Open AccessIdentification and Validation of Candidate Genes Associated with Domesticated and Improved Traits in Soybean
Author(s) -
Zhou Ling,
Luo Longhai,
Zuo JianFang,
Yang Linfeng,
Zhang Li,
Guang Xuanmin,
Niu Yuan,
Jian Jianbo,
Geng QingChun,
Liang Liping,
Song Qijian,
Dunwell Jim M.,
Wu Zhenzhen,
Wen Jia,
Liu YuQin,
Zhang YuanMing
Publication year - 2016
Publication title -
the plant genome
Language(s) - English
Resource type - Journals
SCImago Journal Rank - 1.403
H-Index - 41
ISSN - 1940-3372
DOI - 10.3835/plantgenome2015.09.0090
Subject(s) - domestication , biology , quantitative trait locus , candidate gene , genetics , trait , single nucleotide polymorphism , gene , phenotypic trait , phenotype , genotype , computer science , programming language
Soybean, an important source of vegetable oils and proteins for humans, has undergone significant phenotypic changes during domestication and improvement. However, there is limited knowledge about genes related to these domesticated and improved traits, such as flowering time, seed development, alkaline‐salt tolerance, and seed oil content (SOC). In this study, more than 106,000 single nucleotide polymorphisms (SNPs) were identified by restriction site associated DNA sequencing of 14 wild, 153 landrace, and 119 bred soybean accessions, and 198 candidate domestication regions (CDRs) were identified via multiple genetic diversity analyses. Of the 1489 candidate domestication genes (CDGs) within these CDRs, a total of 330 CDGs were related to the above four traits in the domestication, gene ontology (GO) enrichment, gene expression, and pathway analyses. Eighteen, 60, 66, and 10 of the 330 CDGs were significantly associated with the above four traits, respectively. Of 134 trait‐associated CDGs, 29 overlapped with previous CDGs, 11 were consistent with candidate genes in previous trait association studies, and 66 were covered by the domesticated and improved quantitative trait loci or their adjacent regions, having six common CDGs, such as one functionally characterized gene Glyma15 g17480 ( GmZTL3 ). Of the 68 seed size (SS) and SOC CDGs, 37 were further confirmed by gene expression analysis. In addition, eight genes were found to be related to artificial selection during modern breeding. Therefore, this study provides an integrated method for efficiently identifying CDGs and valuable information for domestication and genetic research.