A genome-wide scan for diversifying selection signatures in selected horse breeds

The genetic differentiation of the current horse population was evolutionarily created by natural or artificial selection which shaped the genomes of individual breeds in several unique ways. The availability of high throughput genotyping methods created the opportunity to study this genetic variation on a genome-wide level allowing detection of genome regions divergently selected between separate breeds as well as among different horse types sharing similar phenotypic features. In this study, we used the population differentiation index (FST) that is generally used for measuring locus-specific allele frequencies variation between populations, to detect selection signatures among six horse breeds maintained in Poland. These breeds can be classified into three major categories, including light, draft and primitive horses, selected mainly in terms of type (utility), exterior, performance, size, coat color and appearance. The analysis of the most pronounced selection signals found in this study allowed us to detect several genomic regions and genes connected with processes potentially important for breed phenotypic differentiation and associated with energy homeostasis during physical effort, heart functioning, fertility, disease resistance and motor coordination. Our results also confirmed previously described association of loci on ECA3 (spanning LCORL and NCAPG genes) and ECA11 (spanning LASP1 gene) with the regulation of body size in our draft and primitive (small size) horses. The efficiency of the applied FST-based approach was also confirmed by the identification of a robust selection signal in the blue dun colored Polish Konik horses at the locus of TBX3 gene, which was previously shown to be responsible for dun coat color dilution in other horse breeds. FST-based method showed to be efficient in detection of diversifying selection signatures in the analyzed horse breeds. Especially pronounced signals were observed at the loci responsible for fixed breed-specific features. Several candidate genes under selection were proposed in this study for traits selected in separate breeds and horse types, however, further functional and comparative studies are needed to confirm and explain their effect on the observed genetic diversity of the horse breeds.

当前马种群的遗传分化，是演化进程中自然选择与人工选择共同塑造的结果——二者以多种独特方式形塑了各马品种的基因组。高通量基因分型技术的普及，使得我们得以在全基因组层面探究此类遗传变异，进而能够检测不同马品种间，以及具有相似表型特征的不同马类群之间的趋异选择基因组区域。本研究采用通常用于衡量种群间位点特异性等位基因频率变异的群体分化指数（FST），对波兰境内饲养的6个马品种进行选择信号检测。这些马品种可分为三大类：轻型马、役用挽马与原始型马，其选育主要依据用途、外形、性能、体型、被毛颜色与外观等维度。通过对本研究中鉴定出的最显著选择信号进行分析，我们成功检测到多个基因组区域与基因，它们与马品种表型分化相关的关键生物学过程密切关联，涉及运动过程中的能量稳态、心脏功能、繁殖力、抗病性与运动协调等方面。本研究结果还验证了此前已报道的关联：马3号染色体（ECA3，覆盖LCORL与NCAPG基因）以及马11号染色体（ECA11，覆盖LASP1基因）上的位点，与本次研究中役用挽马及原始型（小型）马的体型调控相关。基于FST的分析方法的有效性，还通过在蓝鹿皮色波兰科尼克马的TBX3基因位点上鉴定出强选择信号得到验证——该基因此前已被证实可导致其他马品种的鹿皮色被毛稀释。基于FST的方法在本次分析的马品种中，能够有效检测趋异选择信号。在控制品种特异性固定性状的位点上，我们观察到尤为显著的选择信号。本研究针对不同马品种与马类群的选育性状，提出了多个处于选择压力下的候选基因，但仍需开展进一步的功能与比较研究，以验证并阐明这些基因对本次观测到的马种群遗传多样性的影响机制。