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

Dezhou Hu,Zhongyi Yang,Wei Hu,Xiaohong He,Guizhen Kan,Derong Hao,Deyue Yu,Fang Huang,Xiao Li,Yali Li,Hui Yang

doi:10.3389/fpls.2019.00811

Dezhou Hu, Zhongyi Yang + Show 9 more

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https://doi.org/10.3389/fpls.2019.00811

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Abstract

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.

Highlights

Soybean [Glycine max (L.) Merr.] is one of the major oil crops and provides edible oil and abundant protein for human beings
The the percentage of pod dehiscence (PPD) for the individual accessions in the association panel ranged from 0 to 0.99, and the average value was between 0.15 and 0.27. h2 was estimated as 78.5% in association panel, which was slightly lower than that found in recombinant inbred lines (RIL) (Kang et al, 2005)
To mine the single nucleotide polymorphisms (SNP) significantly associated with pod dehiscence, genome-wide association analysis (GWAS) was conducted using 201,915 SNPs (NJAU 355K SoySNP array) with the MLM (Q + K) model in an association panel including 211 accessions

Summary

Introduction

Soybean [Glycine max (L.) Merr.] is one of the major oil crops and provides edible oil and abundant protein for human beings. Funatsuki et al (2006) detected this major QTL and named it qPDH1; it was located between the markers Sat_093 and Sat_366 on chromosome 16 and accounted for 50% of the total variance (Funatsuki et al, 2006) This QTL was reported by several other studies that used different populations and genetic backgrounds (Liu et al, 2007; Kang et al, 2009; Yamada et al, 2009; Suzuki et al, 2010; Ju et al, 2017), suggesting that qPDH1 may be the major QTL associated with pod dehiscence. Other QTLs that were deemed to be minor were mapped (Bailey et al, 1997; Liu et al, 2007; Kang et al, 2009; Yamada et al, 2009)

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