Association Analysis Between Constructed SNPLDBs And GCA Effects Of 11 Yield-related Traits In Parents Of Hybrid Rice(Oryza Sativa L.)

Hybrid rice has high grain yield,nutritious value and resistance to biotic and abiotic stresses.Due to a diverse genetic background,the hybrid rice has several good agronomic and yield characteristics which enable them to have an increased 20%yield over other conventional indica and japonica cultivars.The gain in yield depends on the choice of mating parents which is the basis for superior yield performance.Combining ability analysis is an indispensable tool which discriminates the superior mating parents.In previous studies,efforts were made to develop genomic resources for dissection of GCA with molecular markers.In order to move one step forward i.e.to gain a maximum number of beneficial alleles of GCA of parental traits,we uncovered the genetic foundation of GCA with constructed SNPLDBs.Association analysis between constructed SNPLDBs and GCA effects of parental traits is new and unique approach as to previous experiments conducted for identification of GCA alleles.In our study,The GCA effect values of 14 indica and 19 japonica CMS and restorer lines for 11 yield-related traits were estimated by phenotyping of 48 indica and 78 japonica developed hybrids.The genotype data were obtained by performing the genotyping by sequencing of parental genomes.The single factor ANOVA method of marker-trait association in SAS/STAT software was implemented for association analysis between constructed SNPLDBs and GCA effects of 11 yield-related traits.With this background,the objectives of our study were suggested as;(a)Assess the GCA effects of 33 parents of hybrid rice for 11 yield-related traits(b)discover genome-wide SNPs in parents of hybrid rice using genotyping by sequencing method(c)detect significant SNPLDBs of GCA of parental traits and select superior alleles.1.PERFORMANCES OF GCA OF PARENTS OF HYBRID RICE FOR 11 YIELD-RELATED TRAITSTo examine the GCA effects of 14 indica and 19 japonica parents of hybrid rice,48 indica and 78 japonica crosses were created and evaluated for 11 yield-related traits.Following F1 population was being developed using North Carolina mating design Ⅱ,the means demonstrated significant differences for all the traits of indica and japonica developed hybrids.The parents of hybrid rice showed positive and negative GCA effect values for each of the 11 yield-related trait.Among the indica parental lines,CMS 256A had higher GCA effects for traits,whereas restorer Huizi 04 had higher GCA effects for traits.Subsequently,in japonica parents of hybrid rice,CMS Qingkong A depicts maximum GCA effect values,whereas,restorer C418 showed maximum GCA effect values for all the studied 11 traits.Our results suggest that the parental lines with maximum GCA effect values are the elite mating parents of three line breeding system for developing of indica and japonica hybrids of superior performances.2.SNP DISCOVERY AND CONSTRUCTION OF SNPLDB MARKERSThe sequenced data of 33 parents of hybrid rice revealed 64.6%of unique mapping onto the Nipponbare genome.The successfully mapped short reads discovered a total of 292,074 genome-wide SNPs at 30081 chromosomal positions that distributed unevenly across 12 chromosomes of rice.The annotation of SNPs concluded that 56.9%,28.6%and 16.6%of SNPs were existed within intergenic,exon and intron regions of the genome,respectively.In our study,transition substitutions were significantly found higher than transversion substitutions.Furthermore,the GBS data were imputed and optimized for the construction of 2612 SNPLDB markers,based on the linkage disequilibrium informations.The constructed SNPLDBs were distributed all over the 12 chromosomes.The constructed SNPLDBs were recognized as markers and tested in association analysis with GCA effects of parents of hybrid rice for 11 yield-related traits.Our analysis proved that GBS is an efficient and costs effective sequencing method for discovery of genome-wide SNPs,to exploit the genetic diversity of closely related cultivars,and to provide valuable marker resources for conducting marker-trait association analysis.3.ASSOCIATION ANALYSIS BETWEEN CONSTRUCTED SNPLDBs AND GCA EFFECTSThe association analysis between 2612 constructed SNPLDBs and GCA effect values of 33 parental lines confirmed a total of 99 significant SNPLDBs of GCA of 11 yield-related traits.The identified associations were distributed all over the 12 chromosomes of rice.The number of associated SNPLBDs for each trait varied and showed both negative and positive GCA effects on parental traits.The phenotypic variations explained by the associated SNPLDBs were considerably high that ranged from 19.8%to 52.3%.We detected several positive GCA alleles at the associated loci of SNPLDBs.The superior GCA alleles for 11 yield-related traits were counted as 50 that were distributed throughout the parental genomes.Among the indica parents of hybrid rice,CMS Ⅱ-32A and restorer Hui 9368 possessed a maximum number of superior GCA alleles for most of the studied traits.Likewise,among the japonica parents of hybrid rice,CMS Qingkong A and restorer Yunhui 4 hao contained a maximum number of positive GCA alleles for the studied traits.Moreover,the genes lies within the interval regions of associated SNPLDBs revealed their biological functions in growth and metabolisms,biosynthetic,transport and cellular and in plant modification and development processes.Similarly,the molecular functions of these genes were involved in hydrolase,catalytic,transporter and protein binding activates.In conclusion,the genotyping of GCA with SNPLDBs increase the power and efficiency of association analysis for the discovery of beneficial alleles of GCA of rice traits.The insights of our study provide useful information’s for improving the heterotic values of parents of hybrid rice by pyramiding of identified GCA alleles into CMS or restorer parent(recurrent parents)for development elite hybrid rice cultivars.