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    Creating large EMS populations for functional genomics and breeding in wheat

    Wenqiang Wang, Xizhen Guan, Yong Gan, Guojun Liu, Chunhao Zou, Weikang Wang, Jifa Zhang, Huifei Zhang, Qunqun Hao, Fei Ni, Jiajie Wu, Lynn Epstein, Daolin Fu
    2024, 23 (02): 484-493.   DOI: 10.1016/j.jia.2023.05.039
    Abstract462)      PDF in ScienceDirect      

    Wheat germplasm is a fundamental resource for basic research, applied studies, and wheat breeding, which can be enriched normally by several paths, such as collecting natural lines, accumulating breeding lines, and introducing mutagenesis materials.  Ethyl methane sulfonate (EMS) is an alkylating agent that can effectively introduce genetic variations in a wide variety of plant species.  In this study, we created a million-scale EMS population (MEP) that started with the Chinese wheat cultivars ‘Luyan 128’, ‘Jimai 38’, ‘Jimai 44’, and ‘Shannong 30’.  In the M1 generation, the MEP had numerous phenotypical variations, such as >3,000 chlorophyll-deficient mutants, 2,519 compact spikes, and 1,692 male sterile spikes.  There were also rare mutations, including 30 independent tillers each with double heads.  Some M1 variations of chlorophyll-deficiency and compact spikes were inheritable, appearing in the M2 or M3 generations.  To advance the entire MEP to higher generations, we adopted a single-seed descendent (SSD) approach.  All other seed composites of M2 were used to screen other agronomically important traits, such as the tolerance to herbicide quizalofop-P-methyl.  The MEP is available for collaborative projects, and provides a valuable toolbox for wheat genetics and breeding for sustainable agriculture.

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    OsNPF3.1, a nitrate, abscisic acid and gibberellin transporter gene, is essential for rice tillering and nitrogen utilization efficiency

    Junnan Hang, Bowen Wu, Diyang Qiu, Guo Yang, Zhongming Fang, Mingyong Zhang
    2024, 23 (04): 1087-1104.   DOI: 10.1016/j.jia.2023.04.024
    Abstract354)      PDF in ScienceDirect      

    Low-affinity nitrate transporter genes have been identified in subfamilies 4–8 of the rice nitrate transporter 1 (NRT1)/peptide transporter family (NPF), but the OsNPF3 subfamily responsible for nitrate and phytohormone transport and rice growth and development remains unknown.  In this study, we described OsNPF3.1 as an essential nitrate and phytohormone transporter gene for rice tillering and nitrogen utilization efficiency (NUtE).  OsNPF3.1 possesses four major haplotypes of its promoter sequence in 517 cultivars, and its expression is positively associated with tiller number.  Its expression was higher in the basal part, culm, and leaf blade than in other parts of the plant, and was strongly induced by nitrate, abscisic acid (ABA) and gibberellin 3 (GA3) in the root and shoot of rice.  Electrophysiological experiments demonstrated that OsNPF3.1 is a pH-dependent low-affinity nitrate transporter, with rice protoplast uptake assays showing it to be an ABA and GA3 transporter.  OsNPF3.1 overexpression significantly promoted ABA accumulation in the roots and GA accumulation in the basal part of the plant which inhibited axillary bud outgrowth and rice tillering, especially at high nitrate concentrations.  The NUtE of OsNPF3.1-overexpressing plants was enhanced under low and medium nitrate concentrations, whereas the NUtE of OsNPF3.1 clustered regularly interspaced short palindromic repeats (CRISPR) plants was increased under high nitrate concentrations.  The results indicate that OsNPF3.1 transports nitrate and phytohormones in different rice tissues under different nitrate concentrations.  The altered OsNPF3.1 expression improves NUtE in the OsNPF3.1-overexpressing and CRISPR lines at low and high nitrate concentrations, respectively.

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    Identification and characterization of the chalkiness endosperm gene CHALK-H in rice (Oryza sativa L.)
    PIAO Ri-hua, CHEN Mo-jun, MENG Fan-mei, QI Chun-yan, KOH Hee-Jong, GAO Meng-meng, SONG An-qi, JIN Yong-mei, YAN Yong-feng
    2023, 22 (10): 2921-2933.   DOI: 10.1016/j.jia.2023.04.020
    Abstract329)      PDF in ScienceDirect      

