Abstract
BackgroundThe general combining ability (GCA) of parents in hybrid rice affects not only heterotic level of grain yield and other important agronomic traits, but also performance of grain quality traits of F2 bulk population which is the commodity consumed by humans. In order to make GCA improvement for quality traits in parents of hybrid rice by molecular marker assisted selection feasible, genome-wide GCA loci for quality traits in parents were detected through association analysis between the effects of GCA and constructed single nucleotide polymorphism linkage disequilibrium blocks (SNPLDBs), by using unhusked rice grains harvested from F1 plants of 48 crosses of Indica rice and 78 crosses of Japonica rice. GCA-SNPLDBs association analysis.ResultsAmong the 8 CMS and 6 restorer lines of indica rice subspecies, CMS lines Zhenpin A, Zhenshan97 A, and 257A, and restorers Kanghui98, Minghui63 and Yanhui559 were recognized as good general combiners based on their GCA effect values for the 9 quality traits (brown rice rate, milled rice rate, head rice rate, percentage of chalky grains, chalky area size, chalkiness degree, gelatinization temperature, gel consistency and amylose content). Among the 13 CMS and 6 restorer lines of japonica rice subspecies, CMS 863A, 6427A and Xu 2A, and restorers C418, Ninghui8hao and Yunhui4hao showed elite GCA effect values for the 9 traits. GCA-SNPLDB association analysis revealed 39 significant SNPLDB loci associated with the GCA of the 9 quality-related traits, and the numbers of SNPLDB loci located on chromosome 1, 2, 3, 4, 5, 8, 9, 11 and 12 were 1, 4, 3, 9, 6, 5, 5, 4 and 2, respectively. Number of superior GCA alleles for the 9 traits among the 33 parents ranged from 1 to 26.ConclusionsThirty-nine significant SNPLDBs loci were identified associated with the GCA of 9 quality-related traits, and the superior SNPLDB alleles could be used to improve the GCA of parents for the traits in the future by molecular marker assisted selection. The genetic basis of trait GCA in parents is different from that of trait itself.
Highlights
The general combining ability (GCA) of parents in hybrid rice affects heterotic level of grain yield and other important agronomic traits, and performance of grain quality traits of F2 bulk population which is the commodity consumed by humans
The mean performances of 9 quality-related traits in 78 hybrids obtained from 13 japonica rice Cytoplasmic male sterile (CMS) crossed with 6 japonica restorers are presented in Additional file 2: Table S2
The cross between CMS 731A and restorer Yanhui R50 recorded the least percentage of chalky grains (30.5%), chalky area size (11.5%) and gelatinization temperature (1.1ASS), whereas, the least amylose content (9.6%) was detected in Liuyan 189A × Yanhui R50
Summary
The general combining ability (GCA) of parents in hybrid rice affects heterotic level of grain yield and other important agronomic traits, and performance of grain quality traits of F2 bulk population which is the commodity consumed by humans. Due to the increase in their living standards, people started to demand high-quality rice, including high eating and cooking quality, with various preferences in different geographic regions. Breeding researcher more centered on enhancing the quality of rice to cope with the demanded quality standards of direct consumers, and the other various commercial uses. Grain quality in rice is determined through many factors, e.g., nutritional value, grain appearance, cooking and eating quality. Grain quality of hybrid rice has its speciality since the commodity consumed by people is a F2 bulk population
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