Genetic architecture of soybean yield and agronomic traits

Authors: DIERS, BRIAN - University Of Illinois; SPECHT, JAMES - University Of Nebraska; RAINEY, KATY - Retired ARS Employee; CREGAN, PERRY - Retired ARS Employee; Song, Qijian; RAMASUBRAMANIAN, VISHNU - University Of Illinois; GRAEF, GEORGE - University Of Nebraska; NELSON, RANDALL - University Of Illinois; SCHAPAUGH, WILLIAM - Kansas State University; WANG, ECHUN - Michigan State University; SHANNON, GROVER - University Of Missouri; MCHALE, LEAH - The Ohio State University; KANTARTZI, STELLA - Southern Illinois University; XAVIER, ALENCAR - Dow Agrosciences; Mian, Rouf; STUPAR, ROBERT - University Of Minnesota; MICHNO, JEAN-MICHEL - University Of Minnesota; An, Yong-Qiang - Charles; GOETTEL, WOLFGANG - Danforth Plant Science Center; WARD, RUSSELL - University Of Illinois; FOX, CAROLYN - University Of Illinois; LIPKA, ALEXANDER - University Of Illinois; HYTEN, DAVID - University Of Nebraska; CARY, TROY - University Of Illinois; BEAVIS, WILLIAM - Iowa State University

Submitted to: G3, Genes/Genomes/Genetics
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 8/16/2018
Publication Date: 10/1/2018
Citation: Diers, B.W., Specht, J., Rainey, K., Cregan, P., Song, Q., Ramasubramanian, V., Graef, G., Nelson, R., Schapaugh, W., Wang, E., Shannon, G., McHale, L., Kantartzi, S., Xavier, A., Mian, R.M., Stupar, R., Michno, J., An, Y., Goettel, W., Ward, R., Fox, C., Lipka, A.E., Hyten, D., Cary, T., Beavis, W.D. 2018. Genetic architecture of soybean yield and agronomic traits. G3, Genes/Genomes/Genetics. 8(10):3367-3375. https://doi.org/10.1534/g3.118.200332.
DOI: https://doi.org/10.1534/g3.118.200332

Interpretive Summary: Increasing seed yield is one of the major objectives of soybean breeders. Although soybean yield has been improved in the past decades, the genes that control yield and related agronomic traits have not been fully identified. Previous studies have reported a number of gene regions in soybean DNA that are related to seed yield, but because the regions are too wide and may harbor thousands of genes, the determination of the precise genes of the traits has not occurred. Scientists from universities and USDA-ARS developed a soybean population with 5,600 progeny, the parents of which had high-yield and drought tolerance traits. The progeny were grown in 22 environments in eight Midwestern USA states over three years. Analysis of yield and other traits and analysis of the DNA data determined the genome locations of genes for yield, maturity, plant height, plant lodging, and seed mass. A potential candidate gene underlying both maturity and yield was identified. Other potentially important genes from the parents were identified as well. Scientists, soybean breeders, and geneticists working in the government, private industry, or at universities will use these results and resources to further improve soybean yield and other agronomic traits.

Technical Abstract: Soybean is the world’s leading source of vegetable protein and demand for its seed continues to grow. Breeders have successfully increased soybean yield, but the genetic architecture of yield and key agronomic traits has not been fully explored. To that end, we developed a 40-mating soybean nested association mapping (NAM) population of 5600 single nucleotide polymorphism (SNP)-genotyped inbred soybean lines that were performance-tested in 22 field environments. Analysis of the yield, agronomic, and SNP data revealed 23 significant marker-trait associations (MTA) for yield, 19 for maturity, 15 for plant height, 17 for plant lodging, and 29 for seed mass. A higher frequency of positive yield alleles was evident in the elite parents than in the parents with an exotic pedigree, though one of latter parents had yield alleles not found in the former. Results from this study provided new insights into how to further improve soybean and resources for additional studies.