    Chalkiness is one of the most important agronomic traits in rice breeding, which directly affects the quality of rice seed.  In this study, we identified a chalkiness endosperm mutant, chalk-h, from N-methyl-N-nitrosourea (MNU)-induced japonica rice cultivar Hwacheong (HC).  Compared with wild type (WT)-HC, chalk-h showed severe chalkiness in the endosperm, yellowish green leaves, as well as reduced plant height.  Scanning electron microscopy (SEM) analysis showed that starch grains in the chalk-h mutant were irregular in size and loosely arranged, with large gaps between granules, forming ovoid or orbicular shapes.  MutMap analysis revealed that the phenotype of chalk-h is controlled by a single recessive gene LOC_Os11g39670 encoding seryl-tRNA synthetase, which is renamed as CHALK-H.  A point mutation occurs in chalk-h on the sixth exon (at nucleotide 791) of CHALK-H, in which adenine (A) is replaced by thymidine (T), resulting in an amino acid codon change from glutamine (Glu) to valine (Val).  The chalk-h mutant exhibited a heat-sensitive phenotype from the 3-leaf stage, including yellow-green leaves and reduced pigment content.  The transcriptional expression of starch synthesis-related genes was down-regulated in the chalk-h mutants compared to WT-HC at different grain-filling stages.  With an increase in temperature, the expression of photosynthesis-related genes was down-regulated in the chalk-h mutant compared to WT-HC.  Overexpression of CHALK-H rescued the phenotype of chalk-h, with endosperm and leaf color similar to those of WT-HC.  Our findings reveal that CHALK-H is a causative gene controlling chalkiness and leaf color of the chalk-h mutant.  CHALK-H is the same gene locus as TSCD11, which was reported to be involved in chloroplast development under high temperature.  We suggest that CHALK-H/TSCD11 plays important roles not only in chloroplast development, but also in photosynthesis and starch synthesis during rice growth and development, so it has great application potential in rice breeding for high quality and yield.

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    Dek219 encodes the DICER-LIKE1 protein that affects chromatin accessibility and kernel development in maize
    XIE Si-di, TIAN Ran, ZHANG Jun-jie, LIU Han-mei, LI Yang-ping, HU Yu-feng, YU Guo-wu, HUANG Yu-bi, LIU Ying-hong
    2023, 22 (10): 2961-2980.   DOI: 10.1016/j.jia.2023.02.024
    Abstract316)      PDF in ScienceDirect      

    Chromatin accessibility plays a vital role in gene transcriptional regulation.  However, the regulatory mechanism of chromatin accessibility, as well as its role in regulating crucial gene expression and kernel development in maize (Zea mays) are poorly understood.  In this study, we isolated a maize kernel mutant designated as defective kernel219 (dek219), which displays opaque endosperm and embryo abortion.  Dek219 encodes the DICER-LIKE1 (DCL1) protein, an essential enzyme in miRNA biogenesis.  Loss of function of Dek219 results in significant reductions in the expression levels of most miRNAs and histone genes.  Further research showed that the Heat shock transcription factor17 (Hsf17)-Zm00001d016571 module may be one of the factors affecting the expression of histone genes.  Assay results for transposase-accessible chromatin sequencing (ATAC-seq) indicated that the chromatin accessibility of dek219 is altered compared with that of wild type (WT), which may regulate the expression of crucial genes in kernel development.  By analyzing differentially expressed genes (DEGs) and differentially accessible chromatin regions (ACRs) between WT and dek219, we identified 119 candidate genes that are regulated by chromatin accessibility, including some reported to be crucial genes for kernel development.  Taken together, these results suggest that Dek219 affects chromatin accessibility and the expression of crucial genes that are required for maize kernel development

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    Differential metabolites and their transcriptional regulation in seven major tea cultivars (Camellia sinensis) in China
    GAO Ting, HOU Bing-hao, SHAO Shu-xian, XU Meng-ting, ZHENG Yu-cheng, JIN Shan, WANG Peng-jie, YE Nai-xing
    2023, 22 (11): 3346-3363.   DOI: 10.1016/j.jia.2023.02.009
    Abstract305)      PDF in ScienceDirect      

