant dwarf-related traits. The high-density genetic map and QTLs identification related to dwarf traits can provide a valuable genetic resource and a basis for marker-assisted selection and genomic studies of litchi.

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Transcriptome analysis reveals effects of red and blue lightemitting diodes (LEDs) on the growth, chlorophyll fluorescence and endogenous plant hormones of potato (Solanum tuberosum L.) plantlets cultured in vitro

CHEN Li-li, WANG Hao-ying, GONG Xiao-chen, ZENG Zhao-hai, XUE Xu-zhang, HU Yue-gao

2021, 20 (11): 2914-2931. DOI: 10.1016/S2095-3119(20)63393-7

Abstract （89） PDF in ScienceDirect

Red and blue light illumination has been reported to significantly affect plantlet growth. Potato is an important food and feed crop in the world and potato plantlet cultured in vitro plays an important role in potato production. However, few studies have documented the effects of red and blue light on the growth of potato plantlets revealed at the transcriptome level. The objective of this study was to determine the growth and physiological responses of potato plantlets cultured in vitro under monochromatic red (RR), monochromatic blue (BB) as well as combined red and blue (RB) LEDs using the RNA-Seq technique. In total, 3 150 and 814 differentially expressed genes (DEGs) were detected in potato plantlets under RR and BB, respectively, compared to RB (used as control). Compared to the control, the DEGs enriched in “photosynthesis” and “photosynthesis-antenna proteins” metabolic pathways were up-regulated and down-regulated by BB and RR, respectively, which might be responsible for the increases and decreases of maximum quantum yield (F_v/F_m), photochemical quantum yield (φ_PSII), photochemical quenching (qP) and electron transfer rate (ETR) in BB and RR, respectively. Potato plantlets exhibited dwarfed stems and extended leaves under BB, whereas elongated stems and small leaves were induced under RR. These dramatically altered plantlet phenotypes were associated with variable levels of endogenous plant hormones gibberellin (GAs), indoleacetic acid (IAA) and cytokinins (CKs), as assessed in stems and leaves of potato plantlets. In addition, monochromatic red and blue LEDs trigged the opposite expression profiles of DEGs identified in the “plant hormone signal transduction” metabolic pathway, which were closely related to the endogenous plant hormone levels in potato plantlets. Our results provide insights into the responses of potato plantlets cultured in vitro to red and blue LEDs at the transcriptomic level and may contribute to improvements in the micro-propagation of potato plantlets cultured in vitro from the light spectrum aspect.

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Overexpression of the MADS-box gene SlMBP21 alters leaf morphology and affects reproductive development in tomato

WANG Yun-shu, GUO Peng-yu, ZHANG Jian-ling, XIE Qiao-li, SHEN Hui, HU Zong-li, CHEN Guo-ping

2021, 20 (12): 3170-3185. DOI: 10.1016/S2095-3119(21)63638-9

Abstract （187） PDF in ScienceDirect

Fruit yield is the most important horticultural trait of tomato. SlMBP21, a SEPALLATA subclass MADS-box gene has been reported to have functions in regulating pedicel abscission zone identity and development and controlling sepal size in tomato. However, we generated transgenic tomato plants which overexpress SlMBP21 and found the transformants displayed curly leaves, abnormally shaped flowers with twisted and opened stamens, reduced yield parameters, and small and light seeds. Our studies on the gain-of-function phenotype and gene expression level showed that its novel aspects played important roles in determining leaf morphology, flower and inflorescence architecture, and seed size, as well as the fruit yield. Overexpression of SlMBP21 in tomato resulted in curly leaves with fewer leaflets due to the regulation of the critical leaf polarity genes that cause an imbalance between the midvein adaxial–abaxial cell growth. Defects in the architecture of flowers and inflorescences resulted in reduced fruit set. Furthermore, we demonstrated that SlMBP21 plays its role through inhibiting the expression of the genes involved in the determination of seed development in tomato and SlMBP21 protein can interact with other MADS-box protein (SlAGL11, TAGL1 and SlMBP3) to control seed size. Thus, these results suggest that overexpression of SlMBP21 causes multiple types of damage to plant growth and development, especially fruit yield, in tomato.

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Analysis of genetic diversity and structure across a wide range of germplasm reveals genetic relationships among seventeen species of Malus Mill. native to China

GAO Yuan, WANG Da-jiang, WANG Kun, CONG Pei-hua, LI Lian-wen, PIAO Ji-cheng

2021, 20 (12): 3186-3198. DOI: 10.1016/S2095-3119(20)63421-9

Abstract （134） PDF in ScienceDirect

China is a center of diversity for Malus Mill. with 27 native species including 21 wild species and six domesticated species. We applied a set of 19 simple sequence repeat markers to genotype 798 accessions of 17 species (12 wild species and five cultivated species) of Malus originating from 14 provinces in China. A total of 500 alleles were detected. Diversity statistics indicated a high level of genetic variation as quantified by the average values of the effective allele number (N_e), expected heterozygosity (H_e), and Shannon’s Information Index (I) (10.309, 0.886, and 2.545, respectively). Malus sieversii (MSR; H_e=0.814, I=2.041, N_e=6.054), M. baccata (MBB; H_e=0.848, I=2.350, N_e=8.652), M. toringoides (MTH; H_e=0.663, I=1.355, N_e=3.332), and M. hupehensis (MHR; H_e=0.539, I=0.912, N_e=0.579) showed a higher level of genetic diversity in this study than the previous studies. MSR and MBB contributed to the origin and evolution of some accessions of M. domestica subsp. chinensis (MDC). However, other accessions of MDC showed a closer genetic distance with MBB and cultivated species, especially M. robusta (MRB), M. asiatica (MAN), and M. prunifolia (MPB). Not all accessions of MDC were descended from MSR in Xinjiang Uygur Autonomous Region of China. This research provides novel insights into the genetic relationships of Malus native to China, which will be useful for genetic association studies, germplasm conservation, and breeding programs.

