Molecular diversity and its geographical distribution in core rice germplasm
2003
Xu, W.J. | Yu, S.B. | Singh, S. | Domingo, J. | Bhandari, H. | Lu, Y.F. | Vijayakumar, C.H.M. | Bagali, P. | Sarkarung, S. | Virmani, S.S. | Khush, G.S. | Li, Z.K.
In an effort to develop an international rice molecular breeding program, a large set of 193 rice genotypes from 19 different countries/regions was collected to form a core rice gene pool. To evaluate the genetic diversity of the gene pool and provide DNA polymorphism information for future gene/QTL mapping and marker-assisted breeding, a well-distributed anchor set of 101 simple sequence repeat (SSR) markers was used to genotype these lines. Considerable variation was found in all SSR marker loci, with an overall genetic diversity of 0.687 and an average of 6.2 alleles per SSR locus. SSR loci with prevalent alleles were scattered across the rice genome, except chromosomes 5 and 6. Cluster analysis of the 193 accessions based on the SSR data revealed four cultivar groups. Group I corresponded to the classical indica group, while group IV corresponded to the classical japonica group. Groups II and III represented a portion of the sample that consisted of some modern cultivars, diverse landraces, and traditional japonica varieties. Cultivars in group I (indica) showed the highest level of diversity at all levels. In particular, indica lines from China and India were apparently differentiated from each other, forming two separate subgroups.
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