Warren F. Lamboy

Microsatellite (SSR) markers reveal genetic identities, genetic diversity and relationships in a Malus×domestica borkh. core subset collection

Abstract A collection of 66 Malus×domestica Borkh. accessions from the USDA-ARS Plant Genetic Resources Unit’s core collection was screened with a set of eight SSR (simple sequence repeat) primers developed at the PGRU in order to determine genetic identities, estimate genetic diversity, and to identify genetic relationships among these accessions. All eight primer pairs generated multiple fragments when used in amplification reactions with DNA from these accessions. High levels of variation were detected with a mean of 12.1 alleles per locus and a mean heterozygosity across all eight loci of 0.693. The eight primer pairs utilized in this study unambiguously differentiated all but seven pairs of accessions in this collection of 66 M.×domestica Borkh. genotypes. The probability of matching any two genotypes at all eight loci in this study was approximately 1 in 1 billion. The markers detected two misnamed accessions in the collection. Genetic-identity data produced a genetic-relatedness phenogram which was concordant with geographic origins and/or known pedigree information. These SSR markers show great promise as tools for managing Malus ex situ germplasm collections as well as for collection and preservation strategies concerning wild Malus populations in situ.

Microsatellite (SSR) variation in a collection of Malus (apple) species and hybrids

A collection of 142 accessions of 23 Malus species, derived hybrids and cultivar accessions from the USDA-ARS Plant Genetic Resources Units core collection, which represents an extensive range of Malus species, was screened with a set of previously described SSR (simple sequence repeat) markers. The markers were used to determine genetic identities, estimate genetic diversity, identify genetic relationships among the accessions, and determine the utility of SSR primers developed from Malus ×domestica for making genetic assessments across the whole Malus genus. All eight primer pairs amplified multiple fragments when used in polymerase chain reactions with DNA from these accessions. High levels of variation were detected with a mean of 26.4 alleles per locus and a mean direct count heterozygosity across all eight loci equal to 0.623. The eight primer pairs used in this study unambiguously differentiated all but five pairs of accessions in this collection of 142 accessions of 23 Malus species, derived hybrids and cultivars. These SSR data were not useful in identifying genetic relationships among this diverse collection of accessions, with the majority of the accessions not clustering in ways concordant with taxonomic information and/or geographic origin. The resulting phenogram resolved only two meaningful clusters, for the taxonomically isolated Section Chloromeles and for M. fusca accessions, reflecting genetic relationships arising from geographic origin. The detection of identical accessions in the collection, which were previously considered to be unique, highlights the critical need to further bolster collections of certain Malus species.

Application of isozyme data to the management of the United States national Brassica oleracea L. genetic resources collection

SummaryManagement of a genetic resources collection is more effective if a curator can accurately identify genotypes and accessions as well as assess intraspecific genetic relationships and the genetic structure of species. Consequently, a study was conducted to determine whether data from starch gel electrophoresis of a specific set of isozymes from plants of Brassica oleracea (cole crops) would be useful in answering four questions the answers to which are essential for effective curatorial activities: Can individual plants be identified? Can specific accessions be identified? What are the genetic relationships among botanical varieties within B. oleracea? What is the genetic structure of the species B. oleracea? Six loci from 4 enzyme systems (LAP, PGD, PGI, and PGM) were analyzed. Individuals and accessions could not usefully be identified using these isozymes, but genetic relationships within and genetic structure of the species were easily determined, resulting in specific recommendations for improving collection management. As expected, highly selected commercial lines exhibited less diversity than average, and so may be of limited value when trying to maximize diversity with a minimum number of accessions. In contrast, landraces and weakly selected lines are more diverse than average, and thus are useful in maximizing per accession diversity. Not only was 93% of the genetic variability in B. oleracea found among accessions and a mere 7% among varieties, but also a cluster analysis showed that accessions of a single botanical variety are often more similar to those of a different variety than to each other. These results suggest that in order to create a genetic resources collection of B. oleracea that faithfully represents the diversity in the species, a curator should assemble a broad array of accessions originating from diverse agroecological niches, having different levels of improvement, and representing all botanical varieties.