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

The distribution of recombination events along large cereal chromosomes is uneven and generally restricted to gene-rich telomeric ends. In order to understand how the lack of recombination affects diversity in the large pericentromeric regions, we assembled and analysed deep exome capture data from a panel of 879 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 to wild barley. We observed a mixture of completely and partially differentiated SNPs between domesticated and wild genepools, suggesting the former 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. While most cultivar chromosomes shared a single major pericentromeric haplotype, chromosome 7H clearly differentiated 2-row and 6-row types associated with different geographical origins. Within the pericentromeric regions we identified 22,387 non-synonymous SNPs, of which 92 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’. GO terms associated with the pericentromeric regions revealed housekeeping genes to be over-represented. Overall, our data reveal an unconventional pericentromeric genetic landscape among distinct barley gene pools with different evolutionary processes driving domestication and diversification.大型谷类作物染色体上的重组事件分布并不均匀，且通常局限于基因富集的端粒末端区域。为阐明重组缺失如何影响大型着丝粒旁区域（pericentromeric regions）的遗传多样性，我们对覆盖全球生态地理分布范围的879份栽培大麦、地方品种及野生大麦材料进行了深度外显子组捕获数据（exome capture data）的组装与分析。我们对着丝粒旁区域与非着丝粒旁区域的变异数据进行了定义与比较，观察到染色体内部、染色体间以及种质类群间的遗传多样性均存在显著分化格局。与野生大麦相比，栽培大麦与地方品种的着丝粒旁区域均呈现出显著降低的遗传多样性水平。我们在驯化大麦与野生大麦基因库间观察到完全分化与部分分化的单核苷酸多态性（Single Nucleotide Polymorphisms, SNPs）混合分布模式，表明栽培大麦起源于多个野生祖先类群。全基因组连锁不平衡（linkage disequilibrium）模式、单倍型块（haplotype block）的大小与数量，以及块内变异频率均在不同染色体之间，以及栽培大麦与野生大麦之间呈现出显著差异。尽管大多数栽培大麦染色体共享一个主要的着丝粒旁单倍型，但7号染色体（7H）可明显区分出与不同地理起源相关的二棱与六棱大麦类型。我们在着丝粒旁区域中共鉴定出22387个非同义单核苷酸多态性，其中92个在栽培大麦与野生大麦种质材料间存在固定的替代等位基因差异。令人意外的是，仅在栽培大麦中发现的29个SNPs被预测为‘高度有害’变异。与着丝粒旁区域相关的基因本体（Gene Ontology, GO）术语富集分析显示，持家基因（housekeeping genes）的占比显著偏高。总体而言，本研究的数据揭示了不同大麦基因库间存在非典型的着丝粒旁遗传格局，且驯化与多样化过程由不同的进化机制所驱动。