Unraveling the cryptic genetic variation and population structure of the citrus genotypes with unknown origin

The high diversity of Citrus genotypes can increase the probability of identifying new genetic makeups and even desirable traits. Hence, 76 genotypes with unknown origin and 34 known cultivars from several Citrus species were analyzed by SSR and AFLP markers. Overall, 326 alleles and 545 polymorphic bands were respectively scored for 28 SSR loci and 25 AFLP primer-enzyme combinations. The results of various analyses accomplished with SSR markers were in agreement with AFLP. Accordingly, the true species of citron, mandarin, and pummelo were nested into separate groups. In the studied germplasm, we succeeded in tracking three cryptic origin genomes (2 in SSR and 1 in AFLP analysis) which were distinct from 3 true species, and, interestingly, they contributed to the genetic composition of some control cultivars. The results suggested that the interspecific hybridization and genetic introgression were the main determinants of the Citrus genotypes genetic composition. Hereupon, the share of citron in 36%, mandarin in 34%, and pummelo in 22% of selected accessions estimated more than 50%. Despite the controversy about the origin of lemon and sour orange, the results of different grouping methods suggested that lemon had more affinity with lime, and the genetic contribution of mandarin in sour orange was stronger than that of pummelo. nema