Genome-wide association and epistatic interactions of flowering time in soybean cultivar


Autoři: Kyoung Hyoun Kim aff001;  Jae-Yoon Kim aff001;  Won-Jun Lim aff001;  Seongmun Jeong aff001;  Ho-Yeon Lee aff001;  Youngbum Cho aff001;  Jung-Kyung Moon aff003;  Namshin Kim aff001
Působiště autorů: Genome Editing Research Center, Korea Research Institute of Bioscience and Biotechnology (KRIBB), Daejeon, Republic of Korea aff001;  Department of Bioinformatics, KRIBB School of Bioscience, University of Science and Technology (UST), Daejeon, Republic of Korea aff002;  National Institute of Agricultural Sciences, Rural Development Administration, Jeonju, Republic of Korea aff003
Vyšlo v časopise: PLoS ONE 15(1)
Kategorie: Research Article
doi: 10.1371/journal.pone.0228114

Souhrn

Genome-wide association studies (GWAS) have enabled the discovery of candidate markers that play significant roles in various complex traits in plants. Recently, with increased interest in the search for candidate markers, studies on epistatic interactions between single nucleotide polymorphism (SNP) markers have also increased, thus enabling the identification of more candidate markers along with GWAS on single-variant-additive-effect. Here, we focused on the identification of candidate markers associated with flowering time in soybean (Glycine max). A large population of 2,662 cultivated soybean accessions was genotyped using the 180k Axiom® SoyaSNP array, and the genomic architecture of these accessions was investigated to confirm the population structure. Then, GWAS was conducted to evaluate the association between SNP markers and flowering time. A total of 93 significant SNP markers were detected within 59 significant genes, including E1 and E3, which are the main determinants of flowering time. Based on the GWAS results, multilocus epistatic interactions were examined between the significant and non-significant SNP markers. Two significant and 16 non-significant SNP markers were discovered as candidate markers affecting flowering time via interactions with each other. These 18 candidate SNP markers mapped to 18 candidate genes including E1 and E3, and the 18 candidate genes were involved in six major flowering pathways. Although further biological validation is needed, our results provide additional information on the existing flowering time markers and present another option to marker-assisted breeding programs for regulating flowering time of soybean.

Klíčová slova:

Arabidopsis thaliana – Flowers – Gene regulation – Genome-wide association studies – Molecular genetics – Quantitative trait loci – Soybean – Structural genomics


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2020 Číslo 1