Molecular screening of Southeast Asian rice varieties for diversity and pre-breeding germplasm selection
2019
Rañeses, M.A.M. | Caguiat, X.G.I. | Ferrer, M.C. | Duldulao, M.D. | Alfonso, D.O. | Santiago, J.C. | Nombrere, J.M. | Castro, J.R. | Vilayheuang, K. | Kamaruzaman, R. | Lestari, P. | Sabran, M. | Mulya, K.
Rice is one of the most important food crops for human and genetic information of this germplasm is a prerequisite in crop breeding programs. The aim of the study was to assess the genetic diversity of 100 rice germplasms from Indonesia, Malaysia, Laos and Philippines through SSR and gene-specific SNP markers. A total of 22 SSR markers and ten SNP markers were used. The number of alleles per locus ranged from two to five, averaging 3.27. Polymorphic information content (PIC) values ranged from 0.18 (RM25934) of 0.71 (RM144) with an average of 0.44. Gene-specific include four biotic, one abiotic, two grain quality and three fertility restorer and cytoplasmic male sterility markers. Results showed that three were 40% resistant to blast, one against RTSV and no entries tolerant to submergence. Twenty and 43% of the entries possess allele for fragrance and chalkiness. Forty-four and 70 entries showed presence of restorer factor 2 and CMS alleles, respectively. The UPGMA cluster analysis showed that 100 varieties grouped into two major clusters A-II and B-VII while varieties from Indonesia and Laos are in clusters A-I, B-IV and B-VI and Malaysian rice varieties were grouped in cluster B-V. Highest similarity (0.97) was observed between 'Widas' (Indo20) and 'Inpari Blas' (Indo22). However, lowest similarity (0.25) was observed in Ria (Mal3) and Telurikan (IndoC2), Alaminos (Phil5) and Naia (Phil15), Ca-Ong white (Phil14) and Dicula (Mal4). The study showed variability of the 100-rice germplasm from selected countries of Southeast Asia that would be useful for varietal improvement. Genetic information at molecular level is suitable to identify, develop and acquire genetically unique germplasm that will benefit the plant breeders.
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