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Dissecting the molecular basis of spike traits by integrating gene regulatory networks and genetic variation in wheat

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Plant Communications 2024年第5期5卷 57-74页

作者： guo Ai Chao He Siteng Bi Ziru Zhou Ankui Liu Xin Hu Yanyan Liu Liujie Jin JiaCheng Zhou Heping Zhang Dengxiang Du Hao Chen Xin Gong Sulaiman Saeed Handong Su Caixia Lan Wei Chen Qiang Li Hailiang Mao Lin Li Hao Liu Dijun Chen Kerstin Kaufmann Khaled FAlazab Wenhao Yan national key Laboratory of crop genetic improvement Hubei Hongshan LaboratoryHuazhong Agricultural UniversityWuhan 430070China College of Plant Science and Technology Huazhong Agricultural UniversityWuhan 430070China Shenzhen Institute of Nutrition and Health Huazhong Agricultural UniversityWuhan 430070China Shenzhen Branch Guangdong Laboratory for Lingnan Modern AgricultureGenomeAnalysis Laboratory of the Ministry of AgricultureAgricultural Genomics Institute at ShenzhenChinese Academy of Agricultural SciencesShenzhen 518120China State key Laboratory of Pharmaceutical Biotechnology School of Life SciencesNanjing UniversityNanjing 210023China Department for Plant Cell and Molecular Biology Institute for BiologyHumboldt-Universitat Zu Berlin10115 BerlinGermany Plant Research Department Nuclear Research CenterEgyptian Atomic Energy AuthorityCairo 13759Egypt

Spike architecture inﬂuences both grain weight and grain number per spike,which are the two major components of grain yield in bread wheat(Triticum aestivum L.).However,the complex wheat genome and the inﬂuence of various environmental factors pose challenges in mapping the causal genes that affect spike ***,we systematically identified genes involved in spike trait formation by integrating information on genomic variation and gene regulatory networks controlling young spike development in *** identified 170 loci that are responsible for variations in spike length,spikelet number per spike,and grain number per spike through genome-wide association study and meta-QTL *** constructed gene regulatory networks for young inﬂorescences at the double ridge stage and theﬂoret primordium stage,in which the spikelet meristem and theﬂoret meristem are predominant,respec-tively,by integrating transcriptome,histone modification,chromatin accessibility,eQTL,and protein–pro-tein interactome *** these networks,we identified 169 hub genes located in 76 of the 170 QTL regions whose polymorphisms are significantly associated with variation in spike *** functions of TaZF-B1,VRT-B2,and TaSPL15-A/D in establishment of wheat spike architecture were *** study provides valuable molecular resources for understanding spike traits and demonstrates that combining genetic analysis and developmental regulatory networks is a robust approach for dissection of complex traits.

关键词： bread wheat spike traits genetic variation protein–protein interaction gene regulatory network

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Genomics-based plant germplasm research(GPGR)

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The crop Journal 2017年第2期5卷 166-174页

作者： Jizeng Jia Hongjie Li Xueyong Zhang Zichao Li lijuan qiu key Laboratory of crop Germplasm & Biotechnology Ministry of AgricultureInstitute of Crop ScienceChinese Academy of Agricultural SciencesThe National Key Facility for Crop Gene Resources and Genetic ImprovementNFCRGI beijing key Laboratory of crop genetic improvement Key Laboratory of Crop Heterosis and UtilizationMinistry of EducationChina Agricultural University

Plant germplasm underpins much of crop genetic improvement. Millions of germplasm accessions have been collected and conserved ex situ and/or in situ, and the major challenge is now how to exploit and utilize this abundant resource. Genomics-based plant germplasm research （GPGR） or ＂Cenoplasmics＂ is a novel cross-disciplinary research field that seeks to apply the principles and techniques of genomics to germplasm research. We describe in this paper the concept, strategy, and approach behind GPGR, and summarize current progress in the areas of the definition and construction of core collections, enhancement of germplasm with core collections, and gene discovery from core collections. GPGR is opening a new era in germplasm research. The contribution, progress and achievements of GPGR in the future are predicted.