    Various genetic and biochemical characteristics exist in tea plant cultivars, and they largely determine production suitability and tea quality.  Here, we performed transcriptomic and metabolomic analyses of young shoots of seven tea cultivars and identified major regulatory transcription factors (TFs) for the characteristic metabolites in different cultivars based on weighted gene co-expression network analysis (WGCNA).  Phenotypically, we found that ‘Tieguanyin’ (TGY) and ‘Fujian Shuixian’ (FJSX), which are suitable for oolong tea, had higher catechin contents.  The metabolites of ‘Jinxuan’ (JX) were more prominent, especially the contents of phenolic acids, flavonoids, terpenes, and tannins, which were higher than those of the other six cultivars.  Moreover, ‘Fudingdabai’ (FDDB), which is suitable for white tea, was rich in amino acids, linolenic acid, and saccharides.  At the molecular level, hydroxycinnamoyl CoA quinate hydroxycinnamoyl transferase (HCT) (CsTGY12G0001876, and CsTGY06G0003042) led to the accumulation of chlorogenic acid in TGY.  The main reason for the higher l-ascorbic acid content in FJSX was the high expression levels of L-galactono-1,4-lactone hydrogenase (GalLDH) (CsTGY13G0000389) and Myo-inositol oxygenase (MIOX) (CsTGY14G0001769, and CsTGY14G0001770), which were regulated by WRKY (CsTGY11G0001197).  Furthermore, FDDB, ‘Longjing 43’ (LJ43), ‘Shuchazao’ (SCZ)  and ‘Baihaozao’ (BHZ) had higher free fatty acid contents, among which MYB (CsTGY14G0002344) may be a hub gene for the regulation of palmitoleic acid accumulation.  More importantly, we found that the shoots of TGY were green with purple, mainly due to the accumulation of anthocyanins and the downregulation of the Mg-protoporphyrin IX nonomethyl ester cyclase (MPEC) (CsTGY10G0001989) gene that affects chlorophyll synthesis.  These results will provide a theoretical reference for tea cultivar breeding and suitability.

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    A single nucleotide substitution in the MATE transporter gene regulates plastochron and many noded dwarf phenotype in barley (Hordeum vulgare L.)
    GUO Bao-jian, SUN Hong-wei, QI Jiang, HUANG Xin-yu, HONG Yi, HOU Jian, LÜ Chao, WANG Yu-lin, WANG Fei-fei, ZHU Juan, GUO Gang-gang, XU Ru-gen
    2023, 22 (8): 2295-2305.   DOI: 10.1016/j.jia.2023.02.006
    Abstract297)      PDF in ScienceDirect      
    In higher plants, the shoot apical meristem produces lateral organs in a regular spacing (phyllotaxy) and timing (plastochron).  The molecular analysis of mutants associated with phyllotaxy and plastochron would increase our understanding of the mechanism of shoot architecture formation.  In this study, we identified mutant mnd8ynp5 that shows an increased rate of leaf emergence and a larger number of nodes in combination with a dwarfed growth habit from an EMS-treated population of the elite barley cultivar Yangnongpi 5.  Using a map-based cloning strategy, the mnd8 gene was narrowed down to a 6.7-kb genomic interval on the long arm of chromosome 5H.  Sequence analysis revealed that a C to T single-nucleotide mutation occurred at the first exon (position 953) of HORVU5Hr1G118820, leading to an alanine (Ala) to valine (Val) substitution at the 318th amino acid site.  Next, HORVU5Hr1G118820 was defined as the candidate gene of MND8 encoding 514 amino acids and containing two multidrug and toxic compound extrusion (MATE) domains.  It is highly homologous to maize Bige1 and has a conserved function in the regulation of plant development by controlling the leaf initiation rate.  Examination of modern barely varieties showed that Hap-1 was the dominant haplotype and was selected in barley breeding around the world.  Collectively, our results indicated that mnd8ynp5 is a novel allele of the HORVU5Hr1G118820 gene that is possibly responsible for the shortened plastochron and many noded dwarf phenotype in barley.
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    Estimation of the potential geographical distribution of a new potato pest (Schrankia costaestrigalis) in China under climate change
    XIAN Xiao-qing, ZHAO Hao-xiang, GUO Jian-yang, ZHANG Gui-fen, LIU Hui, LIU Wan-xue, WAN Fang-hao
    2023, 22 (8): 2441-2455.   DOI: 10.1016/j.jia.2022.08.023
    Abstract281)      PDF in ScienceDirect      

    Global food security is threatened by the impacts of the spread of crop pests and changes in the complex interactions between crops and pests under climate change.  Schrankia costaestrigalis is a newly-reported potato pest in southern China.  Early-warning monitoring of this insect pest could protect domestic agriculture as it has already caused regional yield reduction and/or quality decline in potato production.  Our research aimed to confirm the potential geographical distributions (PGDs) of Scostaestrigalis in China under different climate scenarios using an optimal MaxEnt model, and to provide baseline data for preventing agricultural damage by Scostaestrigalis.  Our findings indicated that the accuracy of the optimal MaxEnt model was better than the default-setting model, and the minimum temperature of the coldest month, precipitation of the driest month, precipitation of the coldest quarter, and the human influence index were the variables significantly affecting the PGDs of Scostaestrigalis.  The highly- and moderately-suitable habitats of Scostaestrigalis were mainly located in eastern and southern China.  The PGDs of Scostaestrigalis in China will decrease under climate change.  The conversion of the highly- to moderately-suitable habitat will also be significant under climate change.  The centroid of the suitable habitat area of Scostaestrigalis under the current climate showed a general tendency to move northeast and to the middle-high latitudes in the 2030s.  The agricultural practice of plastic film mulching in potato fields will provide a favorable microclimate for Scostaestrigalis in the suitable areas.  More attention should be paid to the early warning and monitoring of Scostaestrigalis in order to prevent its further spread in the main areas in China’s winter potato planting regions.

