山西谷子核心资源群体结构及主要农艺性状关联分析

Population Structure and Association Analysis of Main Agronomic Traits of Shanxi Core Collection in Foxtail Millet

【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。

【Objective】The objective of this study is to detect the SSR markers associated with agronomic trait and analyzegenetic diversity and genetic structure of foxtail millet landrace in Shanxi province. The results will be helpful for hybridizationcombination of parent materials and molecular marker assisted breeding.【Method】96 SSR markers on 9 chromosomes were genome-wide screened for polymorphism in core collection of 595 accessions. PowerMarker 3.25 software was used to estimate thepolymorphism information of population. Population structure was analyzed using STRUCTURE 2.3.4 software. Then the data wereassociated with 96 SSR markers by GLM (general linear model, Q) and MLM (mixed linear model, Q+K).【Result】Totally 828alleles were found with 96 SSR markers and 8.6 alleles were revealed with each marker in average ranged from 2-26. The genediversity was from 0.005 to 0.941, averagely 0.610. The polymorphism information content (PIC) value ranged from 0.005 to 0.938with the mean of 0.577. Heterozygosity per locus on average was 0.016, ranging from 0 to 0.050. All the 595 accessions weredivided into three subgroups by analysis of population genetic structure. There was linkage disequilibrium (LD) among linked lociand unlinked loci pairs, and 1 955 out of 4 560 loci pairs (42.9%) had significant LD (P < 0.01) with average D′ value of 0.23. A totalof 12 locus found by GLM method significantly at the level of P<0.01 which explained 2.34%-13.94% of the phenotypic varianceand the mean value was 6.33%. CAAS2050 (R2=13.94%) and B153(R2=11.36%) kept the max value. Meanwhile, 9 loci were foundby MLM method significantly at the level of P<0.01 which explained 2.80%-9.22% of the phenotypic variance and the mean valuewas 5.16%. P89(R2=9.22%) and P3*(R2=8.28%) kept the max value. A total of 7 loci were detected in common by GLM and MLM.【Conclusion】Genetic diversity and population structure of 595 accessions were analyzed through SSR markers. In the twoassociation analysis models, 12 markers were associated with nine traits including stem node number, plant height, peduncle length,diameter of main stem, panicle length, panicle diameter, primary branch number per panicle, spikelet number per primary branch,protein content by GLM. Nine markers were associated with eight traits including stem node number, peduncle length, leaf width,diameter of main stem, panicle diameter, primary branch number per panicle, spikelet number per primary branch, 1000-grain weightby MLM.