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

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Abstract

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.

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Fig. 1

Source https://upload.wikimedia.org/wikipedia/commons/4/47/Mindanao_regions.PNG. as of March 2020

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Acknowledgements

We thank Department of Science and Technology—Accelerated Science and Technology Human Resource Development Program-National Science Consortium (DOST-ASTHRDP-NSC) and Department of Science and Technology—Philippine Council for Agriculture, Aquatic, and Natural Resources Research and Development (DOST-PCAARRD) for the financial support of this study. We would also like to thank Genetic Resources Division and Molecular Biotechnology Laboratory staffs of PhilRice-CES and Los Baños for their invaluable assistance. To Mr. Bernard O. Budot, for disease evaluation; and Ms. Gina Balleras for assistance in the insect pest’s data collection.

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  1. Institute of Crop Science, College of Agriculture and Food Science, University of the Philippines Los Baños (UPLB), 4031 College, Laguna, Philippines

    Mary Valerie G. Embate, Mark Ian C. Calayugan, Renerio P. Gentallan Jr., Pompe C. Sta Cruz, Jose E. Hernandez & Teresita H. Borromeo

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  1. Mary Valerie G. Embate
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Embate, M.V.G., Calayugan, M.I.C., Gentallan, R.P. et al. Genetic diversity of selected pigmented traditional rice (Oryza sativa L.) varieties from Mindanao, Philippines using agromorphological traits and simple sequence repeats markers. J. Crop Sci. Biotechnol. 24, 259–277 (2021). https://doi.org/10.1007/s12892-020-00075-0

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