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    Pig macrophages with site-specific edited CD163 decrease the susceptibility to infection with porcine reproductive and respiratory syndrome virus
    XU Kui, ZHOU Yan-rong, SHANG Hai-tao, XU Chang-jiang, TAO Ran, HAO Wan-jun, LIU Sha-sha, MU Yu-lian, XIAO Shao-bo, LI Kui
    2023, 22 (7): 2188-2199.   DOI: 10.1016/j.jia.2022.11.010
    Abstract260)      PDF in ScienceDirect      
    Porcine reproductive and respiratory syndrome (PRRS) is recognized as one of the most infectious viral diseases of swine. Although Cluster of differentiation 163 (CD163) is identified as an essential receptor for mediating PRRS virus (PRRSV) infection, the important residues involved in infection on CD163 are still unclear. Therefore, it is very important to identify these key residues to study the mechanism of PRRSV infection and to generate anti-PRRSV pigs. In this study, we first generated immortalized porcine alveolar macrophage (IPAM) cell lines harboring 40-residues (residues 523–562, including R561 (arginine (R) at position 561)) deletion of CD163. PRRSV infection experiments showed that these IPAM cell lines were completely resistant to PRRSV infection. We then generated cloned pigs carrying CD163- R561A (an arginine (R) to alanine (A) substitution at position 561 of CD163). PRRSV challenge experiments in porcine alveolar macrophages (PAMs) isolated from the CD163-R561A pigs showed significantly lower susceptibility to PRRSV than that of CD163-R561 PAMs. Through this study, we show that CD163 523–562 contains essential residues for mediating PRRSV infection, and that CD163 R561 significantly contributes to PRRSV infection but is not essential for infection. These functional sites can therefore serve as new targets for understanding the mechanism of PRRSV infection. Furthermore, CD163-R561A pigs can be used as an important model for improving pig germplasm with resistance against PRRSV.
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    A stable and major QTL region on chromosome 2 conditions pod shape in cultivated peanut (Arachis hyopgaea L.)
    ZHANG Sheng-zhong, HU Xiao-hui, WANG Fei-fei, CHU Ye, YANG Wei-qiang, XU Sheng, WANG Song, WU Lan-rong, YU Hao-liang, MIAO Hua-rong, FU Chun, CHEN Jing
    2023, 22 (8): 2323-2334.   DOI: 10.1016/j.jia.2023.02.005
    Abstract247)      PDF in ScienceDirect      
    Peanut pod shape is a heritable trait which affects the market acceptance of in-shell peanut products.  In order to determine the genetic control of pod shape, six component traits of pod shape (pod length, pod width, pod length/width ratio, pod roundness, beak degree and constriction degree) were measured using an image-based phenotyping method.  A recombinant inbred line (RIL) population consisting of 181 lines was phenotyped across three environments.  Continuous distributions and transgressive segregations were demonstrated in all measured traits and environments.   Significant correlations were found among most component traits with broad-sense heritability ranging from 0.87 to 0.95.  Quantitative trait locus (QTL) analysis yielded 26 additive QTLs explaining 3.79 to 52.37% phenotypic variations.  A novel, stable and major QTL region conditioning multiple shape features was detected on chromosome 2, which spans a 10.81-Mb genomic region with 543 putative genes.  Bioinformatics analysis revealed several candidate genes in this region.  In addition, 73 pairs of epistatic interactions involving 92 loci were identified for six component traits explaining 0.94–6.45% phenotypic variations.  These results provide new genetic loci to facilitate genomics-assisted breeding of peanut pod shape.
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    A 2-bp frameshift deletion at GhDR, which encodes a B-BOX protein that co-segregates with the dwarf-red phenotype in Gossypium hirsutum L.
    WANG Xue-feng, SHAO Dong-nan, LIANG Qian, FENG Xiao-kang, ZHU Qian-hao, YANG Yong-lin, LIU Feng, ZHANG Xin-yu, LI Yan-jun, SUN Jie, XUE Fei
    2023, 22 (7): 2000-2014.   DOI: 10.1016/j.jia.2022.10.007
    Abstract243)      PDF in ScienceDirect      
    Plant architecture and leaf color are important factors influencing cotton fiber yield. In this study, based on genetic analysis, stem paraffin sectioning, and phytohormone treatments, we showed that the dwarf-red (DR) cotton mutant is a gibberellin-sensitive mutant caused by a mutation in a single dominant locus, designated GhDR. Using bulked segregant analysis (BSA) and genotyping by target sequencing (GBTS) approaches, we located the causative mutation to a ~197-kb genetic interval on chromosome A09 containing 25 annotated genes. Based on gene annotation and expression changes between the mutant and normal plants, GH_A09G2280 was considered to be the best candidate gene responsible for the dwarf and red mutant phenotypes. A 2-nucleotide deletion was found in the coding region of GhDR/GH_A09G2280 in the DR mutant, which caused a frameshift and truncation of GhDR. GhDR is a homolog of Arabidopsis AtBBX24, and encodes a B-box zinc finger protein. The frameshift deletion eliminated the C-terminal nuclear localization domain and the VP domain of GhDR, and altered its subcellular localization. A comparative transcriptome analysis demonstrated downregulation of the key genes involved in gibberellin biosynthesis and the signaling transduction network, as well as upregulation of the genes related to gibberellin degradation and the anthocyanin biosynthetic pathway in the DR mutant. The results of this study revealed the potential molecular basis by which plant architecture and anthocyanin accumulation are regulated in cotton.  