关键词： Plant germplasm Genomics Genomics-based plant germplasm research(GPGR) Genoplasmics

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大豆新品种黑农84品质性状的环境稳定性分析

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大豆科学 2024年第1期43卷 1-12页

作者：王婉刘鑫磊孙君明栾晓燕邱丽娟中国农业科学院作物科学研究所/农作物基因资源与遗传改良国家重大科学工程/农业部北京大豆生物学重点实验室北京100081 黑龙江省农业科学院大豆研究所黑龙江哈尔滨150086

为明确黑农84的品质稳定性,为新品种的推广应用提供依据,本研究分析了黑农84不同年份、不同地点种植的品质性状变异。结果显示:黑农84是具备高蛋白、低脂肪、高亚麻酸、高异黄酮、高蔗糖和低水苏糖特性的优质功能型品种。在检测的27个... 详细信息

为明确黑农84的品质稳定性,为新品种的推广应用提供依据,本研究分析了黑农84不同年份、不同地点种植的品质性状变异。结果显示:黑农84是具备高蛋白、低脂肪、高亚麻酸、高异黄酮、高蔗糖和低水苏糖特性的优质功能型品种。在检测的27个品质性状中,16个性状(蛋白质和脂肪含量,蛋脂总量,棕榈酸、硬脂酸、油酸、亚油酸和亚麻酸含量,维生素E含量,水溶性糖,γ-维生素E,δ-维生素E,果糖、葡萄糖、蔗糖和水苏糖含量)的变异系数小于10%,较为稳定。两年的遗传多样性指数变异范围分别为1.08~1.98和1.07~1.73,平均值分别为1.62和1.59,其中α-大豆苷的遗传多样性指数最高(1.98和1.73),棉子糖的遗传多样性指数均最小(1.08和1.07)。黑农84品质性状聚类均可以分为两类,第一类中蛋白质和α-维生素E含量较高,脂肪和异黄酮含量较低;第二类中大豆苷、m-大豆苷、α-大豆苷和m-染料木苷含量较低。黑农84优质性状的环境稳定性为该品种的遗传育种和加工应用等提供了理论依据。

关键词：黑农84 品质性状遗传多样性指数聚类分析环境稳定性

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genetic diversity of Chinese summer soybean germplasm revealed by SSR markers

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Chinese Science Bulletin 2005年第6期50卷 526-535页

作者： XIE Hua GUAN Rongxia CHANG Ruzhen qiu lijuan Institute of crop Germplasm resources Chinese Academy of Agri-cultural Sciences/Key Laboratory of Crop Germplasm&Biotechnol-ogyMinistry of AgricultureBeijing 100081China beijing Agro-biotechnology Research Center Beijing 100089China

There are abundant soybean germplasm in china. In order to assess genetic diversity of Chinese sum- mer soybean germplasm, 158 Chinese summer soybean ac- cessions from the primary core collection of G. max were used to analyze genetic variation at 67 SSR loci. A total of 460 alleles were detected, in which 414 and 419 alleles oc- curred in the 80 Huanghuai and the 78 Southern summer accessions, respectively. The average number of alleles per locus was 6.9 for all the summer accessions, and 6.2 for both Huanghuai and Southern summer accessions. Marker diver- sity (D) per locus ranged from 0.414 to 0.905 with an average of 0.735 for all the summer accessions, from 0.387 to 0.886 with an average of 0.708 for the Huanghuai summer acces- sions, and from 0.189 to 0.884 with an average of 0.687 for the Southern summer accessions. The Huanghuai and Southern summer germplasm were different in the specific alleles, allelic-frequencies and pairwise genetic similarities. UPGMA cluster analysis based on the similarity data clearly separated the Huanghuai from Southern summer soybean accessions, suggesting that they were different gene pools. The results indicate that Chinese Huanghuai and Southern summer soybean germplasm can be used to enlarge genetic basis for developing elite summer soybean cultivars by ex- changing their germplasm.

关键词：遗传多样性大豆胚质农作物 NDA 核酸基因

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Functional genomics of Brassica napus:Progresses,challenges,and perspectives

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Journal of Integrative Plant Biology 2024年第3期66卷 484-509页

作者： Zengdong Tan Xu Han Cheng Dai Shaoping Lu Hanzi He Xuan Yao Peng Chen Chao Yang Lun Zhao Qing-Yong Yang Jun Zou Jing Wen Dengfeng Hong Chao Liu Xianhong Ge Chuchuan Fan Bing Yi Chunyu Zhang Chaozhi Ma Kede Liu Jinxiong Shen Jinxing Tu Guangsheng Yang Tingdong Fu Liang guo Hu Zhao national key Laboratory of crop genetic improvement Hubei Hongshan LaboratoryHuazhong Agricultural UniversityWuhan 430070China Yazhouwan national Laboratory Sanya 572025China

Brassica napus,commonly known as rapeseed or canola,is a major oil crop contributing over 13%to the stable supply of edible vegetable oil *** and understanding the gene functions in the *** genome is crucial for genomic breeding.A group of genes controlling agronomic traits have been successfully cloned through functional genomics studies in *** this review,we present an overview of the progress made in the functional genomics of ***,including the availability of germplasm resources,omics databases and cloned functional *** on the current progress,we also highlight the main challenges and perspectives in this *** advances in the functional genomics of *** contribute to a better understanding of the genetic basis underlying the complex agronomic traits in *** and will expedite the breeding of high quality,high resistance and high yield in *** varieties.

