Genetic diversity and population structure of hybrid parent lines

The information on genetic diversity and relationships of parent lines is very important in hybrid rice development because it will expedite the parental selection and formation of heterotic groups. This study aimed to characterize and analyze the diversity and population structure of maintainer and restorer lines of tropical rice hybrids developed from Philippine Rice Research Institute and International Rice Research Institute. Out of 384 rice oligonucleotide pooled assay (OPA 3.1) set of SNP markers, 344 polymorphic markers across the 12 rice chromosomes were used to genotype the 29 maintainer and 124 restorer lines. The allele frequency, polymorphic information content (PIC), heterozygosity and gene diversity were determined using Power marker 3.25 software. Values of PIC of polymorphic markers ranged from 0.0065-0.5576 with an average value of 0.0974 whereas gene diversity varied from 0.0065-0.6349, with mean value of 0.1049. The average heterozygosity is 0.102 and the average allele frequency is 0.9358. Marker-based genetic relatedness was calculated using SPAGeDi 1.3, where a high mean kinship value of 0.84 was obtained. The results using STRUCTURE 2.3 Bayesin model-based software revealed two groups defining maintainer and restorer lines indicating a clear differentiation between-these lines in our breeding program. At k=4 (k=no. subpopulations), 42 restorer lines form a distinct groups, while the rest of the lines mixed with maintainer lines. At k=5, the 10 maintainer lines and 44 restorer lines form a distinct individual groupings. As observed, at both k the remaining restorer and maintainer lines have combined and grouped together which might be the result of shared ancestry during the development of maintainer and restorer lines. This information is very useful in exploitation of hybrid parent lines and in breeding heterotic hybrids which is highly correlated to high yielding parent lines.