康尼马拉小马（CP）是一种爱尔兰品种，在过去的五十年里，经过养殖者的不同选择，从传统的强健小马转变为灵活的运动员。我们将这些小马与研究充分的温血马（WB）进行比较，后者也是为了运动表现而有选择地繁殖，但其人口普查数量要大得多。利用116匹WB（包括94匹英国WB和22匹欧洲WB）和36匹CP（包括33匹英国CP和3匹美国CP）的全基因组单核苷酸多态性（SNP）和全基因组测序数据，我们研究了这些品种的基因组多样性、近亲交配和种群结构。k-means 聚类方法将CP和WB两个群体分为四个遗传群体。CP的遗传群体1（C1）与非注册CP相关，C4与美国CP相关，WB的遗传群体1（W1）与荷兰士兵马相关，W3与英国和欧洲WB相关。两种品种的最大和平均连锁不平衡（LD）之间存在显著差异（对于CP的平均值从0.077到0.130，对于WB的平均值从0.016到0.370），但是CP的LD衰减速度通常比WB慢。所有遗传群体的LD区块大小分布峰值为225 kb，大部分LD区块不超过1 Mb。当比较四个CP遗传群体时，前0.5％的谐振均值两两固定指数（FST）值识别出与癌症风险相关的本体术语。与WB的遗传群体相比，四个CP遗传群体的近亲交配程度较低，但是C2、C3和C4的较短同源性区段（ROH）比例较低（74到76％<4 Mb），而四个WB遗传群体的比例较高（80到85％<4 Mb），表明CP有较近期的近亲交配。CP和WB的遗传群体在每个品种内都显示出不同的遗传群体，而在WB中，这些遗传群体更好地反映了种马册或起源国的种群亚结构。CP遗传群体之间的选择标记识别了与免疫和炎症反应相关的本体术语，虽然CP的近亲交配程度较低，但证据指出近期近亲交配的程度更大。CP和WB的每个有效育种者数（Neb）与有效种群大小（Ne）的比例相似，表明在CP和WB中，受欢迎种马的影响是相似的。 ©2023.'Institut National de Recherche en Agriculture, Alimentation et Environnement（INRAE）。

The Connemara pony (CP) is an Irish breed that has experienced varied selection by breeders over the last fifty years, with objectives ranging from the traditional hardy pony to an agile athlete. We compared these ponies with well-studied Warmblood (WB) horses, which are also selectively bred for athletic performance but with a much larger census population. Using genome-wide single nucleotide polymorphism (SNP) and whole-genome sequencing data from 116 WB (94 UK WB and 22 European WB) and 36 CP (33 UK CP and 3 US CP), we studied the genomic diversity, inbreeding and population structure of these breeds.The k-means clustering approach divided both the CP and WB populations into four genetic groups, among which the CP genetic group 1 (C1) associated with non-registered CP, C4 with US CP, WB genetic group 1 (W1) with Holsteiners, and W3 with Anglo European and British WB. Maximum and mean linkage disequilibrium (LD) varied significantly between the two breeds (mean from 0.077 to 0.130 for CP and from 0.016 to 0.370 for WB), but the rate of LD decay was generally slower in CP than WB. The LD block size distribution peaked at 225 kb for all genetic groups, with most of the LD blocks not exceeding 1 Mb. The top 0.5% harmonic mean pairwise fixation index (FST) values identified ontology terms related to cancer risk when the four CP genetic groups were compared. The four CP genetic groups were less inbred than the WB genetic groups, but C2, C3 and C4 had a lower proportion of shorter runs of homozygosity (ROH) (74 to 76% < 4 Mb) than the four WB genetic groups (80 to 85% < 4 Mb), indicating more recent inbreeding. The CP and WB genetic groups had a similar ratio of effective number of breeders (Neb) to effective population size (Ne).Distinct genetic groups of individuals were revealed within each breed, and in WB these genetic groups reflected population substructure better than studbook or country of origin. Ontology terms associated with immune and inflammatory responses were identified from the signatures of selection between CP genetic groups, and while CP were less inbred than WB, the evidence pointed to a greater degree of recent inbreeding. The ratio of Neb to Ne was similar in CP and WB, indicating the influence of popular sires is similar in CP and WB.© 2023. ’Institut National de Recherche en Agriculture, Alimentation et Environnement (INRAE).