Identification of a major quantitative trait locus and its candidate underlying genetic variation for rice stigma exsertion rate
2019
Shouling Xu | Yunchao Zheng | Yang Liu | Xiaohao Guo | Yuanyuan Tan | Qiuping Qian | Qingyao Shu | Jianzhong Huang
Stigma exsertion in male sterile lines of hybrid rice is important for seed yield. In the present study, ZS616 [Oryza sativa subsp. Xian (indica)], a male sterile line with a stigma exsertion rate (SER) as high as 94.5%, was crossed to DS552, a japonica line with almost no exserted stigmas. F3 plants with extremely low and high SER were sequenced to identify SER-associated quantitative trait loci (QTL). A major QTL for SER, qSER-3.1, was identified along with other QTL on chromosome 3 in a 3.9 Mb region. A total of 307 nonsynonymous single-nucleotide polymorphisms (SNPs) and 27 frame-shift insertion/deletions (InDels) differentiating ZS616 and DS552 were identified in the region containing qSER-3.1. Most SNPs (294) and InDels (25) were excluded after further analysis because they were shared by ZS616 and low (<2.0%) SER accessions in the Huazhong Agricultural University (HAU) core rice collection. Association analysis using the full HAU collection identified a 17-bp InDel in OS03G0689400 as the most likely causal genetic variant underlying qSER-3.1. ZS616-type accessions (n = 54, with the 17-bp insertion) in the HAU collection had minimum (16.5%) and mean (39.6%) SERs significantly greater than those (n = 424) without the insertion (with minimum and mean SERs of 0.2% and 20.6%, respectively). Thus, this study identified a major QTL for stigma exsertion and revealed the mutation in a candidate gene for the QTL. Keywords: Hybrid rice, Stigma exsertion, Seed production, QTL-seq, qSER-3.1, GS3
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