Genome-wide association mapping combined with gene-based haplotype analysis identify a novel gene for shoot length in rice (Oryza sativa L.)

Abstract

Key message Genome-wide association mapping revealed a novel QTL for shoot length across multiple environments. Its causal gene, LOC_Os01g68500, was identified firstly through gene-based haplotype analysis, gene expression and knockout transgenic verification. 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 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 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 novel QTL qSL-1f on chromosome 1 could be stably detected across all three cultivation methods in the whole population and indica subpopulation. Through gene-based haplotype analysis of the annotated genes within the putative region of qSL-1f, and validated by gene expression and knockout transgenic experiments, LOC_Os01g68500 (i.e., Os01g0913100 in RAP-DB) was identified as the causal gene for SL, which has a single-base variation (C-to-A transversion) in its CDS 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.

The Function of SD1 on Shoot Length and its Pyramiding Effect on Shoot Length and Plant Height in Rice (Oryza sativa L.)

“…The SLs of the mutants were significantly shorter than that of their wild type ( P < 0.05), indicating that SD1 is the causal gene for SL in rice. Comparing the effects of SD1 (this study) and LOC_Os01g68500 (Yang et al 2023 ) on SL, no significant difference was found (Fig. 3 C).…”

“…In our previous study, qSL-1d could be stably identified across multiple environments and exhibited potential value in improving SL (Yang et al 2023 ). To accurately obtain the favorable haplotypes for the desired SL, it is essential to identify the causal gene underlying qSL-1d .…”

“…Therefore, it is necessary to develop rice varieties with strong seedling vigor, which is an imperative trait for stable seedling establishment and enhancing weed competitiveness in rice direct seeding system (Zhang et al 2005 ; Mahender et al 2015 ). However, seedling vigor is a complex trait controlled by multiple genes (Zhang et al 2005 ; Sandhu et al 2015 ; Yang et al 2021 , 2023 ; Zeng et al 2021 ), thus, it is difficult to develop rice varieties with strong seedling vigor using the conventional breeding methods. Understanding its genetic basis and carrying out molecular breeding is an efficient and effective way to develop rice varieties with strong seedling vigor.…”

“…Varieties with long SL can not only enhance seedling emergence, but also improve their advantage in competition of nutrient and light energy, and effectively suppress the growth of weeds (Abe et al 2012 ; Lu et al 2016 ; Rao et al 2007 ; Singh et al 2017 ; Dimaano et al 2020 ). To date, more than 100 QTLs for seedling vigor in rice have been identified by QTL analysis in bi-parental populations (Redona et al 1996 ; Zhang et al 2005 ; Lu et al 2007 ; Zhou et al 2007 ; Cairns et al 2009 ; Abe et al 2012 ; Yano et al 2012 ; Diwan et al 2013 ; Sandhu et al 2015 ; Cordero-Lara et al 2016 ; Singh et al 2017 ; Zhang et al 2017 ; Dimaano et al 2020 ; Yang et al 2021 ) and genome-wide association study (GWAS) in diverse natural populations (Dang et al 2014 ; Anandan et al 2016 ; Lu et al 2016 ; Chen et al 2019 ; Zhao et al 2019 ; Zeng et al 2021 ; Ma et al 2022 ; Yang et al 2023 ). However, most of the reported QTLs were identified in a single environment, and their reliability and stability remain unclear, and more importantly, few of their functional genes have been identified except OsGA20ox1 (Abe et al 2012 ; Yano et al 2012 ) and LOC_Os01g68500 (Yang et al 2023 ).…”

“…In our previous study, two tightly linked and stably expressed QTLs for SL, qSL-1d and qSL-1f were identified in a diverse population by GWAS, and the causal gene underlying qSL-1f , LOC_Os01g68500 was identified through gene-based haplotype analysis, gene expression and knockout transgenic verification (Yang et al 2023 ). In this study, we further identified LOC_Os01g66100 as the causal gene underlying qSL-1d , which controlled SL at the seedling stage.…”