In multiloci-based genetic association studies of complex diseases, a powerful and high efficient tool for analyses oflinkage disequilibrium (LD) between markers, haplotype distributions and many chi-square/p values w...In multiloci-based genetic association studies of complex diseases, a powerful and high efficient tool for analyses oflinkage disequilibrium (LD) between markers, haplotype distributions and many chi-square/p values with a large numberof samples has been sought for long. In order to achieve the goal of obtaining meaningful results directly from raw data,we developed a robust and user-friendly software platform with a series of tools for analysis in association study withhigh efficiency. The platform has been well evaluated by several sets of real data.展开更多
The inference of genome ancestry and the estimation of molecular relatedness are of great importance for breeding efficiency and association studies. Seventy SSR loci, evenly distributed in 10 chromosomes, were assaye...The inference of genome ancestry and the estimation of molecular relatedness are of great importance for breeding efficiency and association studies. Seventy SSR loci, evenly distributed in 10 chromosomes, were assayed for polymorphism among 187 commonly used maize （Zea mays L.） inbreds which represent the genetic diversity in China. The identified 290 alleles served as raw data for estimating population structure using the coalescent linked loci, based on the ADMIXTURE model. Population number, K, has been inferred to be between five and seven. Specifying five subpopulations （K = 5） led to a distinct decrease and specifying K to be greater than six resulted in only minimal increases in the likelihood value. Therefore, population number, K, has been inferred into six subpopulations, which are PA, BSSS （includes Reid）, PB, Lan （Lancaster Sure Crop）, LRC （Luda Reb Cob, a Chinese landrace, and its derivatives）, and SPT （Si-ping-tou, a Chinese landrace and its derivatives）. The Kullback-Leibler distance of pairwise subpopulation was also inferred as n × p （187 ×6） Q matrices, which gave a detailed percentage of genetic composition of six subpopulations and molecular relatedness of each line. The genome-wide linkage disequilibrium （LD） indicated that the asso- ciation studies in QTLs and/or candidate genes might avoid nonfunctional and spurious associations, as most of the LD blocks were broken among diverse germplasm. The defined population structure has given us a clear genetic structure of these lines for breeding practice and established a good basis for association analysis.展开更多
Vitiligo is an acquired disease characterized principally by patchy depigmentation of skin and overlying hair. Generalized vitiligo （GV）, the predominant form of the disorder, results from autoimmune loss of melanoc...Vitiligo is an acquired disease characterized principally by patchy depigmentation of skin and overlying hair. Generalized vitiligo （GV）, the predominant form of the disorder, results from autoimmune loss of melanocytes from affected regions. GV is a ＂complex trait＂, inherited in a non-Mendelian polygenic, multifactorial manner. GV is epidemiologically associated with other autoimmune diseases, both in GV patients and in their close relatives, suggesting that shared genes underlie susceptibility to this group of diseases. Early candidate gene association studies yielded a few successes, such as PTPN22, but most such reports now appear to be false-positives. Subsequent genomewide linkage studies identified NLRP1 and XBP1, apparent true GV susceptibility genes involved in immune regulation, and recent genome-wide association studies （GWAS） of GV in Caucasian and Chinese populations have yielded a large number of additional validated GV susceptibility genes. Together, these genes highlight biological systems and pathways that reach from the immune cells to the melanocyte, and provide insights into both disease pathogenesis and potential new targets for both treatment and even prevention of GV and other autoimmune diseases in genetically susceptible individuals.展开更多
