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    园艺作物基因功能与分子调控机制Horticulture — Gene function · Molecular mechanism

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    StOFP20 regulates tuber shape and interacts with TONNEAU1 Recruiting Motif proteins in potato
    AI Ju, WANG Ye, YAN Ya-wen, LI Chen-xiao, LUO Wei, MA Ling, SHANG Yi, GAO Dong-li
    2023, 22 (3): 752-761.   DOI: 10.1016/j.jia.2022.08.069
    Abstract368)      PDF in ScienceDirect      

    The OVATE family proteins (OFPs) are plant-specific proteins that modulate diverse aspects of plant growth and development.  In tomato, OFP20 has been shown to interact with TONNEAU1 Recruiting Motif (TRM) proteins to regulate fruit shape.  In this study, we demonstrated that the mutation of StOFP20 caused a shift from round to oval shaped tubers in a diploid accession C151, supporting the role of StOFP20 in controlling tuber shape.  Its expression reached a maximum in the tuber initiation stage and then decreased as the tuber develops.  To help elucidate the mechanism of tuber shape regulation by StOFP20, 27 TONNEAU1 Recruiting Motif (TRM) proteins were identified and 23 of them were successfully amplified in C151.  A yeast two-hybrid assay identified three TRM proteins that interacted with StOFP20, which was confirmed by firefly luciferase complementation in tobacco leaves.  The OVATE domain was indispensable for the interactions, while the necessity of the M10 motif in TRM proteins varied among the interactions between StOFP20 and the three TRMs.  In summary, both StOFP20 and SlOFP20 directed interactions with TRM proteins, but the corresponding interactants were not completely consistent, implying that they exert regulatory roles through mechanisms that are only partially overlapping.  

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    Evaluation of the early defoliation trait and identification of resistance genes through a comprehensive transcriptome analysis in pears
    SHAN Yan-fei, LI Meng-yan, WANG Run-ze, LI Xiao-gang, LIN Jing, LI Jia-ming, ZHAO Ke-jiao, WU Jun
    2023, 22 (1): 120-138.   DOI: 10.1016/j.jia.2022.08.040
    Abstract292)      PDF in ScienceDirect      

    Early defoliation, which usually occurs during summer in pear trees, is gradually becoming a major problem that poses a serious threat to the pear industry in southern China.  However, there is no system for evaluating the responses of different cultivars to early defoliation, and our knowledge of the potential molecular regulation of the genes underlying this phenomenon is still limited.  In this study, we conducted field investigations of 155 pear accessions to assess their resistance or susceptibility to early defoliation.  A total of 126 accessions were found to be susceptible to early defoliation, and only 29 accessions were resistant.  Among them, 19 resistant accessions belong to the sand pear species (Pyrus pyrifolia).  To identify the resistance genes related to early defoliation, the healthy and diseased samples of two sand pear accessions, namely, the resistant early defoliation accession ‘Whasan’ and the susceptible early defoliation accession ‘Cuiguan’, were used to perform RNA sequencing.  Compared with ‘Cuiguan’, a total of 444 genes were uniquely differentially expressed in ‘Whasan’.  Combined with GO and KEGG enrichment analyses, we found that early defoliation was closely related to the stress response.  Furthermore, a weighted gene co-expression network analysis revealed a high correlation of WRKY and ethylene responsive factor (ERF) transcription factors with early defoliation resistance.  This study provides useful resistant germplasm resources and new insights into potentially essential genes that respond to early defoliation in pears, which may facilitate a better understanding of the resistance mechanism and molecular breeding of resistant pear cultivars

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    PpMAPK6 regulates peach bud endodormancy release through interactions with PpDAM6

    ZHANG Yu-zheng, XU Chen, LU Wen-li, WANG Xiao-zhe, WANG Ning, MENG Xiang-guang, FANG Yu-hui, TAN Qiu-ping, CHEN Xiu-de, FU Xi-ling, LI Ling
    2023, 22 (1): 139-148.   DOI: 10.1016/j.jia.2022.09.010
    Abstract195)      PDF in ScienceDirect      

    The MADS-box (DAM) gene PpDAM6, which is related to dormancy, plays a key role in bud endodormancy release, and the expression of PpDAM6 decreases during endodormancy release.  However, the interaction network that governs its regulation of the endodormancy release of flower buds in peach remains unclear.  In this study, we used yeast two-hybrid (Y2H) assays to identify a mitogen-activated protein kinase, PpMAPK6, that interacts with PpDAM6 in a peach dormancy-associated SSHcDNA library.  PpMAPK6 is primarily located in the nucleus, and Y2H and bimolecular fluorescence complementation (BiFC) assays verified that PpMAPK6 interacts with PpDAM6 by binding to the MADS-box domain of PpDAM6.  Quantitative real-time PCR (qRT-PCR) analysis showed that the expression of PpMAPK6 was opposite that of PpDAM6 in the endodormancy release of three cultivars with different chilling requirements (Prunus persica ‘Chunjie’, Prunus persica var. nectarina ‘Zhongyou 5’, Prunus persica ‘Qingzhou peach’).  In addition, abscisic acid (ABA) inhibited the expression of PpMAPK6 and promoted the expression of PpDAM6 in flower buds.  The results indicated that PpMAPK6 might phosphorylate PpDAM6 to accelerate its degradation by interacting with PpDAM6.  The expression of PpMAPK6 increased with decreasing ABA content during endodormancy release in peach flower buds, which in turn decreased the expression of PpDAM6 and promoted endodormancy release.

