Genetic diversity of selected pigmented traditional rice (Oryza sativa L.) varieties from Mindanao, Philippines using agromorphological traits and simple sequence repeats markers

Philippine pigmented traditional rice varieties (TRVs) offer potential novel genes for genetic improvement. In this study, forty-three pigmented traditional rice varieties (TRVs) from Region X, XII and XIII in Mindanao were evaluated using 47 agromorphological (22 qualitative and 25 quantitative) traits, grain chemical properties, disease reaction, insect pests, and 64 SSR markers. The standardized Shannon–Weaver diversity index for phenotypic diversity averaged at 0.30 for qualitative and 0.88 for quantitative traits. Desirable traits observed in the TRVs include erect flag leaf, pubescent leaf blade, and strong culm for lodging resistance. Three TRVs, Malagkit (CollNo. 4555), Dinorado (CollNo. 11071), and Canayo (CollNo. 12794) showed resistance to blast. While Kabuyok (CollNo. 1091), Kabuyog (CollNo. 11052), Dinorado (CollNo. 12786), Lubang (Red) (CollNo. 4541), Manganahaw (CollNo. 4570), Palawenyo (CollNo. 6361), Boringan (CollNo. 4291), Mixture from Kabuyok (CollNo. 11070) and Mimis (CollNo. 1092) recorded intermediate resistance to whiteheads. Tapul (CollNo. 5156) was identified to have blast resistance with desirable grain chemical properties: intermediate amylose content, low gelatinization temperature and medium cooked rice. The PIC values revealed that RM26550, RM28166, RM10665, RM27492 and RM23251 could be the best markers for genetic diversity estimation of these TRVs. The diversity at gene level showed average of 3.48 alleles ranging from 2 to 11 per locus. Mean gene diversity (H) value for all SSR loci was at 0.34, indicates moderate genetic diversity of TRVs used in the study. These pigmented TRVs can be tapped for pests/diseases resistance, and grain quality research, direct utilization or as parents in specific breeding purposes.