Analysis of bulked and redundant accessions of Brassica germplasm using assignment tests of microsatellite markers

Abstract

This study was conducted to determine if Brassica germplasm bulks created and maintained by the USDA-ARS North Central Plant Introduction Station (NCRPIS) were made with genetically indistinguishable component accessions and to examine newly identified putative duplicate accessions to determine if they can be bulked. Using ten microsatellite primer pairs, we genotyped two bulks of B. rapa L. ssp. dichotoma (Roxb.) Hanelt comprising four accessions and three bulks of B. rapa L. ssp. trilocularis (Roxb.) Hanelt comprising fourteen accessions, as well as four pairs of putatively duplicate accessions of B.␣napus L. Assignment tests on ten individual plants per accession were conducted using a model-based clustering method to arrive at probabilities of likelihood of accession assignment. The assignment tests indicated that one of the two bulks of B. rapa ssp. dichotoma involves genetically heterogeneous accessions. It was observed in the B. rapassp. trilocularis bulks that the component accessions could be differentiated into groups, with misassignments observed most frequent within groups. In B. napus, only one of the four pairs of putative duplicates showed significant genetic differentiation. The other three pairs of putative duplicates lack differences and support the creation of bulks. The results of the assignment tests were in agreement with cluster analyses and tests of population differentiation. Implications of these results in terms of germplasm management include the maintenance and/or re-creation of someBrassica germplasm bulks by excluding those accessions identified as being unique in this study. Abstract This study was conducted to determine if Brassica germplasm bulks created and maintained by the USDA-ARS North Central Plant Introduction Station (NCRPIS) were made with genetically indistinguishable component accessions and to examine newly identified putative duplicate accessions to determine if they can be bulked. Using ten microsatellite primer pairs, we genotyped two bulks of B. rapa L. ssp. dichotoma (Roxb.) Hanelt comprising four accessions and three bulks of B. rapa L. ssp. trilocularis (Roxb.) Hanelt comprising fourteen accessions, as well as four pairs of putatively duplicate accessions of B. napus L. Assignment tests on ten individual plants per accession were conducted using a model-based clustering method to arrive at probabilities of likelihood of accession assignment. The assignment tests indicated that one of the two bulks of B. rapa ssp. dichotoma involves genetically heterogeneous accessions. It was observed in the B. rapa ssp. trilocularis bulks that the component accessions could be differentiated into groups, with misassignments observed most frequent within groups. In B. napus, only one of the four pairs of putative duplicates showed significant genetic differentiation. The other three pairs of putative duplicates lack differences and support the creation of bulks. The results of the assignment tests were in agreement with cluster analyses and tests of population differen...

Development of DArT Marker Platforms and Genetic Diversity Assessment of the U.S. Collection of the New Oilseed Crop Lesquerella and Related Species

“…Molecular markers have been very useful in efforts to accurately identify gaps and redundancy within and among individual germplasm collections and have helped resolve important genebank management issues [10], [11], [12]. Examples of markers used in specific Brassicaceae collections include microsatellites for examining diversity in B. napus [13], [14], [15], lesquerella [16] and wild relatives such as Capsella , Crambe and Sinapis [17]; AFLPs in B. oleracea [18] and Lepidium [19]; and RAPD markers in Raphanus [20].…”

Duplication assessments inBrassicavegetable accessions

“…(2009) proposed a strategy to structure genebank collections to avoid under- and over-representation of accessions within each of its different components, building on the concept of core collection, to facilitate a relevant collection for users. In cases with extensive overlap in diversity, duplicates could be removed or bulked (Van Hintum et al ., 2002; Cruz et al ., 2006). In our case, most putative duplicate accessions are maintained by different genebanks and bulking is not an option, but only one of three similar accessions might be selected to become part of the European Collection.…”

“…users. In cases with extensive overlap in diversity, duplicates could be removed or bulked (Van Hintum et al, 2002;Cruz et al, 2006). In our case, most putative duplicate accessions are maintained by different genebanks and bulking is not an option, but only one of three similar accessions might be selected to become part of the European Collection.…”

Optimization of the composition of crop collections for ex situ conservation

“…In addition to removing and adding accessions to collections, optimization may also be achieved by combining accessions with extensive overlap in genetic diversity (Sackville Hamilton et al , 2002; van Hintum et al , 2002). The development of guidelines is needed for the bulking of accessions based on phenotypic and molecular marker data (van Treuren et al , 2001; Cruz et al , 2006), and considering effects of regeneration on the genetic constitution of accessions (van Hintum et al , 2007).…”