QTL mapping and candidate gene analysis of low temperature germination in rice ( Oryza sativa L.) using a genome wide association study

PeerJ

article

Feng Mao¹  Depeng Wu²  Fangfang Lu²  Xin Yi²  Yujuan Gu²  Bin Liu²  Fuxia Liu²  Tang Tang²  Jianxin Shi⁴  Xiangxiang Zhao²  Lei Liu²  Lilian Ji¹ 

[1] School of Chemistry and Life Sciences, Suzhou University of Science and Technology;Jiangsu Key Laboratory for Eco-Agriculture Biotechnology around Hongze Lake, Huaiyin Normal University;Jiangsu Collaborative Innovation Center of Regional Modern Agriculture and Environment Protection, Huaiyin Normal University;School of Life Sciences and Biotechnology, Shanghai Jiao Tong University

关键词: Genome wide association study;    Low temperature germination;    Haplotype analysis;    Rice;   

DOI  :  10.7717/peerj.13407

学科分类：社会科学、人文和艺术（综合）

来源: Inra

【 摘 要 】

Low temperature germination (LTG) is a key agronomic trait in rice (Oryza sativa L.). However, the genetic basis of natural variation for LTG is largely unknown. Here, a genome-wide association study (GWAS) was performed using 276 accessions from the 3,000 Rice Genomes (3K-RG) project with 497 k single nucleotide polymorphisms (SNPs) to uncover potential genes for LTG in rice. In total, 37 quantitative trait loci (QTLs) from the 6th day (D6) to the 10th day (D10) were detected in the full population, overlapping with 12 previously reported QTLs for LTG. One novel QTL, namely qLTG1-2, was found stably on D7 in both 2019 and 2020. Based on two germination-specific transcriptome datasets, 13 seed-expressed genes were isolated within a 200 kb interval of qLTG1-2. Combining with haplotype analysis, a functional uncharacterized gene, LOC_Os01g23580, and a seed germination-associated gene, LOC_Os01g23620 (OsSar1a), as promising candidate genes, both of which were significantly differentially expressed between high and low LTG accessions. Collectively, the candidate genes with favorable alleles may be useful for the future characterization of the LTG mechanism and the improvement of the LTG trait in rice breeding.

【 授权许可】

CC BY