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

Abstract

Rice varieties are required to have high yield and good grain quality. Grain chalkiness and grain shape are two important traits of rice grain quality. Low chalkiness slender grains are preferred by most rice consumers. Here, we dissected two closely linked quantitative trait loci (QTLs) controlling grain chalkiness and grain shape on rice chromosome 8 by substitution mapping. Two closely linked QTLs controlling grain chalkiness and grain shape were identified using single-segment substitution lines (SSSLs). The two QTLs were then dissected on rice chromosome 8 by secondary substitution mapping. qPGC8.1 was located in an interval of 1382.6 kb and qPGC8.2 was mapped in a 2057.1 kb region. The maximum distance of the two QTLs was 4.37 Mb and the space distance of two QTL intervals was 0.72 Mb. qPGC8.1 controlled grain chalkiness and grain width. qPGC8.2 was responsible for grain chalkiness, grain length and width. The additive effects of qPGC8.1 and qPGC8.2 on grain chalkiness were not affected by higher temperature. Two closely linked QTLs qPGC8.1 and qPGC8.2 were dissected on rice chromosome 8. They controlled the phenotypes of grain chalkiness and grain shape. The two QTLs were insensitive to higher temperature.

The Next Generation of Rice: Inter-Subspecific Indica-Japonica Hybrid Rice

“…The HJX74-SSSL library consists of 2,360 SSSLs, which collects rich gene resources from donors with genetic diversity ( Zhang et al, 2004 ; Xi et al, 2006 ; He et al, 2017 ; Zhao et al, 2019 ; Zhang, 2021 ). The HJX74-SSSLs have been used to detect QTLs for complex traits ( Zhang et al, 2012 ; Yang et al, 2016 , 2021a , 2021b ; Zhou et al, 2017 ; Tan et al, 2020 , 2021 , 2022 ; Pan et al, 2021 ), to clone genes of agronomic importance and to assess allelic variation ( Wang et al, 2008 , 2012 , 2015 ; Teng et al, 2012 ; Sui et al, 2019 ; Zhang et al, 2020 ; Gao et al, 2021 ). Using the HJX74-SSSL library as platform for rice breeding by design, several CMS, maintainer and restorer lines have been developed ( Dai et al, 2015 , 2016 ; Luan et al, 2019 ).…”

Reconstruction of the High Stigma Exsertion Rate Trait in Rice by Pyramiding Multiple QTLs

“…We have developed an SSSL library, which includes 2,360 SSSLs derived from 43 donors of 7 species of rice AA genome in the Huajingxian 74 (HJX74) genetic background (Zhang et al, 2004 ; Xi et al, 2006 ; Zhang, 2021 ). The HJX74-SSSLs were widely used to detect QTLs for traits of agronomic importance (Zhang et al, 2012 ; Zhu et al, 2014 , 2018 ; Yang et al, 2016 , 2021a , b ; Zhou et al, 2017b ; Pan et al, 2021 ; Zhan et al, 2021 ; Fu et al, 2022 ), to clone genes of functional importance, and to mine alleles of functional variants (Zeng et al, 2006 ; Teng et al, 2012 ; Wang et al, 2012 ; Fang et al, 2019 ; Sui et al, 2019 ; Gao et al, 2021 ; Zhan et al, 2022 ). Using the HJX74-SSSL library as a platform for rice design, a series of cytoplasmic male sterility (CMS), maintainer and restorer lines, and wide-compatible indica lines (WCILs) were developed (Dai et al, 2015 , 2016 ; Luan et al, 2019 ; Guo et al, 2022 ).…”

Introgression Lines: Valuable Resources for Functional Genomics Research and Breeding in Rice (Oryza sativa L.)

“…Although the genetic diversity within rice subspecies is lower than that between subspecies, there are still large phenotypic differences among varieties from different regions with different genealogical relationships in the same subspecies. Several IL libraries from intrasubspecific crosses have been developed in rice to genetically dissect complex traits such as yield-related traits ( Shen and Xing, 2014 ; Hori et al, 2021a ; Kato and Hirayama, 2021 ), quality-related traits ( Yang et al, 2021b ), root traits ( Anis et al, 2019 ), resistance to preharvest sprouting ( Hori et al, 2010 ; Mizuno et al, 2018 ), and heterosis ( Lin et al, 2020 ). For example, a set of 202 CSSLs of an elite hybrid, Shanyou 63, were developed in the Zhenshan 97 background, and QTLs for heading date and plant height were detected ( Shen and Xing, 2014 ; Shen et al, 2014 ).…”