Molecular diversity in the primary and secondary gene pools of genus Oryza

The objective of the present investigation was to assess the genetic relationships among the species of Oryza that belong to the primary gene pool (sativa complex) and the secondary gene pool (officinalis complex) using three marker systems such as RAPDs, ISSRs and SSRs. A total of 432 clear and reproducible bands were amplified from 18 RAPD primers; 113 bands were detected from 8 ISSR primers and 78 alleles were found to be amplified across the Oryza species from 13 SSR primer pairs. All the three dendrograms constructed, using UPGMA from the genetic similarity matrices based on the three marker data sets, were similar in their groupings. In all the three trees, two accessions of Oryza sativa formed an exclusive group indicating its genomic differentiation from its wild ancestors through the process of domestication. Distinctness between the wild species of the sativa and officinalis complexes was evident in all the trees derived from different markers. The groupings obtained among the species of the sativa complex were in perfect concordance with the species relationships established through classical crossability and cytogenetic analysis. This study has brought out some information on the species relationship between the diploid and tetraploid genomes of the officinalis complex possessing BB, CC and DD genomes. The higher level of similarity observed between the species possessing C and D genomes supports the view of many earlier authors that these two genomes might have originated from a single hybridization event. The results of this study also show that the diploid species possessing C genomes such as Oryza officinalis, Oryza rhizomatis and Oryza eichingeri are distinct from their allotetraploid counterparts possessing BBCC and CCDD genomes indicating a wider genomic differentiation in their evolutionary process.