The evolutionary patterns of barley pericentromeric chromosome regions, as shaped by linkage disequilibrium and domestication.
The evolutionary patterns of barley pericentromeric chromosome regions, as shaped by linkage disequilibrium and domestication.
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DOI：
10.1111/tpj.15908
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发表时间：
2022-09
期刊：
影响因子：
7.2
通讯作者：
Russell, Joanne R.
中科院分区：
文献类型：
--
作者：
Chen, Yun-Yu;Schreiber, Miriam;Bayer, Micha M.;Dawson, Ian K.;Hedley, Peter E.;Lei, Li;Akhunova, Alina;Liu, Chaochih;Smith, Kevin P.;Fay, Justin C.;Muehlbauer, Gary J.;Steffenson, Brian J.;Morrell, Peter L.;Waugh, Robbie;Russell, Joanne R.
重组事件沿着大的谷物染色体的分布是不均匀的，并且通常限于基因丰富的端粒末端。为了了解缺乏重组如何影响大型近着丝粒区域的多样性，我们分析了来自815个大麦品种，地方品种和野生大麦的最后一组深层外显子组捕获数据，这些数据来自其生态地理范围。我们定义并比较了着丝粒周围和非着丝粒周围区域的变异数据，观察到染色体和种质组内和之间的多样性的明确划分。显着减少多样性被发现在两个品种和地方品种的pericentromeres相比，野生大麦。我们观察到驯化和野生基因库之间完全和部分分化的单核苷酸多态性（SNP）的混合物，表明驯化基因库来自多个野生祖先。全基因组连锁不平衡模式、单倍型块大小和数量以及块内变异频率显示出个体染色体之间以及栽培大麦和野生大麦之间的明显差异。虽然大多数栽培品种的染色体共享一个主要的近着丝粒单倍型，染色体7H清楚地区分了与不同地理起源相关的两行和六行类型。在着丝粒周围区域内，我们鉴定了22387个非同义SNP，其中92个在栽培品种与野生品种中固定为替代等位基因。令人惊讶的是，只有29个SNPs发现专门在品种被预测为“高度敏感”。总的来说，我们的数据揭示了不同的大麦基因库之间的非常规的近着丝粒遗传景观，不同的进化过程驱动驯化和多样化。我们已经探索了基因组区域的遗传变异，这些区域在遗传上是不可接近的，将野生祖先与驯化大麦进行比较。这项研究提供了一个更细致入微的理解，以帮助在未来的开发育种改良。
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. We have explored genetic variation in regions of the genome that have been genetically inaccessible, comparing wild progenitors with domesticated barleys. This study provides a more nuanced understanding to help in the future exploitation of breeding improvement.
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