Genome-wide association study reveals GmFulb as candidate gene for maturity time and reproductive length in soybeans (Glycine max)

Authors: ESCAMILLA, DIANA - Purdue University; DIETZ, NICHOLAS - University Of Missouri; Bilyeu, Kristin; Hudson, Karen; RAINEY, KATY MARTIN - Purdue University

Submitted to: PLOS ONE
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 1/10/2024
Publication Date: 1/23/2024
Citation: Escamilla, D., Dietz, N., Bilyeu, K.D., Hudson, K.A., Rainey, K. 2024. Genome-wide association study reveals GmFulb as candidate gene for maturity time and reproductive length in soybeans (Glycine max). PLOS ONE. 19(1). Article e0294123. https://doi.org/10.1371/journal.pone.0294123.
DOI: https://doi.org/10.1371/journal.pone.0294123

Interpretive Summary: The highest soybean yields are achieved by optimizing plant developmental stages to different environments, and this situation has led to the establishment of maturity group designations that provide soybean producers with information about variety selection that suits their environments. In the past decade, much progress has been made in identifying the major genes in soybean that impact plant developmental stages, but those major effect genes have masked the ability to identify additional important minor effect genes. The research here aimed to explore the genetic architecture for soybean flowering time, maturity, and reproductive length and identify potential candidate genes underlying those traits. The experiments relied on a custom accession panel, extensive multi-environment phenotyping, and the application of new bioinformatic tools and strategies. The results revealed important new candidate genes and alleles that may contribute to minor, but important effects that were previously masked. The information can be used to fine tune soybean adaptation in diverse environments for cultivar development.

Technical Abstract: The ability of soybean [Glycine max (L.) Merr.] to adapt to different latitudes is attributed to genetic variation in major E genes and quantitative trait loci (QTLs) determining flowering time (R1), maturity (R8), and reproductive length (RL). Fully revealing the genetic basis of R1, R8, and RL in soybeans is necessary to enhance genetic gains in soybean yield improvement. Here, we performed a genome-wide association analysis (GWA) with 31,689 single nucleotide polymorphisms (SNPs) to detect novel loci for R1, R8, and RL using a soybean panel of 329 accessions with the same genotype for three major E genes (e1-as/E2/E3). he studied accessions were grown in nine environments and observed for R1, R8 and RL in all environments. This study identified two stable peaks on Chr 4, simultaneously controlling R8 and RL. In addition, we identified a third peak on Chr 10 controlling R1. Association peaks overlap with previously reported QTLs for R1, R8, and RL. Considering the alternative alleles, significant SNPs caused RL to be two days shorter, R1 two days later and R8 two days earlier, respectively. We identified association peaks acting independently over R1 and R8, suggesting that trait-specific minor effect loci are also involved in controlling R1 and R8. From the 111 genes highly associated with the three peaks detected in this study, we selected six candidate genes as the most likely cause of R1, R8, and RL variation. High correspondence was observed between a modifying variant SNP at position 04:39294836 in GmFulb and an association peak on Chr 4. Further studies using map-based cloning and fine mapping are necessary to elucidate the role of the candidates we identified for soybean maturity and adaptation to different latitudes and to be effectively used in the marker-assisted breeding of cultivars with optimal yield-related traits.