Molecular Phylogeny of Upland Rice (oryza Sativa L.) Varieties Based on Ribulose Carboxylase(rbcl) Barcoding Sequences

Breeding of high yielding and quality cultivars of rice (genus Oryza) relies on genetic resources from both cultivated and wild species which are collected and maintained in seed banks. Phylogenetic relationships were determined in the AA genome lineage which contains cultivated rice now found mainly in the Asiatic and African continents. The sequences of 2,463 bases of the rbcl gene of CpDNA was determined from three, upland rice varieties (FARO 56, 59 and 65). Phylogenetic trees determined by the neighbour joining method revealed that the three rice varieties are well defined by rbcl sequences and identified the species as Oryza sativa. The three species formed a monophyletic clade and it's monophyly is supported upto 100% in boostrap value. (This is in line with the reports of Ge et al., (1999) who noted a monophyly of each of the genome groups in Oryza species. The phylogeny also agrees with Wambugu et al. (2018) who opined that species with the O. sativa complex constitute the Oryza primary gene pool and is the most recently diverged being at the basal clade). The result showed that Pairwise divergence values were generally low; (0.000 - 0.0030). However, FARO 56 and 65 diverged more (0.0000) than FARO 59, (0.0030. (In line with Herbert et al, 2003). Divergences between conspecific individuals were always small as family values average around 0.25%. They may be a problem with lack of taxon density because we used small numbers of species as such using more species should be necessary to resolve further the phylogeny of Oryza species.