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    Functional analysis of MdSUT2.1, a plasma membrane sucrose transporter from apple
    ZHANG Bo, FAN Wen-min, ZHU Zhen-zhen, WANG Ying, ZHAO Zheng-yang
    2023, 22 (3): 762-775.   DOI: 10.1016/j.jia.2022.09.012
    Abstract260)      PDF in ScienceDirect      

    Sugar content is a determinant of apple (Malus×domestica Borkh.) sweetness.  However, the molecular mechanism underlying sucrose accumulation in apple fruit remains elusive.  Herein, this study reported the role of the sucrose transporter MdSUT2.1 in the regulation of sucrose accumulation in apples.  The MdSUT2.1 gene encoded a protein with 612 amino acid residues that could be localized at the plasma membrane when expressed in tobacco leaf protoplasts.  MdSUT2.1 was highly expressed in fruit and was positively correlated with sucrose accumulation during apple fruit development.  Moreover, complementary growth assays in a yeast mutant validated the sucrose transport activity of MdSUT2.1.  MdSUT2.1 overexpression in apples and tomatoes resulted in significant increases in sucrose, fructose, and glucose contents compared to the wild type (WT).  Further analysis revealed that the expression levels of sugar metabolism- and transport-related genes SUSYs, NINVs, FRKs, HXKs, and TSTs increased in apples and tomatoes with MdSUT2.1 overexpression compared to WT.  Finally, unlike the tonoplast sugar transporters MdTST1 and MdTST2, the promoter of MdSUT2.1 was not induced by exogenous sugars.  These findings provide valuable insights into the molecular mechanism underlying sugar accumulation in apples.

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    Identification and functional analysis of arabinogalactan protein expressed in pear pollen tubes
    JIAO Hui-jun, WANG Hong-wei, RAN Kun, DONG Xiao-chang, DONG Ran, WEI Shu-wei, WANG Shao-min
    2023, 22 (3): 776-789.   DOI: 10.1016/j.jia.2023.02.007
    Abstract183)      PDF in ScienceDirect      

    Arabinogalactan proteins (AGPs) are widely distributed in the plant kingdom and play a vital role during the process of plant sexual reproduction.  In this study, we performed a comprehensive identification of the PbrAGPs expressed in pear pollen and further explored their influences on pollen tube growth.  Among the 187 PbrAGPs that were found to be expressed in pear pollen tubes, 38 PbrAGPs were specifically expressed in pollen according to the RNA-seq data.  The PbrAGPs were divided into two groups of highly expressed and specifically expressed in pear pollen.  We further tested their expression patterns using RT-PCR and RT-qPCR.  Most of the PbrAGPs were expressed in multiple tissues and their expression levels were consistent with reads per kilobase per million map reads (RPKM) values during pollen tube growth, implying that PbrAGPs might be involved in the regulation of pear pollen tube growth.  We also constructed phylogenetic trees to identify the functional genes in pear pollen tube growth.  Therefore, 19 PbrAGPs (PbrAGP1 to PbrAGP19) were selected to test their influences on pollen tube growth.  Recombinant proteins of the 19 PbrAGP-His were purified and used to treat pear pollen, and 11 of the PbrAGP-His recombinant proteins could promote pear pollen tube growth.  Additionally, pollen tube growth was inhibited when the expression levels of PbrAGP1 and PbrAGP5 were knocked down using an antisense oligonucleotide assay.  PbrAGP1 and PbrAGP5 were localized in the plasma membrane and might not alter the distribution of pectin in the pollen tube.  In summary, this study identified the PbrAGPs expressed in pear pollen and lays the foundation for further exploring their functions in pollen tube growth.

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    Molecular characterization of the SAUR gene family in sweet cherry and functional analysis of PavSAUR55 in the process of abscission
    HOU Qian-dong, HONG Yi, WEN Zhuang, SHANG Chun-qiong, LI Zheng-chun, CAI Xiao-wei, QIAO Guang, WEN Xiao-peng
    2023, 22 (6): 1720-1739.   DOI: 10.1016/j.jia.2023.04.031
    Abstract241)      PDF in ScienceDirect      

    Small auxin up RNA (SAUR) is a large gene family that is widely distributed among land plants.  In this study, a comprehensive analysis of the SAUR family was performed in sweet cherry, and the potential biological functions of PavSAUR55 were identified using the method of genetic transformation.  The sweet cherry genome encodes 86 SAUR members, the majority of which are intron-less.  These genes appear to be divided into seven subfamilies through evolution.  Gene duplication events indicate that fragment duplication and tandem duplication events occurred in the sweet cherry.  Most of the members mainly underwent purification selection pressure during evolution.  During fruit development, the expression levels of PavSAUR16/45/56/63 were up-regulated, and conversely, those of PavSAUR12/61 were down-regulated.  Due to the significantly differential expressions of PavSAUR13/16/55/61 during the fruitlet abscission process, they might be the candidate genes involved in the regulation of physiological fruit abscission in sweet cherry.  Overexpression of PavSAUR55 in Arabidopsis produced earlier reproductive growth, root elongation, and delayed petal abscission.  In addition, this gene did not cause any change in the germination time of seeds and was able to increase the number of lateral roots under abscisic acid (ABA) treatment.  The identified SAURs of sweet cherry play a crucial role in fruitlet abscission and will facilitate future insights into the mechanism underlying the heavy fruitlet abscission that can occur in this fruit crop.

