Assessment Of Genetic Diversity In Upland Rice Germplasm From Southwest China Using SSR Markers

Upland rice is a special ecotype of cultivated rice.The cultivation of upland rice in China has a long history and it is rich in natural resources, it distributes concentratedly in the four provinces (autonomous regions) of Yunnan, Guangxi, Guizhou and Hainan which have relative more minorities. Upland rice has the traits of strong drought resistance and less water demand, which is one of the best drought-resistant crops for implementing water-saving agriculture and dry farming. The genetic diversity in upland rice germplasm was mainly evaluated by SSR molecular markers in this paper, which would be of great theoretical significance and value in conservation, using, construction of core collection, and genetic breeding for upland rice. The main results were summarized as follows:1. Phenol reaction was applied to identify the subspecies of upland rice. The 221 upalnd rice accessions were divided into two subspecies of indica and japonica, in which 167 accessions were japonica, and 54 accessions were indica.2. 28 SSR markers were screened out from 50 SSR markers, and they were applied to study the genetic diversity of 221 upland rice and 15 lowland rice accessions. A total of 269 alleles were detected among 221 UR accessions (9.6 alleles / locus), the polymorphism information content (PIC) value ranged from 0.25 to 0.89, with the average of 0.63; 155 alleles were detected among the 15 lowland rice accessions, the average PIC value was also 0.63. According to the result of phenol reaction for upland rice, the average number of alleles detected in japonica (8.2) was larger than that of indica (7.4), while the average PIC value in indica (0.64) was much higer than that of japonica (0.49), with the significant at 0.01 level.This indicated the upland rice germplasm had a relative high level of genetic diversity, and the genetic diversity of indica upland rice was more exuberance than that of japonica one.3. The results from the genetic distance-based clustering revealed a clear divide of the 221 upland rice germplasm into indica and japonica groups, which was completely same with the result of phenol reaction. The upland rice germplasm selected from the same or adjacent geographical areas could no be clustered together very well. The result of PCA sustained that of NJ clustering. These results suggested that the protection of upland rice germplasm should break the geographic restriction.4. The analysis of molecular variance (AMOVA) showed that 68.6%and 31.4% of genetic variation was existed within subspecies and between subspecies respectively in upland rice germplasm, with significant at 0.01 level. The 28 SSRs had significant differentiation between upland rice subspecies, showing a strong specificity between indica and japonica, which could be used as classification markers for upland rice subspecies.5. Using the data of SSRs, a diverse subset of 50 accessions were screened out from the 221 upland rice, it embodied 90.3% alleles of the total sample, and the average PIC value reached 0.73, which could represent the genetic variety of the 221 upland rice, and it potentially could be used as candidate germplasm for constructing a core collection of upland rice in China.