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Genome-wide identification and characterization of the abiotic-stress-responsive lipoxygenase gene family in diploid woodland strawberry (Fragaria vesca)

LI Zhi-qi, Xie Qian, YAN Jia-hui, CHEN Jian-qing, CHEN Qing-xi

2022, 21 (7): 1982-1996. DOI: 10.1016/S2095-3119(21)63819-4

Abstract （197） PDF in ScienceDirect

Lipoxygenase (LOXs) is a kind of dioxygenase without heme and iron, which plays an important role in the development and adaptation of many plants to the environment. However, the study of strawberry LOX gene family has not been reported. In this study, 14 LOX genes were identified from the diploid woodland strawberry genome. The phylogenetic tree divides the FvLOX gene into two subfamilies: 9-LOX and 13-LOX. Gene duplication event analysis showed that whole-genome duplication (WGD)/segmental duplication and dispersed duplication effectively promoted the expansion of strawberry LOX family. QRT-PCR analysis showed that FvLOX genes were expressed in different tissues. Expression profile analysis showed that FvLOX1 and FvLOX8 were up-regulated under low temperature stress, FvLOX3 and FvLOX7 were up-regulated under drought stress, FvLOX6 and FvLOX9 were up-regulated under salt stress, FvLOX2, FvLOX3 and FvLOX6 were up-regulated under salicylic acid (SA) treatment, FvLOX3, FvLOX11 and FvLOX14 were up-regulated under methyl jasmonate (MeJA) treatment, FvLOX4 and FvLOX14 were up-regulated under abscisic acid (ABA) treatment. Promoter analysis showed that FvLOX genes were involved in plant growth and development and stress response. We analyzed and identified the whole genome of strawberry FvLOX family and characterized a variety of FvLOX candidate genes involved in abiotic stress response. This study laid a theoretical and empirical foundation for the response mechanism of strawberry to abiotic stress.

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Tomato SlPti5 plays a regulative role in the plant immune response against Botrytis cinerea through modulation of ROS system and hormone pathways

TANG Qiong, ZHENG Xiao-dong, GUO Jun, YU Ting

2022, 21 (3): 697-709. DOI: 10.1016/S2095-3119(21)63630-4

Abstract （105） PDF in ScienceDirect

While SlPti5 has been shown to play a crucial role in the regulation of antagonistic genes in Solanum lycopersicum and Arabidopsis against pathogen infection, there have been no comprehensive studies on the effects of SlPti5 on the regulatory response mechanism of reactive oxygen species (ROS) system and hormone pathways during growth and disease resistance of tomato plants. Here, we investigated the function of SlPti5 in the defense response of tomato against Botrytis cinerea utilizing a virus-induced gene silencing (VIGS)-based system. Expression profile analysis showed that SlPti5 was significantly induced upon B. cinerea infection, with high expression levels in the leaves and fruit of tomato. VIGS-based silencing of SlPti5 inhibited early vegetative growth, increased the plant’s susceptibility to infection, promoted the development of ROS, affected the expression of genes involved in the ROS scavenging system, and attenuated the expression of genes associated with pathogenesis and the ethylene/jasmonic acid signaling pathways. In sum, our data demonstrated that SlPti5 stimulates the immune response of tomato plant to Botrytis cinerea infection by involving the ethylene (ET)- and jasmonic acid (JA)-mediated pathways and modulating the expression of some key pathogenesis-related (PR) genes.

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Genome-wide identification, evolutionary selection, and genetic variation of DNA methylation-related genes in Brassica rapa and Brassica oleracea

AN Feng, ZHANG Kang, ZHANG Ling-kui, LI Xing, CHEN Shu-min, WANG Hua-sen, CHENG Feng

2022, 21 (6): 1620-1632. DOI: 10.1016/S2095-3119(21)63827-3

Abstract （160） PDF in ScienceDirect

DNA methylation plays an important role in plant growth and development, and in regulating the activity of transposable elements (TEs). Research on DNA methylation-related (DMR) genes has been reported in Arabidopsis, but little research on DMR genes has been reported in Brassica rapa and Brassica oleracea, the genomes of which exhibit significant differences in TE content. In this study, we identified 78 and 77 DMR genes in Brassica rapa and Brassica oleracea, respectively. Detailed analysis revealed that the numbers of DMR genes in different DMR pathways varied in B. rapa and B. oleracea. The evolutionary selection pressure of DMR genes in B. rapa and B. oleracea was compared, and the DMR genes showed differential evolution between these two species. The nucleotide diversity (π) and selective sweep (Tajima’s D) revealed footprints of selection in the B. rapa and B. oleracea populations. Transcriptome analysis showed that most DMR genes exhibited similar expression characteristics in B. rapa and B. oleracea. This study dissects the evolutionary differences and genetic variations of the DMR genes in B. rapa and B. oleracea, and will provide valuable resources for future research on the divergent evolution of DNA methylation between B. rapa and B. oleracea.

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Versatile physiological functions of the Nudix hydrolase family in berry development and stress response in grapevine

WANG Pei-pei, WANG Zhao-ke, GUAN Le, Muhammad Salman HAIDER, Maazullah NASIM, YUAN Yong-bing, LIU Geng-sen, LENG Xiang-peng

2022, 21 (1): 91-112. DOI: 10.1016/S2095-3119(20)63490-6

Abstract （194） PDF in ScienceDirect

Nudix hydrolases are widely distributed across all classes of organisms and provide the potential capacity to hydrolyze a wide range of organic pyrophosphates. Although Nudix hydrolases are involved in plant detoxification processes in response to abiotic and biotic stresses, the biological functions of Nudix hydrolases remain largely unclear in grapevine. In the present study, a total of 25 putative grapevine Nudix hydrolases (VvNUDXs) were identified by bioinformatics analysis and classified into eight subfamilies based to their preferred substrates. Both tandem and segmental duplications were responsible for the evolution and expansion of the NUDX gene family in grapevine. To investigate the regulatory roles of VvNUDX genes during growth and development, as well as in response to abiotic and biotic stresses in grapevine, the expression patterns were revealed in publicly available microarray data. The spatial and temporal expression patterns of the VvNUDX genes indicated that they might play important roles in multiple developmental processes. Transcriptome and qRT-PCR analyses showed that ten VvNUDX genes were specifically expressed in grapevine berries, suggesting potential roles in grapevine berry development. Expression and phylogenetic analyses demonstrated that VvNUDX1 and VvNUDX3 might be involved in terpenoid biosynthesis in grapevine. Furthermore, most VvNUDX genes active toward the ADP-ribose/NADH showed different patterns in response to various abiotic and biotic stresses, such as salinity and drought, as well as different types of biotic treatments, such as Erysiphe necator, Bois Noir phytoplasma and leaf-roll-associated virus-3 (GLRaV-3). These results indicated that VvNUDX genes were associated with plant detoxification processes in response to abiotic and biotic stresses, and regulate the disease immunity and resistance pathways. The information obtained here may provide good opportunities to explore the physiological functions of VvNUDX genes in berry development and stress response networks in grapevine.

