J Integr Plant Biol.

• Research Article •    

Differential SW16.1 allelic effects and genetic backgrounds contributed to increased seed weight after soybean domestication

Xianlian Chen1†, Cheng Liu1†, Pengfei Guo1, Xiaoshuai Hao1, Yongpeng Pan1, Kai Zhang1, Wusheng Liu2, Lizhi Zhao1, Wei Luo1, Jianbo He1, Yanzhu Su1, Ting Jin1, Fenfen Jiang1, Si Wang1, Fangdong Liu1, Rongzhou Xie1, Changgen Zhen1, Wei Han1, Guangnan Xing1, Wubin Wang1*, Shancen Zhao3*, Yan Li1* and Junyi Gai1*   

  1. 1. State Key Laboratory of Crop Genetics and Germplasm Enhancement, National Center for Soybean Improvement, Key Laboratory for Biology and Genetic Improvement of Soybean(General, Ministry of Agriculture), Jiangsu Collaborative Innovation Center for Modern Crop Production, Nanjing Agricultural University, Nanjing 210095, China
    2. Department of Horticultural Science, North Carolina State University, Raleigh North Carolina 27606, USA
    3. BGI Genomics, BGI-Shenzhen, Shenzhen 518083, China
    These authors contributed equally to this work.
    *Correspondences:Wubin Wang(wangbean@njau.edu.cn);Shancen Zhao(zhaoshancen@genomics.cn);Yan Li(yanli1@njau.edu.cn, Dr. Li is responsible for queries related to this article);Junyi Gai(sri@njau.edu.cn, Prof. Gai is responsible for material distribution)
  • Received:2023-10-21 Accepted:2023-03-06 Online:2023-05-12

Abstract: Although seed weight has increased following domestication from wild soybean (Glycine soja) to cultivated soybean (Glycine max), the genetic basis underlying this change is unclear. Using mapping populations derived from chromosome segment substitution lines of wild soybean, we identified SW16.1 as the causative gene underlying a major quantitative trait locus controlling seed weight. SW16.1 encodes a nucleus-localized LIM domain-containing protein. Importantly, the GsSW16.1 allele from wild soybean accession N24852 had a negative effect on seed weight, whereas the GmSW16.1 allele from cultivar NN1138-2 had a positive effect. Gene expression network analysis, reverse-transcription quantitative polymerase chain reaction, and promoter-luciferase reporter transient expression assays suggested that SW16.1 regulates the transcription of MT4, a positive regulator of seed weight. The natural variations in SW16.1 and other known seed weight genes were analyzed in soybean germplasm. The SW16.1 polymorphism was associated with seed weight in 247 soybean accessions, showing much higher frequency of positive-effect alleles in cultivated soybean than in wild soybean. Interestingly, gene allele matrix analysis of the known seed weight genes revealed that G. max has lost 38.5% of the G. soja alleles and that most of the lost alleles had negative effects on seed weight. Our results suggest that eliminating negative alleles from G. soja led to a higher frequency of positive alleles and changed genetic backgrounds in G. max, which contributed to larger seeds in cultivated soybean after domestication from wild soybean. Our findings provide new insights regarding soybean domestication and should assist current soybean breeding programs.

Key words: domestication, natural variation, positional cloning, QTL, seed weight, soybean, SW16.1

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