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

Abstract

Key message Through substitution mapping strategy, two pairs of closely linked QTLs controlling stigma exsertion rate were dissected from chromosomes 2 and 3 and the four QTLs were fine mapped. Abstract Stigma exsertion rate (SER) is an important trait affecting the outcrossing ability of male sterility lines in hybrid rice. This complex trait was controlled by multiple QTLs and affected by environment condition. Here, we dissected, respectively, two pairs of tightly linked QTLs for SER on chromosomes 2 and 3 by substitution mapping. On chromosome 2, two linkage QTLs, qSER-2a and qSER-2b, were located in the region of 1288.0 kb, and were, respectively, delimited to the intervals of 234.9 kb and 214.3 kb. On chromosome 3, two QTLs, qSER-3a and qSER-3b, were detected in the region of 3575.5 kb and were narrowed down to 319.1 kb and 637.3 kb, respectively. The additive effects of four QTLs ranged from 7.9 to 9.0%. The epistatic effect produced by the interaction of qSER-2a and qSER-2b was much greater than that of qSER-3a and qSER-3b. The open reading frames were identified within the maximum intervals of qSER-2a, qSER-2b and qSER-3a, respectively. These results revealed that there are potential QTL clusters for SER in the two regions of chromosome 2 and chromosome 3. Fine mapping of the QTLs laid a foundation for cloning of the genes of SER.

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

“…On chromosome 2, two linkage QTLs, qSER-2a and qSER-2b , were located in the region of 1288.0 kb, and were respectively delimited to the intervals of 234.9 kb and 214.3 kb. On chromosome 3, two QTLs, qSER-3a and qSER-3b , were detected in the region of 3575.5 kb and were narrowed down to 319.1 kb and 637.3 kb, respectively (Tan et al 2021a ). Together, those results indicated that substitution mapping using SSSLs is a powerful tool for dissection of closely linked QTLs for complex traits.…”

“…Substitution mapping is a powerful tool to detect QTLs for complex traits (Tan et al 2021a , b ; Yang et al 2021 ). Like near-isogenic lines (NILs), single-segment substitution lines (SSSLs) carry only one substitution segment from donors in the recipient genetic background (Zhang et al 2004 ; Keurentjes et al 2007 ).…”

“…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 , 2021 ). 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 , 2018b ; Yang et al 2016 , 2021 ; Zhou et al 2017 ; Fang et al 2019 ; Sui et al 2019 ; Tan et al 2020 , 2021a , b ). Recently, the SSSLs were used to detect QTLs controlling stigma exsertion rate (SER) of rice.…”

“…Recently, the SSSLs were used to detect QTLs controlling stigma exsertion rate (SER) of rice. Two pairs of tightly linked QTLs for SER, qSER-2a and qSER-2b on chromosome 2 and qSER-3a and qSER-3b on chromosome 3, were dissected by substitution mapping (Tan et al 2021a ). In previous study, we fine-mapped two QTLs qPGC9 and qPGC11 for grain chalkiness on rice chromosomes 9 and 11, which were sensitive to high temperature (Yang et al 2021 ).…”

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.…”