Linkage disequilibrium (LD) is a key parameter to study the history of populations and to identify and fine map quantitative trait loci (QTL) and it has been studied for many years in animal populations. The advent of new genotyping technologies has allowed whole-genome LD studies in most cattle populations. However, to date, long-range LD (LRLD) between distant variants on the genome has not been investigated in detail in cattle. Here, we present the first comprehensive study of LRLD in French beef cattle by analysing data on 672 Charolais (CHA), 462 Limousine (LIM) and 326 Blonde d’Aquitaine (BLA) individuals that were genotyped on the Illumina BovineHD Beadchip. Furthermore, whole-genome LD and haplotype block structure were analysed in these three breeds. We computed linkage disequilibrium (r2) values for 5.9, 5.6 and 6.0 billion pairs of SNPs on the 29 autosomes of CHA, LIM and BLA, respectively. Mean r2 values drop to less than 0.1 for distances between SNPs greater than 120 kb. However, for the first time, we detected the existence of LRLD in the three main French beef breeds. In total, 598, 266, and 795 LRLD events (r2 ≥ 0.6) were detected in CHA, LIM and BLA, respectively. Each breed had predominantly population-specific LRLD interactions, although shared LRLD events occurred in a number of regions (55 LRLD events were shared between two breeds and nine between the three breeds). Examples of possible functional gene interactions and QTL co-location were observed with some of these LRLD events, which suggests epistatic selection. We identified long-range linkage disequilibrium for the first time in French beef cattle populations. Epistatic selection may be the main source of the observed LRLD events, but other forces may also be involved. LRLD information should be accounted for in genome-wide association studies.

中文翻译：

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法国肉牛品种的远距离连锁不平衡

连锁不平衡（LD）是研究种群历史、识别和精确定位数量性状基因座（QTL）的关键参数，在动物种群中已研究多年。新基因分型技术的出现使得在大多数牛群中进行全基因组 LD 研究成为可能。然而，迄今为止，尚未在牛中详细研究基因组上远距离变异之间的远程 LD (LRLD)。在这里，我们通过分析在 Illumina BovineHD Beadchip 上进行基因分型的 672 头夏洛莱 (CHA)、462 头豪华轿车 (LIM) 和 326 头金发阿奎坦 (BLA) 个体的数据，首次对法国肉牛的 LRLD 进行了全面研究。此外，分析了这三个品种的全基因组 LD 和单倍型块结构。我们计算了 5.9、5.6 和 6 的连锁不平衡 (r2) 值。CHA、LIM 和 BLA 的 29 个常染色体上分别有 0 亿对 SNP。对于大于 120 kb 的 SNP 之间的距离，平均 r2 值下降到小于 0.1。然而，我们第一次在三个主要的法国牛肉品种中检测到 LRLD 的存在。总共分别在 CHA、LIM 和 BLA 中检测到 598、266 和 795 次 LRLD 事件（r2 ≥ 0.6）。每个品种主要具有特定种群的 LRLD 相互作用，尽管在许多地区发生了共同的 LRLD 事件（两个品种之间共有 55 个 LRLD 事件，三个品种之间共有 9 个）。在这些 LRLD 事件中的一些事件中观察到了可能的功能基因相互作用和 QTL 共定位的例子，这表明存在上位选择。我们首次在法国肉牛种群中发现了远距离连锁不平衡。上位选择可能是观察到的 LRLD 事件的主要来源，但也可能涉及其他力量。在全基因组关联研究中应考虑 LRLD 信息。