Identification of a major quantitative trait locus and its candidate underlying genetic variation for rice stigma exsertion rate

Abstract

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