A de novo evolved gene contributes to rice grain shape difference between indica and japonica

Rujia Chen, Ning Xiao, Yue Lu, Tianyun Tao, Qianfeng Huang, Shuting Wang, Zhichao Wang, Mingli Chuan, Qing Bu, Zhou Lu, Hanyao Wang, Yanze Su, Yi Ji, Jianheng Ding, Ahmed Gharib, Huixin Liu, Yong Zhou, Shuzhu Tang, Guohua Liang, Honggen Zhang, Chuandeng Yi, Xiaoming Zheng, Zhukuan Cheng, Yang Xu, Pengcheng Li, Chenwu Xu (), Jinling Huang (), Aihong Li () and Zefeng Yang ()
Additional contact information
Rujia Chen: Agriculture College of Yangzhou University
Ning Xiao: Institute of Agricultural Sciences for Lixiahe Region in Jiangsu
Yue Lu: Agriculture College of Yangzhou University
Tianyun Tao: Agriculture College of Yangzhou University
Qianfeng Huang: Agriculture College of Yangzhou University
Shuting Wang: Agriculture College of Yangzhou University
Zhichao Wang: Agriculture College of Yangzhou University
Mingli Chuan: Agriculture College of Yangzhou University
Qing Bu: Agriculture College of Yangzhou University
Zhou Lu: Agriculture College of Yangzhou University
Hanyao Wang: Agriculture College of Yangzhou University
Yanze Su: Agriculture College of Yangzhou University
Yi Ji: Agriculture College of Yangzhou University
Jianheng Ding: Agriculture College of Yangzhou University
Ahmed Gharib: Agriculture College of Yangzhou University
Huixin Liu: Agriculture College of Yangzhou University
Yong Zhou: Agriculture College of Yangzhou University
Shuzhu Tang: Agriculture College of Yangzhou University
Guohua Liang: Agriculture College of Yangzhou University
Honggen Zhang: Agriculture College of Yangzhou University
Chuandeng Yi: Agriculture College of Yangzhou University
Xiaoming Zheng: Chinese Academy of Agricultural Sciences
Zhukuan Cheng: Agriculture College of Yangzhou University
Yang Xu: Agriculture College of Yangzhou University
Pengcheng Li: Agriculture College of Yangzhou University
Chenwu Xu: Agriculture College of Yangzhou University
Jinling Huang: East Carolina University
Aihong Li: Institute of Agricultural Sciences for Lixiahe Region in Jiangsu
Zefeng Yang: Agriculture College of Yangzhou University

Nature Communications, 2023, vol. 14, issue 1, 1-13

Abstract: Abstract The role of de novo evolved genes from non-coding sequences in regulating morphological differentiation between species/subspecies remains largely unknown. Here, we show that a rice de novo gene GSE9 contributes to grain shape difference between indica/xian and japonica/geng varieties. GSE9 evolves from a previous non-coding region of wild rice Oryza rufipogon through the acquisition of start codon. This gene is inherited by most japonica varieties, while the original sequence (absence of start codon, gse9) is present in majority of indica varieties. Knockout of GSE9 in japonica varieties leads to slender grains, whereas introgression to indica background results in round grains. Population evolutionary analyses reveal that gse9 and GSE9 are derived from wild rice Or-I and Or-III groups, respectively. Our findings uncover that the de novo GSE9 gene contributes to the genetic and morphological divergence between indica and japonica subspecies, and provide a target for precise manipulation of rice grain shape.

Date: 2023
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DOI: 10.1038/s41467-023-41669-w

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