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    Genome-wide identification and function analysis of the sucrose phosphate synthase MdSPS gene family in apple
    ZHANG Li-hua, ZHU Ling-cheng, XU Yu, LÜ Long, LI Xing-guo, LI Wen-hui, LIU Wan-da, MA Feng-wang, LI Ming-jun, HAN De-guo
    2023, 22 (7): 2080-2093.   DOI: 10.1016/j.jia.2023.05.024
    Abstract233)      PDF in ScienceDirect      

    Sucrose phosphate synthase (SPS) is a rate-limiting enzyme that works in conjunction with sucrose-6-phosphate phosphatase (SPP) for sucrose synthesis, and it plays an essential role in energy provisioning during growth and development in plants as well as improving fruit quality.  However, studies on the systematic analysis and evolutionary pattern of the SPS gene family in apple are still lacking.  In the present study, a total of seven MdSPS and four MdSPP genes were identified from the Malus domestica genome GDDH13 v1.1.  The gene structures and their promoter cis-elements, protein conserved motifs, subcellular localizations, physiological functions and biochemical properties were analyzed.  A chromosomal location and gene-duplication analysis demonstrated that whole-genome duplication (WGD) and segmental duplication played vital roles in MdSPS gene family expansion.  The Ka/Ks ratio of pairwise MdSPS genes indicated that the members of this family have undergone strong purifying selection during domestication.  Furthermore, three SPS gene subfamilies were classified based on phylogenetic relationships, and old gene duplications and significantly divergent evolutionary rates were observed among the SPS gene subfamilies.  In addition, a major gene related to sucrose accumulation (MdSPSA2.3) was identified according to the highly consistent trends in the changes of its expression in four apple varieties (‘Golden Delicious’, ‘Fuji’, ‘Qinguan’ and ‘Honeycrisp’) and the correlation between gene expression and soluble sugar content during fruit development.  Furthermore, the virus-induced silencing of MdSPSA2.3 confirmed its function in sucrose accumulation in apple fruit.  The present study lays a theoretical foundation for better clarifying the biological functions of the MdSPS genes during apple fruit development.

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    The PcERF5 promotes anthocyanin biosynthesis in red-fleshed pear (Pyrus communis) through both activating and interacting with PcMYB transcription factors
    CHANG Yao-jun, CHEN Guo-song, YANG Guang-yan, SUN Cong-rui, WEI Wei-lin, Schuyler S. KORBAN, WU Jun
    2023, 22 (9): 2687-2704.   DOI: 10.1016/j.jia.2023.07.007
    Abstract216)      PDF in ScienceDirect      

    As there is a strong interest in red-skinned pears, the molecular mechanism of anthocyanin regulation in red-skinned pears has been widely investigated; however, little is known about the molecular mechanism of anthocyanin regulation in red-fleshed pears due to limited availability of such germplasm, primarily found in European pears (Pyrus communis).  In this study, based on transcriptomic analysis in red-fleshed and white-fleshed pears, we identified an ethylene response factor (ERF) from Pcommunis, PcERF5, of which expression level in fruit flesh was significantly correlated with anthocyanin content.  We then verified the function of PcERF5 in regulating anthocyanin accumulation by genetic transformation in both pear skin and apple calli.  PcERF5 regulated anthocyanin biosynthesis by different regulatory pathways.  On the one hand, PcERF5 can activate the transcription of flavonoid biosynthetic genes (PcDFR, PcANS and PcUFGT) and two key transcription factors encoding genes PcMYB10 and PcMYB114.  On the other hand, PcERF5 interacted with PcMYB10 to form the ERF5-MYB10 protein complex that enhanced the transcriptional activation of PcERF5 on its target genes.  Our results suggested that PcERF5 functioned as a transcriptional activator in regulating anthocyanin biosynthesis, which provides new insights into the regulatory mechanism of anthocyanin biosynthesis.  This new knowledge will provide guidance for molecular breeding of red-fleshed pear.

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    Functional prediction of tomato PLATZ family members and functional verification of SlPLATZ17
    XU Min, GAO Zhao, LI Da-long, ZHANG Chen, ZHANG Yu-qi, HE Qian, QI Ying-bin, ZHANG He, JIANG Jing-bin, XU Xiang-yang, ZHAO Ting-ting
    DOI: doi.org/10.1016/j.jia.2023.08.003 Online: 03 August 2023
    Abstract0)      PDF in ScienceDirect      

    PLATZ is a novel zinc finger DNA-binding protein that plays an important role in regulating plant growth and development and resisting abiotic stress. However, there has been very little research on the function of this family gene in tomatoes, which limits its application in germplasm resource improvement. Therefore, the PLATZ gene family was identified and analyzed in tomato, and its roles were predicted and verified to provide a basis for in-depth research on SlPLATZ gene function. In this study, the PLATZ family members of tomato were identified in the whole genome, and 19 SlPLATZ genes were obtained. Functional prediction was conducted based on gene and promoter structure analysis and RNA-seq-based expression pattern analysis. SlPLATZ genes that responded significantly under different abiotic stresses or were significantly differentially expressed among multiple tissues were screened as functional gene resources. SlPLATZ17 was selected for functional verification by experiment-based analysis. The results showed that the downregulation of SlPLATZ17 gene expression reduced the drought and salt tolerance of tomato plants. Tomato plants overexpressing SlPLATZ17 had larger flower sizes and long, thin petals, adjacent petals were not connected at the base, and the stamen circumference was smaller. This study contributes to understanding the functions of the SlPLATZ family in tomato and provides a reference for functional gene screening.

