Genetic diversity and heterotic grouping of Philippine inbred rice germplasm: implications to Philippine hybrid rice breeding

The available genetic variation in the breeders pool and an efficient selection strategy for germplasm are considered as major factors for success in hybrid rice breeding. Understanding the genetic structure and diversity in the gene pools with which breeders work is critical for the choice of parents, construction of heterotic groups and, thus, for the development of hybrids. In this study, genetic diversity of 182 PhilRice inbred lines were assessed using single nucleotide polymorphism (SNP) markers and results were merged to IRRI hybrid parental germplasm SNP analysis for the purpose of developing heterotic groups. Results showed that Philippine inbred lines have low diversity as indicated by different diversity indexes used. Mean gene diversity across the markers used was 0.21 while average genetic distance between pairs of the Philrice inbred rice was 0.19. On the other hand, average polymorphism information content was 0.17 and mean heterozygosity was likewise very low at 0.02. Model-based structure analysis assigned the inbred lines into five groups where PhilRice inbred lines grouped together. Likewise, only 26% of the PhilRice lines belonged to any of the conferred five-model based group at 0.8 membership probability further indicating high similarity of the genetic background and shared ancestries among the breeding lines at PhilRice. In order to determine the possible contribution of the genetic diversity of Philippine inbred lines in hybrid rice breeding, SNP data of the 182 PhilRice inbred lines and the 372 hybrid parental germplasm of the International Rice Research Institute (IRRI) was merged. Results showed that merging the two groups of lines increased genetic diversity. Mean genetic distance obtained likewise increased from 0.19 for the PhilRice lines to 0.31 for the merged PhilRice and IRRI lines. The STRUCTURE analysis performed for the combined PhilRice and IRRI lines generated five major groups, clustering together the lines according to line classification and breeding group that developed the lines. The grouping derived was used in choosing parents for the determination of heterotic groups among Philippine inbred and IRRI hybrid parental lines. From the groupings generated, 26 parents representing the identified groups were used for the combining ability test using the line x tester analysis. Twenty-six parents from PhilRice and IRRI hybrid lines, 135 derived hybrids, and a hybrid and an inbred check were evaluated in 5 environments. Results showed that hybrid yield, heterosis and combining ability were statistically significant among the parents and hybrids. Mean yield advantage of hybrids was 32%, 20% and 9% against the means of the parents, inbred check and hybrid check respectively. For this set of lines, three IRRI groups formed heterotic hybrids with the PhilRice inbred lines and four promising hybridization patterns were identified based on the marker grouping and the field testing done. The study confirmed that the grouping identified in the PhilRice and IRRI lines by SNP markers represents heterotic groups and is useful in selecting parents in hybrid rice breeding. Results likewise showed the high potential of the SNP markers used in grouping the germplasm materials. The information generated in the study will be useful in developing heterotic groups in the PhilRice germplasm and gives a guide on how to possibly attain high yield heterosis in Philippine hybrid rice varieties.