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Genome-wide analysis of the CCCH zinc finger family in longan: Characteristic identification and expression profiles in Dimocarpus longan Lour

SU Li-yao, XIAO Xue-chen, JIANG Meng-qi, HUANG Shu-qi, XUE Xiao-dong, LI Xue, LAI Zhong-xiong, LIN Yu-ling

2022, 21 (1): 113-130. DOI: 10.1016/S2095-3119(20)63460-8

Abstract （429） PDF in ScienceDirect

CCCH (C3H) Zinc finger (Znf) transcription factors (TFs), as a novel type of Znf gene, regulate the expression of genes by binding to their mRNAs and play important roles in plant growth and development and abiotic stress resistance. Longan (Dimocarpous longan) is a tropical/subtropical fruit tree of great economic importance in Southeast Asia. However, genomic information on C3H and their functions in longan are still unknown. In this study, a comprehensive analysis of the longan C3H (DlC3H) gene family was carried out. A total of 49 DlC3H genes in three clades were identified from the longan genome database. Characteristics of the genes were analyzed with respect to gene structure, motif composition, phylogenetic tree and potential functions. The analysis of alternative splicing (AS) events suggested that AS events in DlC3H genes were related to the transformation from longan non-embryonic to embryonic cultures. Promoter analysis indicated that most of the DlC3H genes included cis-acting elements associated with hormones and stresses responses. Quantitative real-time PCR (qRT-PCR) analysis indicated that 26 of the 49 DlC3Hs, which possess methyl jasmonate (MeJA) and abscisic acid (ABA) responsive cis-acting elements, showed differential expression patterns under treatment with ABA, MeJA and their endogenous inhibitors, suggesting that DlC3Hs might be involved in the ABA and MeJA signaling pathways. The expression profiles of 17 of the 49 DlC3Hs in non-embryonic callus and three tissues of embryonic cultures showed that only five of the 17 DlC3Hs had the same expression trends as the FPKM trends in transcriptome data; the expression levels of DlC3H07/14/16/36/49 in embryogenic callus and DlC3H04/38 in globular embryos were high, suggesting that they have different functions in embryonic development. Further, we verified that DlC3H01/03/05/11/19/39 were regulated by sRNAs by a modified 5´ RLM-RACE method. This study provides the first systematic analysis of C3H genes in longan, and found that C3H genes may be involved in hormone and stress responses, and somatic embryogenesis. Our preliminary investigation may provide clues to further studies on the characteristics and functions of this family in longan.

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Constructing the wolfberry (Lycium spp.) genetic linkage map using AFLP and SSR markers

YIN Yue, AN Wei, ZHAO Jian-hua, LI Yan-long, FAN Yun-fang, CHEN Jin-huan, CAO You-long, ZHAN Xiang-qiang

2022, 21 (1): 131-138. DOI: 10.1016/S2095-3119(21)63610-9

Abstract （130） PDF in ScienceDirect

Genetic linkage maps are important for quantitative trait locus (QTL) and marker-assisted selection breeding. The wolfberry (Lycium spp.) is an important food and traditional medicine in China. However, few construction genetic linkage maps have been reported because of the lack of genomic and genetic resources. In this study, a population of 89 F₁ seedings was derived from a cross between two heterozygous parents, L. chinense var. potaninii ‘BF-01’ (female) and L. barbarum var. auranticarpum ‘NH-01’ (male), in order to construct a genetic linkage map using simple sequence repeat (SSR) and amplified fragment length polymorphism (AFLP) markers based on the double pseudo-test cross mapping strategy. The resulting genetic map consisted of 165 markers (74 AFLPs and 91 SSRs) distributed across 12 linkage groups and spanned a total length of 557.6 cM with an average distance of 3.38 cM between adjacent markers. The 12 linkage groups contained 3 to 21 markers and ranged in length from 8.6 to 58.3 cM. Twenty-nine segregated markers distributed in the map were mainly located on LG4 and LG9 linkage groups at P<0.05. This is the first linkage map of Lycium species using SSR and AFLP markers, which can serve as basis for improving genes and selective breeding of the genome assembly.

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Genome-wide identification and expression analysis of GDSL esterase/lipase genes in tomato

SUN Yao-guang, HE Yu-qing, WANG He-xuan, JIANG Jing-bin, YANG Huan-huan, XU Xiang-yang

2022, 21 (2): 389-406. DOI: 10.1016/S2095-3119(20)63461-X

Abstract （324） PDF in ScienceDirect

The GDSL esterase/lipase family contains many functional genes that perform important biological functions in growth and development, morphogenesis, seed oil synthesis, and defense responses in plants. The expression of GDSL esterase/lipase genes can respond to biotic and abiotic stresses. Although GDSL esterase/lipase family genes have been identified and studied in other plants, they have not been identified and their functions remain unclear in tomato. This study is the first to identify 80 GDSL esterase/lipase family genes in tomato, which were named SlGELP1–80. These genes were mapped to their positions on the chromosomes and their physical and chemical properties, gene structure, phylogenetic relationships, collinear relationships, and cis-acting elements were analyzed. The spatiotemporal expression characteristics of the SlGELP genes in tomato were diverse. In addition, RNA-seq analysis indicated that the expression patterns of the SlGELP genes in tomato differed before and after inoculation with Stemphylium lycopersici. qRT-PCR was used to analyze the expression of five SlGELP genes after treatments with S. lycopersici, salicylic acid and jasmonic acid. Finally, this study was the first to identify and analyze GDSL esterase/lipase family genes in tomato via bioinformatics approaches, and these findings provide new insights for improving the study of plant disease resistance.

