Molecular characterization of avocado germplasm with a new set of SSR and EST-SSR markers: genetic diversity, population structure, and identification of race-specific markers in a group of cultivated genotypes

Although molecular characterization of the avocado germplasm started with the early development of molecular markers, the genetic relationships among the three botanical races are still uncertain. Here, we report the development of 47 new microsatellites in avocado (Persea americana Mill) and the results of various genetic studies carefully designed to address the unsolved questions. Forty high-quality, single-locus markers (25 simple sequence repeats (SSRs) and 15 expressed sequence tag-SSRs (EST-SSRs)) were evaluated in a selected group of 42 cultivated accessions, which represent the three described botanical races. A total of 455 alleles (11.4 alleles per locus) have been detected. The mean expected and observed heterozygosities averaged 0.831 and 0.674, respectively. All the analyzed genotypes could be unequivocally distinguished with an accumulated probability of identity value of 6.36 x 10(-50). Seventy-five percent of the loci showed a significant departure from Hardy-Weinberg equilibrium, most likely due to the substructure of the accession set and kinship among some of the accessions. The genetic relationships among the accessions were explored using different methods. We demonstrate that the correct allocation of the avocado cultivars requires the complementary use of distance-based and model-based methods. All of the results agreed with the existence of three groups to which accessions were assigned based on their botanical race, with 25 % of the detected variation being partitioned among the groups. The diversity analysis within each group has allowed for the identification of unique alleles that are useful as race-specific markers. The effects of the different experimental parameters on the results are discussed.