Integrative omics analysis elucidates the genetic basis underlying seed weight and oil content in soybean

Author:

Yuan Xiaobo1ORCID,Jiang Xinyu1ORCID,Zhang Mengzhu1ORCID,Wang Longfei1ORCID,Jiao Wu1ORCID,Chen Huatao2ORCID,Mao Junrong1ORCID,Ye Wenxue1ORCID,Song Qingxin1ORCID

Affiliation:

1. State Key Laboratory of Crop Genetics & Germplasm Enhancement and Utilization, Jiangsu Collaborative Innovation Center for Modern Crop Production, Nanjing Agricultural University , No. 1 Weigang, Nanjing, Jiangsu 210095 , China

2. Institute of Industrial Crops, Jiangsu Academy of Agricultural Sciences , No. 50 Zhongling, Nanjing, Jiangsu 210014 , China

Abstract

Abstract Synergistic optimization of key agronomic traits by traditional breeding has dramatically enhanced crop productivity in the past decades. However, the genetic basis underlying coordinated regulation of yield- and quality-related traits remains poorly understood. Here, we dissected the genetic architectures of seed weight and oil content by combining genome-wide association studies (GWAS) and transcriptome-wide association studies (TWAS) using 421 soybean (Glycine max) accessions. We identified 26 and 33 genetic loci significantly associated with seed weight and oil content by GWAS, respectively, and detected 5,276 expression quantitative trait loci (eQTLs) regulating expression of 3,347 genes based on population transcriptomes. Interestingly, a gene module (IC79), regulated by two eQTL hotspots, exhibited significant correlation with both seed weigh and oil content. Twenty-two candidate causal genes for seed traits were further prioritized by TWAS, including Regulator of Weight and Oil of Seed 1 (GmRWOS1), which encodes a sodium pump protein. GmRWOS1 was verified to pleiotropically regulate seed weight and oil content by gene knockout and overexpression. Notably, allelic variations of GmRWOS1 were strongly selected during domestication of soybean. This study uncovers the genetic basis and network underlying regulation of seed weight and oil content in soybean and provides a valuable resource for improving soybean yield and quality by molecular breeding.

Funder

National Key Research and Development Program of China

National Natural Science Foundation of China

Publisher

Oxford University Press (OUP)

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