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
利用57个SSR和InDel标记,对80份大白菜自交系及110份F1杂交种材料的基因组DNA进行扩增。通过群体遗传结构分析,将供试材料分为3个亚群体,亚群体的划分与群体遗传关系和性状相关联;采用TASSEL软件的GLM(general linear model)方法进行标...利用57个SSR和InDel标记,对80份大白菜自交系及110份F1杂交种材料的基因组DNA进行扩增。通过群体遗传结构分析,将供试材料分为3个亚群体,亚群体的划分与群体遗传关系和性状相关联;采用TASSEL软件的GLM(general linear model)方法进行标记与抽薹时间和开花时间的关联作图分析,发现13个标记的17个位点与抽薹时间和开花时间相关,其中15个与抽薹时间相关,12个与开花时间相关。10个位点同时与两个性状相关联。展开更多
Exploring the elite al eles and germplasm acces-sions related to fiber quality traits wil accelerate the breeding of cotton for fiber quality improvement. In this study, 99 Gossypium hirsutum L. accessions with divers...Exploring the elite al eles and germplasm acces-sions related to fiber quality traits wil accelerate the breeding of cotton for fiber quality improvement. In this study, 99 Gossypium hirsutum L. accessions with diverse origins were used to perform association analysis of fiber quality traits using 97 polymorphic microsatel ite marker primer pairs. A total of 107 significant marker-trait associations were detected for three fiber quality traits under three different environments, with 70 detected in two or three environments and 37 detected in only one environment. Among the 70 significant marker-trait associations, 52.86% were reported previously, implying that these are stable loci for target traits. Furthermore, we detected a large number of elite al eles associated simulta-neously with two or three traits. These elite al eles were mainly from accessions col ected in China, introduced to China from the United States, or rare al eles with a frequency of less than＆amp;nbsp;5%. No one cultivar contained more than half of the elite al eles, but 10 accessions were col ected from China and the two introduced from the United States did contain more than half of these al eles. Therefore, there is great potential for mining elite al eles from germplasm accessions for use in fiber quality improvement in modern cotton breeding.展开更多
Maize seedlings are very sensitive to chilling, especially during the transition phase from heterotrophic to autotrophic growth. Genetic dissection of the genetic basis of chilling tolerance would provide useful infor...Maize seedlings are very sensitive to chilling, especially during the transition phase from heterotrophic to autotrophic growth. Genetic dissection of the genetic basis of chilling tolerance would provide useful information for genetic improvement of maize inbreds. In this study, genome-wide association analysis was conducted to explore the genetic architecture of maize chilling tolerance at the seed germination and seedling stages with an association panel of 125 inbreds. Ten tolerance indices （ratios of the performance of 10 germination rates and seedling growth-related traits under chilling stress and control conditions） were investigated to assess the ability of chilling tolerance of the inbreds, and a total of 43 single nucleotide polymorphisms associated with chilling tolerance were detected, with none of them being related to chilling tolerance at both the germination and seedling stages simultaneously. Correlation analysis also revealed that the genetic basis of chilling tolerance at the seed germination stage is generally different from that at the seedling stage. In addition, a total of 40 candidate genes involving 31 of the 43 single nucleotide polymorphisms were predicted, and were grouped into five categories according to their functions. The possible roles of these candidate genes in chilling tolerance were also discussed.展开更多
The main objective of this study was to evaluate the potential of a sesame （Sesamum indicum L.） panel for association analysis, and investigate the genetic basis of oil content （OC）, protein content, oleic acid co...The main objective of this study was to evaluate the potential of a sesame （Sesamum indicum L.） panel for association analysis, and investigate the genetic basis of oil content （OC）, protein content, oleic acid concentration, and linoleic acid concentration using association mapping. A panel of 216 sesame accessions was phenotyped in a multi-environment trial and fingerprinted with 608 polymorphic loci produced by 79 primers, including simple sequence repeats （SSRs）, sequence-related amplified polymorphisms （SRAPs）, and amplified fragment length polymorphisms （AFLPs）. Population structure analysis revealed two subgroups in the population. The Q model performed better for its ability to re-identify associations for the four traits at highly significant P-values compared to the other three mixed models. And a total of 35 and 25 associations for the four traits in 2010 and 2011 were identified, respectively, with the Q model after Bonferroni correction. Among those associations, only one for OC was re-identified in two environments, and several markers associated simultaneously with multiple traits were discovered. These results suggest the power and stability of the Q model for association analysis of nutritional traits in this sesame panel for its slight population stratification and familial relationship, which could aid in dissecting complex traits, and could help to develop strategies for improving nutritional quality.展开更多