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    The nitrate-responsive transcription factor MdNLP7 regulates callus formation by modulating auxin response
    LI Tong, FENG Zi-quan, ZHANG Ting-ting, YOU Chun-xiang, ZHOU Chao, WANG Xiao-Fei
    2023, 22 (10): 3022-3033.   DOI: 10.1016/j.jia.2023.08.007
    Abstract188)      PDF in ScienceDirect      

    Under appropriate culture conditions, plant cells can regenerate new organs or even whole plants.  De novo organ regeneration is an excellent biological system, which usually requires additional growth regulators, including auxin and cytokinin.  Nitrate is an essential nutrient element for plant vegetative and reproductive development.  It has been reported that nitrate is involved in auxin biosynthesis and transport throughout the growth and development of plants.  In this study, we demonstrated that the ectopic expression of the MdNLP7 transcription factor in Arabidopsis could regulate the regeneration of root explants.  MdNLP7 mainly participated in the regulation of callus formation, starting with pericycle cell division, and mainly affected auxin distribution and accumulation in the regulation process.  Moreover, MdNLP7 upregulated the expression of genes related to auxin biosynthesis and transport in the callus formation stage.  The results demonstrated that MdNLP7 may play a role in the nitrate-modulated regeneration of root explants.  Moreover, the results revealed that nitrate–auxin crosstalk is required for de novo callus initiation and clarified the mechanisms of organogenesis.

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    A mutation in the promoter of the yellow stripe-like transporter gene in cucumber results in a yellow cotyledon phenotype

    Jiawei Pan, Jia Song, Rahat Sharif, Xuewen Xu, Shutong Li, Xuehao Chen
    2024, 23 (3): 849-862.   DOI: 10.1016/j.jia.2023.11.024
    Abstract151)      PDF in ScienceDirect      
    Leaf color mutants in higher plants are considered to be ideal materials for studying the chlorophyll biosynthesis, photosynthesis mechanism and chloroplast development.  Herein, we identified a spontaneous mutant, yc412, in cultivated cucumber that exhibited yellow cotyledons.  The yellow-lethal mutant was diagnosed with an abnormal chloroplast ultrastructure, and reduced photosynthetic capacity and pigment content.  Through bulked segregant analysis-based whole-genome sequencing and fine genetic mapping, we narrowed the yellow cotyledons (yc) locus to a 96.8 kb interval on chromosome 3.  By resequencing and molecular cloning, we showed that Csyc is a potential candidate gene, which encodes a yellow stripe-like (YSL) transporter.  The T to C mutation in the promoter region of Csyc caused the yellow cotyledon phenotype in yc412.  Compared to YZU027A (WT), the expression of Csyc was significantly downregulated in the cotyledons of yc412.  Silencing of Csyc in cucumber via virus-induced gene silencing resulted in chlorotic leaves, mainly by suppressing the chlorophyll content.  Furthermore, a comparative transcriptome analysis revealed that chloroplast-related genes and chlorophyll biosynthesis genes were significantly downregulated in yc412 cotyledons.  Our results provide new insights into the molecular function of the YSL transporter in plant chloroplast development and chlorophyll synthesis.
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    Alternative splicing of the PECTINESTERASE gene encoding a cell wall-degrading enzyme affects postharvest softening in grape

    Hainan Liu, Maosong Pei, Charles Ampomah-Dwamena, Yaxin Shang, Yihe Yu, Tonglu Wei, Qiaofang Shi, Dalong Guo
    2024, 23 (3): 863-875.   DOI: 10.1016/j.jia.2023.11.023
    Abstract159)      PDF in ScienceDirect      

    The firmness of table grape berries is a crucial quality parameter.  Despite extensive research on postharvest fruit softening, its precise molecular mechanisms remain elusive.  To enhance our comprehension of the underlying molecular factors, we initially identified differentially expressed genes (DEGs) by comparing the transcriptomes of folic acid (FA)-treated and water-treated (CK) berries at different time points.  We then analyzed the sequences to detect alternatively spliced (AS) genes associated with postharvest softening.  A total of 2,559 DEGs were identified and categorized into four subclusters based on their expression patterns, with subcluster-4 genes exhibiting higher expression in the CK group compared with the FA treatment group.  There were 1,045 AS-associated genes specific to FA-treated berries and 1,042 in the CK-treated berries, respectively.  Gene Ontology (GO) annotation indicated that the AS-associated genes in CK-treated berries were predominantly enriched in cell wall metabolic processes, particularly cell wall degradation processes.  Through a comparison between treatment-associated AS genes and subcluster-4 DEGs, we identified eight genes, including Pectinesterase 2 (VvPE2, Vitvi15g00704), which encodes a cell wall-degrading enzyme and was predicted to undergo an A3SS event.  The reverse transcription polymerase chain reaction further confirmed the presence of a truncated transcript variant of VvPE2 in the FA-treated berries.  Our study provides a comprehensive analysis of AS events in postharvest grape berries using transcriptome sequencing and underscores the pivotal role of VvPE2 during the postharvest storage of grape berries.

