Abstract
BackgroundChromosome segment substitution lines (CSSLs) can be used to dissect complex traits, from which single-segment substitution lines (SSSLs) containing a target quantitative trait loci (QTL) can be developed, and they are thus important for functional analysis and molecular breeding.ResultsA rice line with short wide grains, CSSL-Z563, was isolated from advanced-generation backcross population (BC3F6) derived from ‘Xihui 18’ (the recipient parent) and ‘Huhan 3’ (the donor parent). Z563 carried seven segments from ‘Huhan 3’, distributed on chromosomes 3, 7, and 8, with average substitution length of 5.52 Mb. Eleven QTLs for grain size were identified using secondary F2 population of ‘Xihui 18’/Z563. The QTLs qGL3–1, qGL3–2, and qGL7 control grain length in Z563 and have additive effects to reduce grain length; qGW3–1 and qGW3–2 control grain width in Z563 and have additive effects to increase grain width. Four SSSLs, three double-segment substitution lines (D1–D3), and two triple-segment substitution lines (T1 and T2) were developed containing the target QTLs. The genetic stability of eight QTLs, including qGL3–2, qGL3–1, and qGL7, was verified by the SSSLs. D1 (containing qGL3–2 and qGL3–1), D2 (qGL3–1 and qGL7), and T1 (qGL3–2, qGL3–1, and qGL7) had positive epistatic effects on grain length, and their grain length was shorter than that of the corresponding SSSLs. The QTL qGL3–2 was fine-mapped to a 696 Kb region of chromosome 3 containing five candidate genes that differed between ‘Xihui 18’ and Z563. These results are important for functional research on qGL3–2 and molecular breeding of hybrid rice cultivars.ConclusionsThe short and wide grain of Z563 was mainly controlled by qGL3–1, qGL3–2, qGL7, qGW3–1 and qGW3–2. The major QTL qGL3–2 was fine-mapped to a 696 Kb region of chromosome 3 containing five candidate genes. Different QTLs pyramiding displayed various phenotypes. In essence, the performance after pyramiding of genes depended on the comparison between the algebraic sum of the additive and epistatic effects of QTLs in the pyramidal line and the additive effect value of the single QTL. The results lay good foundation in the functional analysis of qGL3–2 and molecular design breeding of novel hybrid rice cultivars.
Highlights
Chromosome segment substitution lines (CSSLs) can be used to dissect complex traits, from which single-segment substitution lines (SSSLs) containing a target quantitative trait loci (QTL) can be developed, and they are important for functional analysis and molecular breeding
Identification of Substitution Segments in Z563 Following the previous development of Z563, the substitution segments and purity of the genetic backgrounds were investigated with 10 plants of Z563 using 13 markers on the substitution segment and 24 markers outside the substitution segment
In essence, the performance after pyramiding of genes depended on the comparison between the algebraic sum of the additive and epistatic effects of QTLs in the pyramidal line and the additive effect value of the single QTL
Summary
Chromosome segment substitution lines (CSSLs) can be used to dissect complex traits, from which single-segment substitution lines (SSSLs) containing a target quantitative trait loci (QTL) can be developed, and they are important for functional analysis and molecular breeding. Rice grain size and shape are complex quantitative traits that include grain length, grain width, and grain length-to-width ratio These traits affect directly both the yield and the quality of rice (Wang et al 2020). Some regulate positively regulate rice grain size, such as OsBZR1 (Zhu et al 2015), OsMCA1/PAD (Liu et al 2015a), OsMKK4 (Guo et al 2018), OsLG3 (Yu et al 2017), OsMKB3/OsGIF1 (Lu et al 2020), AFG1 (Yu et al 2020), OsACOT (Zhao et al 2019), and OsUBP15 (Shi et al 2019). Numerous genes have been identified in rice, compared with the phenotypic diversity of the grain and the complex underlying molecular mechanisms, identification of additional genes associated with grain size is necessary to satisfy growing calls to improve grain quality in rice breeding
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