Genetic Dissection of the Major Quantitative Trait Locus (qSE11), and Its Validation As the Major Influence on the Rate of Stigma Exsertion in Rice (Oryza sativa L.)

Abstract

The rate of stigma exsertion (SE) is an important trait in rice breeding because the efficiency of hybrid rice seed production can be improved by increasing the percentage of stigmas that exsert. In this study, we developed a near isogenic line (NIL) from two parents, XieqingzaoB (XQZB) and Zhonghoi9308 (ZH9308), which have high and low SE rates in that order. In our previous study, we employed 75 chromosome segment substitution lines (CSSLs) and analyzed quantitative trait loci (QTLs) for their influence on SE rate. The single gene QTL (qSE11), which is located on chromosome 11, was responsible for this trait. In this study, we focused on one of the CSSLs (C65), namely, the NIL (qSE11XB). It contains an introgression segment of XQZB in the genetic background of ZH9308, and exhibits a significantly higher SE rate than that of the parents. We demonstrated that qSE11 regulated both the single and the dual SE rates. They both contribute to the total SE rate. Genetic analysis revealed that qSE11 acted as a single Mendelian factor and that the allele from XQZB increased the SE rate. The validity of our conclusions was established when C65 was used to develop secondary F2 (BC5F2) and F2:3 (BC5F2:3) populations by backcrossing to ZH9308, with subsequent selfing. We entered 3600 plants from the F2 population and 3200 from the F2:3 populations into a genetic dissection program and dissected the major QTL qSE11 to a 350.7-kb region located on chromosome 11. This study will contribute to the future isolation of candidate genes of SE and will play a vital role in future hybrid rice seed production programs.

Fine mapping and target gene identification of qSE4, a QTL for stigma exsertion rate in rice (Oryza sativa L.)

“…Using the single-segment substitution line created by the maintainer line IR66897B, qSER-2a , qSER2b, and qSER3a , qSER3b were mapped on chromosomes 2 and 3, respectively ( Tan et al, 2021 ). From the maintainer XieqingzaoB, qSE7 ( Zhang et al, 2018 ) and qSE11 ( Rahman et al, 2017 ) were mapped on chromosomes 7 and 11, respectively. Many QTLs for SER, such as qPEST-5 , qPEST-8 , qRES-5 ( Uga et al, 2003 ), qRES-10 ( Uga et al, 2003 ), qSER-2 ( Bakti and Tanaka, 2019 ), qSER-3 ( Bakti and Tanaka, 2019 ), qPES-9 , and qSER-1a ( Tan et al, 2020 ) have been found in wild rice, which is an important germplasm resource ( Marathi et al, 2015 ; Marathi and Jena, 2015 ).…”

Linkage mapping and association analysis to identify a reliable QTL for stigma exsertion rate in rice

“…With the continuous advancement of molecular marker technologies over the past several years, researchers have successfully mapped multiple SER-related QTLs in rice utilizing various types of segregating populations, including chromosome segment substitution lines (Rahman et al, 2017 ; Zhang et al, 2018 ; Tan et al, 2020 , 2021 ), doubled haploid lines (Hittalmani et al, 2002 ; Li et al, 2003 ), F 2 populations (Xiong et al, 1999 ; Yue et al, 2009 ; Li et al, 2010 , 2017 ; Xu et al, 2019 ), backcrossing populations (Li et al, 2001 ; Miyata et al, 2007 ), and recombinant inbred lines (RILs) (Uga et al, 2003 ; Yamamoto et al, 2003 ; Li et al, 2014 ). Several studies have identified one particular QTL that co-localized with the GS3 gene, which controls grain size, stigma length, and stigma exsertion (Miyata et al, 2007 ; Takano-Kai et al, 2011 ).…”

Dissection of closely linked QTLs controlling stigma exsertion rate in rice by substitution mapping

“…Because of high SER, MSLs or their maintainer lines were usually used to detect QTLs for SER. From the cytoplasmic male sterile (CMS) maintainer line XieqingzaoB, qSE7 was located on chromosome 7 (Zhang et al 2018 ), and qSE11 was mapped on chromosome 11 (Rahman et al 2017 ). From the CMS maintainer line II-32B, qSER-7 was identified on chromosome 7 (Liu et al 2019 ).…”