Shade tolerance is essential for soybeans in inter/relay cropping systems.A genome-wide association study(GWAS)integrated with transcriptome sequencing was performed to identify genes and construct a genetic network g...Shade tolerance is essential for soybeans in inter/relay cropping systems.A genome-wide association study(GWAS)integrated with transcriptome sequencing was performed to identify genes and construct a genetic network governing the trait in a set of recombinant inbred lines derived from two soybean parents with contrasting shade tolerance.An improved GWAS procedure,restricted two-stage multi-locus genome-wide association study based on gene/allele sequence markers(GASM-RTM-GWAS),identified 140 genes and their alleles associated with shade-tolerance index(STI),146 with relative pith cell length(RCL),and nine with both.Annotation of these genes by biological categories allowed the construction of a protein–protein interaction network by 187 genes,of which half were differentially expressed under shading and non-shading conditions as well as at different growth stages.From the identified genes,three ones jointly identified for both traits by both GWAS and transcriptome and two genes with maximum links were chosen as beginners for entrance into the network.Altogether,both STI and RCL gene systems worked for shade-tolerance with genes interacted each other,this confirmed that shadetolerance is regulated by more than single group of interacted genes,involving multiple biological functions as a gene network.展开更多
关联作图是一种利用连锁不平衡(linkage disequilibrium,LD)检测自然群体中基因位点及其等位变异的方法。利用60个SSR标记,对全国大豆地方品种群体(393份代表性材料)和野生大豆群体(196份代表性材料)的基因组变异进行扫描,分析两类群体...关联作图是一种利用连锁不平衡(linkage disequilibrium,LD)检测自然群体中基因位点及其等位变异的方法。利用60个SSR标记,对全国大豆地方品种群体(393份代表性材料)和野生大豆群体(196份代表性材料)的基因组变异进行扫描,分析两类群体的连锁不平衡位点、群体结构,并采用TASSEL软件的GLM(general linear model)方法对16个农艺、品质性状观测值进行标记与性状的关联分析。结果表明:(1)在公共图谱上不论共线性的或是非共线性的SSR位点组合都有一定程度的LD,说明历史上发生过连锁群间的重组;栽培群体的连锁不平衡成对位点数较野生群体多,但野生群体位点间连锁不平衡程度高,随距离的衰减慢。(2)群体SSR数据遗传结构分析发现,栽培群体和野生群体分别由9和4个亚群体组成,亚群的划分与群体地理生态类型相关联,证实地理生态类型划分有其遗传基础。(3)栽培群体中累计有27个位点与性状相关;野生大豆种质中累计有34个位点与性状相关。部分标记在两类群体中都表现与同一性状关联,检出的位点有一致性,也有互补性;一些标记同时与2个或多个性状相关联,可能是性状相关乃至一因多效的遗传基础;关联位点中累计有24位点(次)与遗传群体连锁分析定位的QTL一致。展开更多
大豆贮藏蛋白主要成分是7S和11S球蛋白,大豆贮藏蛋白组分及其亚基组成决定了蛋白质的品质和加工特性。本研究选用134对细胞核SSR标记,对166份栽培大豆微核心种质进行基因分型,运用一般线性回归(general linear model,GLM)和复合线性回归...大豆贮藏蛋白主要成分是7S和11S球蛋白,大豆贮藏蛋白组分及其亚基组成决定了蛋白质的品质和加工特性。本研究选用134对细胞核SSR标记,对166份栽培大豆微核心种质进行基因分型,运用一般线性回归(general linear model,GLM)和复合线性回归(mixed linear model,MLM)方法进行标记与性状的关联分析,定位大豆蛋白亚基的相关基因。结果表明,2年均检测到的且与蛋白亚基相关联的SSR位点有14个,以MLM方法检测到5个SSR位点(Sat_062、Satt583、Satt291、Satt234和Satt595)与蛋白亚基相关联;7S组分各亚基变异程度较大,是引起11S/7S变异的主要原因;表型变异较大的亚基可能因为相关基因进化中发生重组较多,LD衰减距离较小,导致检测到较少的相关位点。本研究结果对蛋白亚基相关性状的标记辅助选择育种有重要的利用价值。展开更多
基金This work was financially supported by the grants from the National Key Research and Development Program of China(2021YFF1001204,2021YFD1201602)the MOE 111 Project(B08025)+2 种基金the MOA CARS-04 program,the Program of Jiangsu province(JBGS-2021-014)the Guangxi Scientific Research and Technology Development Plan(14125008-2-16)the Guidance Foundation of Sanya Institute of Nanjing Agricultural University(NAUSY-ZZ02,NAUSY-MS05).