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Effects of exogenous paclobutrazol and sampling time on the efficiency of in vitro embryo rescue in the breeding of new seedless grape varieties

XU Teng-fei, GUO Yu-rui, YUAN Xiao-jian, CHU Yan-nan, WANG Xiao-wei, HAN Yu-lei, WANG Wen-yuan, WANG Yue-jin, SONG Rui, FANG Yu-lin, WANG Lu-jun, XU Yan

2022, 21 (6): 1633-1644. DOI: 10.1016/S2095-3119(21)63815-7

Abstract （305） PDF in ScienceDirect

Embryo rescue technology plays an important role in seedless grape breeding. However, the efficiency of embryo rescue, including the embryo formation, germination, and seedling rates, is closely related to the parental genotypes, degree of abortion, growth medium, and plant growth regulators. In this study, we investigated the effects of different concentrations of paclobutrazol (PAC), a plant growth regulator, and embryo collection times on the embryo formation, germination, and seedling rates for different hybrid combinations of grape breeding varieties used for their aroma and cold-resistance traits. The results showed that the different PAC concentrations had varying impacts on the development of ovules and embryos from the different grape varieties. The embryo formation rates of the ‘Sultanina Rose’×‘Beibinghong’ and ‘Kunxiang Seedless’×‘Taishan-2’ crosses were the highest under the 5.1 μmol L^–1 PAC treatment. The 1.0 μmol L^–1 PAC treatment was optimal for the germination and seedling development of the ‘Sultanina Rose’×‘Beibinghong’ embryos, whereas the 0.2 μmol L^–1 PAC treatment induced the highest germination rate for the ‘Sultanina Rose’×‘Kunxiang Seedless’ cross. The optimal sampling times for each cross varied as 39 d after pollination (DAP) for the ‘Flame Seedless’×‘Muscat Hamburg’ cross, 46 DAP for the ‘Kunxiang Seedless’×‘Beibinghong’ cross, and 41 DAP for the ‘Ruby Seedless’×‘Beibinghong’ and ‘Fantasy Seedless’×‘Shuangyou’ crosses. Moreover, the medium modified with 0.5 g L^–1 of indole-3-butyric acid allowed the malformed seedlings to develop into plantlets and achieve larger progenies. This study provides a useful basis for further studies into grape embryo rescue and could improve breeding efforts for new seedless grape varieties.

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Genome-wide characterization and expression analysis of WRKY family genes during development and resistance to Colletotrichum fructicola in cultivated strawberry (Fragaria×ananassa Duch.)

ZOU Xiao-hua, DONG Chao, LIU Hai-ting, GAO Qing-hua

2022, 21 (6): 1658-1672. DOI: 10.1016/S2095-3119(21)63816-9

Abstract （332） PDF in ScienceDirect

Based on the recently published whole-genome sequence of cultivated strawberry ‘Camarosa’, in this study, 222 FaWRKY genes were identified in the ‘Camarosa’ genome. Phylogenetic analysis showed that the 222 FaWRKY candidate genes were classified into three groups, of which 41 were in group I, 142 were in group II, and 39 were in group III. The 222 FaWRKY genes were evenly distributed among the seven chromosomes. The exon–intron structures and motifs of the WRKY genes had evolutionary diversity in different cultivated strawberry genomes. Regarding differential expression, the expression of FaWRKY133 was relatively high in leaves, while FaWRKY63 was specifically expressed in roots. FaWRKY207, 59, 46, 182, 156, 58, 39, 62 and 115 were up-regulated during achene development from the green to red fruit transition. FaWRK181, 166 and 211 were highly expressed in receptacles at the ripe fruit stage. One interesting finding was that FaWRKY179 and 205 were significantly repressed after Colletotrichum fructicola inoculation in both ‘Benihoppe’ and ‘Sweet Charlie’ compared with Mock. The data reported here provide a foundation for further comparative genomics and analyses of the distinct expression patterns of FaWRKY genes in various tissues and in response to C. fructicola inoculation.

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PbPH5, an H⁺ P-ATPase on the tonoplast, is related to malic acid accumulation in pear fruit

SONG Jun-xing, CHEN Ying-can, LU Zhao-hui, ZHAO Guang-ping, WANG Xiao-li, ZHAI Rui, WANG Zhi-gang, YANG Cheng-quan, XU Ling-fei

2022, 21 (6): 1645-1657. DOI: 10.1016/S2095-3119(21)63790-5

Abstract （152） PDF in ScienceDirect

Organic acids are one of the most important factors influencing fruit flavors. The predominant organic acid in most pear cultivars is malic acid, but the mechanism controlling its accumulation remains unclear. In this study, by comparing gene expression levels and organic acid content, we revealed that the expression of PbPH5, which encodes a P_3A-ATPase, is highly correlated with malic acid accumulation in different pear species, with correlation coefficients of 0.932^**, 0.656^*, 0.900^**, and 0.518^* (^*, P<0.05 or ^**, P<0.01) in Pyrus bretschneideri Rehd., P. communis Linn., P. pyrifolia Nakai., and P. ussuriensis Maxim., respectively. Moreover, the overexpression of PbPH5 in pear significantly increased the malic acid content. In contrast, silencing PbPH5 via RNA interference significantly decreased its transcript level and the pear fruit malic acid content. A subcellular localization analysis indicated that PbPH5 is located in the tonoplast. Additionally, a phylogenetic analysis proved that PbPH5 is a PH5 homolog gene that is clustered with Petunia hybrida, Malus domestica, and Citrus reticulata genes. Considered together, these findings suggest PbPH5 is a functionally conserved gene. Furthermore, the accumulation of malic acid in pear fruits is at least partly related to the changes in PbPH5 transcription levels.

