Genetic diversity of released Malaysian rice varieties based on single nucleotide polymorphism markers

Understanding of genetic diversity is a main key for crop improvement and genetic resource management. In this study, we aim to evaluate the genetic diversity of released Malaysian rice varieties using single nucleotide polymorphism (SNP) markers. A total of 46 released Malaysian rice varieties were genotyped using 1536 SNP markers to evaluate their diversity. Out of 1536 SNPs, only 932 SNPs (60.7%) represented high quality alleles, whereas the remainder either failed to amplify or had low call rates across the samples. Analysis of the 932 SNPs revealed that a total of 16 SNPs were monomorphic. The analysis of SNPs per chromosome revealed that the average of polymorphic information content (PIC) value ranged from 0.173 for chromosome 12 to 0.259 for chromosome 11, with an average of 0.213 per locus. Genetic analysis of the 46 released Malaysian rice varieties using an unweighted pair group method with arithmetic mean (UPGMA) dendrogram revealed the presence of two major groups.  The analysis was supported by the finding from the STRUCTURE analysis which indicated the ∆K value to be at the highest peak at K = 2,followed by K = 4. The pairwise genetic distance of shared alleles showed that the value ranged from 0.000 (MR159↔MR167) to 0.723 (MRIA↔Setanjung), which suggested that MR159 and MR167 were identical, and that the highest dissimilarity detected between MRIA 1 and Setanjung. The results of the study will be very useful for variety identification, proper management and conservation of the genetic resources, and exploitation and utilization in future breeding programs.

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