关键词： accelerate breeding Brassica napus functional genomics high resistance high yield

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A pan-TE map highlights transposable elements underlying domestication and agronomic traits in Asian rice

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national Science Review 2024年第6期11卷 105-118页

作者： Xiaoxia Li Xiaofan Dai Huiying He Yang Lv Longbo Yang Wenchuang He Congcong Liu Hua Wei Xiangpei Liu Qiaoling Yuan Xianmeng Wang Tianyi Wang Bintao Zhang Hong Zhang Wu Chen Yue Leng Xiaoman Yu Hongge Qian Bin Zhang Mingliang guo Zhipeng Zhang Chuanlin Shi Qianqian Zhang Yan Cui Qiang Xu Xinglan Cao Dandan Chen Yongfeng Zhou Qian Qian Lianguang Shang Shenzhen Branch Guangdong Laboratory of Lingnan Modern AgricultureGenome Analysis Laboratory of the Ministry of Agriculture and Rural AffairsAgricultural Genomics Institute at ShenzhenChinese Academy of Agricultural Sciences Rice Research Institute Shenyang Agricultural University Yazhouwan national Laboratory State key Laboratory of Rice Biology China National Rice Research Institute national key Laboratory of Tropical crop Breeding Tropical Crops Genetic Resources InstituteChinese Academy of Tropical Agricultural Sciences

Transposable elements(TEs) are ubiquitous genomic components and hard to study due to being highly repetitive. Here we assembled 232 chromosome-level genomes based on long-read sequencing *** the 232 genomes with 15 existing assemblies, we developed a pan-TE map comprising both cultivated and wild Asian rice. We detected 177 084 high-quality TE variations and inferred their derived state using outgroups. We found TEs were one source of phenotypic variation during rice domestication and differentiation. We identified 1246 genes whose expression variation was associated with TEs but not single-nucleotide polymorphisms(SNPs), such as Os Rboh B, and validated Os Rboh B's relative expression activity using a dual-Luciferase(LUC) reporter assays system. Our pan-TE map allowed us to detect multiple novel loci associated with agronomic traits. Collectively, our findings highlight the contributions of TEs to domestication, differentiation and agronomic traits in rice, and there is massive potential for gene cloning and molecular breeding by the high-quality Asian pan-TE map we generated.

关键词： transposable element super pan-genome pan-TE rice

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水稻苗期耐低钾品种筛选及相关性状的QTL定位

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植物遗传资源学报 2019年第5期20卷 1262-1270页

作者：罗曦吴方喜林强连玲何炜谢鸿光陈丽萍朱永生魏毅东蒋家焕谢华安张建福福建省农业科学院水稻研究所福州350019 闽台作物有害生物生态防控国家重点实验室/农业部华南杂交水稻种质创新与分子育种重点实验室/福州(国家)水稻改良分中心/福建省作物种质创新与分子育种省部共建国家重点实验室培育基地/杂交水稻国家重点实验室华南研究基地/福建省作物分子育种工程实验室/福建省水稻分子育种重点实验室/水稻国家工程实验室福州350003

对159份遗传差异较大的水稻品种进行耐低钾筛选,根据综合指数筛选出18份耐低钾和10份低钾敏感的水稻品种。利用筛选得到的耐低钾水稻品种台农67和低钾敏感品种制西构建重组自交系,对耐低钾相关性状进行QTL分析和定位,共检测到27个耐低... 详细信息

对159份遗传差异较大的水稻品种进行耐低钾筛选,根据综合指数筛选出18份耐低钾和10份低钾敏感的水稻品种。利用筛选得到的耐低钾水稻品种台农67和低钾敏感品种制西构建重组自交系,对耐低钾相关性状进行QTL分析和定位,共检测到27个耐低钾相关性状的QTL,LOD值为2.52~9.23,可解释表型变异为2.22%~7.25%,其中贡献率最高的QTL是qKC-2,该QTL定位在水稻2号染色体上,可能是1个控制水稻钾含量的未知基因,可进一步通过构建次级群体对该基因进行精细定位和克隆。本研究中设计的Indel标记可快速筛选水稻育种材料中的耐低钾基因型,缩短育种时间,而且重组自交系中可以选出农艺性状好又耐低钾的株系直接应用于育种。

关键词：水稻品种耐低钾 QTL 综合指数

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Association mapping combined with linkage analysis for seed coat color in soybean(Glycine max)

Association mapping combined with linkage analysis for seed ...

