A Novel Function of GW5 on Controlling the Early Growth Vigor and its Haplotype Effect on Shoot Dry Weight and Grain Size in Rice (Oryza sativa L.)

Tifeng Yang; Jingfang Dong; Xijuan Xiong; Longting Zhang; Jian Wang; Haifei Hu; Lian Zhou; Wu Yang; Yamei Ma; Hua Fu; Jiansong Chen; Wenhui Li; Shuai Nie; Ziqiang Liu; Bin Liu; Feng Wang; Junliang Zhao; Shaohong Zhang

doi:10.1186/s12284-024-00728-6

Rice (Aug 2024)

A Novel Function of GW5 on Controlling the Early Growth Vigor and its Haplotype Effect on Shoot Dry Weight and Grain Size in Rice (Oryza sativa L.)

Tifeng Yang,
Jingfang Dong,
Xijuan Xiong,
Longting Zhang,
Jian Wang,
Haifei Hu,
Lian Zhou,
Wu Yang,
Yamei Ma,
Hua Fu,
Jiansong Chen,
Wenhui Li,
Shuai Nie,
Ziqiang Liu,
Bin Liu,
Feng Wang,
Junliang Zhao,
Shaohong Zhang

Affiliations

Tifeng Yang: Rice Research Institute, Guangdong Key Laboratory of New Technology in Rice Breeding, Rice Engineering Laboratory, Key Laboratory of Genetics and Breeding of High Quality Rice in Southern China (Co-construction by Ministry and Province), Ministry of Agriculture and Rural Affairs, Guangdong Academy of Agricultural Sciences
Jingfang Dong: Rice Research Institute, Guangdong Key Laboratory of New Technology in Rice Breeding, Rice Engineering Laboratory, Key Laboratory of Genetics and Breeding of High Quality Rice in Southern China (Co-construction by Ministry and Province), Ministry of Agriculture and Rural Affairs, Guangdong Academy of Agricultural Sciences
Xijuan Xiong: Rice Research Institute, Guangdong Key Laboratory of New Technology in Rice Breeding, Rice Engineering Laboratory, Key Laboratory of Genetics and Breeding of High Quality Rice in Southern China (Co-construction by Ministry and Province), Ministry of Agriculture and Rural Affairs, Guangdong Academy of Agricultural Sciences
Longting Zhang: Rice Research Institute, Guangdong Key Laboratory of New Technology in Rice Breeding, Rice Engineering Laboratory, Key Laboratory of Genetics and Breeding of High Quality Rice in Southern China (Co-construction by Ministry and Province), Ministry of Agriculture and Rural Affairs, Guangdong Academy of Agricultural Sciences
Jian Wang: Rice Research Institute, Guangdong Key Laboratory of New Technology in Rice Breeding, Rice Engineering Laboratory, Key Laboratory of Genetics and Breeding of High Quality Rice in Southern China (Co-construction by Ministry and Province), Ministry of Agriculture and Rural Affairs, Guangdong Academy of Agricultural Sciences
Haifei Hu: Rice Research Institute, Guangdong Key Laboratory of New Technology in Rice Breeding, Rice Engineering Laboratory, Key Laboratory of Genetics and Breeding of High Quality Rice in Southern China (Co-construction by Ministry and Province), Ministry of Agriculture and Rural Affairs, Guangdong Academy of Agricultural Sciences
Lian Zhou: Rice Research Institute, Guangdong Key Laboratory of New Technology in Rice Breeding, Rice Engineering Laboratory, Key Laboratory of Genetics and Breeding of High Quality Rice in Southern China (Co-construction by Ministry and Province), Ministry of Agriculture and Rural Affairs, Guangdong Academy of Agricultural Sciences
Wu Yang: Rice Research Institute, Guangdong Key Laboratory of New Technology in Rice Breeding, Rice Engineering Laboratory, Key Laboratory of Genetics and Breeding of High Quality Rice in Southern China (Co-construction by Ministry and Province), Ministry of Agriculture and Rural Affairs, Guangdong Academy of Agricultural Sciences
Yamei Ma: Rice Research Institute, Guangdong Key Laboratory of New Technology in Rice Breeding, Rice Engineering Laboratory, Key Laboratory of Genetics and Breeding of High Quality Rice in Southern China (Co-construction by Ministry and Province), Ministry of Agriculture and Rural Affairs, Guangdong Academy of Agricultural Sciences
Hua Fu: Rice Research Institute, Guangdong Key Laboratory of New Technology in Rice Breeding, Rice Engineering Laboratory, Key Laboratory of Genetics and Breeding of High Quality Rice in Southern China (Co-construction by Ministry and Province), Ministry of Agriculture and Rural Affairs, Guangdong Academy of Agricultural Sciences
Jiansong Chen: Rice Research Institute, Guangdong Key Laboratory of New Technology in Rice Breeding, Rice Engineering Laboratory, Key Laboratory of Genetics and Breeding of High Quality Rice in Southern China (Co-construction by Ministry and Province), Ministry of Agriculture and Rural Affairs, Guangdong Academy of Agricultural Sciences
Wenhui Li: Rice Research Institute, Guangdong Key Laboratory of New Technology in Rice Breeding, Rice Engineering Laboratory, Key Laboratory of Genetics and Breeding of High Quality Rice in Southern China (Co-construction by Ministry and Province), Ministry of Agriculture and Rural Affairs, Guangdong Academy of Agricultural Sciences
Shuai Nie: Rice Research Institute, Guangdong Key Laboratory of New Technology in Rice Breeding, Rice Engineering Laboratory, Key Laboratory of Genetics and Breeding of High Quality Rice in Southern China (Co-construction by Ministry and Province), Ministry of Agriculture and Rural Affairs, Guangdong Academy of Agricultural Sciences
Ziqiang Liu: College of Agriculture, South China Agricultural University
Bin Liu: Rice Research Institute, Guangdong Key Laboratory of New Technology in Rice Breeding, Rice Engineering Laboratory, Key Laboratory of Genetics and Breeding of High Quality Rice in Southern China (Co-construction by Ministry and Province), Ministry of Agriculture and Rural Affairs, Guangdong Academy of Agricultural Sciences
Feng Wang: Rice Research Institute, Guangdong Key Laboratory of New Technology in Rice Breeding, Rice Engineering Laboratory, Key Laboratory of Genetics and Breeding of High Quality Rice in Southern China (Co-construction by Ministry and Province), Ministry of Agriculture and Rural Affairs, Guangdong Academy of Agricultural Sciences
Junliang Zhao: Rice Research Institute, Guangdong Key Laboratory of New Technology in Rice Breeding, Rice Engineering Laboratory, Key Laboratory of Genetics and Breeding of High Quality Rice in Southern China (Co-construction by Ministry and Province), Ministry of Agriculture and Rural Affairs, Guangdong Academy of Agricultural Sciences
Shaohong Zhang: Rice Research Institute, Guangdong Key Laboratory of New Technology in Rice Breeding, Rice Engineering Laboratory, Key Laboratory of Genetics and Breeding of High Quality Rice in Southern China (Co-construction by Ministry and Province), Ministry of Agriculture and Rural Affairs, Guangdong Academy of Agricultural Sciences

