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

Mengrou Niu; Kewei Tian; Qiang Chen; Chunyan Yang; Mengchen Zhang; Shiyong Sun; Xuelu Wang

doi:10.3389/fpls.2023.1302359

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

Front Plant Sci. 2024 Jan 8:14:1302359. doi: 10.3389/fpls.2023.1302359. eCollection 2023.

Authors

Mengrou Niu^#^{1

2

3

4}, Kewei Tian^#^{1

2

3

4}, Qiang Chen⁵, Chunyan Yang⁵, Mengchen Zhang⁵, Shiyong Sun^{2

3

4}, Xuelu Wang^{2

3

4}

Affiliations

¹ Center of Integrative Biology, College of Life Science and Technology, Huazhong Agricultural University, Wuhan, Hubei, China.
² Sanya Institute of Henan University, Henan University, Sanya, Hainan, China.
³ State Key Laboratory of Crop Stress Adaptation and Improvement, School of Life Science, Henan University, Zhengzhou, China.
⁴ The Academy for Advanced Interdisciplinary Studies, Henan University, Zhengzhou, China.
⁵ Institute of Cereal and Oil Crops, Hebei Academy of Agriculture and Forestry Sciences/Hebei Laboratory of Crop Genetics and Breeding, Shijiazhuang, Hebei, China.

^# Contributed equally.

Abstract

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.

Keywords: GWAS; agronomic traits; architecture; branch angle; soybean.

Grants and funding

The author(s) declare financial support was received for the research, authorship, and/or publication of this article. This research was supported by grants from the National Key Research and Development Program (Grant No. 2022YFA0912100 to XW and SS), the National Natural Science Foundation of China (Grant No. U21A20181 to XW), the Innovation Scientists and Technicians Troop Construction Projects of Henan Province (grant no. 224000510001 to XW), and the Outstanding Talents Fund of Henan University (Grant no. CX3050A092004 to XW), the Program for Innovative Research Team (in Science and Technology) in University of Henan Province (Grant No. 23IRTSTHN020 to SS) and the Natural Science Foundation of Henan Province (Grant No. 212300410001 to SS).