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Comparative analysis of genetic diversity and differentiation of cauliflower (Brassica oleracea var. botrytis) accessions from two ex situ genebanks

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  • Eltohamy A A Yousef
  • Thomas Müller
  • Andreas Börner
  • Karl J Schmid

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 (

Suggested Citation

  • Eltohamy A A Yousef & Thomas Müller & Andreas Börner & Karl J Schmid, 2018. "Comparative analysis of genetic diversity and differentiation of cauliflower (Brassica oleracea var. botrytis) accessions from two ex situ genebanks," PLOS ONE, Public Library of Science, vol. 13(2), pages 1-19, February.
    • Handle: RePEc:plo:pone00:0192062
    DOI: 10.1371/journal.pone.0192062
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    1. Agnieszka A. Golicz & Philipp E. Bayer & Guy C. Barker & Patrick P. Edger & HyeRan Kim & Paula A. Martinez & Chon Kit Kenneth Chan & Anita Severn-Ellis & W. Richard McCombie & Isobel A. P. Parkin & An, 2016. "The pangenome of an agronomically important crop plant Brassica oleracea," Nature Communications, Nature, vol. 7(1), pages 1-8, December.
    2. Dray, Stéphane & Dufour, Anne-Béatrice, 2007. "The ade4 Package: Implementing the Duality Diagram for Ecologists," Journal of Statistical Software, Foundation for Open Access Statistics, vol. 22(i04).
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