【目的】分析山西谷子地方品种遗传多样性和群体遗传结构,筛选与谷子农艺性状相关联的分子标记,为谷子杂交组合亲本选配及分子标记辅助育种提供依据。【方法】利用96对SSR标记对595份山西谷子核心资源进行全基因组扫描,采用PowerMarker ...【目的】分析山西谷子地方品种遗传多样性和群体遗传结构,筛选与谷子农艺性状相关联的分子标记,为谷子杂交组合亲本选配及分子标记辅助育种提供依据。【方法】利用96对SSR标记对595份山西谷子核心资源进行全基因组扫描,采用PowerMarker 3.25软件分析群体遗传多样性,利用STRUCTURE 2.3.4软件分析群体遗传结构,使用TASSEL 2.1软件中GLM(general linear model,Q)和MLM(mixed linear model,Q+K)2种方法,进行表型和标记关联分析。【结果】96对SSR引物共扩增出828个等位变异,平均每对引物扩增到8.6个,变化范围为2—26;基因多样性指数变化范围为0.005—0.941,平均为0.610;多态信息量变化范围为0.005—0.938,平均为0.577;各位点杂合度变化范围为0—0.050,平均位点杂合度仅为0.016。群体结构分析将595份核心资源分为3个亚群。4560个SSR位点成对组合中,共线性组合和非共线性组合之间都存在一定的连锁不平衡。D′统计概率(P<0.01)支持的LD成对位点1955个,占全部位点组合的42.9%,D′平均值为0.23。通过GLM方法共检测到12个极显著性位点(P<0.01),表型变异解释率为2.34%—13.94%,平均为6.33%,贡献率较高的等位变异位点是CAAS2050(R2=13.94%)和B153(R2=11.36%);通过MLM方法共检测到9个极显著性位点(P<0.01),表型变异解释率为2.80%—9.22%,平均为5.16%,贡献率较高的等位变异位点是P89(R2=9.22%)和P3*(R2=8.28%);2种方法共同检测到的极显著性位点有7个。【结论】利用SSR标记分析了595份山西谷子核心资源的遗传多样性和群体遗传结构。2种关联分析模型中,GLM方法关联到12个标记与节数、株高、颈长、茎粗、穗长、穗粗、码数、码粒数、蛋白质含量9个性状相关;MLM方法关联到9个标记与节数、颈长、叶宽、茎粗、穗粗、码数、码粒数、千粒重8个性状相关。展开更多
Using 219 F2 Individuals developed by crossing the genetic standard line TM-1 and the multiple dominant marker line T586 In Gossyplum hirsutum L., a genetic linkage map with 19 linkage groups was constructed based on ...Using 219 F2 Individuals developed by crossing the genetic standard line TM-1 and the multiple dominant marker line T586 In Gossyplum hirsutum L., a genetic linkage map with 19 linkage groups was constructed based on simple sequence repeat （SSR） markers. Compared with our tetraploid backboned molecular genetic map from a （TM-1xHal 7124）xTM-1 BC1 population, 17 of the 19 I｜nkage groups were combined and anchored to 12 chromosomes （sub-genomes）. Of these groups, four morphological marker genes In T586 had been mapped Into the molecular linkage map. Meanwhile, three quantitative trait loci for lint percentage were tagged and mapped separately on the A03 linkage group and chromosome 6.展开更多
Soybean mosaic virus（SMV） disease is one of the most serious and broadly distributed soybean（Glycine max（L.） Merr.） diseases. Here, we combine the advantages of association and linkage analysis to identify and f...Soybean mosaic virus（SMV） disease is one of the most serious and broadly distributed soybean（Glycine max（L.） Merr.） diseases. Here, we combine the advantages of association and linkage analysis to identify and fine-map the soybean genes associated with resistance to SMV strain SC7.A set of 191 soybean accessions from different geographic origins and 184 recombinant inbred lines（RILs） derived from Kefeng No.1（resistant） Nannong 1138-2（susceptible） were used in this study. The SC7 resistance genes were previously mapped to a 2.65 Mb region on chromosome 2 and a 380 kb region on chromosome 13. Among 19 single nucleotide polymorphisms（SNPs） detected via association analysis in the study, the SNP BARC-021625-04157 was located in the2.65 Mb region, and the SNP BARC-041671-08065 was located near the 380 kb region; three genes harboring the SNPs were probably related to SC7 resistance. The resistance gene associated with BARC-021625-04157 was then finemapped to a region of approximately 158 kb on chromosome2 using 184 RILs. Among the 15 genes within this region, one NBS-LRR type gene, one HSP40 gene and one serine carboxypeptidase-type gene might be candidate SC7 resistance genes. These results will be useful for map-based cloning and marker-assisted selection in soybean breeding programs.展开更多
基金This work was supported by the Major State Basic Research Development program of Chinathe National High Technology Research and Development Program of China.