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Overexpression of MdMIPS1 enhances drought tolerance and water-use efficiency in apple

HU Ling-yu, YUE Hong, ZHANG Jing-yun, LI Yang-tian-su, GONG Xiao-qing, ZHOU Kun, MA Feng-wang

2022, 21 (7): 1968-1981. DOI: 10.1016/S2095-3119(21)63822-4

Abstract （211） PDF in ScienceDirect

Myo-inositol and its derivatives play important roles in the tolerance of higher plants to abiotic stresses, and myo-inositol-1-phosphate synthase (MIPS) is the rate-limiting enzyme in myo-inositol biosynthesis. In this study, we found that increased myo-inositol biosynthesis enhanced drought tolerance in MdMIPS1-overexpressing apple lines under short-term progressive drought stress. The effect of myo-inositol appeared to be mediated by the increased accumulation of osmoprotectants such as glucose, sucrose, and proline, and by the increased activities of antioxidant enzymes that eliminate reactive oxygen species. Moreover, enhanced water-use efficiency (WUE) was observed in MdMIPS1-overexpressing apple lines under long-term moderate water deficit conditions that mimicked the water availability in the soil of the Loess Plateau. Enhanced WUE may have been associated with the synergistic regulation of osmotic balance and stomatal aperture mediated by increased myo-inositol biosynthesis. Taken together, our findings shed light on the positive effects of MdMIPS1-mediated myo-inositol biosynthesis on drought tolerance and WUE in apple.

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Nodulin 26-like intrinsic protein CsNIP2;2 is a silicon influx transporter in Cucumis sativus L.

DUAN Yao-ke, SU Yan HAN Rong, SUN Hao, GONG Hai-jun

2022, 21 (3): 685-696. DOI: 10.1016/S2095-3119(21)63748-6

Abstract （194） PDF in ScienceDirect

Nodulin 26-like intrinsic proteins (NIPs) are a family of channel-forming transmembrane proteins that function in the transport of water and other small molecules. Some NIPs can mediate silicon transport across plasma membranes and lead to silicon accumulation in plants, which is beneficial for the growth and development of plants. Cucumber is one of the most widely consumed vegetables; however, the functions of NIPs in this crop are still largely unknown. Here, we report the functional characteristics of CsNIP2;2. It was found that CsNIP2;2 is a tandem repeat of CsNIP2;1, which had been demonstrated to be a silicon influx transporter gene. CsNIP2;2 has a selectivity filter composed of cysteine, serine, glycine and arginine (CSGR), which is different from all previously characterized silicon influx transporters in higher plants at the second helix position. Xenopus laevis oocytes injected with CsNIP2;2 cRNA demonstrated a higher uptake of silicon than the control, and the uptake remained unchanged under low temperature. CsNIP2;2 was found to be expressed in the root, stem, lamina and petiole, and exogenous silicon treatment decreased its expression in the stem but not in other tissues. Transient expression of CsNIP2;2-eGFP fusion sequence in onion epidermal cells showed that CsNIP2;2 was localized to the cell nucleus, plasma membrane and an unknown structure inside the cell. The results suggest that CsNIP2;2 is a silicon influx transporter in cucumber, and its subcellular localization and the selectivity filter are different from those of the previously characterized silicon influx transporters in other plants. These findings may be helpful for understanding the functions of NIPs in cucumber plants.

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The impact of tandem duplication on gene evolution in Solanaceae species

HUANG Yi-le, ZHANG Ling-kui, ZHANG Kang, CHEN Shu-min, HU Jian-bin, CHENG Feng

2022, 21 (4): 1004-1014. DOI: 10.1016/S2095-3119(21)63698-5

Abstract （201） PDF in ScienceDirect

Whole genome duplication (WGD) and tandem duplication (TD) are important modes of gene amplification and functional innovation, and they are common in plant genome evolution. We analyzed the genomes of three Solanaceae species (Solanum lycopersicum, Capsicum annuum, and Petunia inflata), which share a common distant ancestor with Vitis vinifera, Theobroma cacao, and Coffea canephora but have undergone an extra whole genome triplication (WGT) event. The analysis was used to investigate the phenomenon of tandem gene evolution with (S. lycopersicum) or without WGT (V. vinifera). Among the tandem gene arrays in these genomes, we found that V. vinifera, which has not experienced the WGT event, retained relatively more and larger tandem duplicated gene (TDG) clusters than the Solanaceae species that experienced the WGT event. Larger TDG clusters tend to be derived from older TD events, so this indicates that continuous TDGs (absolute dosage) accumulated during long-term evolution. In addition, WGD and TD show a significant bias in the functional categories of the genes retained. WGD tends to retain dose-sensitive genes related to biological processes, including DNA-binding and transcription factor activity, while TD tends to retain genes involved in stress resistance. WGD and TD also provide more possibilities for gene functional innovation through gene fusion and fission. The TDG cluster containing the tomato fusarium wilt resistance gene I3 contains 15 genes, and one of these genes, Solyc07g055560, has undergone a fusion event after the duplication events. These data provide evidence that helps explain the new functionalization of TDGs in adapting to environmental changes.

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Genome-wide analysis of OVATE family proteins in cucumber (Cucumis sativus L.)

HAN Li-jie, SONG Xiao-fei, WANG Zhong-yi, LIU Xiao-feng, YAN Li-ying, HAN De-guo, ZHOU Zhao-yang, ZHANG Xiao-lan

2022, 21 (5): 1321-1331. DOI: 10.1016/S2095-3119(21)63788-7

Abstract （181） PDF in ScienceDirect

OVATE family proteins (OFPs) are plant-specific proteins with a conserved OVATE domain that regulate plant growth and development. Although OFPs have been studied in several species, their biological functions remain largely unknown in cucumber (Cucumis sativus L.). This study identified 19 CsOFPs distributed on seven chromosomes in cucumber. Most CsOFP genes were expressed in reproductive organs, but with different expression patterns. Ectopic expression of CsOFP12-16c in Arabidopsis resulted in shorter and blunt siliques. The overall results indicated that CsOFP12-16c regulates silique development in Arabidopsis and may have a similar function in cucumber.

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Genome-wide identification of WOX gene family in apple and a functional analysis of MdWOX4b during adventitious root formation

XU Xiao-zhao, CHE Qin-qin, CHENG Chen-xia, YUAN Yong-bing, WANG Yong-zhang

2022, 21 (5): 1332-1345. DOI: 10.1016/S2095-3119(21)63768-1

Abstract （338） PDF in ScienceDirect

The plant-specific WUSCHEL-related homeobox (WOX) genes are crucial for plant growth and development. Here, we systematically identified the MdWOX gene family in apple at the genome-wide level, and analyzed the phylogenetic relationships, conserved motifs, gene structure, and syntenic relationships of the MdWOX genes. A total of 18 MdWOX genes were identified and phylogenetic analysis placed them into three clades. The phylogenetic relationships among the WOXs were further supported by the analyses of gene structure and conserved motifs. Chromosomal distribution and synteny analysis revealed that whole-genome and segmental duplications have played key roles in MdWOX gene family expansion. Moreover, the MdWOX genes exhibit tissue-specific expression patterns and MdWOX4a, MdWOX4b, MdWOX5b, MdWOX11/12a, and MdWOX11/12b may play essential roles in adventitious root development. The adventitious rooting ability was enhanced in MdWOX4b transgenic tobacco lines. The results of this study provide useful information for future functional studies on MdWOXs in the development of apple rootstocks.

