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Kanin J. Routson, Ann A. Reilley, Adam D. Henk and Gayle M. Volk

Many apple varieties commonly planted in the United States a century ago can no longer be found in today's orchards and nurseries. Abandoned farmsteads and historic orchards harbor considerable agrobiodiversity, but the extent and location of that diversity is poorly understood. We assessed the genetic diversity of 280 apple (Malus ×domestica Borkh.) trees growing in 43 historic farmstead and orchard sites in Arizona, Utah, and New Mexico using seven microsatellite markers. We compared the samples to 109 cultivars likely introduced into the southwest in the late 19th and early 20th centuries. Genetic analysis revealed 144 genotypes represented in the 280 field samples. We identified 34 of these 144 genotypes as cultivars brought to the region by Stark Brothers Nursery and by USDA agricultural experiment stations. One hundred twenty of the total samples (43%) had DNA fingerprints that suggested they were representative of these 34 cultivars. The remaining 160 samples—representing 110 genotypes—had unique fingerprints that did not match any of the fingerprinted cultivars. The results of this study confirm for the first time that a high diversity of historic apple genotypes remain in homestead orchards in the U.S. southwest. Future efforts targeting orchards in the southwest should focus on conservation for all unique genotypes as a means to sustain both cultural heritage and biological genetic diversity.

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Gayle M. Volk, Christopher M. Richards, Adam D. Henk, Ann A. Reilley, Nahla V. Bassil and Joseph D. Postman

Edible european pears (Pyrus communis L. ssp. communis) are derived from wild relatives native to the Caucasus Mountain region and eastern Europe. Microsatellite markers (13 loci) were used to determine the relationships among 145 wild and cultivated individuals of P. communis maintained in the National Plant Germplasm System (NPGS). A Bayesian clustering method grouped the individual pear genotypes into 12 clusters. Pyrus communis ssp. caucasica (Fed.) Browicz, native to the Caucasus Mountains of Russia, Crimea, and Armenia, can be genetically differentiated from P. communis ssp. pyraster L. native to eastern European countries. The domesticated pears cluster closely together and are most closely related to a group of genotypes that are intermediate to the P. communis ssp. pyraster and the P. communis ssp. caucasica groups. Based on the high number of unique alleles and heterozygosity in each of the 12 clusters, we conclude that genetic diversity of wild P. communis is not fully represented at the NPGS. Additional diversity may be present in seed accessions stored in the NPGS and more pear diversity could be captured through supplementary collection trips to eastern Europe, the Caucasus Mountains, and the surrounding countries.

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Gayle M. Volk, Christopher M. Richards, Ann A. Reilley, Adam D. Henk, Philip L. Forsline and Herb S. Aldwinckle

Seeds and scionwood of Malus sieversii Lebed. have been collected from wild populations of apple trees in Kazakhstan. Seedlings and grafted trees were planted in the orchards at the U.S. Dept. of Agriculture Plant Genetic Resources Unit in Geneva, N.Y. We developed core collections to capture the genetic and phenotypic diversity represented in the trees from each of two of the Kazakhstan collection sites. These core collections capture more than 90% of the genetic diversity of the original populations, as determined using seven unlinked simple sequence repeat markers and 19 quantitative traits. Since phenotypic evaluations of these materials have been completed, the 35 trees within each population will be used as parents in crosses so that the genetic diversity in the orchard populations can be captured as seed for long-term ex situ conservation. This strategy of storing seeds, rather than maintaining costly field collections, could be applied to other collections of wild plant materials in the National Plant Germplasm System.

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Gayle M. Volk, Christopher M. Richards, Adam D. Henk, Ann A. Reilley, Patrick A. Reeves, Philip L. Forsline and Herb S. Aldwinckle

Seeds from wild Malus orientalis trees were collected during explorations to Armenia (2001, 2002), Georgia (2004), Turkey (1999), and Russia (1998). Seedling orchards with between eight and 171 individuals from each collection location were established at the U.S. Department of Agriculture–Agricultural Research Service Plant Genetic Resources Unit (PGRU) in Geneva, NY. Genotypic (seven microsatellite markers) and disease resistance data were collected for the 776 M. orientalis trees. The genetic diversity of the 280 individuals from Armenia and Georgia was compared with data previously published for the M. orientalis individuals from Russia and Turkey. A total of 106 alleles were identified in the trees from Georgia and Armenia and the average gene diversity ranged from 0.47 to 0.85 per locus. The genetic differentiation among sampling locations was greater than that found between the two countries. Six individuals from Armenia exhibited resistance to fire blight (Erwinia amylovora), apple scab (Venturia inaequalis), and cedar apple rust (Gymnosporangium juniperi-virginianae). The allelic richness across all loci in the individuals from Armenia and Georgia was statistically the same as that across all loci in the individuals from Russia and Turkey. A core set of 27 trees was selected to capture 93% of the alleles represented by the entire PGRU collection of 776 M. orientalis trees. This core set representing all four countries was selected based on genotypic data using a modified maximization algorithm. The trees selected for the M. orientalis core collection will be added to the main field collection at the PGRU.

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Christopher M. Richards, Gayle M. Volk, Patrick A. Reeves, Ann A. Reilley, Adam D. Henk, Philip L. Forsline and Herb S. Aldwinckle

We estimate the minimum core size necessary to maximally represent a portion of the U.S. Department of Agriculture's National Plant Germplasm System apple (Malus) collection. We have identified a subset of Malus sieversii individuals that complements the previously published core subsets for two collection sites within Kazakhstan. We compared the size and composition of this complementary subset with a core set composed without restrictions. Because the genetic structure of this species has been previously determined, we were able to identify the origin of individuals within this core set with respect to their geographic location and genetic lineage. In addition, this core set is structured in a way that samples all of the major genetic lineages identified in this collection. The resulting panel of genotypes captures a broad range of phenotypic and molecular variation throughout Kazakhstan. These samples will provide a manageable entry point into the larger collection and will be critical in developing a long-term strategy for ex situ wild Malus conservation.

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Gayle M. Volk, Christopher M. Richards, Ann A. Reilley, Adam D. Henk, Patrick A. Reeves, Philip L. Forsline and Herb S. Aldwinckle

Genetic diversity and disease resistance are described for 496 seedlings from wild populations of Malus orientalis Uglitzh. collected in southern Russia and Turkey in 1998 and 1999. Eighty-five half-sib families were genotyped using seven microsatellite markers, and disease resistance was determined for apple scab (Venturia inaequalis Cooke), cedar apple rust (Gymnosporangium juniperi-virginianae Schwein), and fire blight (Erwinia amylovora Burrill). Individuals from the two Russian Caucasus collection locations were homogeneous compared with populations from the four Turkish collection locations. Within three of the Turkish collection locations, some half-sib families were highly diverse and several of these families had unusually high levels of disease resistance. In all, twenty individuals exhibited resistance to all three diseases. Bayesian analyses of the population structure revealed six distinct clusters. Most of the individuals segregated into two clusters, one containing individuals primarily from southern Russia and the other containing individuals from both Russia and northern Turkey. Individuals in the four small clusters were specific to Turkish collection locations. These data suggest wild populations of M. orientalis from regions around the Black Sea are genetically distinguishable and show high levels of diversity.