Phylogenetic analysis of eleven Malaysian rice cultivars using a chloroplastic DNA marker

Abstract

To date, both the morphological and molecular characteristics of Malaysian rice cultivars are not well documented resulting in difficulty to identify cultivars with specific origin or traits. Although some rice information are available, the information are mostly not systematically organized with limited accessibility. Thus in this work, a chloroplastic DNA (cpDNA) marker gene, the large subunit of ribulose- 1,5 - bisphosphate carboxylase (rbcL) gene were used to construct a phylogenetic tree of eleven Malaysian rice (Oryza sativa L.) cultivars. cpDNA is most commonly used in phylogenetic and barcoding study for plant species because of its high success rate in PCR amplification, appropiate length and a base substitution rate for inferring phylogeny at higher levels. The rbcL gene was amplified from genomic DNA of the 11 rice cultivars, cloned and sequenced. The sequences obtained was analyzed and aligned using software MEGA 6. Then, the phylogenetic analysis was constructed by using method Maximum Parsimony. The result revealed that rbcL gene of eleven Malaysian rice cultivars are ~1400 bp in size. Based on the tree constructed, the eleven Malaysian rice cultivars studied can be classified into two major clades. The first clade consists of MR 220 CL2, MR 219, Putih and Wai while MR 269, MR 263, MR 220, Merah Udang, Pulut Bukit, MR Q76 and Bukit Hitam falled into the second clade. Bootstrap support (BS) value in some of the branches were a bit low and these value is reflected by the small number of informative character (844 were conserved and 319 were potentially informative) to design the tree. The formation of several subclades in the tree is due to its similar genetic pattern and thus support the system classification. In overall, this study suggested that rbcL gene can serve as a good candidate gene to distinguish the phylogenetic relationship in Malaysian rice cultivars.