Identification of interspecific hybrids among domesticated apple and its wild relatives

Authors: Gross, Briana; Henk, Adam; Forsline, Philip; Richards, Christopher; Volk, Gayle

Submitted to: Tree Genetics and Genomes
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 4/10/2012
Publication Date: 12/1/2012
Citation: Gross, B.L., Henk, A.D., Forsline, P.L., Richards, C.M., Volk, G.M. 2012. Identification of interspecific hybrids among domesticated apple and its wild relatives. Tree Genetics and Genomes. 8(6):1223-1235. DOI: 10.1007/s11295-012-0509-4.

Interpretive Summary: Problem: Potential interspecific hybrids are identified in natural populations by their proximity to two interbreeding species or their intermediate phenotypes. Hybridization can then be confirmed by comparing molecular markers in putative hybrids to the genetic makeup of pure species. Identifying interspecific hybrids in ex situ collections is more difficult because we often lack species-specific phenotypic data and fine-scale geographic information that would normally indicate the presence of a possible hybrid individual. Instead, we must rely purely on molecular data. Accomplishment: This manuscript describes the detection of interspecific hybrids among domesticated apple and three of its close wild relatives using over 400 accessions genotyped at 19 molecular markers. We show that while most samples of domesticated apple are correctly labeled as pure species, over 10% of each of the wild species are either mislabeled or the result of interspecific hybridization. For many of these hybrid individuals, there is little phenotypic or other information available that would have indicated their hybrid status. Impact: This work demonstrates the effectiveness of molecular markers for detecting hybrid or mislabeled individuals in large collections, even when phenotypic or fine-scale geographic information is unavailable. The information will be useful for apple breeding efforts, where choosing the wrong species in a breeding program can have negative consequences. In addition, some hybrids were identified in samples that were field collected, so the results suggest that gene flow between domesticated and wild apple may be occurring in the wild – this finding is important for conservation planning.

Technical Abstract: Potential interspecific hybrids are usually identified in natural populations by their proximity to interbreeding species or their intermediate phenotypes; hybridization can then be confirmed by comparing the genetic make-up of putative hybrids to pure species. In contrast, detecting interspecific hybridization and misclassifications in ex situ collections can be difficult because fine-scale geographic locations and species-specific phenotypic data are generally unavailable. Thus, there is little a priori information available to suggest which individuals might be hybrids. Instead, hybrids or misclassified individuals must be identified based on molecular data via population assignment and admixture detection programs. We have applied a variety of population assignment and admixture detection programs to over 400 samples of four closely related Malus species held in the USDA-ARS National Plant Germplasm System that were genotyped at 19 SSR loci. Our findings indicate that over 10% of the samples of the wild species M. sieversii and M. orientalis, and nearly 20% of the samples of the wild species M. sylvestris, may be admixed or misclassified. The percentage of admixed or misclassified samples of the domesticated species, M. × domestica, was much lower, at less than 5%. These findings have important implications for how to detect hybridization and misclassification in large collections using molecular data and, ultimately, how to maximize the utility of the collections. In addition, the presence of wild-collected samples that show admixture with domesticated apple suggests that gene flow may be occurring from the crop into natural populations of the wild species.