Association mapping is a useful tool for the detection of genes selected during plant domestication based on their linkage disequilibrium（LD）. This study was carried out to estimate genetic diversity, population str...Association mapping is a useful tool for the detection of genes selected during plant domestication based on their linkage disequilibrium（LD）. This study was carried out to estimate genetic diversity, population structure and the extent of LD to develop an association framework in order to identify genetic variations associated with drought and salt tolerance traits. 106 microsatellite marker primer pairs were used in 323 Gossypium hirsutum germplasms which were grown in the drought shed and salt pond for evaluation. Polymorphism（PIC=0.53） was found, and three groups were detected（K=3） with the second likelihood ΔK using STRUCTURE software. LD decay rates were estimated to be 13-15 cM at r2 0.20. Significant associations between polymorphic markers and drought and salt tolerance traits were observed using the general linear model（GLM） and mixed linear model（MLM）（P 0.01）. The results also demonstrated that association mapping within the population structure as well as stratification existing in cotton germplasm resources could complement and enhance quantitative trait loci（QTLs） information for marker-assisted selection.展开更多
To find the quantitative trait loci associated with wood density in teak(Tectona grandis L.f.), 21 co-dominant markers including 13 site specific recombinase and 8 EST-based co-dominant markers designed from lignin bi...To find the quantitative trait loci associated with wood density in teak(Tectona grandis L.f.), 21 co-dominant markers including 13 site specific recombinase and 8 EST-based co-dominant markers designed from lignin biosynthesis genes were applied to 174 teak plus tree clones at the National Germplasm Bank, Chandrapur,India. The germplasm bank exhibited 10.6% coefficient of variation for wood densities with 84.5 ± 31.3 genetic polymorphism(%). The highly panmictic set of genotypes(FST= 0.035 ± 0.004) harbored 96.47 ± 0.40 genetic variability(%). The average allelic frequency of the 21 codominant markers was 0.65 ± 0.11 with 12.9% pairs of loci in significant LD(p\0.05, R^2 values [ 0.1), confirming their suitability for a strong marker-trait association study. The marker CCoAMT-1 was significantly(p\0.01) associated with wood density showing stability by both GLM and MLM models and explained 4.3% of the phenotypic effect. The marker from the EST representing CCoAMT can be further developed for gene-assisted selection of elite genotypes of teak with greater wood density. Therefore, we believe that the report will help accelerate the genetic improvement and advance the breeding program of the species.展开更多
With completion of the Populus genome sequencing project and the availability of many expressed sequence tags （ESTs） databases in forest trees, attention is now rapidly shifting towards the study of individual genet...With completion of the Populus genome sequencing project and the availability of many expressed sequence tags （ESTs） databases in forest trees, attention is now rapidly shifting towards the study of individual genetic variation in natural populations. The most abundant form of genetic variation in many eukaryotic species is represented by single nucleotide polymorphisms （SNPs）, which can account for heritable inter-individual differences in complex phenotypes. Unlike humans, the linkage disequilibrium （LD） rapidly decays within candidate genes in forest trees. Thus, SNPs-based candidate gene association studies are considered to be a most effective approach to dissect the complex quantitative traits in forest trees. The present study demonstrates that LD mapping can be used to identify alleles associated with quantitative traits and suggests that this new approach could be particularly useful for performing breeding programs in forest trees. In this review, we will describe the fundamentals, patterns of SNPs distribution and frequency, summarize recent advances in SNPs discovery and LD and comment on the application of LD in the dissection of complex quantitative traits in forest tress. We also put forward the outlook for future SNPs-based association analysis of quantitative traits in forest trees.展开更多
筛选与小麦重要农艺性状相关联的SSR标记,对小麦分子标记辅助育种有重要的实践意义。本研究利用多态性较高的80个SSR标记,对南大2419及其71份衍生后代品种(系)进行基因型分析,采用TASSEL软件的MLM(Mixed linear model)方法对籽粒产量、...筛选与小麦重要农艺性状相关联的SSR标记,对小麦分子标记辅助育种有重要的实践意义。本研究利用多态性较高的80个SSR标记,对南大2419及其71份衍生后代品种(系)进行基因型分析,采用TASSEL软件的MLM(Mixed linear model)方法对籽粒产量、千粒重、有效穗、穗粒数等8个主要农艺性状进行SSR标记与性状的关联分析。结果表明:(1)该群体由6个亚群组成;(2)群体SSR数据分析发现,无论是连锁还是非连锁SSR位点组合都存在不同程度的连锁不平衡(Linkage disequilibrium,LD);在各基因组选择标记数基本相同的情况下,D基因组中显著LD位点比例(8.9%)明显低于A基因组(15.3%)和B基因组(13.8%),但D基因组的LD水平较高;(3)群体中共20个SSR位点与8个农艺性状显著关联,4个位点2年被检测到与同一性状显著相关(p<0.01),10个位点位于家系连锁定位的QTL区间或附近,多数位点/性状关联结果与前人研究一致;13个标记位点同时与2个或多个性状关联。展开更多
基金supported by the National Natural Science Foundation of China(31201246)the Project of International Science and Technology Cooperation and Exchange from the Ministry of Science and Technology,China(2010DFR30620-3)
文摘Association mapping is a useful tool for the detection of genes selected during plant domestication based on their linkage disequilibrium（LD）. This study was carried out to estimate genetic diversity, population structure and the extent of LD to develop an association framework in order to identify genetic variations associated with drought and salt tolerance traits. 106 microsatellite marker primer pairs were used in 323 Gossypium hirsutum germplasms which were grown in the drought shed and salt pond for evaluation. Polymorphism（PIC=0.53） was found, and three groups were detected（K=3） with the second likelihood ΔK using STRUCTURE software. LD decay rates were estimated to be 13-15 cM at r2 0.20. Significant associations between polymorphic markers and drought and salt tolerance traits were observed using the general linear model（GLM） and mixed linear model（MLM）（P 0.01）. The results also demonstrated that association mapping within the population structure as well as stratification existing in cotton germplasm resources could complement and enhance quantitative trait loci（QTLs） information for marker-assisted selection.