文摘In multiloci-based genetic association studies of complex diseases, a powerful and high efficient tool for analyses oflinkage disequilibrium (LD) between markers, haplotype distributions and many chi-square/p values with a large numberof samples has been sought for long. In order to achieve the goal of obtaining meaningful results directly from raw data,we developed a robust and user-friendly software platform with a series of tools for analysis in association study withhigh efficiency. The platform has been well evaluated by several sets of real data.
文摘The inference of genome ancestry and the estimation of molecular relatedness are of great importance for breeding efficiency and association studies. Seventy SSR loci, evenly distributed in 10 chromosomes, were assayed for polymorphism among 187 commonly used maize （Zea mays L.） inbreds which represent the genetic diversity in China. The identified 290 alleles served as raw data for estimating population structure using the coalescent linked loci, based on the ADMIXTURE model. Population number, K, has been inferred to be between five and seven. Specifying five subpopulations （K = 5） led to a distinct decrease and specifying K to be greater than six resulted in only minimal increases in the likelihood value. Therefore, population number, K, has been inferred into six subpopulations, which are PA, BSSS （includes Reid）, PB, Lan （Lancaster Sure Crop）, LRC （Luda Reb Cob, a Chinese landrace, and its derivatives）, and SPT （Si-ping-tou, a Chinese landrace and its derivatives）. The Kullback-Leibler distance of pairwise subpopulation was also inferred as n × p （187 ×6） Q matrices, which gave a detailed percentage of genetic composition of six subpopulations and molecular relatedness of each line. The genome-wide linkage disequilibrium （LD） indicated that the asso- ciation studies in QTLs and/or candidate genes might avoid nonfunctional and spurious associations, as most of the LD blocks were broken among diverse germplasm. The defined population structure has given us a clear genetic structure of these lines for breeding practice and established a good basis for association analysis.
基金supported in part by the grants R01 AR45585 and R01 AR056292 from the National Institutes of Health,USA
文摘Vitiligo is an acquired disease characterized principally by patchy depigmentation of skin and overlying hair. Generalized vitiligo （GV）, the predominant form of the disorder, results from autoimmune loss of melanocytes from affected regions. GV is a ＂complex trait＂, inherited in a non-Mendelian polygenic, multifactorial manner. GV is epidemiologically associated with other autoimmune diseases, both in GV patients and in their close relatives, suggesting that shared genes underlie susceptibility to this group of diseases. Early candidate gene association studies yielded a few successes, such as PTPN22, but most such reports now appear to be false-positives. Subsequent genomewide linkage studies identified NLRP1 and XBP1, apparent true GV susceptibility genes involved in immune regulation, and recent genome-wide association studies （GWAS） of GV in Caucasian and Chinese populations have yielded a large number of additional validated GV susceptibility genes. Together, these genes highlight biological systems and pathways that reach from the immune cells to the melanocyte, and provide insights into both disease pathogenesis and potential new targets for both treatment and even prevention of GV and other autoimmune diseases in genetically susceptible individuals.