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    Genome-wide identification of the CONSTANS-LIKE (COL) family and mechanism of fruit senescence regulation by PpCOL8 in sand pear (Pyrus pyrifolia)

    Yue Xu, Shurui Song, Huiying Wang, Xilong Cao, Xinran Zhao, Wenli Wang, Liyue Huo, Yawei Li, Misganaw Wassie, Bin Lu, Liang Chen, Haiyan Shi
    2024, 23 (4): 1222-1237.   DOI: 10.1016/j.jia.2024.01.011
    Abstract126)      PDF in ScienceDirect      
    Pyrus pyrifolia Nakai ‘Whangkeumbae’ is a sand pear fruit with excellent nutritional quality and taste.  However, the industrial development of pear fruit is significantly limited by its short shelf life.  Salicylic acid (SA), a well-known phytohormone, can delay fruit senescence and improve shelf life.  However, the mechanism by which SA regulates CONSTANS-LIKE genes (COLs) during fruit senescence and the role of COL genes in mediating fruit senescence in sand pear are poorly understood.  In this study, 22 COL genes were identified in sand pear, including four COLs (PpCOL8, PpCOL9a, PpCOL9b, and PpCOL14) identified via transcriptome analysis and 18 COLs through genome-wide analysis.  These COL genes were divided into three subgroups according to the structural domains of the COL protein.  PpCOL8, with two B-box motifs and one CCT domain, belonged to the first subgroup.  In contrast, the other three PpCOLs, PpCOL9a, PpCOL9b, and PpCOL14, with similar conserved protein domains and gene structures, were assigned to the third subgroup.  The four COLs showed different expression patterns in pear tissues and were preferentially expressed at the early stage of fruit development.  Moreover, the expression of PpCOL8 was inhibited by exogenous SA treatment, while SA up-regulated the expression of PpCOL9a and PpCOL9b.  Interestingly, PpCOL8 interacts with PpMADS, a MADS-box protein preferentially expressed in fruit, and SA up-regulated its expression.  While the production of ethylene and the content of malondialdehyde (MDA) were increased in PpCOL8-overexpression sand pear fruit, the antioxidant enzyme (POD and SOD) activity and the expression of PpPOD1 and PpSOD1 in the sand pear fruits were down-regulated, which showed that PpCOL8 promoted sand pear fruit senescence.  In contrast, the corresponding changes were the opposite in PpMADS-overexpression sand pear fruits, suggesting that PpMADS delayed sand pear fruit senescence.  The co-transformation of PpCOL8 and PpMADS also delayed sand pear fruit senescence.  The results of this study revealed that PpCOL8 can play a key role in pear fruit senescence by interacting with PpMADS through the SA signaling pathway.
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    Silencing of early auxin responsive genes MdGH3-2/12 reduces the resistance to Fusarium solani in apple
    Qianwei Liu, Shuo Xu, Lu Jin, Xi Yu, Chao Yang, Xiaomin Liu, Zhijun Zhang, Yusong Liu, Chao Li, Fengwang Ma
    2024, 23 (9): 3012-3024.   DOI: 10.1016/j.jia.2024.03.003
    Abstract87)      PDF in ScienceDirect      
    Apple replant disease (ARD) has led to severe yield and quality reduction in the apple industry.  Fusarium solani (Fsolani) has been identified as one of the main microbial pathogens responsible for ARD.  Auxin (indole-3-acetic acid, IAA), an endogenous hormone in plants, is involved in almost all plant growth and development processes and plays a role in plant immunity against pathogens.  Gretchen Hagen3 (GH3) is one of the early/primary auxin response genes.  The aim of this study was to evaluate the function of MdGH3-2 and MdGH3-12 in the defense response of Fsolani by treating MdGH3-2/12 RNAi plants with Fsolani.  The results show that under Fsolani infection, RNAi of MdGH3-2/12 inhibited plant biomass accumulation and exacerbated root damage.  After inoculation with Fsolani, MdGH3-2/12 RNAi inhibited the biosynthesis of acid-amido synthetase.  This led to the inhibition of free IAA combining with amino acids, resulting in excessive free IAA accumulation.  This excessive free IAA altered plant tissue structure, accelerated fungal hyphal invasion, reduced the activity of antioxidant enzymes (SOD, POD and CAT), increased the reactive oxygen species (ROS) level, and reduced total chlorophyll content and photosynthetic ability, while regulating the expression of PR-related genes including PR1, PR4, PR5 and PR8.  It also changed the contents of plant hormones and amino acids, and ultimately reduced the resistance to Fsolani.  In conclusion, these results demonstrate that MdGH3-2 and MdGH3-12 play an important role in apple tolerance to Fsolani and ARD.


