A genome-wide association study of seed protein and oil content in soybean

BMC Genomics

Research Article

James E Specht¹  Eun-Young Hwang²  Jose Costa³  Perry B Cregan⁴  Qijian Song⁴  Gaofeng Jia⁴  David L Hyten⁵ 

[1] Agronomy & Horticulture Department, University of Nebraska, 68583, Lincoln, NE, USA;Department of Plant Science and Landscape Architecture, University of Maryland, 20742, College Park, MD, USA;Department of Plant Science and Landscape Architecture, University of Maryland, 20742, College Park, MD, USA;USDA-ARS, Crop Production and Protection, GWCC-BLTSVL, 20705, Beltsville, MD, USA;USDA, Agricultural Research Service, Soybean Genomics and Improvement Lab, 20705, Beltsville, MD, USA;USDA, Agricultural Research Service, Soybean Genomics and Improvement Lab, 20705, Beltsville, MD, USA;DuPont Pioneer, PO Box 7060, 8305 NW 62nd Ave., 50131, Johnston, IA, USA;

关键词: GWAS;    Glycine max;    Seed protein and oil content;    Single nucleotide polymorphism;    Linkage disequilibrium;   

DOI  :  10.1186/1471-2164-15-1

 received in 2013-08-29, accepted in 2013-12-21,  发布年份 2014

来源: Springer

【 摘 要 】

BackgroundAssociation analysis is an alternative to conventional family-based methods to detect the location of gene(s) or quantitative trait loci (QTL) and provides relatively high resolution in terms of defining the genome position of a gene or QTL. Seed protein and oil concentration are quantitative traits which are determined by the interaction among many genes with small to moderate genetic effects and their interaction with the environment. In this study, a genome-wide association study (GWAS) was performed to identify quantitative trait loci (QTL) controlling seed protein and oil concentration in 298 soybean germplasm accessions exhibiting a wide range of seed protein and oil content.ResultsA total of 55,159 single nucleotide polymorphisms (SNPs) were genotyped using various methods including Illumina Infinium and GoldenGate assays and 31,954 markers with minor allele frequency >0.10 were used to estimate linkage disequilibrium (LD) in heterochromatic and euchromatic regions. In euchromatic regions, the mean LD (r2) rapidly declined to 0.2 within 360 Kbp, whereas the mean LD declined to 0.2 at 9,600 Kbp in heterochromatic regions. The GWAS results identified 40 SNPs in 17 different genomic regions significantly associated with seed protein. Of these, the five SNPs with the highest associations and seven adjacent SNPs were located in the 27.6-30.0 Mbp region of Gm20. A major seed protein QTL has been previously mapped to the same location and potential candidate genes have recently been identified in this region. The GWAS results also detected 25 SNPs in 13 different genomic regions associated with seed oil. Of these markers, seven SNPs had a significant association with both protein and oil.ConclusionsThis research indicated that GWAS not only identified most of the previously reported QTL controlling seed protein and oil, but also resulted in narrower genomic regions than the regions reported as containing these QTL. The narrower GWAS-defined genome regions will allow more precise marker-assisted allele selection and will expedite positional cloning of the causal gene(s).

【 授权许可】

Unknown   
© Hwang et al.; licensee BioMed Central Ltd. 2014. This article is published under license to BioMed Central Ltd. This is an open access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/2.0), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.