文摘【目的】分析山西谷子地方品种遗传多样性和群体遗传结构,筛选与谷子农艺性状相关联的分子标记,为谷子杂交组合亲本选配及分子标记辅助育种提供依据。【方法】利用96对SSR标记对595份山西谷子核心资源进行全基因组扫描,采用PowerMarker 3.25软件分析群体遗传多样性,利用STRUCTURE 2.3.4软件分析群体遗传结构,使用TASSEL 2.1软件中GLM(general linear model,Q)和MLM(mixed linear model,Q+K)2种方法,进行表型和标记关联分析。【结果】96对SSR引物共扩增出828个等位变异,平均每对引物扩增到8.6个,变化范围为2—26;基因多样性指数变化范围为0.005—0.941,平均为0.610;多态信息量变化范围为0.005—0.938,平均为0.577;各位点杂合度变化范围为0—0.050,平均位点杂合度仅为0.016。群体结构分析将595份核心资源分为3个亚群。4560个SSR位点成对组合中,共线性组合和非共线性组合之间都存在一定的连锁不平衡。D′统计概率(P<0.01)支持的LD成对位点1955个,占全部位点组合的42.9%,D′平均值为0.23。通过GLM方法共检测到12个极显著性位点(P<0.01),表型变异解释率为2.34%—13.94%,平均为6.33%,贡献率较高的等位变异位点是CAAS2050(R2=13.94%)和B153(R2=11.36%);通过MLM方法共检测到9个极显著性位点(P<0.01),表型变异解释率为2.80%—9.22%,平均为5.16%,贡献率较高的等位变异位点是P89(R2=9.22%)和P3*(R2=8.28%);2种方法共同检测到的极显著性位点有7个。【结论】利用SSR标记分析了595份山西谷子核心资源的遗传多样性和群体遗传结构。2种关联分析模型中,GLM方法关联到12个标记与节数、株高、颈长、茎粗、穗长、穗粗、码数、码粒数、蛋白质含量9个性状相关;MLM方法关联到9个标记与节数、颈长、叶宽、茎粗、穗粗、码数、码粒数、千粒重8个性状相关。
基金Supported by the Hi-Tech Research and Development （863） Program of China （2004AA211172）, the Program for Changjiang Scholars and Innovative Research Team in University of the Ministry of Education （IRT0432） and the National Natural Science Foundation of China （30070483 and 30270806）.
文摘Using 219 F2 Individuals developed by crossing the genetic standard line TM-1 and the multiple dominant marker line T586 In Gossyplum hirsutum L., a genetic linkage map with 19 linkage groups was constructed based on simple sequence repeat （SSR） markers. Compared with our tetraploid backboned molecular genetic map from a （TM-1xHal 7124）xTM-1 BC1 population, 17 of the 19 I｜nkage groups were combined and anchored to 12 chromosomes （sub-genomes）. Of these groups, four morphological marker genes In T586 had been mapped Into the molecular linkage map. Meanwhile, three quantitative trait loci for lint percentage were tagged and mapped separately on the A03 linkage group and chromosome 6.
基金supported in part by the National Basic Research Program of China(973 Program)(2010CB125906)the National Natural Science Foundation of China(31171573,31301342,31370034)+2 种基金the Jiangsu Provincial Support Program(BE2012328)the Program for Changjiang Scholarsthe Innovative Research Team in University(PCSIRT13073)
文摘Soybean mosaic virus（SMV） disease is one of the most serious and broadly distributed soybean（Glycine max（L.） Merr.） diseases. Here, we combine the advantages of association and linkage analysis to identify and fine-map the soybean genes associated with resistance to SMV strain SC7.A set of 191 soybean accessions from different geographic origins and 184 recombinant inbred lines（RILs） derived from Kefeng No.1（resistant） Nannong 1138-2（susceptible） were used in this study. The SC7 resistance genes were previously mapped to a 2.65 Mb region on chromosome 2 and a 380 kb region on chromosome 13. Among 19 single nucleotide polymorphisms（SNPs） detected via association analysis in the study, the SNP BARC-021625-04157 was located in the2.65 Mb region, and the SNP BARC-041671-08065 was located near the 380 kb region; three genes harboring the SNPs were probably related to SC7 resistance. The resistance gene associated with BARC-021625-04157 was then finemapped to a region of approximately 158 kb on chromosome2 using 184 RILs. Among the 15 genes within this region, one NBS-LRR type gene, one HSP40 gene and one serine carboxypeptidase-type gene might be candidate SC7 resistance genes. These results will be useful for map-based cloning and marker-assisted selection in soybean breeding programs.
