Understanding genetic diversity is a main key for crop improvement and genetic resource management. In this study, we aim to evaluate the genetic diversity of the 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 the SNPs per chromosome revealed that the average of the 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. The 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 findings 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 the 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 was detected between MRIA 1 and Setanjung. The results of the study will be very useful for the variety identification, the proper management and conservation of the genetic resources, and the exploitation and utilisation in future breeding programmes.

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Genetic based information of different traits plays important role in varietal improvement of rice. Twenty rice accessions (Oryza sativa L.) obtained from National Rice Gene Bank were evaluated during main season 2015/2016 to estimate heritability, genetic variability and genetic advance for seven grain physical properties. Among the traits, milled grain length/width ratio, milled grain length, milled grain length after cooking and grain length exhibited high estimates of phenotypic coefficient of variation (PCV), and genotypic coefficient of variation (GCV). Highest broad sense heritability and genetic advance was obtained for grain length (98.66% and 62.25%), milled grain length (98.95% and 67.31%), milled grain length/width ratio (98.50% and 80.41%) and milled grain length after cooking (98.93% and 65.44%) which suggest these traits are most probably controlled by additive gene action and hence they can be fixed by selection. However, kernel elongation ratio showed lowest value of broad sense heritability and genetic advance (11.76% and 1.38%, respectively) and may suggest non-additive gene action in their inheritance and selection of this trait may difficult due to high environmental influences. Therefore, improvement of high quality rice with kernel elongation ability may require molecular marker application as it is highly affected by environment for precise selection.

The research was conducted at MARDI Seberang Perai research plot during main-season 2011/2012 and off-season 2012. Varieties such as MR 272, MR 278, MR 283 and MR 284 showed high yield potential as compared to the control varieties namely MR 211, MR 219, MR 253 and MR 263. According to correlation analysis, traits such as flag leaf width (r = 0.36, p = 0.01), percentage filled grain (r = 0.43, p = 0.002) and spikelets number/panicle (r = -0.43, p = 0.002) showed association toward yield potential. As a result, high rate of photosynthesis is depend to high leaf surface area. In addition, low number of spikelets /panicle can enhance the grain filling.

Genetic characterization refers to variation detection using genetic markers. In this study, 28 simple sequence repeat (SSR) markers were used to characterize five selected Sarawak rice cultivars, namely Bali1, Bali2, Bali3, Bubok, and Mamut. An analysis based on these 28 polymorphic SSR markers revealed that the number of alleles ranged from 2 (RM312, RM510, and RM536) to 9 (RM307) with an average of 3.86. The polymorphism information content (PIC) values ranged from 0.0175 (RM489) to 0.8174 (RM19) with an average of 0.5179. A dendogram constructed on the basis of the genetic similarity to Nei's 1983 genetic distance showed a high similarity between Bali2 and Bali3, which was further supported by a principal coordinate analysis (PCoA). The population structure analysis illustrated the log likelihood peaking at K = 2, indicating that the entire population could be divided into two distinct groups. To develop an SSR fingerprinting panel, 10 SSR markers were selected on the basis of a high PIC value. As this panel provides a better discrimination power in cultivar identification, it could be an efficient and effective tool in cultivar identification, particularly for these selected Sarawak varieties, thus helping breeders to protect their intellectual property rights (IPR). Moreover, the markers could be used to evaluate the seed purity of the selected rice cultivars.