Association analysis uncovers the genetic basis of general combining ability of 11 yield-related traits in parents of hybrid rice

Abstract

Association analysis between constructed single nucleotide polymorphism linkage disequilibrium blocks (SNPLDBs) and general combining ability (GCA) effects is a novel approach to uncover the genetic basis of GCA within the sequence genomes of parents of hybrid rice. Here, we calculated the GCA effect values of 33 parents of hybrid rice and sequenced them to identify genome-wide single nucleotide polymorphisms (SNPs). In total, 64.6 % of the uniquely mapped paired-end short reads revealed a final total of 291 959 SNPs between the 33 parental genomes and the Nipponbare reference genome. The identified SNPs were non-randomly distributed among all chromosomes of rice, whereas one-fourth of the SNPs were situated in the exonic regions with 16 % being non-synonymous. Further, the identified SNPs were merged and optimized for construction of 2612 SNPLDB markers, using linkage disequilibrium information. The single-factor analysis of variance-based association method between the constructed SNPLDB markers and GCA effects values detected 99 significant SNPLDBs for GCA of 11 yield-related traits. The associated SNPLDB markers explained 26.4 % of phenotypic variations with traits, on average. We mined 50 favourable GCA alleles at the associated SNPLDBs regions, distributed across the 33 parental genomes. The parental genomes possessed a small number of favourable GCA alleles for studied traits, with the exception of days to heading and plant height. Our results suggest that the identified GCA alleles could be used to improve the GCA performance of parents of hybrid rice through optimal crossing design. Moreover, favourable GCA alleles should be incorporated in the parental genomes through marker-assisted selection experiments, and the parental lines carrying more alleles could be utilized in breeding as superior parents for developing rice hybrids of desirable characteristics.

Genetic Dissection of the General Combining Ability of Yield-Related Traits in Maize

“…qRN3-1 and qRN6, two pleiotropic loci, were associated with the GCA effects of RN, KW, and HKW rather than these per se performances for the traits. The two loci were not been identified in previous study (Qi et al, 2013), the specificities in additive effects might be caused by diverse testers (Qu et al, 2012), the identified loci occurred due to the presence of potential GCA coverage in the potential genomic regions (Zaid et al, 2019). Furthermore, qKT1-2 and qHKW5-1 were two stable loci for GCA effects of KT and HKW respectively, but no significant loci were detected for corresponding per se performances for the traits in multiple environments.…”

Exploiting heterosis and combining ability in two-line hybrid rice

“…GCA analysis seeks to facilitate breeding through effective and efficient selection of inbred lines for a cross based on additive and additive × additive gene effects. Moreover, GCA analysis maximize additive gene effect that increases the selection efficiency of breeders in selecting elite inbred parents with better performance (Ullah Zaid et al, 2019)we calculated the GCA effect values of 33 parents of hybrid rice and sequenced them to identify genome-wide single nucleotide polymorphisms (SNPs. The RILs from the cross between the maintainer line Zhenshan97B and the restorer line Minghui63 (both parents of the elite hybrid Shanyou63, the classical hybrid of three-line system) was used to create the subsequent immortalized F 2 population, which enabled the comprehensive evaluations of the genetic contributions of dominance, over-dominance and epistatic effects across the whole rice genome (Liu et al, 2020).…”