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    JrATHB-12 mediates JrMYB113 and JrMYB27 to control the anthocyanin levels in different types of red walnut
    Haifeng Xu, Guifang Wang, Xinying Ji, Kun Xiang, Tao Wang, Meiyong Zhang, Guangning Shen, Rui Zhang, Junpei Zhang, Xin Chen
    2024, 23 (8): 2649-2661.   DOI: 10.1016/j.jia.2024.03.015
    Abstract124)      PDF in ScienceDirect      
    Red walnut has broad market prospects because it is richer in anthocyanins than ordinary walnut.  However, the mechanism driving anthocyanin biosynthesis in red walnut is still unknown.  We studied two types of red walnut, called red walnut 1 (R1), with a red pericarp and seed coat, and red walnut 2 (R2), with a red seed coat only.  R1 mostly contained cyanidin-3-O-galactoside, while R2 contained a various amounts of cyanidin-3-O-galactoside, cyanidin-3-O-arabinoside, and cyanidin-3-O-glucoside.  The LDOX-2 (LOC109007163) and LDOX-3 (LOC109010746) genes, which encode leucoanthocyanidin dioxygenase/anthocyanidin synthase (LDOX/ANS), were preliminarily indicated as the crucial genes for anthocyanin biosynthesis in R1 and R2, respectively.  The MYB differential genes analysis showed that MYB27 and MYB113 are specifically expressed in the red parts of R1 and R2, respectively, and they are regarded as candidate regulatory genes.  Ectopic expression in Arabidopsis and transient injection in walnut showed that both MYB27 and MYB113 were located in the nucleus and promoted anthocyanin accumulation, while MYB27 promoted the expression of LDOX-2, and MYB113 promoted the expression of LDOX-3 and UAGT-3.  Yeast one-hybrid and electrophoretic mobility shift assays showed that MYB27 could only bind to the LDOX-2 promoter, while MYB113 could bind to the promoters of both LDOX-3 and UAGT-3.  In addition, we also identified an HD-Zip transcription factor, ATHB-12, which is specifically expressed in the pericarp.  After silencing the expression of ATHB-12, the R2 pericarp turned red, and MYB113 expression increased.  Further experiments showed that ATHB-12 could specifically interact with MYB113 and bind to its promoter.  This suggests that MYB27 controls R1 coloration by regulating LDOX-2, while MYB113 controls R2 coloration by regulating LDOX-3 and UAGT-3, but ATHB-12 can specifically bind to and inhibit the MYB113 of the R2 pericarp so that it becomes unpigmented.  This study reveals the anthocyanin biosynthetic mechanisms in two different types of red walnut and provides a scientific basis for the selection and breeding of red walnut varieties.


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    Establishing VIGS and CRISPR/Cas9 techniques to verify RsPDS function in radish

    Jiali Ying, Yan Wang, Liang Xu, Tiaojiao Qin, Kai Xia, Peng Zhang, Yinbo Ma, Keyun Zhang, Lun Wang, Junhui Dong, Lianxue Fan, Yuelin Zhu, Liwang Liu
    2024, 23 (5): 1557-1567.   DOI: 10.1016/j.jia.2024.03.059
    Abstract119)      PDF in ScienceDirect      
    Virus-induced gene silencing (VIGS) and clustered regularly interspaced short palindromic repeats/CRISPR-associated protein (CRISPR/Cas) systems are effective technologies for rapid and accurate gene function verification in modern plant biotechnology.  However, the investigation of gene silencing and editing in radish remains limited.  In this study, a bleaching phenotype was generated through the knockdown of RsPDS using tobacco rattle virus (TRV)- and turnip yellow mosaic virus (TYMV)-mediated gene silencing vectors.  The TYMV-mediated gene silencing efficiency was higher than the TRV-based VIGS system in radish.  The expression level of RsPDS was significantly inhibited using VIGS in ‘NAU-067’ radish leaves.  The rootless seedlings of ‘NAU-067’ were infected with Agrobacterium rhizogenes using the 2300GN-Ubi-RsPDS-Cas9 vector with two target sequences.  Nine adventitious roots were blue with GUS staining, and four of these adventitious roots were edited at target sequence 1 of the RsPDS gene as indicated by Sanger sequencing.  Furthermore, albino lines were generated with Atumefaciens-mediated transformation of radish cotyledons.  Five base substitutions and three base deletions occurred at target sequence 2 in Line 1, and three base insertions and three base substitutions occurred at target sequence 1 in Line 2.  This study shows that VIGS and CRISPR/Cas9 techniques can be employed to precisely verify the biological functions of genes in radish, which will facilitate the genetic improvement of vital horticultural traits in radish breeding program
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    Duplicated chalcone synthase (CHS) genes modulate flavonoid production in tea plants in response to light stress

    Mingzhuo Li, Wenzhao Wang, Yeru Wang, Lili Guo, Yajun Liu, Xiaolan Jiang, Liping Gao, Tao Xia
    2024, 23 (6): 1940-1955.   DOI: 10.1016/j.jia.2024.03.060
    Abstract128)      PDF in ScienceDirect      
    In tea plants, the abundant flavonoid compounds are responsible for the health benefits for the human body and define the astringent flavor profile.  While the downstream mechanisms of flavonoid biosynthesis have been extensively studied, the role of chalcone synthase (CHS) in this secondary metabolic process in tea plants remains less clear.  In this study, we compared the evolutionary profile of the flavonoid metabolism pathway and discovered that gene duplication of CHS occurred in tea plants.  We identified three CsCHS genes, along with a CsCHS-like gene, as potential candidates for further functional investigation.  Unlike the CsCHS-like gene, the CsCHS genes effectively restored flavonoid production in Arabidopsis chs-mutants.  Additionally, CsCHS transgenic tobacco plants exhibited higher flavonoid compound accumulation compared to their wild-type counterparts.  Most notably, our examination of promoter and gene expression levels for the selected CHS genes revealed distinct responses to UV-B stress in tea plants.  Our findings suggest that environmental factors such as UV-B exposure could have been the key drivers behind the gene duplication events in CHS.
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    EjGASA6 promotes flowering and root elongation by enhancing gibberellin biosynthesis

    Qian Chen, Shunyuan Yong, Fan Xu, Hao Fu, Jiangbo Dang, Qiao He, Danlong Jing, Di Wu, Guolu Liang, Qigao Guo
    2024, 23 (5): 1568-1579.   DOI: 10.1016/j.jia.2024.03.066
    Abstract110)      PDF in ScienceDirect      

