College of Life Sciences, Jiangxi Normal University, Nanchang 330022, China.
Rice National Engineering Laboratory, Rice Research Institute, Jiangxi Academy of Agricultural Sciences, Nanchang 330022, China.
Genes (Basel). 2021 Nov 19;12(11):1831. doi: 10.3390/genes12111831.
Dongxiang wild rice ( Griff.) (DXWR) has strong seed storability and identifying its elite gene resources may facilitate genetic improvements in rice seed storability. In this study, we developed two backcross inbred lines (BILs) populations, with DXWR as a common donor parent and two rice varieties (F6 and R974) as recipient parents. Bulked segregant analysis via whole genome sequencing (BSA-seq) was used to identify seed storability-related loci in the DXWR and F6 population. Two main genomic regions containing 18,550,000-20,870,000 bp on chromosome 4 and 7,860,000-9,780,000 bp on chromosome 9 were identified as candidate loci of DXWR seed storability; these overlapped partially with seed storability-related quantitative trait loci (QTLs) discovered in previous studies, suggesting that these loci may provide important regions for isolating the responsible genes. In total, 448 annotated genes were predicted within the identified regions, of which 274 and 82 had nonsynonymous and frameshift mutations, respectively. We detected extensive metabolic activities and cellular processes during seed storability and confirmed the effects of the seed storability-related candidate loci using four BILs from DXWR and R974. These results may facilitate the cloning of DXWR seed storability-related genes, thereby elucidating rice seed storability and its improvement potential.
东乡野生稻（Griff.）（DXWR）具有很强的种子贮藏能力，鉴定其优良基因资源可能有助于提高水稻种子贮藏能力。本研究以 DXWR 为共同供体亲本，以两个水稻品种（F6 和 R974）为受体亲本，构建了两个回交自交系（BIL）群体。通过全基因组测序（BSA-seq）进行的 bulked segregant analysis 鉴定了 DXWR 和 F6 群体中与种子贮藏能力相关的位点。在第 4 号染色体上发现了两个主要的基因组区域，包含 18,550,000-20,870,000 bp，在第 9 号染色体上发现了 7,860,000-9,780,000 bp，这两个区域被认为是 DXWR 种子贮藏能力的候选区域；这些区域与先前研究中发现的与种子贮藏能力相关的数量性状位点（QTL）部分重叠，表明这些区域可能为分离相关基因提供了重要区域。总共预测到在鉴定区域内有 448 个注释基因，其中 274 个和 82 个分别具有非同义和移码突变。我们在种子贮藏过程中检测到广泛的代谢活性和细胞过程，并使用来自 DXWR 和 R974 的四个 BIL 验证了与种子贮藏能力相关的候选区域的效果。这些结果可能有助于 DXWR 种子贮藏能力相关基因的克隆，从而阐明水稻种子贮藏能力及其改良潜力。
