Identification of Conserved Orthologous Set Markers in Cultivated Vigna radiata (L.) Wilczek

Identification of Conserved Orthologous Set Markers in Cultivated Vigna radiata (L.) Wilczek

With an aim to develop widely applicable conserved gene markers to identify and tag orthologous genes from related Vigna species to reveal phylogenetic relationships and the nature of genes conserved in genus Vigna across the evolution, low copy nuclear Conserved Ortholog Set (COS) genes were tested to explore the interspecific genetic relationship of Vigna radiata (L.) Wilczek with other species such as V. mungo (L.), V. umbellata Thunb., V. angularis Wild and V. unguiculata (L.) Walp. To detect COS regions, computational approach was followed utilizing the available expressed sequence tags (EST) database of Vigna radiata and its related species. The ESTs were processed to eliminate sequence repeats, contaminants and low-complexity sequences. Upon alignment with Soybean genome, only high quality ESTs were grouped into clusters from which consensus sequences representing putative genes are generated for each Vigna species. From 6443 ESTs, 2550 contigs were acquired to develop 230 primer pairs to amplify conserved orthologous sequences across Vigna species. Among 14 primer pairs used for validation with genotypes of V. radiata, 3 gave double bands (paralogs) and 9 produced single bands indicating single copy orthologs. This infers that DNA sequences identified by this comparative genomics approach would be of great use in analyzing genomic information of related, unexplored crop genomes to augment gene discovery and plant breeding in other legumes.