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Evaluation of genetic variation and population structure between wilds and cultivars is important for understanding their origin and distribution, domestication, and genetic relationship. In this research, sixty-one papayas from eight wild populations and 52 additional samples from three cultivars in Thailand were studied using six polymorphic microsatellite loci. Higher genetic variation was observed in the wilds, especially from the South (mean number of alleles (Na) = 2.333 to 2.833; mean observed heterozygosity (HO) = 0.194 to 0.267; mean expected heterozygosity (HE) = 0.481 to 0.526). This suggests that papayas from the southern part of Thailand could be a potential source population of the other local populations. Conversely, the cultivars have been maintained and selected over a long term. There were low levels of genetic variation (Na = 1.167 to 1.500; HO = 0.081 to 0.167; HE = 0.086 to 0.183) with no private alleles. Cross-fertilisation was indirectly detected in both wilds and cultivars, possibly leading to retaining some polymorphisms. Lastly, genetic clustering of wilds and cultivars (K = 2) was identified; however, approximately 22.95% of wild samples (14 out of 61) were genetically admixed (0.100 ≤ Qwilds ≤ 0.900) and 8.20% (five out of 61) belonged to the cultivar cluster (Qcultivars > 0.900). This suggests that feral papayas could survive in a natural environment.
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