Identification of qGL3.5, a Novel Locus Controlling Grain Length in Rice Through Bulked Segregant Analysis and Fine Mapping

Lan Wang; Lan Wang; Lan Wang; Yang Liu; Yang Liu; Yang Liu; Haiyan Zhao; Haiyan Zhao; Yuebin Zheng; Yuebin Zheng; Yuebin Zheng; Feng Bai; Feng Bai; Feng Bai; Sicheng Deng; Zhixiong Chen; Zhixiong Chen; Zhixiong Chen; Jinwen Wu; Jinwen Wu; Jinwen Wu; Xiangdong Liu; Xiangdong Liu; Xiangdong Liu

doi:10.3389/fpls.2022.921029

Frontiers in Plant Science (Jun 2022)

Identification of qGL3.5, a Novel Locus Controlling Grain Length in Rice Through Bulked Segregant Analysis and Fine Mapping

Lan Wang,
Lan Wang,
Lan Wang,
Yang Liu,
Yang Liu,
Yang Liu,
Haiyan Zhao,
Haiyan Zhao,
Yuebin Zheng,
Yuebin Zheng,
Yuebin Zheng,
Feng Bai,
Feng Bai,
Feng Bai,
Sicheng Deng,
Zhixiong Chen,
Zhixiong Chen,
Zhixiong Chen,
Jinwen Wu,
Jinwen Wu,
Jinwen Wu,
Xiangdong Liu,
Xiangdong Liu,
Xiangdong Liu

Affiliations

Lan Wang: State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, South China Agricultural University, Guangzhou, China
Lan Wang: Guangdong Laboratory for Lingnan Modern Agriculture, Guangzhou, China
Lan Wang: Guangdong Provincial Key Laboratory of Plant Molecular Breeding, College of Agriculture, South China Agricultural University, Guangzhou, China
Yang Liu: State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, South China Agricultural University, Guangzhou, China
Yang Liu: Guangdong Laboratory for Lingnan Modern Agriculture, Guangzhou, China
Yang Liu: Guangdong Provincial Key Laboratory of Plant Molecular Breeding, College of Agriculture, South China Agricultural University, Guangzhou, China
Haiyan Zhao: State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, South China Agricultural University, Guangzhou, China
Haiyan Zhao: Songgang Middle School, Qingyuan, China
Yuebin Zheng: State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, South China Agricultural University, Guangzhou, China
Yuebin Zheng: Guangdong Provincial Key Laboratory of Plant Molecular Breeding, College of Agriculture, South China Agricultural University, Guangzhou, China
Yuebin Zheng: State Key Laboratory of Vegetation and Environmental Change, Institute of Botany, Chinese Academy of Sciences, Beijing, China
Feng Bai: State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, South China Agricultural University, Guangzhou, China
Feng Bai: Guangdong Laboratory for Lingnan Modern Agriculture, Guangzhou, China
Feng Bai: Guangdong Provincial Key Laboratory of Plant Molecular Breeding, College of Agriculture, South China Agricultural University, Guangzhou, China
Sicheng Deng: State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, South China Agricultural University, Guangzhou, China
Zhixiong Chen: State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, South China Agricultural University, Guangzhou, China
Zhixiong Chen: Guangdong Laboratory for Lingnan Modern Agriculture, Guangzhou, China
Zhixiong Chen: Guangdong Provincial Key Laboratory of Plant Molecular Breeding, College of Agriculture, South China Agricultural University, Guangzhou, China
Jinwen Wu: State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, South China Agricultural University, Guangzhou, China
Jinwen Wu: Guangdong Laboratory for Lingnan Modern Agriculture, Guangzhou, China
Jinwen Wu: Guangdong Provincial Key Laboratory of Plant Molecular Breeding, College of Agriculture, South China Agricultural University, Guangzhou, China
Xiangdong Liu: State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, South China Agricultural University, Guangzhou, China
Xiangdong Liu: Guangdong Laboratory for Lingnan Modern Agriculture, Guangzhou, China
Xiangdong Liu: Guangdong Provincial Key Laboratory of Plant Molecular Breeding, College of Agriculture, South China Agricultural University, Guangzhou, China

DOI: https://doi.org/10.3389/fpls.2022.921029
Journal volume & issue: Vol. 13

Abstract

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Grain length (GL) directly affects the yield and quality of rice. Very few cloned GL-related genes are applied in production because their yield-increasing effects are not obvious, and the overall regulatory networks underlying the associated processes remain poorly understood. DNA samples from two bulk DNA pools (L-pool and S-pool) and their parents (KJ01 and Huaye 3) were subjected to high-throughput sequencing. Using bulked segregant analysis (BSA), qGL3.5 was mapped to a 0.34-Mb “hotspot” region on chromosome 3 that contains 37 genes related to various traits. Then, qGL3.5 was mapped to the genomic interval between the flanking markers M2 and M3 using 2786 BC4F2 individuals. Because the region from B5 to B6 was not the associated region under BSA-seq analysis, qGL3.5 was narrowed down to the interval between B6 and M3, which spanned 24.0-kb. Of all 37 genes with non-synonymous single-nucleotide polymorphisms (SNPs) between KJ01 and Huaye 3 based on BSA-seq analysis, only one complete annotated gene, ORF18 (Gene ID: LOC_Os03g42790.1) was found. ORF18 encodes an IBR-RING zinc-finger-related protein, with one really interesting new gene (RING) and two in between ring finger (IBR) domains. The knockout of ORF18 derived from Huaye 3 using clustered, regularly interspaced, short palindromic repeat (CRISPR)/CRISPR-associated 9 (Cas9) editing technology increased the GL of the mutant by approximately 2.2 mm. The novel locus qGL3.5 negatively regulated GL by promoting elongation of the longitudinal cell of the grain outer glume. These results provide a new genetic resource for rice grain shape breeding and a starting point for the functional characterization of the wild rice GL gene.

Published in Frontiers in Plant Science

ISSN: 1664-462X (Online)
Publisher: Frontiers Media S.A.
Country of publisher: Switzerland
LCC subjects: Agriculture: Plant culture
Website: https://www.frontiersin.org/journals/plant-science

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