Genetic Structure of Peach Breeding Germplasm from Embrapa, Brazil

Peach has great economic and social importance in Brazil. The Brazilian genetic resources of peach have diverse origins. This germplasm is composed mainly by local selections in the country and accessions selected from populations developed by the National breeding program, adapted to subtropical climate, with low chill requirement, as well as accessions introduced from several countries. Population structure studies provide additional tools for breeding and it is valuable information for genome-wide association studies (GWAS). In this research, we used 10 SSR markers, selected by their high level of polymorphism, to investigate the genetic structure of a set of 204 accessions from the peach breeding program of the Brazilian Agricultural Research Corporation - Embrapa. PCR products were separated by vertical electrophoresis on 6.5% polyacrylamide gel using 4300 DNA Analyzer LI-COR and Saga Generation 2 software for analysis of the amplified fragments. A total of 80 alleles were obtained, giving an average of eight alleles per locus. The 10 SSR markers were able to discriminate 198 accessions of the 204 target in this study, with an overall average genetic distance of 0.62 between accessions, ranging from 0.16 to 0.97. We analyzed the data by successively increasing the number of subpopulations (K) from 2 to 10. STRUCTURE analysis assigned 162 accessions splitted into two subpopulations based mainly on their fruit traits: melting and non-melting flesh varieties. The remaining accessions, 42, could not be assigned under the 80% membership coefficient criteria. CLUMPP alignment of 20 independent solutions for K = 2 showed a similarity of 99% indicating that the assignment of accessions to the subpopulation was well correlated among runs. Melting flesh subpopulation includes also nectarines and flat peaches. Non-melting flesh subpopulation includes peach and nectarines. The foundation clones clustered together with melting and non-melting flesh peaches, indicating that this germplasm is well represented in modern cultivars. This research is a first step to apply associative mapping studies aiming to implement marker-assisted selection. Potential application of these results in the development of new peach cultivars will be discussed.