The insensitive response to photoperiod and temperature is an important quantitative trait for soybean in wide adaptation breeding. The natural variation in response to photoperiod and temperature was detected using 2...The insensitive response to photoperiod and temperature is an important quantitative trait for soybean in wide adaptation breeding. The natural variation in response to photoperiod and temperature was detected using 275 accessions of soybean [Glycine max （L.） Merrill] from China. Genome-wide association mapping, based on population structure analysis, was carried out using 118 SSR markers by the TASSEL GLM （general linear model） program. Nine SSR markers （P〈0.01） were associated with the value of the response to photoperiod and temperature （VRPT） caused by days to flowering （DF）, among which, Satt308 （LG M）, Sattl50 （LG M） and Satt440 （LG l）, were identified in both 2006 and 2007. Twelve SSR markers （P〈0.01） were associated with VRPT caused by days to maturity （DM）, among which three markers, Satt387 （LG N）, Satt307 （LG C2） and AW310961 （LG J）, were detected in both 2006 and 2007. In addition, a total of 20 elite alleles were screened out over 2006 and 2007 for being associated with an insensitive response to photoperiod and temperature （IRPT） caused by DF and a total of seven different elite alleles were screened out for being associated with IRPT caused by DM. Among these elite alleles, five alleles, Satt150-244, Satt308-164, Satt308-206, Satt440-176, and Satt440-206, were associated with IRPT caused by DF and were identified in both years, but only one allele, Satt307-170, was identified as being associated with an IRPT caused by DM. Based on these elite alleles, a set of typical accessions were screened out. The result about the genetic basis of IRPT is meaningful for soybean wide adaption breeding.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
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。
文摘利用57个SSR和InDel标记,对80份大白菜自交系及110份F1杂交种材料的基因组DNA进行扩增。通过群体遗传结构分析,将供试材料分为3个亚群体,亚群体的划分与群体遗传关系和性状相关联;采用TASSEL软件的GLM(general linear model)方法进行标记与抽薹时间和开花时间的关联作图分析,发现13个标记的17个位点与抽薹时间和开花时间相关,其中15个与抽薹时间相关,12个与开花时间相关。10个位点同时与两个性状相关联。
基金financially supported in part by the National Science Foundation in China(30871558)the National High Technology Research and Development Program of China(863 Program)(2012AA101108-04-04)+1 种基金Jiangsu Agriculture Science and Technology Innovation Fund(cx(13)3059)a project funded by the Priority Academic Program Development of Jiangsu Higher Education Institutions
文摘Exploring the elite al eles and germplasm acces-sions related to fiber quality traits wil accelerate the breeding of cotton for fiber quality improvement. In this study, 99 Gossypium hirsutum L. accessions with diverse origins were used to perform association analysis of fiber quality traits using 97 polymorphic microsatel ite marker primer pairs. A total of 107 significant marker-trait associations were detected for three fiber quality traits under three different environments, with 70 detected in two or three environments and 37 detected in only one environment. Among the 70 significant marker-trait associations, 52.86% were reported previously, implying that these are stable loci for target traits. Furthermore, we detected a large number of elite al eles associated simulta-neously with two or three traits. These elite al eles were mainly from accessions col ected in China, introduced to China from the United States, or rare al eles with a frequency of less than＆amp;nbsp;5%. No one cultivar contained more than half of the elite al eles, but 10 accessions were col ected from China and the two introduced from the United States did contain more than half of these al eles. Therefore, there is great potential for mining elite al eles from germplasm accessions for use in fiber quality improvement in modern cotton breeding.