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    Dissecting the key genomic regions underlying high yield potential in common wheat variety ‘Kenong 9204’
    ZHAO Chun-hua, ZHANG Na, FAN Xiao-li, JI Jun, SHI Xiao-li, CUI Fa, LING Hong-qing, LI Jun-ming
    2023, 22 (9): 2603-2616.   DOI: 10.1016/j.jia.2023.02.013
    Abstract242)      PDF in ScienceDirect      
    The foundation parents play key roles in the genetic improvement of both yield potential and end-use quality in wheat.  Characterizing the genetic basis that underlies certain beneficial traits in the foundation parents will provide theoretical reference for molecular breeding by a design approach.  ‘Kenong 9204’ (KN9204) is a candidate foundation parent characterized by ideotype, high yield potential, and particularly high nitrogen fertilizer utilization.  To better understand the genetic basis of its high yield potential, high throughput whole-genome re-sequencing (10×) was performed on KN9204, its parental lines and its derivatives.  A high-resolution genetic composition map of KN9204 was constructed, which showed the parental origin of the favorable genomic segments based on the identification of excellent yield-related quantitative trait loci (QTL) from a bi-parental mapping population.  Xiaoyan 693 (XY693), a wheat–Thinopyrum ponticum partial amphidiploid, contributed a great deal to the high yield potential of KN9204, and three major stable QTLs from XY693 were fine mapped.  The transmissibility of key genomic segments from KN9204 to its derivatives were delineated, indicating that haplotype blocks containing beneficial gene combinations were conserved along with directional selection by breeders.  Evidence for selection sweeps in the breeding programs was identified.  This study provides a theoretical reference for the breeding of high-yield wheat varieties by a molecular design approach.
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    Host niche, genotype, and field location shape the diversity and composition of the soybean microbiome
    YANG Hong-jun, YE Wen-wu, YU Ze, SHEN Wei-liang, LI Su-zhen, WANG Xing, CHEN Jia-jia, WANG Yuan-chao, ZHENG Xiao-bo
    2023, 22 (8): 2412-2425.   DOI: 10.1016/j.jia.2023.01.006
    Abstract239)      PDF in ScienceDirect      
    Plant-associated microbes represent a key determinant of plant fitness through acquiring nutrients, promoting growth, and resisting to abiotic and biotic stresses.  However, an extensive characterization of the bacterial and fungal microbiomes present in different plant compartments of soybean in field conditions has remained elusive.  In this study, we investigated the effects of four niches (roots, stems, leaves, and pods), four genotypes (Andou 203, Hedou 12, Sanning 16, and Zhonghuang 13), and three field locations (Jining, Suzhou, and Xuzhou) on the diversity and composition of bacterial and fungal communities in soybean using 16S and internal transcribed spacer rRNA amplicon sequencing, respectively.  The soybean microbiome significantly differed across organs.  Host genotypes explained more variation in stem bacterial community composition and leaf fungal community composition.  Field location significantly affected the composition of bacterial communities in all compartments and the effects were stronger in the root and stem than in the leaf and pod, whereas field location explained more variation in stem and leaf fungal community composition than in the root and pod.  The relative abundances of potential soybean fungal pathogens also differed among host organs and genotypes, reflecting the niches of these microbes in the host and probably their compatibility to the host genotypes.  Systematic profiling of the microbiome composition and diversity will aid the development of plant protection technologies to benefit soybean health.  
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    Physiological and transcriptome analyses provide new insights into the mechanism mediating the enhanced tolerance of melatonin-treated rhododendron plants to heat stress
    XU Yan-xia, ZHANG Jing, WAN Zi-yun, HUANG Shan-xia, DI Hao-chen, HE Ying, JIN Song-heng
    2023, 22 (8): 2397-2411.   DOI: 10.1016/j.jia.2023.07.005
    Abstract235)      PDF in ScienceDirect      