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Genome-scale mRNA and miRNA transcriptomic insights into the regulatory mechanism of cucumber corolla opening

SONG Xiao-fei, GE Dan-feng, XIE Yang, LI Xiao-li, SUN Cheng-zhen, CUI Hao-nan, ZHU Xue-yun, LIU Ren-yi, YAN Li-ying

2022, 21 (9): 2603-2614. DOI: 10.1016/j.jia.2022.07.024

Abstract （172） PDF in ScienceDirect

‘Corollas and spines’ is an important trait for fresh market cucumber. In a unique cucumber line, ‘6457’, the super ovary is much larger and corolla opening is delayed by 4–5 days, thus the resulting fruit has a flower that remains on the tip, which has a high commodity value. In this study, to better understand the molecular basis of corolla opening, mRNA and miRNA transcriptome analyses were performed during corolla development of the super and normal ovaries. A total of 234 differentially expressed miRNAs (DEMs) and 291 differentially expressed target genes (DE-target genes) were identified from four developmental stages, and the greatest number of DEMs was found at the yellow bud stage. Thirty of the DE-target genes were regulated by more than five DEMs, among which, CsHD-Zip was regulated by 28 DEMs, followed by DD2X (18). In addition, the expression patterns of miRNA_104, miRNA_157, miRNA_349, miRNA_242, and miRNA_98 were similar during corolla development, and they shared the same target gene, CsCuRX. Moreover, several critical candidate DEMs and DE-target genes were characterized and profiled by a qRT-PCR experiment. Three of the miRNAs, miRNA_157-CsCuRX, miRNA_411-CsGH3.6, and miRNA_161/297/257-CsHD-Zip, might be responsible for corolla opening in the cucumber super ovary. This integrated study on the transcriptional and post-transcriptional profiles can provide insights into the molecular regulatory mechanism underlying corolla opening in the cucumber.

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QTL-seq analysis of seed size trait in grape provides new molecular insight on seedlessness

WANG Li, ZHANG Song-lin, JIAO Chen, LI Zhi, LIU Chong-huai, WANG Xi-ping

2022, 21 (10): 2910-2925. DOI: 10.1016/j.jia.2022.07.047

Abstract （123） PDF in ScienceDirect

Seedlessness in grape (Vitis vinifera) is an important commercial trait for both the fresh and drying markets. However, despite numerous studies, the mechanisms and key genes regulating grape seedlessness are mostly unknown. In this study, we sequenced the genomes of the V. vinifera seeded cultivar ‘Red Globe’, the seedless cultivar ‘Centennial Seedless’, and the derived hybrids. Nonsynonymous single nucleotide polymorphisms (SNPs) were identified by genome sequencing and analyzed using published transcriptome data. Nonsynonymous SNPs occurred in genes related to seed development, which were identified as protein kinases, transcription factors, and cytochrome P450s and showed differential expression during ovule development in both seeded and seedless grapes. These nonsynonymous SNP-associated genes were mainly involved in biological processes such as hormone balance, seed coat and endosperm development, reproductive organ development, oxidation and reduction, senescence and cell death. A potential quantitative trait locus (QTL) region associated with seed size was characterized based on the SNP-index, and expression analysis of candidate genes in the QTL region during ovule development in multiple seeded and seedless grape cultivars were conducted. Three SNPs were further subjected to SNaPshot analysis and one SNP in G8 showed 67.5% efficiency in the grape progeny validation. Overall, the data obtained in this study shed light on the differences in seed development between seeded and seedless progeny at the genomic level, which provides valuable resources for future functional studies and grape breeding.

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Comparative transcriptome analysis provides insights into the mechanism of pear dwarfing

TANG Zi-kai, SUN Man-yi, LI Jia-ming, SONG Bo-bo, LIU Yue-yuan, TIAN Yi-ke, WANG Cai-hong, WU Jun

2022, 21 (7): 1952-1967. DOI: 10.1016/S2095-3119(21)63774-7

Abstract （224） PDF in ScienceDirect

Dwarfism is an important trait which is closely related to the efficiency of fruit orchard management and production. However, dwarfing cannot be widely applied in the cultivation of pears, especially Asian pears. Developing varieties with dwarf characteristics is a goal of paramount importance in pear breeding. In the present study, dwarf phenotype pears (DPPs) and arborescent phenotype pears (APPs) were obtained from the offspring of a cross between ‘Aiyuxiang’ and ‘Cuiguan’ pear cultivars, which exhibited dwarfed and arborescent statures, respectively. When compared with APPs, the heights of DPPs showed a 62.8% reduction, and the internode lengths were significantly shorter. Cross-grafting between DPPs and APPs demonstrated that the dwarfed phenotype of DPPs was primarily induced by the aerial portions of the plant, and independent of the root system. Observations of stem tissue sections showed that DPP cells were arranged chaotically with irregular shapes, and the average length was larger than that of the APP cells. A total of 1 401 differently expressed genes (DEGs) in shoot apices between DPPs and APPs were identified by RNA-sequencing (RNA-Seq), and these DEGs were mainly enriched in the ‘phytohormone-related pathways, cell wall metabolism and cell division’ categories. Moreover, 101 DEGs were identified as transcription factors (TFs). In DPPs, several brassinosteroids (BR) signaling and cell cycle-related genes were significantly down-regulated, while genes involved in BR and GA degradation were up-regulated. Comprehensive analysis of RNA-Seq data and stem tissue sections suggested that the dwarfed phenotype of DPPs could be primarily attributed to deficiencies in cell division. Previous work using simple sequence repeat (SSR) markers narrowed the location of the gene responsible for the dwarf phenotype of ‘Le Nain Vert’. Through combined analysis of our transcriptomic data with the SSR results, we identified four genes as promising candidates for the dwarf phenotype, among which, a DELLA gene could be the most promising. The results presented in this study provide a sound foundation for further exploration into the genetic and molecular mechanisms underlying pear dwarfing.

