Evidence map›Paper›PMID 40522587›Full record

ArticleRice (New York, N.Y.)2025

GWAS Combined with Meta-Analysis Identifies OsDREB6 as a Regulator of Coleoptile Elongation Under Anaerobic Conditions in Rice.

Kai Liu, Dandan Li, Jinrui Li, Shiyi Chen, Di Zhu, Min Guo, Jing Yang, Xueyu Liang, Jiafeng Wang, Hui Wang and 3 more

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Article in Rice (New York, N.Y.), 2025. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Not yet cited in PubMed.

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5 · Who and what money

Authors and funding

13 authors.

Kai Liu *National Engineering Research Center of Plant Space Breeding, College of Agriculture, South China Agricultural University, Guangzhou, 510642, China.
Dandan Li *National Engineering Research Center of Plant Space Breeding, College of Agriculture, South China Agricultural University, Guangzhou, 510642, China.
Jinrui LiNational Engineering Research Center of Plant Space Breeding, College of Agriculture, South China Agricultural University, Guangzhou, 510642, China.
Shiyi ChenNational Engineering Research Center of Plant Space Breeding, College of Agriculture, South China Agricultural University, Guangzhou, 510642, China.
Di ZhuNational Engineering Research Center of Plant Space Breeding, College of Agriculture, South China Agricultural University, Guangzhou, 510642, China.
Min GuoNational Engineering Research Center of Plant Space Breeding, College of Agriculture, South China Agricultural University, Guangzhou, 510642, China.
Jing YangNational Engineering Research Center of Plant Space Breeding, College of Agriculture, South China Agricultural University, Guangzhou, 510642, China.
Xueyu LiangNational Engineering Research Center of Plant Space Breeding, College of Agriculture, South China Agricultural University, Guangzhou, 510642, China.
Jiafeng WangNational Engineering Research Center of Plant Space Breeding, College of Agriculture, South China Agricultural University, Guangzhou, 510642, China.
Hui WangNational Engineering Research Center of Plant Space Breeding, College of Agriculture, South China Agricultural University, Guangzhou, 510642, China.
Chun ChenNational Engineering Research Center of Plant Space Breeding, College of Agriculture, South China Agricultural University, Guangzhou, 510642, China.
Tao GuoNational Engineering Research Center of Plant Space Breeding, College of Agriculture, South China Agricultural University, Guangzhou, 510642, China. guo.tao@vip.163.com.
Yongzhu LiuNational Engineering Research Center of Plant Space Breeding, College of Agriculture, South China Agricultural University, Guangzhou, 510642, China. lively@scau.edu.cn.

Funding

Construction of Cosmic Particle Directed Mutagenesis Technology System and Creation of New Germplasm in Rice 2022YFD1200703Improvement of Conventional Rice Varieties in South China Rice Region CARS-01-06
6 · The paper itself

Abstract

Identifying genes resistant to anaerobic germination can provides key genetic targets for breeding direct seeding rice varieties with anaerobic tolerance. In this study, genome-wide association analysis (GWAS) was performed on coleoptile length (CL) of 591 natural rice populations under anaerobic conditions, and a total of 34 significant QTLs were identified, with eight of them co-localized with previous studies. Furthermore, through meta-analysis of 156 initial QTLs from 21 independent studies related to anaerobic germination, 37 MQTLs were identified, including 4 core MQTLs. Integration of GWAS with meta-analysis revealed the overlap between the physical interval of qCL9.5 on chromosome 9 and MQTL9.2, highlighting it as a reliable locus. Notably, our analysis pinpointed the dehydration-responsive element-binding protein 6 gene, OsDREB6, as a potential regulator impacting anaerobic germination in rice seeds. Phenotypic analysis revealed that the ko-osdreb6-1 and ko-osdreb6-2 mutants exhibited significantly increased CL and germination sprout length under aerobic treatment for 4 days compared to WT. In contrast, disruption of OsDREB6 caused reduced CL in plants seeds under under anaerobic 4-day treatment and anaerobic 3-day treatment after seed dehiscence. Additionally, the relative coleoptile lengths of the mutants after 4 days between anaerobic and aerobic treatments were significantly lower than those of WT. RNA-seq and MapMan analysis of the ko-osdreb6-1 suggested that OsDREB6 may regulate the coleoptile elongation under anaerobic conditions by affecting the expression of related genes involved in the sucrose and starch metabolism. Overall, our study demonstrated that the effectiveness of combining GWAS with meta-analysis of QTL in identifying genetic loci and key genes for improving anaerobic germination tolerance in direct seeding rice breeding.

Indexed as

Anaerobic germinationGenome-wide association analysis (GWAS)Meta-analysis of QTLRiceRNA-seq

Identifiers

PMID40522587
PMCPMC12170972

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