Genetic Resources and Crop Evolution

, Volume 60, Issue 2, pp 543–568

Nuclear and chloroplast microsatellite markers to assess genetic diversity and evolution in hazelnut species, hybrids and cultivars

  • Nahla Bassil
  • Paolo Boccacci
  • Roberto Botta
  • Joseph Postman
  • Shawn Mehlenbacher
Research Article

DOI: 10.1007/s10722-012-9857-z

Cite this article as:
Bassil, N., Boccacci, P., Botta, R. et al. Genet Resour Crop Evol (2013) 60: 543. doi:10.1007/s10722-012-9857-z
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Abstract

The US Department of Agriculture, Agricultural Research Service, National Clonal Germplasm Repository in Corvallis, Oregon, preserves more than 800 accessions of hazelnut (Corylus), including C. avellana cultivars and representatives of 10 other recognized shrub and tree species. Characterization and study of genetic diversity in this collection require cross-transferable markers, such as trinucleotide microsatellite or simple sequence repeat (SSR) markers and universal chloroplast SSR markers. We developed new SSR markers and evaluated 114 Corylus accessions representing 11 species and 44 interspecific hybrids. Eight of 23 SSRs generated easy-to-score alleles in all species and seven were highly polymorphic. For those seven, the average heterozygosity was moderate at 0.49, and mean allele number, genetic diversity and polymorphism information index were high at 11.71, 0.79 and 0.76, respectively. The three most polymorphic SSRs were CaC-C008, CaC-C040 and CaC-C118. Neighbor-joining (NJ) clustering and structure analysis agreed with classical taxonomic analysis and supported inclusion of C. maxima within the large polymorphic species, C. avellana. Analysis also indicated that C. californica is a distinct species rather than a botanical variety of C. cornuta. Six universal cpSSRs were polymorphic in Corylus and generated 21 distinct chlorotypes with an average of 3 alleles per locus. Diversity at these cpSSRs was high and ranged from 0.33 to 0.64, with an average of 0.54. Incongruence in NJ topologies between the nuclear and chloroplast markers could be attributed to chloroplast capture related to hybridization during the ancestral diversification of the genus, or to homoplasy. The phylogeographical relationships among the 21 chlorotypes in the 11 Corylus species support Asia as a refugium where several hazelnut lineages survived during glaciation and from which they continued to evolve after dispersal from Asia through the Mediterranean to Europe, and across the Atlantic and/or the Bering land bridge to North America.

Keywords

CorylusFilbertSimple sequence repeat (SSR) markersUniversal chloroplast SSRs

Supplementary material

10722_2012_9857_MOESM1_ESM.xlsx (25 kb)
Supplementary Table 1. Amplification and polymorphism of twenty-three SSRs developed from a trinucleotide-enriched library (GAA) of hazelnut. Amplification success and polymorphism are indicated with a ‘+’ while failure and monomorphism are indicated by ‘-‘. ‘D’ refers to discarded primer pairs for that species due to poor amplification in tested representatives of that species. Also listed are the SSR motif, primer sequences, expected size, optimum annealing temperature, linkage group location, and citation where available. (XLSX 25 kb)

Copyright information

© Springer Science+Business Media B.V. (outside the USA) 2012

Authors and Affiliations

  • Nahla Bassil
    • 1
  • Paolo Boccacci
    • 2
  • Roberto Botta
    • 3
  • Joseph Postman
    • 1
  • Shawn Mehlenbacher
    • 4
  1. 1.United States Department of Agriculture (USDA)Agricultural Research Service (ARS), National Clonal Germplasm Repository (NCGR)CorvallisUSA
  2. 2.Plant Virology Institute, National Research Council (IVV-CNR), UOS of GrugliascoGrugliascoItaly
  3. 3.Dipartimento di Colture ArboreeUniversità degli Studi di TorinoGrugliascoItaly
  4. 4.Department of HorticultureOregon State UniversityCorvallisUSA