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

• DOI: 10.1111/tpj.15908
• Publication Date: 2022-07-14T17:58:22Z
• Authors: 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
• Keywords: Linkage Disequilibrium; Germ plasm; Nucleotide diversity; Hordeum

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