Table_1_Identification of Loci and Candidate Genes Responsible for Pod Dehiscence in Soybean via Genome-Wide Association Analysis Across Multiple Environments.XLSX

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.

豆荚开裂（Pod dehiscence (shattering)）是大豆机械收获过程中造成严重产量损失的主要原因。深入解析豆荚开裂的遗传结构与分子机制，对大豆育种工作具有重要意义。本研究采用NJAU 355K SoySNP芯片开展全基因组关联分析（Genome-Wide Association Analysis, GWAS），对包含211份种质的关联群体在5种环境下的豆荚开裂性状进行关联位点检测。最终共鉴定到163个与豆荚开裂显著关联的单核苷酸多态性（Single Nucleotide Polymorphism, SNPs）位点。其中，136个位于16号染色体的SNPs落在已知数量性状基因座（Quantitative Trait Locus, QTL）qPDH1区间内；其余SNPs分别分布于1、4、6、8、9、11、17、18、20号染色体，对应位点数量依次为1、1、3、11、3、1、3、3及1个。基于10个功能SNPs，本研究鉴定出优异等位变异与6种单倍型，其中Hap2与Hap3为最优单倍型。此外，依托本次GWAS分析结果，本研究筛选得到候选基因Glyma09g06290。实时荧光定量PCR（Quantitative Real-time PCR, qRT-PCR）结果及多态性分析显示，Glyma09g06290可能参与调控豆荚开裂过程。进一步，本研究为Glyma09g06290开发了1个衍生酶切扩增多态性序列（derived cleaved amplified polymorphic sequences, dCAPS）标记。综上，本研究鉴定的位点与基因将有助于培育抗裂荚大豆种质。