Assessment of genetic diversity and relationships of upland rice accessions from southwest China using microsatellite markers

Upland rice (UR) is a unique rice ecotype that can be grown on upland fields without surface water accumulation in cultivation. Although UR has long been recognised as an important genetic resource for breeding of drought-tolerant rice varieties, it is facing the risk of genetic erosion due to the rapid spread of high-yielding modern rice strains. In this study, genetic diversity and relationships among 221 UR accessions collected from southwest China were evaluated using microsatellite (i.e. simple sequence repeat, SSR) markers. A total of 269 alleles were detected using 28 pairs of SSR primers, and the number of alleles per locus ranged from 2 to 20, with an average of 9.6. The polymorphism information content value, a measure of gene diversity, was 0.63 with a range of 0.25-0.89. Clustering analysis showed that all 236 accessions fell into two groups corresponding to indica and japonica. More than 75% of UR accessions were identified as japonica. We detected no clear relationship between genetic similarity and geographical distances, which may be partially due to the frequent seed exchange by local farmers. Our study revealed relatively high levels of genetic diversity in the Chinese UR germplasm, which could provide invaluable genetic resources for improving economically important traits in rice, such as tolerance to drought stress.