Genome-Wide Single-Nucleotide Polymorphisms in CMS and Restorer Lines Discovered by Genotyping Using Sequencing and Association with Marker-Combining Ability for 12 Yield-Related Traits in Oryza sativa L. subsp. Japonica

Abstract

Heterosis or hybrid vigor is closely related with general combing ability (GCA) of parents and special combining ability (SCA) of combinations. The evaluation of GCA and SCA facilitate selection of parents and combinations in heterosis breeding. In order to improve combining ability (CA) by molecular marker assist selection, it is necessary to identify marker loci associated with the CA. To identify the single nucleotide polymorphisms (SNP) loci associated with CA in the parental genomes of japonica rice, genome-wide discovered SNP loci were tested for association with the CA of 18 parents for 12 yield-related traits. In this study, 81 hybrids were created and evaluated to calculate the CA of 18 parents. The parents were sequenced by genotyping by sequencing (GBS) method for identification of genome-wide SNPs. The analysis of GBS indicated that the successful mapping of 9.86 × 106 short reads in the Nipponbare reference genome consists of 39,001 SNPs in parental genomes at 11,085 chromosomal positions. The discovered SNPs were non-randomly distributed within and among the 12 chromosomes of rice. Overall, 20.4% (8026) of the discovered SNPs were coding types, and 8.6% (3344) and 9.9% (3951) of the SNPs revealed synonymous and non-synonymous changes, which provide valuable knowledge about the underlying performance of the parents. Furthermore, the associations between SNPs and CA indicated that 362 SNP loci were significantly related to the CA of 12 parental traits. The identified SNP loci of CA in our study were distributed genome wide and caused a positive or negative effect on the CA of traits. For the yield-related traits, such as grain thickness, days to heading, panicle length, grain length and 1000-grain weight, a maximum number of positive SNP loci of CA were found in CMS A171 and in the restorers LC64 and LR27. On an individual basis, some of associated loci that resided on chromosomes 2, 5, 7, 9, and 11 recorded maximum positive values for the CA of traits. From our results, we suggest that heterosis in japonica rice would be improved by pyramiding the favorable SNP loci of CA and eliminating the unfavorable loci from parental genomes.

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

“…In this study, the genomic positions of associated SNPLDBs were compared with the reported genomic positions of GCA. The associated SNPLDBs of GCA of PH and ST on chromosomes 6, 7 and 11 were close to the chromosomal regions of previously identified alleles of PH and ST with combining abilities (Zaid et al 2017). Additionally, most of the associated SNPLDBs were located in adjacent intervals of the same chromosome that used a diverse set of ILs (Xiang et al 2016).…”

Association analysis between constructed SNPLDBs and GCA effects of 9 quality-related traits in parents of hybrid rice (Oryza sativa L.)

“…The SNP data of this study were obtained from Zaid et al [39], and are available at NCBI under accession number SRR7250921. The missing genotypes in the sequence data were precisely predict through the fas-tPHASE software [35].…”

Research and Development Strategies for Hybrid japonica Rice

“…Associated loci residing on chromosomes 2, 5, 7, 9, and 11 that recorded maximum positive values for the CA of traits were identified. It was concluded that the strategy to improve the heterosis of hybrid japonica rice involved pyramiding favorable SNP loci of CA and eliminating the unfavorable loci from parental genomes (Zaid et al 2017).…”