基金supported by grants from the National Natural Science Foundation of China(J1103510)the Huazhong Agricultural University Scientific & Technological Self-innovative Foundation(2011SC14)the Fundamental Research Funds for the Central University(2012ZYTS055)
文摘Maize seedlings are very sensitive to chilling, especially during the transition phase from heterotrophic to autotrophic growth. Genetic dissection of the genetic basis of chilling tolerance would provide useful information for genetic improvement of maize inbreds. In this study, genome-wide association analysis was conducted to explore the genetic architecture of maize chilling tolerance at the seed germination and seedling stages with an association panel of 125 inbreds. Ten tolerance indices （ratios of the performance of 10 germination rates and seedling growth-related traits under chilling stress and control conditions） were investigated to assess the ability of chilling tolerance of the inbreds, and a total of 43 single nucleotide polymorphisms associated with chilling tolerance were detected, with none of them being related to chilling tolerance at both the germination and seedling stages simultaneously. Correlation analysis also revealed that the genetic basis of chilling tolerance at the seed germination stage is generally different from that at the seedling stage. In addition, a total of 40 candidate genes involving 31 of the 43 single nucleotide polymorphisms were predicted, and were grouped into five categories according to their functions. The possible roles of these candidate genes in chilling tolerance were also discussed.
基金Financial support for this work was provided by the National Basic Research Program of China(2011 CB1 09304-2)the China Agriculture Research System of Sesame(CARS-15-1- 07)
文摘The main objective of this study was to evaluate the potential of a sesame （Sesamum indicum L.） panel for association analysis, and investigate the genetic basis of oil content （OC）, protein content, oleic acid concentration, and linoleic acid concentration using association mapping. A panel of 216 sesame accessions was phenotyped in a multi-environment trial and fingerprinted with 608 polymorphic loci produced by 79 primers, including simple sequence repeats （SSRs）, sequence-related amplified polymorphisms （SRAPs）, and amplified fragment length polymorphisms （AFLPs）. Population structure analysis revealed two subgroups in the population. The Q model performed better for its ability to re-identify associations for the four traits at highly significant P-values compared to the other three mixed models. And a total of 35 and 25 associations for the four traits in 2010 and 2011 were identified, respectively, with the Q model after Bonferroni correction. Among those associations, only one for OC was re-identified in two environments, and several markers associated simultaneously with multiple traits were discovered. These results suggest the power and stability of the Q model for association analysis of nutritional traits in this sesame panel for its slight population stratification and familial relationship, which could aid in dissecting complex traits, and could help to develop strategies for improving nutritional quality.
基金supported by the National Basic Research Program of China(2009CB118400)the Earmarked Fund for Modern Agro-Industry Technology Research System,China(nycytx-004)
文摘The insensitive response to photoperiod and temperature is an important quantitative trait for soybean in wide adaptation breeding. The natural variation in response to photoperiod and temperature was detected using 275 accessions of soybean [Glycine max （L.） Merrill] from China. Genome-wide association mapping, based on population structure analysis, was carried out using 118 SSR markers by the TASSEL GLM （general linear model） program. Nine SSR markers （P〈0.01） were associated with the value of the response to photoperiod and temperature （VRPT） caused by days to flowering （DF）, among which, Satt308 （LG M）, Sattl50 （LG M） and Satt440 （LG l）, were identified in both 2006 and 2007. Twelve SSR markers （P〈0.01） were associated with VRPT caused by days to maturity （DM）, among which three markers, Satt387 （LG N）, Satt307 （LG C2） and AW310961 （LG J）, were detected in both 2006 and 2007. In addition, a total of 20 elite alleles were screened out over 2006 and 2007 for being associated with an insensitive response to photoperiod and temperature （IRPT） caused by DF and a total of seven different elite alleles were screened out for being associated with IRPT caused by DM. Among these elite alleles, five alleles, Satt150-244, Satt308-164, Satt308-206, Satt440-176, and Satt440-206, were associated with IRPT caused by DF and were identified in both years, but only one allele, Satt307-170, was identified as being associated with an IRPT caused by DM. Based on these elite alleles, a set of typical accessions were screened out. The result about the genetic basis of IRPT is meaningful for soybean wide adaption breeding.
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。
