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Indian Journal of Pure & Applied Biosciences (IJPAB)
Year : 2016 , Volume 4, Issue 1
Page No. : 28-34
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: 23.10Received: 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.
Keywords: Oryza sativa L., SNP marker, Genetic diversity, Malaysian rice landraces
Full Text : PDF; Journal doi : http://dx.doi.org/10.18782/2320-7051.2194
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