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Identifying potential flavonoid biosynthesis regulator in Zanthoxylum bungeanum Maxim. by genome-wide characterization of the MYB transcription factor gene family

WANG Xiang-yuan, TIAN Lu, FENG Shi-jing, WEI An-zhi

2022, 21 (7): 1997-2018. DOI: 10.1016/S2095-3119(21)63747-4

Abstract （136） PDF in ScienceDirect

Plant MYB transcription factors (TFs) play crucial roles in regulating the biosynthesis of flavonoids but current analysis on their role in Zanthoxylum bungeanum Maxim. (ZBM) is far from comprehensive. In this study, we identified 270 MYB genes in ZBM and divided them into four subfamilies. The R2R3-MYB (ZbMYB) category contained 251 genes and was classified into 33 subfamilies according to their phylogenetic results and sequence similarity. These subfamilies included 24 subgroups containing both MYBs of ZBM plants and AtMYBs, and nine subgroups containing only ZBM MYBs or AtMYBs. ZbMYBs with similar functions clustered into the same subgroup, indicating functional conservation. The subcellular localization analysis predicted that most ZbMYB genes were found in the nucleus. The transposed duplications appeared to play a major role in the expansion of the MYB gene family in ZBM. Through phylogenetic analysis and transcriptome profiling, it was found that 28 ZbMYB genes may regulate the biosynthesis of flavonoids in ZBM, and these genes expression presented distinct temporal and spatial expression patterns. In different fruit development stages of ZBM, the expression patterns of EVM0042160 and EVM0033809 genes obtained by qRT-PCR analysis are very similar to the flavonoid and anthocyanin content curves in ZBM. Further correlation analysis showed that the content of flavonoids in different fruit development stages and the transcript abundance levels of 28 ZbMYB genes have different degrees of correlation relationship. These results indicated that the ZbMYB genes might be involved in the flavonoid metabolic pathway. This comprehensive and systematic analysis of MYB family genes provided a solid foundation for further functional analysis of MYB TFs in ZBM.

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Identification of soft rot resistance loci in Brassica rapa with SNP markers

LIU Meng-yang, WU Fang, GE Yun-jia, LU Yin, ZHANG Xiao-meng, WANG Yan-hua, WANG Yang, YAN Jing-hui, SHEN Shu-xing, ZHAO Jian-jun, MA Wei

2022, 21 (8): 2253-2263. DOI: 10.1016/S2095-3119(21)63874-1

Abstract （165） PDF in ScienceDirect

Soft rot caused by Pectobacterium carotovorum (Pc) is a devastating disease of Brassica rapa, causing substantial reductions in crop yield and quality. Identifying genes related to soft rot resistance is the key to solving this problem. To characterize soft rot resistance, we screened a soft rot-susceptible Chinese cabbage (A03), a resistant pakchoi (‘Huaguan’), and a resistant mutant (sr). An F₂ population was generated by crossing susceptible Chinese cabbage A03 and resistant pakchoi ‘Huaguan’ to identify quantitative trait loci (QTLs) that confer soft rot resistance. A high-density genetic map was constructed and the three QTLs identified contain 166 genes. Based on available transcriptome data, we analyzed the expression of the 166 genes during an important defense regulatory period in Pc infection in both A03 and the resistant mutant sr. Among the 166 genes, six candidate genes were related to the soft rot defense response in B. rapa. TIFY10B (JAZ2, BraA07g038660.3C) was located in the major soft rot resistance QTL, DRQTL-3 on A07, and we speculate that this gene may play an important role in the defense mechanism against soft rot in B. rapa. This study lays the foundation for further investigations on the mechanism of soft rot resistance in B. rapa crops.

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Auxin response factor gene MdARF2 is involved in ABA signaling and salt stress response in apple

WANG Chu-kun, ZHAO Yu-wen, HAN Peng-liang, YU Jian-qiang, HAO Yu-jin, XU Qian, YOU Chun-xiang, HU Da-gang

2022, 21 (8): 2264-2274. DOI: 10.1016/S2095-3119(21)63843-1

Abstract （162） PDF in ScienceDirect

Auxin response factors (ARFs) play key roles throughout the whole process of plant growth and development, and mediate auxin response gene transcription by directly binding with auxin response elements (AuxREs). However, their functions in abiotic stresses are largely limited, especially in apples. Here, the auxin response factor gene MdARF2 (HF41569) was cloned from apple cultivar ‘Royal Gala’ (Malus×domestica Borkh.). Phylogenetic analysis showed that ARF2 proteins are highly conserved among different species and MdARF2 is the closest relative to PpARF2 of Prunus persica, but they differ at the DNA level. MdARF2 contains three typical conserved domains including the B3 DNA-binding domain, Auxin_resp domain and AUX_IAA domain. The subcellular localization demonstrated that MdARF2 is localized in the nucleus. The three-dimensional structure prediction of the proteins showed that MdARF2 is highly similar with AtARF2, and they contain helices, folds, and random coils. The promoter of MdARF2 contains cis-acting elements which respond to various stresses, as well as environmental and hormonal signals. Expression analysis showed that MdARF2 is widely expressed in all tissues of apple, with the highest expression of MdARF2 in root. Functional analysis with a series of MdARF2 transgenic apple calli indicated that MdARF2 can reduce the sensitivity to ABA signaling and enhance salt tolerance in apple. In summary, the results of this research provide a new basis for studying the regulation of abiotic stresses by ARFs.

