Substitution mapping of the major quantitative trait loci controlling stigma exsertion rate from Oryza glumaepatula

Abstract

Background: Stigma exsertion rate (SER) is a key determinant for the outcrossing ability of male sterility lines (MSLs) in hybrid rice seed production. In the process of domestication, the outcrossing ability of cultivated rice varieties decreased, while that of wild Oryza species kept strong. Here, we detected the quantitative trait loci (QTLs) controlling SER using a set of single-segment substitution lines (SSSLs) derived from O. glumaepatula , a wild Oryza species. Results: Seven QTLs for SER were located on 5 chromosomes. qSER-1a and qSER-1b were located on chromosome 1. qSER-3a and qSER-3b were mapped on chromosome 3, and qSER-3b was further located at an estimated interval of 898.8kb by secondary substitution mapping. qSER-5 , qSER-9 and qSER-10 were identified on chromosomes 5, 9 and 10, respectively, and qSER-9 was delimited to an estimated region of 551.9kb by secondary substitution mapping. The additive effects of the 7 QTLs ranged from 10.6% to 14.8%, which were higher than those of most loci for SER reported previously. Conclusions: qSER-1a and qSER-1b are novel loci for SER on chromosome 1. All of the 7 QTLs have major effects on SER. The major QTLs of SER will help to develop MSLs with strong outcrossing ability.

GW10, a Member of P450 Subfamily Regulates Grain Size and Grain Number in Rice

“…It was difficult to determine the precise location of QTLs in rice genome by using the F2 plants, Recombinant Inbred Lines (RILs), Backcross Inbred Lines (BILs) and Doubled Haploid Lines (DHLs) (Ashikari et al 2006). Consequently, the development of Nearly Isogenic Lines (NILs), Chromosome Fragment Substitution Line (CSSL) and Single Segment Substitution Line (SSSL) were necessary for QTL fine mapping and gene cloning (Ashikari et al 2006;Guo et al 2016;Zhou et al2017;Wang et al 2018;Yang et al 2018;Luan et al 2019;Tan et al 2020;Tan et al 2021), especially for the minor genes.…”

Substitution Mapping of Two Closely Linked QTLs Controlling Grain Chalkiness and Grain Shape on Rice Chromosome 8

“…The DNA samples were amplified by PCR method. The PCR products were separated by gel electrophoresis on 6% denatured PAGE and detected by the silver staining method (Tan et al 2020). To develop secondary SSSLs or NILs, 03-08 and 15-08 were crossed with the recipient HJX74.…”

“…Minimum length, maximum length and estimated length of a substitution segment were estimated as described by Tan (2020). When PGC showed significant difference between SSSL genotype and HJX74 genotype, a QTL for PGC was detected on the substitution segment of SSSL.…”

“…When PGC showed significant difference between SSSL genotype and HJX74 genotype, a QTL for PGC was detected on the substitution segment of SSSL. When multiple substitution segments overlapped in NILs, the QTL was located in the overlapping region (Eshed and Zamir, 1995;Tan et al 2020). Additive effect of a QTL was defined as the phenotypic difference between SSSL and HJX74 (Zhou et al 2020).…”

“…We have developed a library of 2360 SSSLs, which were derived from 43 donors of 7 species of rice AA genome in the genetic background of Huajingxian 74 (HJX74), an indica elite variety in southern China (Zhang et al 2004;Xi et al 2006;Zhang 2019). These SSSLs were widely used to detect QTLs for complex traits, to clone QTLs of agronomic importance and to mine alleles of different functions (Zeng et al 2006;Teng et al 2012;Wang et al 2012;Zhang et al 2012;Zhu et al 2014;Yang et al 2016;Zhou et al 2017;Zhu et al 2018b;Fang et al 2019;Sui et al 2019;Tan et al 2020;Tan et al 2021;Yang et al 2021). Recently, the SSSLs were used to detect QTLs controlling stigma exsertion rate (SER) of rice.…”