文摘Shade tolerance is essential for soybeans in inter/relay cropping systems.A genome-wide association study(GWAS)integrated with transcriptome sequencing was performed to identify genes and construct a genetic network governing the trait in a set of recombinant inbred lines derived from two soybean parents with contrasting shade tolerance.An improved GWAS procedure,restricted two-stage multi-locus genome-wide association study based on gene/allele sequence markers(GASM-RTM-GWAS),identified 140 genes and their alleles associated with shade-tolerance index(STI),146 with relative pith cell length(RCL),and nine with both.Annotation of these genes by biological categories allowed the construction of a protein–protein interaction network by 187 genes,of which half were differentially expressed under shading and non-shading conditions as well as at different growth stages.From the identified genes,three ones jointly identified for both traits by both GWAS and transcriptome and two genes with maximum links were chosen as beginners for entrance into the network.Altogether,both STI and RCL gene systems worked for shade-tolerance with genes interacted each other,this confirmed that shadetolerance is regulated by more than single group of interacted genes,involving multiple biological functions as a gene network.
文摘关联作图是一种利用连锁不平衡(linkage disequilibrium,LD)检测自然群体中基因位点及其等位变异的方法。利用60个SSR标记,对全国大豆地方品种群体(393份代表性材料)和野生大豆群体(196份代表性材料)的基因组变异进行扫描,分析两类群体的连锁不平衡位点、群体结构,并采用TASSEL软件的GLM(general linear model)方法对16个农艺、品质性状观测值进行标记与性状的关联分析。结果表明:(1)在公共图谱上不论共线性的或是非共线性的SSR位点组合都有一定程度的LD,说明历史上发生过连锁群间的重组;栽培群体的连锁不平衡成对位点数较野生群体多,但野生群体位点间连锁不平衡程度高,随距离的衰减慢。(2)群体SSR数据遗传结构分析发现,栽培群体和野生群体分别由9和4个亚群体组成,亚群的划分与群体地理生态类型相关联,证实地理生态类型划分有其遗传基础。(3)栽培群体中累计有27个位点与性状相关;野生大豆种质中累计有34个位点与性状相关。部分标记在两类群体中都表现与同一性状关联,检出的位点有一致性,也有互补性;一些标记同时与2个或多个性状相关联,可能是性状相关乃至一因多效的遗传基础;关联位点中累计有24位点(次)与遗传群体连锁分析定位的QTL一致。
文摘大豆贮藏蛋白主要成分是7S和11S球蛋白,大豆贮藏蛋白组分及其亚基组成决定了蛋白质的品质和加工特性。本研究选用134对细胞核SSR标记,对166份栽培大豆微核心种质进行基因分型,运用一般线性回归(general linear model,GLM)和复合线性回归(mixed linear model,MLM)方法进行标记与性状的关联分析,定位大豆蛋白亚基的相关基因。结果表明,2年均检测到的且与蛋白亚基相关联的SSR位点有14个,以MLM方法检测到5个SSR位点(Sat_062、Satt583、Satt291、Satt234和Satt595)与蛋白亚基相关联;7S组分各亚基变异程度较大,是引起11S/7S变异的主要原因;表型变异较大的亚基可能因为相关基因进化中发生重组较多,LD衰减距离较小,导致检测到较少的相关位点。本研究结果对蛋白亚基相关性状的标记辅助选择育种有重要的利用价值。
