Genome-wide association mapping combined with gene-based haplotype analysis identify a novel gene for shoot length in rice (Oryza sativa 必威betway中文版入口 L.)
Tifeng Yang† · Jingfang Dong† · Junliang Zhao · Longting Zhang · Lian Zhou · Wu Yang · Yamei Ma ·Jian Wang · Hua Fu · Jiansong Chen · Wenhui Li · Haifei Hu · 必威betways Xianya Jiang · Ziqiang Liu · Bin Liu 必威betway中文版入口 ·Shaohong Zhang*
Theoretical and applied genetics
Abstract
Strong seedling vigor is an important breeding target for rice varieties used in direct seeding. Shoot length (SL) is one of the important traits associated with seedling vigor characterized by rapid growth of seedling, which enhance seedling emergence. Therefore, mining genes for SL and conducting molecular breeding help to develop varieties 必威betway中文版入口 for direct seeding. However, few QTLs for SL have been fine mapped or cloned so far. In this study, a genome-wide association study of SL was performed in a 必威betways diverse rice collection consisting of 391 accessions in two years, using phenotypes generated by different cultivation methods according to the production practice, and a total of twenty-four QTLs for SL were identified. Among them, the 必威betways novel QTL qSL-1f on chromosome 1 could be stably detected across all three cultivation methods in the whole 必威betway中文版入口 population and indica subpopulation. Through gene-based haplotype 必威betway中文版入口 analysis of the annotated genes within the putative region of qSL-1f, and validated by 必威betway中文版入口 gene expression and knockout transgenic experiments, LOC_Os01g68500 (i.e., Os01g0913100 in RAP-DB) was identified as the causal 必威betway中文版入口 gene for SL, which has a single-base variation (C-to-A transversion) in its CDS 必威betway中文版入口 region, resulting in the significant difference in SL of rice. LOC_Os01g68500 encodes a DUF538 (Domain of unknown function) containing protein, and the function of DUF538 protein gene on rice seedling growth is firstly reported in this study. These results provide a new clue for exploring the molecular mechanism regulating SL, and promising gene source for the molecular breeding in rice.