DOI: https://doi.org/10.1186/s12284-024-00728-6
Journal volume & issue: Vol. 17, no. 1
pp. 1 – 16

Abstract

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Abstract Strong early growth vigor is an essential target in both direct seeded rice breeding and high-yielding rice breeding for rice varieties with relatively short growth duration in the double-cropping region. Shoot dry weight (SDW) is one of the important traits associated with early growth vigor, and breeders have been working to improve this trait. Finding stable QTLs or functional genes for SDW is crucial for improving the early growth vigor by implementing molecular breeding in rice. Here, a genome-wide association analysis revealed that the QTL for SDW, qSDW-5, was stably detected in the three cultivation methods commonly used in production practice. Through gene-based haplotype analysis of the annotated genes within the putative region of qSDW-5, and validated by gene expression and knockout transgenic experiments, LOC_Os05g09520, which is identical to the reported GW5/GSE5 controlling grain width (GW) and thousand grain weight (TGW) was identified as the causal gene for qSDW-5. Five main haplotypes of LOC_Os05g09520 were identified in the diverse international rice collection used in this study and their effects on SDW, GW and TGW were analyzed. Phenotypic comparisons of the major haplotypes of LOC_Os05g09520 in the three subpopulations (indica, japonica and aus) revealed the same patterns of wider GW and higher TGW along with higher SDW. Furtherly, the haplotype analysis of 138 rice varieties/lines widely used in southern China showed that 97.8% of the cultivars/lines carry Hap2 LOC_Os05g09520 . These results not only provide a promising gene source for the molecular breeding of rice varieties with strong early growth vigor, but also elucidate the effect of the LOC_Os05g09520 haplotypes on SDW, GW, and TGW in rice. Importantly, this study provides direct genetic evidence that these three traits are significantly correlated, and suggests a breeding strategy for developing high-yielding and slender grain-shaped indica cultivars with strong early growth vigor.

Published in Rice

ISSN: 1939-8425 (Print); 1939-8433 (Online)
Publisher: SpringerOpen
Country of publisher: United Kingdom
LCC subjects: Agriculture: Plant culture
Website: https://thericejournal.springeropen.com/

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