A multi-trait GWAS-based genetic association network controlling soybean architecture and seed traits

Ideal plant architecture is essential for enhancing crop yields. Ideal soybean (Glycine max) architecture encompasses an appropriate plant height, increased node number, moderate seed weight, and compact architecture with smaller branch angles for growth under high-density planting. However, the functional genes regulating plant architecture are far not fully understood in soybean. In this study, we investigated the genetic basis of 12 agronomic traits in a panel of 496 soybean accessions with a wide geographical distribution in China. Analysis of phenotypic changes in 148 historical elite soybean varieties indicated that seed-related traits have mainly been improved over the past 60 years, with targeting plant architecture traits having the potential to further improve yields in future soybean breeding programs. In a genome-wide association study (GWAS) of 12 traits, we detected 169 significantly associated loci, of which 61 overlapped with previously reported loci and 108 new loci. By integrating the GWAS loci for different traits, we constructed a genetic association network and identified 90 loci that were associated with a single trait and 79 loci with pleiotropic effects. Of these 79 loci, 7 hub-nodes were strongly linked to at least three related agronomic traits. qHub_5, containing the previously characterized Determinate 1 (Dt1) locus, was associated not only with plant height and node number (as determined previously), but also with internode length and pod range. Furthermore, we identified qHub_7, which controls three branch angle-related traits; the candidate genes in this locus may be beneficial for breeding soybean with compact architecture. These findings provide insights into the genetic relationships among 12 important agronomic traits in soybean. In addition, these studies uncover valuable loci for further functional gene studies and will facilitate molecular design breeding of soybean architecture.