ARS | Publication request: Genetic diversity and population structure in Malus sieversii, a wild progenitor species of domesticated apple.

Submitted to: Tree Genetics and Genomes
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: August 26, 2008
Publication Date: N/A

Interpretive Summary: Dessert apples are believed to have been domesticated from Malus sieversii (Lebed) M. Roem. and several other wild apple species. The USDA has sponsored several collection trips to obtain seeds from M. sieversii trees within the forests of the Tien Shan mountains of Kazakhstan. Genetic analyses using microsatellite markers were performed to determine the diversity and differentiation of 949 seedlings originating from eight collection sites spanning over a thousand kilometers. Differentiation among the 88 half-sib families was more than three times greater than the differentiation among the eight collection sites. Overall, half-sib families of M. sieversii seedlings are very diverse. In addition, the 949 individuals were grouped into four genetically distinct clusters based on their genotypes. The southern sites had high representations of all four clusters, while the northern collection sites were primarily composed of individuals from one of the clusters. These data suggest that high levels of diversity are present in the southern sites. These results will be useful to plant explorers looking for additional sources of diversity in the wild M. sieversii populations.

Technical Abstract: Malus sieversii (Lebed.)M. Roem. is a wild progenitor species of the domesticated apple. It is found across a mountainous region of central Asia and has been the focus of several collection expeditions by the USDA. This study used SSR variation at seven loci to estimate diversity and differentiation within Malus sieversii using several complimentary approaches. Multi-locus genotypes were amplified from 949 individuals representing seedling trees from 88 half-sib families from eight M. sieversii populations collected in Kazakhstan. Apportioning of genetic variation was estimated at both the family and site level. Analyses using a hierarchical model to estimate Fst showed that differentiation among individual families is more than three times greater than differentiation among sites. In addition, average gene diversity and allelic richness varied significantly among sites. A rendering of a genetic network among all sites showed that differentiation is largely congruent with geographical location. In addition, non-hierarchical Bayesian assignment methods were used to infer genetic clusters across the collection area. We detected four genetic clusters in the data set. The quality of these assignments was evaluated over multiple MCMC runs using both posterior likelihood and stability of the assignments. The spatial pattern of genetic assignments among the eight collection sites shows two broadly distributed and two narrowly distributed clusters. These data indicate that the southwestern collection sites are more admixed and more diverse than the northern sites.