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Stigma exsertion is a key determinant to increase the efficiency of commercial hybrid rice seed production. The major quantitative trait locus (QTL)  qSE7  for stigma exsertion rate was previously detected on the chromosome 7 using 75 Chromosome Segment Substitution Lines (CSSLs) derived from a cross between the high stigma exsertion  indica  maintainer XieqingzaoB (XQZB) and low stigma exsertion  indica  restorer Zhonghui9308 (ZH9308). The C51 line, a CSSL population with an introgression from XQZB, was backcrossed with ZH9308 to produce the secondary F 2  (BC 5 F 2 ) and F 2:3  (BC 5 F 2:3 ) populations. As a result, the Near Isogenic Line (NIL  qSE7   XB  ) was developed. Analysis indicated  qSE7  acted as a single Mendelian factor and decreased the stigma exsertion. We hypothesized  qSE7  regulates single, dual, and total stigma exsertion rate, provided experimental support.  qSE7  was mapped and localized between RM5436 and RM5499 markers, within a physical distance of 1000-kb. With use of new insertion-deletion (InDel) markers and analysis of the heterozygous and phenotypic data, it was ultimately dissected to a 322.9-kb region between InDel SER4-1 and RM5436. The results are useful for additional identification and isolation of this candidate gene controlling stigma exsertion rate, and provide a basis for further fine mapping, gene cloning, and Marker Assisted Selection (MAS) breeding later.

qSE7 is a major quantitative trait locus (QTL) influencing stigma exsertion rate in rice (Oryza sativa L.)