Identification of Loci and Candidate Genes Responsible for Pod Dehiscence in Soybean via Genome-Wide Association Analysis Across Multiple Environments
Identification of Loci and Candidate Genes Responsible for Pod Dehiscence in Soybean via Genome-Wide Association Analysis Across Multiple Environments
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通过跨多个环境的全基因组关联分析鉴定导致大豆豆荚开裂的基因座和候选基因
DOI：
10.3389/fpls.2019.00811
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发表时间：
2019-06-21
影响因子：
5.6
通讯作者：
Yu, Deyue
中科院分区：
文献类型：
--
作者：
Hu, Dezhou;Kan, Guizhen;Yu, Deyue
豆荚开裂（破碎）是大豆机械收获过程中造成严重产量损失的主要原因。深入了解豆荚开裂的遗传结构和分子机制对大豆育种具有重要意义。在这项研究中，使用NJAU 355K SoySNP阵列进行全基因组关联分析（GWAS），以检测与豆荚开裂相关的单核苷酸多态性（snp），该关联面板包含5个环境中的211个接入。共鉴定出163个snp与荚果开裂显著相关。其中，在16号染色体上发现的136个snp位于已知QTL qPDH1上。1、1、3、11、3、1、3、3和1个SNPs分别分布在第1、4、6、8、9、11、17、18和20号染色体上。从10个功能性snp中鉴定出有利snp和6个单倍型；其中Hap2和Hap3被认为是最优单倍型。此外，基于GWAS结果，鉴定候选基因Glyma09g06290。实时荧光定量PCR （qRT-PCR）和多态性分析表明，Glyma09g06290可能参与了荚果开裂。此外，还开发了Glyma09g06290的衍生的cleaved扩增多态性序列（dCAPS）标记。总的来说，本研究所鉴定的位点和基因将有助于大豆品种的抗荚果开裂育种。
Pod dehiscence (shattering) is the main cause of serious yield loss during the soybean mechanical harvesting process. A better understanding of the genetic architecture and molecular mechanisms of pod dehiscence is of great significance for soybean breeding. In this study, genome-wide association analysis (GWAS) with NJAU 355K SoySNP array was performed to detect single nucleotide polymorphisms (SNPs) associated with pod dehiscence in an association panel containing 211 accessions across five environments. A total of 163 SNPs were identified as significantly associated with pod dehiscence. Among these markers, 136 SNPs identified on chromosome 16 were located in the known QTL qPDH1. One, one, three, eleven, three, one, three, three and one SNPs were distributed on chromosome 1, 4, 6, 8, 9, 11, 17, 18, and 20, respectively. Favorable SNPs and six haplotypes were identified based on ten functional SNPs; among those Hap2 and Hap3 were considered as optimal haplotypes. In addition, based on GWAS results, the candidate gene Glyma09g06290 was identified. Quantitative real-time PCR (qRT-PCR) results and polymorphism analysis suggested that Glyma09g06290 might be involved in pod dehiscence. Furthermore, a derived cleaved amplified polymorphic sequences (dCAPS) marker for Glyma09g06290 was developed. Overall, the loci and genes identified in this study will be helpful in breeding soybean accessions resistant to pod dehiscence.