Tree Genetics & Genomes

, Volume 8, Issue 6, pp 1223–1235

Identification of interspecific hybrids among domesticated apple and its wild relatives


  • Briana L. Gross
    • USDA-ARS National Center for Genetic Resources Preservation
  • Adam D. Henk
    • USDA-ARS National Center for Genetic Resources Preservation
  • Philip L. Forsline
    • USDA-ARS Plant Genetic Resources Unit
  • Christopher M. Richards
    • USDA-ARS National Center for Genetic Resources Preservation
    • USDA-ARS National Center for Genetic Resources Preservation
Original Paper

DOI: 10.1007/s11295-012-0509-4

Cite this article as:
Gross, B.L., Henk, A.D., Forsline, P.L. et al. Tree Genetics & Genomes (2012) 8: 1223. doi:10.1007/s11295-012-0509-4


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 makeup 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 US Department of Agriculture–Agricultural Research Service National Plant Germplasm System that were genotyped at 19 simple sequence repeat loci. Our findings indicate that over 10 % of the samples of the wild species Malus sieversii and Malus orientalis and nearly 20 % of the samples of the wild species Malus sylvestris may be admixed or misclassified. The percentage of admixed or misclassified samples of the domesticated species, Malus × domestica, was much lower, at <5 %. These findings provide an illustration of how to detect hybridization and misclassification in ex situ collections using molecular data and, ultimately, should help 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.


AdmixtureInterspecific hybridizationTree domesticationPerennial cropMalus × domesticaApple

Supplementary material

11295_2012_509_MOESM1_ESM.pdf (217 kb)
Online resource 1Species assignments and admixture analyses from all separate analyses. See color coding for key. The two columns at the end of the table (Admixed Overall; Admixed with Overall) correspond to the results in Table 2 (PDF 216 kb)
11295_2012_509_MOESM2_ESM.pdf (175 kb)
Online resource 2Primer names, sequences, observed size range and number of alleles, approximate annealing temperature, repeat type, map location, and reference for each SSR (PDF 174 kb)
11295_2012_509_MOESM3_ESM.pdf (598 kb)
Online resource 3Graphical representations of results from STRUCTURE, BAPS, FLOCK, and DARwin conducted on the full dataset and the dataset excluding known families. For STRUCTURE, BAPS, and FLOCK, species groups, analysis method and levels of K indicated are below each plot. Each bar (not delineated) represents a sample, and the colors represent the estimated membership in the genetic clusters identified by the programs. Species groups are delineated with black lines. There are three graphical representations of the STRUCTURE results for K = 4 without families; one shows the average of all 10 runs, one shows the average of six runs that converged on one solution and one shows the average of four runs that converged on alternate solution. For DARwin, each sample is represented as a terminal node in the neighbor-joining tree, and the samples are color-coded according to their original species designations in GRIN; clades of species are labeled with text. *K was set equal to four for the BAPS analyses, so the level of K was not estimated by the program (PDF 598 kb)
11295_2012_509_MOESM4_ESM.xls (274 kb)
Online resource 4Allele frequencies for each species and overall allele frequencies for all 19 SSR loci, calculated after the removal of all misclassified or admixed samples from the dataset. See color coding for key. Note that the total number of samples will differ for each locus due to missing data (XLS 274 kb)
11295_2012_509_MOESM5_ESM.pdf (3.9 mb)
Online resource 5All available photos of admixed or misclassified samples, as well as a representative sample of each species, labeled with PI number, cultivar name (if applicable), currently assigned species status, and species they are admixed with in parentheses (dom = M. × domestica, ori = M. orientalis, sie = M. sieversii, syl = M. sylvestris). Images are resized to roughly the same scale (1 cm grid is shown with dots in the background of each photo) (PDF 3986 kb)

Copyright information

© Springer-Verlag (outside the USA) 2012