    The Gibberellic Acid-stimulated Arabidopsis (GASA) gene family is involved in the regulation of gene expression and plant growth, development, and stress responses.  To investigate the function of loquat GASA genes in the growth and developmental regulation of plants, a loquat EjGASA6 gene homologous to Arabidopsis AtGASA6 was cloned.  EjGASA6 expression was induced by gibberellin, and ectopic transgenic plants containing this gene exhibited earlier bloom and longer primary roots since these phenotypic characteristics are related to higher gibberellin content.  Transcriptome analysis and qRT-PCR results showed that the expression levels of GA3ox1 and GA20ox1, which encode key enzymes in gibberellin biosynthesis, were significantly increased.  Furthermore, we confirmed that EjGASA6 could promote the expression of GA20ox1 via the luciferase reporter system.  Overall, our results suggest that EjGASA6 promotes blooming and main-root elongation by positively regulating gibberellin biosynthesis.  These findings broaden our understanding of the role of GASAs in plant development and growth, and lay the groundwork for future research into the functions of EjGASA6 in regulating loquat growth and development.

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    A novel histone methyltransferase gene CgSDG40 positively regulates carotenoid biosynthesis during citrus fruit ripening
    Jialing Fu, Qingjiang Wu, Xia Wang, Juan Sun, Li Liao, Li Li, Qiang Xu
    2024, 23 (8): 2633-2648.   DOI: 10.1016/j.jia.2024.03.068
    Abstract74)      PDF in ScienceDirect      
    The flesh color of pummelo (Citrus maxima) fruits is highly diverse and largely depends on the level of carotenoids, which are beneficial to human health.  It is vital to investigate the regulatory network of carotenoid biosynthesis to improve the carotenoid content in pummelo.  However, the molecular mechanism underlying carotenoid accumulation in pummelo is not fully understood.  In this study, we identified a novel histone methyltransferase gene, CgSDG40, involved in carotenoid regulation by analyzing the flesh transcriptome of typical white-fleshed pummelo, red-fleshed pummelo and extreme-colored F1 hybrids from a segregated pummelo population.  Expression of CgSDG40 corresponded to flesh color change and was highly coexpressed with CgPSY1.  Interestingly, CgSDG40 and CgPSY1 are located physically adjacent to each other on the chromosome in opposite directions, sharing a partially overlapping promoter region.  Subcellular localization analysis indicated that CgSDG40 localizes to the nucleus.  Overexpression of CgSDG40 significantly increased the total carotenoid content in citrus calli relative to that in wild type.  In addition, expression of CgPSY1 was significantly activated in overexpression lines relative to wild type.  Taken together, our findings reveal a novel histone methyltransferase regulator, CgSDG40, involved in the regulation of carotenoid biosynthesis in citrus and provide new strategies for molecular design breeding and genetic improvement of fruit color and nutritional quality.
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    Enhancer of Shoot Regeneration 2 (ESR2) regulates pollen maturation and vitality in watermelon (Citrullus lanatus)
    Hu Wang, Lihong Cao, Yalu Guo, Zheng Li, Huanhuan Niu
    2024, 23 (10): 3506-3521.   DOI: 10.1016/j.jia.2024.05.032
    Abstract82)      PDF in ScienceDirect      
    Watermelon (Citrullus lanatus) holds global significance as a fruit with high economic and nutritional value.  Exploring the regulatory network of watermelon male reproductive development is crucial for developing male sterile materials and facilitating cross-breeding.  Despite its importance, there is a lack of research on the regulation mechanism of male reproductive development in watermelon.  In this study, we identified that ClESR2, a VIIIb subclass member in the APETALA2/Ethylene Responsive Factor (AP2/ERF) superfamily, was a key factor in pollen development.  RNA in situ hybridization confirmed significant ClESR2 expression in the tapetum and pollen during the later stage of anther development.  The pollens of transgenic plants showed major defects in morphology and vitality at the late development stage.  The RNA-seq and protein interaction assay confirmed that ClESR2 regulates pollen morphology and fertility by interacting with key genes involved in pollen development at both transcriptional and protein levels.  These suggest that Enhancer of Shoot Regeneration 2 (ESR2) plays an important role in pollen maturation and vitality.  This study helps understand the male reproductive development of watermelon, providing a theoretical foundation for developing male sterile materials.


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    An allelic variation in the promoter of the LRR-RLK gene, qSS6.1, is associated with melon seed size
    Xiaoxue Liang, Jiyu Wang, Lei Cao, Xuanyu Du, Junhao Qiang, Wenlong Li, Panqiao Wang, Juan Hou, Xiang Li, Wenwen Mao, Huayu Zhu, Luming Yang, Qiong Li, Jianbin Hu
    2024, 23 (10): 3522-3536.   DOI: 10.1016/j.jia.2024.07.012
    Abstract90)      PDF in ScienceDirect      

