The evolutionary patterns of barley pericentromeric chromosome regions, as shaped by linkage disequilibrium and domestication

Yun-Yu Chen, Miriam Schreiber, Micha M. Bayer, Ian K. Dawson, Peter E. Hedley, Li Lei, Alina Akhunova, Chaochih Liu, Kevin P. Smith, Justin C. Fay, Gary J. Muehlbauer, Brian J. Steffenson, Peter L. Morrell, Robbie Waugh, Joanne R. Russell (Lead / Corresponding author)

Research output: Contribution to journalArticlepeer-review

5 Citations (Scopus)
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The distribution of recombination events along large cereal chromosomes is uneven and is generally restricted to gene-rich telomeric ends. To understand how the lack of recombination affects diversity in the large pericentromeric regions, we analysed deep exome capture data from a final panel of 815 Hordeum vulgare (barley) cultivars, landraces and wild barleys, sampled from across their eco-geographical ranges. We defined and compared variant data across the pericentromeric and non-pericentromeric regions, observing a clear partitioning of diversity both within and between chromosomes and germplasm groups. Dramatically reduced diversity was found in the pericentromeres of both cultivars and landraces when compared with wild barley. We observed a mixture of completely and partially differentiated single-nucleotide polymorphisms (SNPs) between domesticated and wild gene pools, suggesting that domesticated gene pools were derived from multiple wild ancestors. Patterns of genome-wide linkage disequilibrium, haplotype block size and number, and variant frequency within blocks showed clear contrasts among individual chromosomes and between cultivars and wild barleys. Although most cultivar chromosomes shared a single major pericentromeric haplotype, chromosome 7H clearly differentiated the two-row and six-row types associated with different geographical origins. Within the pericentromeric regions we identified 22 387 non-synonymous SNPs, 92 of which were fixed for alternative alleles in cultivar versus wild accessions. Surprisingly, only 29 SNPs found exclusively in the cultivars were predicted to be ‘highly deleterious’. Overall, our data reveal an unconventional pericentromeric genetic landscape among distinct barley gene pools, with different evolutionary processes driving domestication and diversification.

Original languageEnglish
Pages (from-to)1580-1594
Number of pages15
JournalPlant Journal
Issue number6
Early online date14 Jul 2022
Publication statusPublished - Sept 2022


  • Hordeum vulgare
  • SNPs
  • diversity
  • domestication
  • evolution
  • pericentromeric regions

ASJC Scopus subject areas

  • Genetics
  • Plant Science
  • Cell Biology


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