海南短日照条件下谷子穗部性状的全基因组关联分析

Genome-Wide Association Analysis of Panicle Traits of Foxtail Millet under Hainan Short-day Condition

定位短日照条件下控制谷子穗部性状的QTL位点,筛选候选基因,为揭示短日照条件下谷子穗部性状形成的遗传机制奠定基础。2015年10月—2016年2月于海南省乐东县九所镇调查98份谷子材料的穗长、穗粗、穗码数、穗粒质量、千粒质量5个性状,同时对98份谷子材料进行重测序开发SNP标记,利用开发的SNP标记用STRUCTURE软件对98份谷子材料进行群体结构分析,用VCFtools软件进行SNP标记间的连锁不平衡分析,最后用GAPIT软件进行SNP与性状间的关联分析。结果表明,对98份谷子材料进行重测序开发了4 482 208个高质量的SNP标记,群体结构分析将98份谷子材料划分为3个组,连锁不平衡(LD)分析发现谷子基因组LD衰退距离为47. 5 kb,适合进行关联分析研究。全基因组关联分析检测到与穗长、穗粗、穗码数、穗粒质量、千粒质量关联的SNP位点数分别是27、95、18、22、28个,这些位点分布在大多数谷子染色体上;在关联位点候选区域内发现,与穗长、穗粗、穗码数、穗粒质量、千粒质量关联的候选基因数分别为24、33、18、18、22个,经在NR、GO、KEGG等数据库注释,每个性状筛选出4~9个主要候选基因,这些基因主要参与泛素-蛋白酶系统介导的蛋白质降解过程、防御反应、木质素合成、信号传导,少数参与脂肪酸合成以及氨基酸、锌离子运输等,其中位于6号染色体的泛素E3-蛋白连接酶基因XB3和位于3号染色体的蛋白磷酸酶基因PP2C可能分别与谷子穗粒质量、千粒质量密切相关。

Locating the QTL loci responsible for panicle traits in foxtail millet under short-day condition,and screening candidate genes are to provide foundation for uncovering the genetic mechanism underlying the formation of panicle traits.98 foxtail millet varieties were selected to investigate five panicle traits including panicle length,panicle diameter,branch number per panicle,grain weight per panicle and 1 000-grain weight at Jiusuo town,Ledong county,Hainan province from October,2015 to February,2016.At the same time re-sequencing was performed for the 98 foxtail millet varieties to exploit SNP markers.Population structure of the 98 foxtail millet varieties was analyzed by STRUCTURE software based on the SNP data and LD analysis of the SNPs was performed by VCFtools software.Finally,association analysis between SNPs and traits was performed by GAPIT software.The results showed that 4 482 208 high-quality SNPs were exploited by re-sequencing of 98 foxtail millet varities.The 98 foxtail millet varities were divided into three groups by population structure analysis.Linkage disequilibrium(LD)analysis showed that the LD decline distance of foxtail millet genome was 47.5 kb,which was suitable for association analysis.Genome-wide association analysis detected 27,95,18,22,28 SNPs associated with panicle length,panicle diameter,branch number per panicle,grain weight per panicle and 1 000-grain weight,respectively.The associated SNPs distributed on most of the nine chromosomes.In the associated regions,24,33,18,18 and 22 genes corresponding to panicle length,panicle diameter,branch number per panicle,grain weight per panicle and 1 000-grain weight were found.After annotation of these genes in NR,GO and KEGG databases,4-9 important candidate genes per trait were filtered out,and these genes were mainly participated in ubiquitin-protein enzyme system-mediated protein degradation process,defense response,lignin synthesis,signal transduct,the remaining fewer were participated in fatty acid synthesis,amino acid and Zn ion transportation and so on.Among them,the ubiquitin E3-protein ligase gene XB 3 locating on chromosome 6 and the protein phosphatase gene PP 2 C locating on chromosome 3 may be closely related to grain weight per panicle and 1 000-grain weight.