    Rhododendron is a well-known genus consisting of commercially valuable ornamental woody plant species.  Heat stress is a major environmental factor that affects rhododendron growth.  Melatonin was recently reported to alleviate the effects of abiotic stress on plants.  However, the role of melatonin in rhododendron plants is unknown.  In this study, the effect of melatonin on rhododendron plants exposed to heat stress and the potential underlying mechanism were investigated.  Analyses of morphological characteristics and chlorophyll a fluorescence indicated 200 µmol L–1 was the optimal melatonin concentration for protecting rhododendron plants from heat stress.  To elucidate how melatonin limits the adverse effects of high temperatures, melatonin contents, photosynthetic indices, Rubisco activity, and adenosine triphosphate (ATP) contents were analyzed at 25, 35, and 40°C, respectively.  Compared with the control, exogenous application of melatonin improved the melatonin contents, electron transport rate, photosystem II and I activities, Rubisco activity, and ATP contents under heat stress.  The transcriptome analysis revealed many of the heat-induced differentially expressed genes were associated with the photosynthetic pathway; the expression of most of these genes was down-regulated by heat stress more in the melatonin-free plants than in the melatonin-treated plants.  We identified RhPGR5A, RhATPB, RhLHCB3, and RhRbsA as key genes.  Thus, we speculate that melatonin promotes photosynthetic electron transport, improves Calvin cycle enzyme activities, and increases ATP production.  These changes lead to increased photosynthetic efficiency and CO2 assimilation under heat stress conditions via the regulated expression of specific genes, including RhRbsA.  Therefore, the application of exogenous melatonin may increase the tolerance of rhododendron to heat stress.

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    CRISPR/Cas9-mediated knockout of SLC15A4 gene involved in the immune response in bovine rumen epithelial cells
    JIANG Mao-cheng, HU Zi-xuan, WANG Ke-xin, YANG Tian-yu, LIN Miao, ZHAN Kang, ZHAO Guo-qi
    2023, 22 (10): 3148-3158.   DOI: 10.1016/j.jia.2023.06.016
    Abstract222)      PDF in ScienceDirect      

    The objective of this study was to determine the role of SLC15A4 in the muramyl dipeptide (MDP)-mediated inflammatory response of bovine rumen epithelial cells (BRECs).  First, changes in the mRNA expression of pro-inflammatory factor genes in BRECs following 10 μg mL–1 MDP treatments were examined.  RT-qPCR results showed that the expression of pro-inflammatory factor (IL-1β, IL-6, and TNF-α) mRNAs were significantly increased under MDP stimulation (P<0.001).  Moreover, SLC15A4-Knockout (SLC15A4-KO) cells were obtained through lentivirus packaging, transfection, screening, and cell monoclonal culture.  In order to gain further insight into the potential function of SLC15A4, we utilized transcriptome data, which revealed a change in the genes between WT-BRECs and SLC15A4-KO.  Five down-regulated pro-inflammatory genes and 13 down-regulated chemokine genes related to the inflammatory response were identified.  Meanwhile, the down-regulated genes were mostly enriched in the nuclear factor κB (NF-κB) and mitogen-activated protein kinase (MAPK) signaling pathways.  The results of RT-qPCR also verified these detected changes.  To further determine the mechanism of how WT and SLC15A4-KO BRECs are involved in inflammatory responses, we investigated the inflammatory responses of cells exposed to MDP.  WT-BRECs and SLC15A4-KO were treated with a culture medium containing 10 μg mL–1 MDP, in comparison to a control without MDP.  Our results show that SLC15A4-KO BRECs had reduced the expression of genes (IL-6, TNF-α, CXCL2, CXCL3, CXCL9, and CCL2) and proteins (p-p65 and p-p44/42) from the MDP-mediated inflammatory response compared to WT-BRECs (P<0.05).  In this experiment, CRISPR-Cas9 was used to KO the di/tripeptide transporter SLC15A4, and its role was confirmed via the MDP-induced inflammatory response in BRECs.  This work will provide a theoretical basis for studying the pro-inflammatory mechanism of MDP and its application in the prevention and treatment of subacute rumen acidosis in dairy cows.