基金partially funded in the form of Senior Research Fellowship(vide No.09/1164(0001)/2016-EMR-I)awarded to the first author(Vivek Vaishnav)by Government of India Council of Scientific and Industrial Research,New Delhi,which is gratefully acknowledged
文摘To find the quantitative trait loci associated with wood density in teak(Tectona grandis L.f.), 21 co-dominant markers including 13 site specific recombinase and 8 EST-based co-dominant markers designed from lignin biosynthesis genes were applied to 174 teak plus tree clones at the National Germplasm Bank, Chandrapur,India. The germplasm bank exhibited 10.6% coefficient of variation for wood densities with 84.5 ± 31.3 genetic polymorphism(%). The highly panmictic set of genotypes(FST= 0.035 ± 0.004) harbored 96.47 ± 0.40 genetic variability(%). The average allelic frequency of the 21 codominant markers was 0.65 ± 0.11 with 12.9% pairs of loci in significant LD(p\0.05, R^2 values [ 0.1), confirming their suitability for a strong marker-trait association study. The marker CCoAMT-1 was significantly(p\0.01) associated with wood density showing stability by both GLM and MLM models and explained 4.3% of the phenotypic effect. The marker from the EST representing CCoAMT can be further developed for gene-assisted selection of elite genotypes of teak with greater wood density. Therefore, we believe that the report will help accelerate the genetic improvement and advance the breeding program of the species.
文摘With completion of the Populus genome sequencing project and the availability of many expressed sequence tags （ESTs） databases in forest trees, attention is now rapidly shifting towards the study of individual genetic variation in natural populations. The most abundant form of genetic variation in many eukaryotic species is represented by single nucleotide polymorphisms （SNPs）, which can account for heritable inter-individual differences in complex phenotypes. Unlike humans, the linkage disequilibrium （LD） rapidly decays within candidate genes in forest trees. Thus, SNPs-based candidate gene association studies are considered to be a most effective approach to dissect the complex quantitative traits in forest trees. The present study demonstrates that LD mapping can be used to identify alleles associated with quantitative traits and suggests that this new approach could be particularly useful for performing breeding programs in forest trees. In this review, we will describe the fundamentals, patterns of SNPs distribution and frequency, summarize recent advances in SNPs discovery and LD and comment on the application of LD in the dissection of complex quantitative traits in forest tress. We also put forward the outlook for future SNPs-based association analysis of quantitative traits in forest trees.
文摘筛选与小麦重要农艺性状相关联的SSR标记,对小麦分子标记辅助育种有重要的实践意义。本研究利用多态性较高的80个SSR标记,对南大2419及其71份衍生后代品种(系)进行基因型分析,采用TASSEL软件的MLM(Mixed linear model)方法对籽粒产量、千粒重、有效穗、穗粒数等8个主要农艺性状进行SSR标记与性状的关联分析。结果表明:(1)该群体由6个亚群组成;(2)群体SSR数据分析发现,无论是连锁还是非连锁SSR位点组合都存在不同程度的连锁不平衡(Linkage disequilibrium,LD);在各基因组选择标记数基本相同的情况下,D基因组中显著LD位点比例(8.9%)明显低于A基因组(15.3%)和B基因组(13.8%),但D基因组的LD水平较高;(3)群体中共20个SSR位点与8个农艺性状显著关联,4个位点2年被检测到与同一性状显著相关(p<0.01),10个位点位于家系连锁定位的QTL区间或附近,多数位点/性状关联结果与前人研究一致;13个标记位点同时与2个或多个性状关联。
