Development and transferability analysis of SSR primers in wild rice Zizania latifolia (Poaceae)

Zizania latifolia Turcz., also known as Manchurian wild rice, is a member of the tribe Oryzeae, and a major wild ecological and genetic resource. In this study, nuclear SSR primers were developed in silico based on part of the existing genome sequences of Z. latifolia. Five wild populations of the species from different regions across China were selected to screen 64 developed primers. Results showed that 15 primer pairs were polymorphic in at least one population. In addition, we identified a total of 84 alleles, with an average of 5.6 alleles per locus. For the different populations, the level of observed and expected heterozygosity ranged from 0.000 to 0.941 and 0.072 to 0.625, respectively. Relatively high genetic differentiation between populations (F_ST=0.432) was found, as evidenced by low levels of gene flow (N_m=0.576) among populations. These newly developed markers will facilitate further study of the level and pattern of genetic diversity, and the development of germplasm resource conservation strategies for natural extant Z. latifolia populations. In the cross-species transferability test, eight and nine of the 15 loci were successfully amplified in Oryza sativa L. and O. rufipogon Griff., respectively.