International Journal of Pure & Applied Bioscience (IJPAB)
Year : 2016, Volume : 4, Issue : 1
First page : (28) Last page : (34)
Article doi: http://dx.doi.org/10.18782/2320-7051.2194
Genetic Diversity of Malaysian Rice Landraces Based on Single Nucleotide Polymorphism (SNP) Markers
Shahril Ab Razak1*, Siti Norhayati Ismail1, Azwan Jaafar1, Muhammad Fairuz Mohd Yusof1, Rahiniza Kamaruzaman2, Site Noorzuraini Abd Rahman3, Khairun Hisam Nasir1 and Norzihan Abdullah1
1Centre for Marker Discovery and Validation, Biotechnology and Nanotechnology Research Centre, MARDI Headquarters, 43400 Serdang, Selangor, Malaysia
2Rice Research Centre, MARDI Seberang Perai, 13200 Kepala Batas, Pulau Pinang
3MARDI Rice Gene Bank, MARDI Seberang Perai, 13200 Kepala Batas, Pulau Pinang
*Corresponding Author E-mail: shahrilf@mardi.gov.my
Received: 17.01.2016 | Revised: 26.01.2016 | Accepted: 04.02.2016
Abstract
A collection of 42 Malaysian rice cultivars which consists of 40 traditional rice varieties and two Malaysian elite varieties were genotyped using a set of 96 SNP markers to understand their diversity levels. Forty of the traditional rice cultivars originated from Peninsular Malaysia, Sabah and Sarawak. Out of 96 SNPs genotyped, only 67 SNPs were used for statistical analysis since the rest of the markers were either monomorphic or could not amplify most of the samples. The polymorphism information content (PIC) values ranged from 0.0232 to 0.3748 with an average of 0.1496. The gene diversity and heterozygosity values ranged from 0.0235 to 0.4997 and 0.0000 to 0.1429 with an average of 0.1703 and 0.0362, respectively. These low values of gene diversity and heterozygosity suggested low genetic diversity in the studied collections. The UPGMA dendogram showed the cultivar collections could be clustered into two major groups. The results were further supported by principal co-ordinate analysis (PCoA). The results from this study allow the characterization of germplasm collections which can aid in better genetic conservation management and selection of parental lines for breeding programs.
Key words: Oryza sativa L., SNP marker, Genetic diversity, Malaysian rice landraces
Full Text : PDF; Journal doi : http://dx.doi.org/10.18782
Cite this article: Razak, S.Ab., Ismail, S.N., Jaafar, A., Yusof, M.F., Kamaruzaman, R., Rahman, S.N.Ab., Nasir, K.H. and Abdullah, N., Genetic Diversity of Malaysian Rice Landraces Based on Single Nucleotide Polymorphism (SNP) Markers, Int. J. Pure App. Biosci. 4(1): 28-34 (2016). doi: http://dx.doi.org/10.18782/2320-7051.2194
