Abstract
Cauliflower (Brassica oleracea var. botrytis) is an important vegetable crop for human nutrition. We characterized 192 cauliflower accessions from the USDA and IPK genebanks with genotyping by sequencing (GBS). They originated from 26 different countries and represent about 44% of all cauliflower accessions in both genebanks. The analysis of genetic diversity revealed that accessions formed two major groups that represented the two genebanks and were not related to the country of origin. This differentiation was robust with respect to the analysis methods that included principal component analysis, ADMIXTURE and neighbor-joining trees. Genetic diversity was higher in the USDA collection and significant phenotypic differences between the two genebanks were found in three out of six traits investigated. GBS data have a high proportion of missing data, but we observed that the exclusion of single nucleotide polymorphisms (SNPs) with missing data or the imputation of missing SNP alleles produced very similar results. The results indicate that the composition and type of accessions have a strong effect on the structure of genetic diversity of ex situ collections, although regeneration procedures and local adaptation to regeneration conditions may also contribute to a divergence. Fst-based outlier tests of genetic differentiation identified only a small proportion (<1%) of SNPs that are highly differentiated between the two genebanks, which indicates that selection during seed regeneration is not a major cause of differentiation between genebanks. Seed regeneration procedures of both genebanks do not result in different levels of genetic drift and loss of genetic variation. We therefore conclude that the composition and type of accessions mainly influence the level of genetic diversity and explain the strong genetic differentiation between the two ex situ collections. In summary, GBS is a useful method for characterizing genetic diversity in cauliflower genebank material and our results suggest that it may be useful to incorporate routine genotyping into accession management and seed regeneration to monitor the diversity present in ex situ collections and to reduce the loss of genetic diversity during seed regeneration.
Highlights
The extent and type of genetic variation present in the germplasm of a crop is an important component of efficient breeding programs, because it provides useful information for the broadening of breeding pools, the utilization of heterosis and the selection of parental lines
Our study outlined the usefulness of genotyping by sequencing (GBS) to characterize the genetic diversity of genebank accessions of a minor crop like cauliflower
The low cost of GBS and low-coverage genome sequencing suggest that a lack of passport information can be substituted by high-resolution genotyping and suitable analysis methods to characterize the diversity of germplasm from different sources
Summary
The extent and type of genetic variation present in the germplasm of a crop is an important component of efficient breeding programs, because it provides useful information for the broadening of breeding pools, the utilization of heterosis and the selection of parental lines This information helps breeders to narrow the search for new alleles at loci of interest and assists in the identification of markers linked to desirable traits for introgression into new varieties [1]. PGR often experience a loss of genetic diversity, stronger inbreeding depression (especially in outcrossing crops) and accumulation of deleterious alleles because of small population sizes of individual genebank accessions These processes may negatively affect the success of ex situ conservation after several regeneration cycles [4, 5]. Strong selection caused by adaptation to the seed regeneration environment may further reduce genetic variation
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