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An assessment of the genetic diversity of pear (Pyrus L.) germplasm resources based on the fruit phenotypic traits

ZHANG Ying, CAO Yu-fen, HUO Hong-liang, XU Jia-yu, TIAN Lu-ming, DONG Xing-guang, QI Dan, LIU Chao

2022, 21 (8): 2275-2290. DOI: 10.1016/S2095-3119(21)63885-6

Abstract （162） PDF in ScienceDirect

Germplasm resources are an important basis for genetic breeding and analysis of complex traits, and research on genetic diversity is conducive to the exploration and creation of new types of germplasm. In this study, the distribution frequency, coefficient of variation, Shannon–Wiener index, and variance and cluster analyses were used to analyze the diversity and trait differences of 39 fruit phenotypic traits from 570 pear accessions, which included 456 pear accessions from 11 species and 114 interspecific hybrid cultivars that had been stored in the National Germplasm Repository of Apple and Pear (Xingcheng, China). The comprehensive evaluation indices were screened by correlation, principal component and regression analyses. A total of 132 variant types were detected in 28 categorical traits of pear germplasm fruit, which indicate a rich diversity. The diversity indices in decreasing order were: fruit shape (1.949), attitude of calyx (1.908), flesh texture type (1.700), persistency of calyx (1.681), russet location (1.658), relief of area around eye basin (1.644), flavor (1.610) and ground color (1.592). The coefficient of variation of titratable acidity in the 11 numerical traits of pear germplasm fruit was as high as 128.43%, which could more effectively reflect the differences between pear accessions. The phenotypic differentiation coefficient V_st (66.4%) among the five cultivated pear species, including Pyrus bretschneideri (White Pear), P. pyrifolia (Sand Pear), P. ussuriensis (Ussurian Pear), P. sinkiangensis (Xinjiang Pear), and P. communis (European Pear), was higher than the within population phenotypic differentiation coefficient V_st(33.6%). The variation among populations was the main source of variation in pear fruit traits. A hierarchical cluster analysis divided the 389 accessions of six cultivated pear species, including P. pashia (Himalayan Pear), into six categories. There were certain characteristics within the populations, and the differences between populations were not completely clustered by region. For example, Sand Pear cultivars from Japan and the Korean Peninsula clustered together with those from China. Most of the White Pear cultivars clustered with the Sand Pear, and a few clustered with the Ussurian Pear cultivars. The Ussurian Pear and European Pear cultivars clustered separately. The Xinjiang Pear and Himalayan Pear did not cluster together, and neither did the cultivars. Seventeen traits, three describing fruit weight and edible rate (fruit diameter, fruit length and fruit core size), five describing outer quality and morphological characteristics (over color, amount of russeting, dot obviousness, fruit shape, and stalk length), and nine describing inner quality (flesh color, juiciness of flesh, aroma, flavor, flesh texture, flesh texture type, soluble solid contents, titratable acidity, and eating quality) were selected from the 39 traits by principal component and stepwise regression analyses. These 17 traits could reflect 99.3% of the total variation and can be used as a comprehensive evaluation index for pear germplasm resources.

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A novel long non-coding RNA, DIR, increases drought tolerance in cassava by modifying stress-related gene expression

DONG Shi-man, XIAO Liang, LI Zhi-bo, SHEN Jie, YAN Hua-bing, LI Shu-xia, LIAO Wen-bin, PENG Ming

2022, 21 (9): 2588-2602. DOI: 10.1016/j.jia.2022.07.022

Abstract （201） PDF in ScienceDirect

Cassava is an important tropical cash crop. Severe drought stresses affect cassava productivity and quality, and cause great economic losses in agricultural production. Enhancing the drought tolerance of cassava can effectively improve its yield. Long non-coding RNAs (lncRNAs) are present in a wide variety of eukaryotes. Recently, increasing evidence has shown that lncRNAs play a critical role in the responses to abiotic stresses. However, the function of cassava lncRNAs in the drought response remains largely unknown. In this study, we identified a novel lncRNA, DROUGHT-INDUCED INTERGENIC lncRNA (DIR). Gene expression analysis showed that DIR was significantly induced by drought stress treatment, but did not respond to abscisic acid (ABA) or jasmonic acid (JA) treatments. In addition, overexpression of the DIR gene enhanced proline accumulation and drought tolerance in transgenic cassava. RNA-seq analysis revealed that DIR preferentially affected drought-related genes that were linked to transcription and metabolism. Moreover, RNA pull-down mass spectrometry analysis showed that DIR interacted with 325 proteins. A protein–protein interaction (PPI) analysis found a marked enrichment in proteins associated with the mRNA export and protein quality control pathways. Collectively, these results suggest that DIR and its interacting proteins that regulate mRNA or protein metabolism are involved in mediating the drought stress response. Thus, regulating DIR expression has potential for improving cassava yield under drought conditions.

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Comparative transcriptomic analysis of Rosa sterilis inflorescence branches with different trichome types reveals an R3-MYB transcription factor that negatively regulates trichome formation

MA Wen-tao, LU Min, AN Hua-ming, YI Yin

2022, 21 (10): 2926-2942. DOI: 10.1016/j.jia.2022.07.050

Abstract （99） PDF in ScienceDirect

Rosa sterilis S. D. Shi is an important economic tree in China that produces fruits with high nutritional and medicinal value. Many of R. sterilis’ organs are covered with different types of trichomes or prickles that directly affect fruit appearance and plant management. This study used RNA sequencing technology to analyze the transcriptomes of two parts of the inflorescence branch, namely inflorescence stems with flagellated trichomes and pedicels with both flagellated and glandular trichomes. Comparative transcriptomic analysis showed that many transcription factors (TFs) are potentially involved in the formation and development of trichomes. The accumulation of RsETC1, a TF of the R3-MYB family, was significantly higher in inflorescence stems than in pedicels; quantitative reverse transcription PCR (qRT-PCR) verified that its expression was significantly higher in inflorescence stems than in pedicels during the first three development stages, indicating its inhibitory action on the initiation of glandular trichomes in R. sterilis. The mRNA level of RsETC1 accumulated to significantly higher levels in trichomeless tissues than in tissues with trichromes, suggesting that this gene may inhibit the formation of trichomes in R. sterilis. Over-expression of RsETC1 in Arabidopsis resulted in glabrous phenotypes, and the expression of trichome-related endogenous genes, except for TTG1, was markedly reduced. In addition, the contents of the phytohormones jasmonic acid (JA), gibberellin A3 (GA₃), and cytokinins (CKs) in pedicels were significantly higher than those in inflorescence stems, and the expression patterns of the genes related to hormone biosynthesis and signal transduction presented consistent responses, suggesting that the transduction of these hormones might be crucial for trichome initiation and development. These data provide a new perspective for revealing the molecular mechanism of trichome formation in R. sterilis.

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