Genetic Architecture of Soybean Yield and Agronomic Traits

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 is poorly understood. We developed a 40-mating soybean nested association mapping (NAM) population of 5,600 inbred lines that were characterized by single nucleotide polymorphism (SNP) markers and six agronomic traits in field trials in 22 environments. Analysis of the yield, agronomic, and SNP data revealed 23 significant marker-trait associations for yield, 19 for maturity, 15 for plant height, 17 for plant lodging, and 29 for seed mass. A higher frequency of estimated positive yield alleles was evident from elite founder parents than from exotic founders, although unique desirable alleles from the exotic group were identified, demonstrating the value of expanding the genetic base of US soybean breeding.

Quantitative Disease Resistance Loci towards Phytophthora sojae and Three Species of Pythium in Six Soybean Nested Association Mapping Populations

“…The parents of the SoyNAM population were not originally selected for resistance to biotic stress (Diers et al, 2018) but will serve as a rich resource as these studies continue to target and dissect QDRL for resistance to soilborne pathogens. However, this study indicates that these soilborne pathogens, which have very similar pathogenic styles and sites of infection, have different QDRL and potentially mechanisms of resistance.…”

“…However, this study indicates that these soilborne pathogens, which have very similar pathogenic styles and sites of infection, have different QDRL and potentially mechanisms of resistance. The parents of the SoyNAM population were not originally selected for resistance to biotic stress (Diers et al, 2018) but will serve as a rich resource as these studies continue to target and dissect QDRL for resistance to soilborne pathogens.…”

“…The Soybean Nested Association Mapping (SoyNAM) Project developed and made available to the soybean research community a large nested association mapping (NAM) population composed of 40 RIL populations derived from crosses between one common, high-yielding hub parent (IA3023) and exotic germplasm, plant introductions, and high-yielding breeding lines with the goal of identifying QTL associated with yield and other desirable traits (Grant et al, 2009;Diers, 2014;Xavier et al, 2017aXavier et al, , 2017bXavier et al, , 2018Diers et al, 2018;www.soybase.org/ SoyNAM). The parents and the 40 related F 5 RIL populations were previously genotyped with the SoySNP6K Illumina Infinium BeadChip genotyping array and the linkage maps developed for each NAM RIL population (Song et al, 2017), which are publicly available at SoyBase (http://soybase.org, accessed April 2017).…”

Evolutionary and ecological functional genomics, from lab to the wild

“…Mapping populations have been generated for a wide array of plant species, and have remained important resources for uncovering the genetic architecture of traits of interest. Examples of these species are the model plant Arabidopsis thaliana (Ehrenreich et al ., ), crops such as maize (Buckler et al ., ), rice (Zhou et al ., ) and soybeans (Diers et al ., ), and ecologically and evolutionarily interesting species such as Mimulus spp. (Monnahan and Kelly, ) and Helianthus spp.…”

Quantitative Genomic Dissection of Soybean Yield Components

“…The first large-scale genetic assessment of complex traits was performed in the SoyNAM population, where 5600 genotypes from 40 bi-parental families sharing a common parent were phenotyped for various agronomic traits (Xavier et al 2016, Xavier et al 2017a, Diers et al 2018). Whereas soybeans have constrained genetic diversity (Carter et al 2004), the SoyNAM is a relatively rich panel of locally adapted genotypes that represents an invaluable resource for the breeding community.…”