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ARS Home » Northeast Area » Beltsville, Maryland (BARC) » Beltsville Agricultural Research Center » Soybean Genomics & Improvement Laboratory » Research » Publications at this Location » Publication #316486

Title: Genome-wide association study and marker-based selection for seed weight in soybean (Glycine max)

item ZHANG, JIAOPING - South Dakota State University
item Song, Qijian
item CREGAN, PERRY - Retired ARS Employee
item JIANG, GUO-LIANG - Virginia State University

Submitted to: Theoretical and Applied Genetics
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 9/29/2015
Publication Date: 10/30/2015
Citation: Zhang, J., Song, Q., Cregan, P., Jiang, G. 2015. Genome-wide association study and marker-based selection for seed weight in soybean (Glycine max). Theoretical and Applied Genetics. doi: 10.1007/s00122-015-2614-x.

Interpretive Summary: Seed weight is an important trait in soybean that influences seed yield, however, our knowledge of genes controlling the seed weight remains limited. To better understand the genetic control of seed weight in soybean, we conducted a genetic study using a group of 309 soybean accessions from the USDA Soybean Germplasm Collection. Each accession was analyzed with more than 50,000 single nucleotide polymorphism (SNP) DNA markers. The analysis of the resulting DNA marker data identified 22 positions on the 20 pairs of soybean chromosomes that appear to be associated with seed weight. In particular, the region on soybean chromosome 19 that had previously been identified as influencing seed weight was identified. These regions contain genes involved in seed development and other genes that would be expected to influence seed weight. Our Results should enhance our understanding of genetic control of the trait, and facilitate the identification of genes controlling seed weight in soybean. The genes identified in this study could be used to develop soybean varieties with greater seed weight and yield.

Technical Abstract: Seed weight (SW) is important for the yield and quality in food/vegetable uses of soybean (Glycine max), a worldwide major crop. However, our knowledge of genes controlling SW remains limited. To better understand the molecular mechanism of the trait and identify DNA markers usable in marker-based breeding, we conducted a genome-wide association study (GWAS) for SW using 309 soybean germplasm accessions genotyped with the Illumina Infinium SoySNP50K BeadChip, and estimated the accuracy of genomic selection (GS) and marker-assisted selection (MAS). Twenty-two loci on 12 chromosomes were identified to be associated with SW. The mixed model containing these loci explained 83.4% of phenotypic variation. Fifteen of the identified loci, including the hotspot loci on Gm04, Gm10 and Gm19, were previously reported and were refined. Candidate genes with Arabidopsis orthologs conditioning SW were also identified. The accuracy of MAS based on 15 selected loci was 0.74 and 0.58 for the association panel and the panels obtained from the Germplasm Resources Information Network (GRIN) with early to medium maturities, respectively. The results also suggested that MAS with selected loci might be more appropriate than GS, if a low similarity of genetic composition exists between the training and validation populations and/or if the trait under selection is controlled by a small number of loci. This study helps to enhance our knowledge of the genetic basis of genes controlling SW and facilitates the identification of these genes in soybean. The markers identified should be useful in MAS for SW as well as yield improvement in soybean.