Data from: Commercial chicken breeds exhibit highly divergent patterns of linkage disequilibrium

The analysis of linkage disequilibrium (LD) underpins the development of effective genotyping technologies, trait mapping and understanding of biological mechanisms such as those driving recombination and the impact of selection. We apply the Malécot-Morton model of LD to create additive LD maps which describe the high-resolution LD landscape of commercial chickens. We investigated LD in chickens (Gallus gallus) at the highest resolution to date for broiler, white egg and brown egg layer commercial lines. There is minimal concordance between breeds of fine scale LD patterns (correlation coefficient < 0.21), and even between discrete broiler lines. Regions of LD breakdown, which may align with recombination hotspots, are enriched near CpG islands and transcription start sites (p < 2.2x10-16), consistent with recent evidence described in finches, but concordance in hotspot locations between commercial breeds is only marginally greater than random. As in other birds functional elements in the chicken genome are associated with recombination, but, unlike evidence from other bird species, the LD landscape is not stable in the populations studied. The development of optimal genotyping panels for genome-led selection programmes will depend on careful analysis of the LD structure of each line of interest. Further study is required to fully elucidate the mechanisms underlying highly divergent LD patterns found in commercial chickens.

连锁不平衡（linkage disequilibrium, LD）分析是开发高效基因分型技术、开展性状定位以及解析诸如重组驱动机制与选择影响等生物学过程的核心基础。本研究借助马莱科特-莫顿（Malécot-Morton）连锁不平衡模型构建加性连锁不平衡图谱，以此刻画商品鸡的高分辨率连锁不平衡格局。我们以迄今最高的分辨率，针对肉鸡、白壳蛋鸡与褐壳蛋鸡三类商品鸡品系的家鸡（Gallus gallus）展开连锁不平衡分析。结果显示，不同品系（乃至不同肉鸡品系之间）的精细尺度连锁不平衡模式仅存在极微弱的一致性（相关系数<0.21）。可能与重组热点重合的连锁不平衡衰退区域，在CpG岛与转录起始位点附近呈现显著富集（p < 2.2×10⁻¹⁶），这与此前在雀类中报道的研究结果相符；但不同商品鸡品系间重组热点位置的一致性仅略高于随机水平。与其他鸟类的研究结果一致，家鸡基因组中的功能元件与重组存在关联，但与其他鸟类的已有证据不同的是，本研究涉及的种群中连锁不平衡格局并不稳定。面向基因组选择育种项目的最优基因分型检测组合的开发，有赖于对目标品系连锁不平衡结构的精准分析。仍需开展进一步研究，以全面阐明商品鸡中观测到的高度分化连锁不平衡模式背后的分子机制。