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第十四届全国植物基因组学大会

作者： Jian Song Yong guo lijuan qiu The national key facility for crop gene resources and genetic improvement(NFCRI) Institute of Crop ScienceChinese Academy of Agricultural Sciences

Color is one of the most widely used phenotypic markers in the study of genetic, molecular and biochemical processes,due to their easy *** coat color of soybean is also an important evolutionary trait other than its u... 详细信息

关键词： soybean seed coat color genetic mapping association analysis

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Molecular characterization of GmNHX2,a Na^+/H^+ antiporter gene homolog from soybean,and its heterologous expression to improve salt tolerance in Arabidopsis

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Chinese Science Bulletin 2009年第19期54卷 3536-3545页

作者： ZHOU guoAn GUAN RongXia LI YingHui CHANG RuZhen qiu lijuan national key facility for crop gene resources and genetic improvement (NFCRI)/key Lab of Germplasm & Biotechnology (MOA) Institute of Crop Science Chinese Academy of Agricultural Sciences Beijing 100081 China

Na+/H+ antiporters have been well documented to enhance plant salt tolerance by regulating cellular ion homeostasis. Here, a putative Na+/H+ antiporter gene homolog GmNHX2 from soybean was cloned and predicted to encode a protein of 534 amino acids with 10 putative transmembrane domains. GmNHX2 was expressed in all soybean plant tissues but enriched in roots and its expression was induced by NaCl and polyethylene glycol (PEG) treatments. GmNHX2 exhibits greater sequence similarity with LeNHX2 and AtNHX6 than that of AtNHX1 and AtSOS1. Although phylogenetic analysis clustered GmNHX2 with organellar (tonoplast and vesicles) antiporters, the GmNHX2-EGFP (enhanced green fluorescent protein) fusion protein was possibly localized in the plasma membrane or organelle membrane of transgenic plant cells. Furthermore, transgenic Arabidopsis plants expressing GmNHX2 were more tolerant to high NaCl concentrations during germination and seedling stages when compared with wild-type plants. These results suggest that GmNHX2 is a membrane Na+/H+ antiporter and may function to regulate ion homeostasis under salt stress.

关键词：植物耐盐基因工程盐胁迫离子分布植物组织 GmNHX2

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QTL mapping of qSCN3-1 for resistance to soybean cyst nematode in soybean line Zhongpin 03-5373

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The crop Journal 2021年第2期9卷 351-359页

作者： Lei Yang Yu Tian Yulin Liu Jochen C.Reif Yinghui Li lijuan qiu The national key facility for crop gene resources and genetic improvement(NFCRI)/key Lab of Germplasm Utilization(MOA) Institute of Crop SciencesChinese Academy of Agricultural SciencesBeijing 100081China College of Forestry Northwest A&F UniversityYangling 712100ShaanxiChina Department of Breeding Research Leibniz Institute of Plant Genetics and Crop Plant Research(IPK)GaterslebenGermany

Soybean cyst nematode(SCN,Heterodera glycines Ichinohe)is one of the most economically destructive *** soybean line Zhongpin03-5373(ZP),which combines resistance genes from several donors,is highly resistant to SCN race 3(SCN3).In our previous study,two QTL(rhg1 and GmSNAP11)were identified in a population of recombinant inbred lines derived from a cross between ZP and the susceptible parent Zhonghuang *** two QTL explained around one-third of the resistance,suggesting the presence of further QTL contributing to SCN *** the present study,we used an improved version of the geneticmap comprising the previously applied 1062 molecular markers and 47 newly developed InDel(insertion-deletion)*** improved map revealed a novel locus contributing to SCN3 resistance:qSCN3-1,flanked by InDelmarker InDel1-7 and SNPmarker Map-0047,explained 4.55%of the phenotypic variance for resistance to SCN3 and was not involved in digenic epistatic interaction with rhg1 and *** of Map-0047_CAPS(a CAPS marker developed for Map-0047)and InDel1-7 were significantly associated with SCN3 resistance in a panel of 209 resistant and susceptible *** further allele-combination analysis for three functional markers representing three cloned resistance genes(rhg1,Rhg4,andGmSNAP11)and twomarkers flanking qSCN3-1,we found that adding the resistance allele of qSCN3-1 greatly increased soybean resistance to SCN,even in diverse genetic *** qSCN3-1 locus will be useful for marker-assisted polygene pyramid breeding and should be targeted for the future identification of candidate genes.

关键词： Allelic combination InDel Pyramid Soybean cyst nematode

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