    Seed size is an important agronomic trait in melons that directly affects seed germination and subsequent seedling growth.  However, the genetic mechanism underlying seed size in melon remains unclear.  In the present study, we employed Bulked-Segregant Analysis sequencing (BSA-seq) to identify a candidate region (~1.35 Mb) on chromosome 6 that corresponds to seed size.  This interval was confirmed by QTL mapping of three seed size-related traits from an F2 population across three environments.  This mapping region represented nine QTLs that shared an overlapping region on chromosome 6, collectively referred to as qSS6.1.  New InDel markers were developed in the qSS6.1 region, narrowing it down to a 68.35 kb interval that contains eight annotated genes.  Sequence variation analysis of the eight genes identified a SNP with a C to T transition mutation in the promoter region of MELO3C014002, a leucine-rich repeat receptor-like kinase (LRR-RLK) gene.  This mutation affected the promoter activity of the MELO3C014002 gene and was successfully used to differentiate the large-seeded accessions (C-allele) from the small-seeded accessions (T-allele).  qRT-PCR revealed differential expression of MELO3C014002 between the two parental lines.  Its predicted protein has typical LRR-RLK family domains, and phylogenetic analyses reveled its similarity with the homologs in several plant species.  Altogether, these findings suggest MELO3C014002 as the most likely candidate gene involved in melon seed size regulation.  Our results will be helpful for better understanding the genetic mechanism regulating seed size in melons and for genetically improving this important trait through molecular breeding pathways. 

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    Physiological and molecular mechanisms of cytokinin involvement in nitrate-mediated adventitious root formation in apples
    Muhammad Mobeen Tahir, Li Fan, Zhimin Liu, Humayun Raza, Usman Aziz, Asad Shehzaib, Shaohuan Li, Yinnan He, Yicen Lu, Xiaoying Ren, Dong Zhang, Jiangping Mao
    2024, 23 (12): 4046-4057.   DOI: 10.1016/j.jia.2024.07.045
    Abstract127)      PDF in ScienceDirect      
    Potassium nitrate (KNO3) promotes adventitious root (AR) formation in apple stem cuttings.  However, evidence for the possible involvement of cytokinin (CK) in KNO3-mediated AR formation in apples is still lacking.  In this study, we cultured GL-3 apple microshoots in different treatment combinations.  While the T1 (KNO3 9.4 mmol L–1+6-benzyl adenine (6-BA) 2.22 μmol L–1) and T3 (6-BA 2.22 μmol L–1) treatments completely inhibited AR formation, the control, T2 (KNO3 9.4 mmol L–1), and T4 (KNO3 9.4 mmol L–1+lovastatin (Lov) 1.24 μmol L–1) treatments developed ARs.  However, T4-treated microshoots developed fewer and shorter ARs, indicating that optimum CK synthesis is needed for normal AR growth.  This also suggests that these fewer and shorter ARs developed because of the presence of KNO3 in the same medium.  The anatomy of the stem basal part indicated that the inhibition of CK biosynthesis delayed AR primordia formation.  The endogenous levels of indole‐3‐acetic acid (IAA) and zeatin riboside (ZR) were higher in T2-treated microshoots, while the abscisic acid (ABA), gibberellic acid 3 (GA3), and brassinosteroid (BR) levels were higher in T4-treated microshoots.  The expression levels of MdNRT1.1 and MdNRT2.1 were higher in T2-treated microshoots at 3 and 8 days, while MdRR2 and MdCKX5 were higher at 8 and 16 days, respectively.  Furthermore, higher IAA levels increased MdWOX11 expression, which in turn increased MdLBD16 and MdLBD29 expression in response to T2.  The combined expression of these genes stimulated adventitious rooting by upregulating cell cycle-related genes (MdCYCD1;1 and MdCYCD3;1) in response to T2 treatment.  This study shows that specific genes and hormonal pathways contribute to KNO3-CK-mediated adventitious rooting in apples.


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    Whole-genome characterization of CKX genes in Prunus persica and their role in bud dormancy and regrowth 
    Xuehui Zhao, Jianting Liu, Xiling Fu, Long Xiao, Qingjie Wang, Chaoran Wang, Zhizhang Chen, Jiakui Li, Changkun Lu, Hui Cao, Ling Li
    2024, 23 (12): 4058-4073.   DOI: 10.1016/j.jia.2024.09.002
    Abstract135)      PDF in ScienceDirect      
    Bud dormancy is a complex physiological process of perennial woody plants living in temperate regions, and it can be affected by various phytohormones.  Cytokinin oxidase/dehydrogenases (CKXs) are a group of enzymes essential for maintaining cytokinin homeostasis, yet a comprehensive analysis of these enzymes in peach remains lacking.  Here, a total of 51 CKX members from different species, including six from peach, eleven from apple, nine from poplar, seven from Arabidopsis, eight from strawberry, and ten from rice, were identified using the Simple HMM Search tool of TBtools and a BLASTP program and classified into four groups using phylogenetic analysis.  Conserved motif and gene structure analysis of these 51 CKX members showed that 10 conserved motifs were identified, and each CKX gene contained at least two introns.  Cis-element analysis of PpCKXs showed that all PpCKX genes have light-responsive elements and at least one hormone-responsive element.  The changed relative expression levels of six PpCKX genes in peach buds from endodormancy to bud-break were observed by qRT-PCR.  Among them, the expression trend of PpCKX6 was almost opposite that of PpEBB1, a positive bud-break regulator in woody plants, around the bud-break stage.  Y1H, EMSA, and dual-luciferase assays indicated that PpEBB1 negatively regulated PpCKX6 through direct binding to a GCC box-like element located in the promoter region of PpCKX6.  In addition, a transient assay showed that overexpression of PpCKX6 delayed the bud-break of peach.  These results indicate that the PpCKX genes play an essential role in the dormancy-regrowth process, and PpCKX6 may act downstream of PpEBB1 directly to regulate the bud-break process, which further improves the hormone-regulatory network of dormancy-regrowth of woody plants, and provides new insights for molecular breeding and genetic engineering of peach.
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