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    SNP-based identification of QTLs for thousand-grain weight and related traits in wheat 8762/Keyi 5214 DH lines
    HUANG Feng, LI Xuan-shuang, DU Xiao-yu, LI Shun-cheng, LI Nan-nan, LÜ Yong-jun, ZOU Shao-kui, ZHANG Qian, WANG Li-na, NI Zhong-fu, HAN Yu-lin, XING Jie-wen
    2023, 22 (10): 2949-2960.   DOI: 10.1016/j.jia.2023.03.004
    Abstract216)      PDF in ScienceDirect      

    As important yield-related traits, thousand-grain weight (TGW), grain number per spike (GNS) and grain weight per spike (GWS) are crucial components of wheat production.  To dissect their underlying genetic basis, a double haploid (DH) population comprised of 198 lines derived from 8762/Keyi 5214 was constructed.  We then used genechip to genotype the DH population and integrated the yield-related traits TGW, GNS and GWS for QTL mapping.  Finally, we obtained a total of 18 942 polymorphic SNP markers and identified 41 crucial QTLs for these traits.  Three stable QTLs for TGW were identified on chromosomes 2D (QTgw-2D.3 and QTgw-2D.4) and 6A (QTgw-6A.1), with additive alleles all from the parent 8762, explaining 4.81–18.67% of the phenotypic variations.  Five stable QTLs for GNS on chromosomes 3D, 5B, 5D and 6A were identified.  QGns-5D.1 was from parent 8762, while the other four QTLs were from parent Keyi 5214, explaining 5.89–7.08% of the GNS phenotypic variations.  In addition, a stable GWS genetic locus QGws-4A.3 was detected from the parent 8762, which explained 6.08–6.14% of the phenotypic variations.  To utilize the identified QTLs, we developed STARP markers for four important QTLs, Tgw2D.3-2, Tgw2D.4-1, Tgw6A.1 and Gns3D.1.  Our results provide important basic resources and references for the identification and cloning of genes related to TGW, GNS and GWS in wheat.

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    A high-quality genome of Actinidia eriantha provides new insight into ascorbic acid regulation
    LIAO Guang-lian, HUANG Chun-hui, JIA Dong-feng, ZHONG Min, TAO Jun-jie, QU Xue-yan, XU Xiao-biao
    2023, 22 (11): 3244-3255.   DOI: 10.1016/j.jia.2023.07.018
    Abstract208)      PDF in ScienceDirect      

    Actinidia eriantha is one of the species of kiwifruit with a particularly high ascorbic acid (AsA) content.  However, the molecular mechanism driving AsA richness in fruit remains unclear.  In order to reveal the molecular mechanism of AsA richness in Aeriantha, this study constructed a regulatory network related to AsA metabolism by combining genomics, metabolomics and transcriptomics.  We assembled a high-quality genome of Aeriantha ‘Ganlv 1’ with only five remaining gaps.  The assembly is comprised of 29 pseudochromosomes with a total size of 615.95 Mb, and contig N50 of 20.35 Mb. Among them, 24 of the pseudochromosomes were obtained directly from telomere-to-telomere.  The LTR assembly index score and consensus quality value were 21.34 and 39.90%, respectively.  Subsequently, 61 metabolites and 2 092 genes were found to be differentially accumulated/expressed during fruit development by metabolome and transcriptome assays, respectively.  AsA metabolism and the cyclic regeneration pathway were found to have high expression levels throughout fruit growth and development, suggesting its crucial role in the regulation of AsA.  Furthermore, the AsA contents are highly associated with ascorbate peroxidase genes.  The genome obtained in this study provides genomic resources for the genetic and breeding research of Aeriantha, and the constructed regulatory network can provide a public data platform for future research on kiwifruit.

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    Advancing approach and toolbox in optimization of chloroplast genetic transformation technology
    LIU Yu-xin, LI Fan, GAO Liang, TU Zhang-li, ZHOU Fei, LIN Yong-jun
    2023, 22 (7): 1951-1966.   DOI: 10.1016/j.jia.2023.02.031
    Abstract205)      PDF in ScienceDirect      

    Chloroplast is a discrete, highly structured, and semi-autonomous cellular organelle. The small genome of chloroplast makes it an up-and-coming platform for synthetic biology. As a special means of synthetic biology, chloroplast genetic engineering shows excellent potential in reconstructing various sophisticated metabolic pathways within the plants for specific purposes, such as improving crop photosynthetic capacity, enhancing plant stress resistance, and synthesizing new drugs and vaccines. However, many plant species exhibit limited efficiency or inability in chloroplast genetic transformation. Hence, new transformation technologies and tools are being constantly developed. In order to further expand and facilitate the application of chloroplast genetic engineering, this review summarizes the new technologies in chloroplast genetic transformation in recent years and discusses the choice of appropriate synthetic biological elements  for the construction of efficient chloroplast transformation vectors.

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    Effect of delayed sowing on grain number, grain weight, and protein concentration of wheat grains at specific positions within spikes
    CHU Jin-peng, GUO Xin-hu, ZHENG Fei-na, ZHANG Xiu, DAI Xing-long, HE Ming-rong
    2023, 22 (8): 2359-2369.   DOI: 10.1016/j.jia.2023.02.002
    Abstract204)      PDF in ScienceDirect      

    Delays in sowing have significant effects on the grain yield, yield components, and grain protein concentrations of winter wheat.  However, little is known about how delayed sowing affects these characteristics at different positions in the wheat spikes.  In this study, the effects of sowing date were investigated in a winter wheat cultivar, Shannong 30, which was sown in 2019 and 2020 on October 8 (normal sowing) and October 22 (late sowing) under field conditions.  Delayed sowing increased the partitioning of 13C-assimilates to spikes, particularly to florets at the apical section of a spike and those occupying distal positions on the same spikelet.  Consequently, the increase in grain number was the greatest for the apical sections, followed by the basal and central sections.  No significant differences were observed between sowing dates in the superior grain number in the basal and central sections, while the number in apical sections was significantly different.  The number of inferior grains in each section also increased substantially in response to delayed sowing.  The average grain weights in all sections remained unchanged under delayed sowing because there were parallel increases in grain number and 13C-assimilate partitioning to grains at specific positions in the spikes.  Increases in grain number m–2 resulted in reduced grain protein concentrations as the limited nitrogen supply was diluted into more grains.  Delayed sowing caused the greatest reduction in grain protein concentration in the basal sections, followed by the central and apical sections.  No significant differences in the reduction of the grain protein concentration were observed between the inferior and superior grains under delayed sowing.  In conclusion, a 2-week delay in sowing improved grain yield through increased grain number per spike, which originated principally from an increased grain number in the apical sections of spikes and in distal positions on the same spikelet.  However, grain protein concentrations declined in each section because of the increased grain number and reduced N uptake.

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    The HD-Zip transcription factor GhHB12 represses plant height by regulating the auxin signaling in cotton
    LIU Yan, WANG Wei-ping, ZHANG Lin, ZHU Long-fu, ZHANG Xian-long, HE Xin
    2023, 22 (7): 2015-2024.   DOI: 10.1016/j.jia.2022.09.022
    Abstract197)      PDF in ScienceDirect      
    Upland cotton (Gossypium hirsutum L.) is the most important natural textile fiber crop worldwide. Plant height (PH) is a significant component of plant architecture, strongly influencing crop cultivation patterns, overall yield, and economic coefficient. However, cotton genes regulating plant height have not been fully identified. Previously, an HD-Zip gene (GhHB12) was isolated and characterized in cotton, which regulates the abiotic and biotic stress responses and the growth and development processes. In this study, we showed that GhHB12 was induced by auxin. Moreover, overexpression of GhHB12 induces the expression of HY5, ATH1, and HAT4, represses the spatial-temporal distribution, polar transport, and signaling of auxin, alters the expression of genes involved in cell wall expansion, and restrains the plant height in cotton. These results suggest a role of GhHB12 in regulating cotton plant height, which could be achieved by affecting the auxin signaling and cell wall expansion.
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    Population genetic variation and historical dynamics of the natural enemy insect Propylea japonica (Coleoptera: Coccinellidae) in China
    WANG Meng-qi, ZHANG Hong-rui, XI Yu-qiang, WANG Gao-ping, ZHAO Man, ZHANG Li-juan, GUO Xian-ru
    2023, 22 (8): 2456-2469.   DOI: 10.1016/j.jia.2022.08.025
    Abstract196)      PDF in ScienceDirect      

    Propylea japonica (Coleoptera: Coccinellidae) is a natural enemy insect with a wide range of predation in Chinese mainland and is commonly used in pest management.  However, its genetic pattern (i.e., genetic variation, genetic structure, and historical population dynamics) is still unclear, impeding the development of biological control of insect pests.  Population genetic research has the potential to optimize strategies at different stages of the biological control processes.  This study used 23 nuclear microsatellite sites and mitochondrial COI genes to investigate the population genetics of Propylea japonica based on 462 specimens collected from 30 sampling sites in China.  The microsatellite dataset showed a moderate level of genetic diversity, but the mitochondrial genes showed a high level of genetic diversity.  Populations from the Yellow River basin were more genetically diverse than those in the Yangtze River basin.  Propylea japonica has not yet formed a significant genealogical structure in China, but there was a population structure signal to some extent, which may be caused by frequent gene flow between populations.  The species has experienced population expansion after a bottleneck, potentially thanks to the tri-trophic plant–insect–natural enemy relationship.  Knowledge of population genetics is of importance in using predators to control pests.  Our study complements existing knowledge of an important natural predator in agroecosystems through estimating its genetic diversity and population differentiation and speculating about historical dynamics.

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