PDF(Pubmed)
Abstract：
BACKGROUND: The Icelandic horse and Exmoor pony are ancient, native breeds, adapted to harsh environmental conditions and they have both undergone severe historic bottlenecks. However, in modern days, the selection pressures on these breeds differ substantially. The aim of this study was to assess genetic diversity in both breeds through expected (HE) and observed heterozygosity (HO) and effective population size (Ne). Furthermore, we aimed to identify runs of homozygosity (ROH) to estimate and compare genomic inbreeding and signatures of selection in the breeds.
RESULTS: HO was estimated at 0.34 and 0.33 in the Icelandic horse and Exmoor pony, respectively, aligning closely with HE of 0.34 for both breeds. Based on genomic data, the Ne for the last generation was calculated to be 125 individuals for Icelandic horses and 42 for Exmoor ponies. Genomic inbreeding coefficient (FROH) ranged from 0.08 to 0.20 for the Icelandic horse and 0.12 to 0.27 for the Exmoor pony, with the majority of inbreeding attributed to short ROHs in both breeds. Several ROH islands associated with performance were identified in the Icelandic horse, featuring target genes such as DMRT3, DOCK8, EDNRB, SLAIN1, and NEURL1. Shared ROH islands between both breeds were linked to metabolic processes (FOXO1), body size, and the immune system (CYRIB), while private ROH islands in Exmoor ponies were associated with coat colours (ASIP, TBX3, OCA2), immune system (LYG1, LYG2), and fertility (TEX14, SPO11, ADAM20).
CONCLUSIONS: Evaluations of genetic diversity and inbreeding reveal insights into the evolutionary trajectories of both breeds, highlighting the consequences of population bottlenecks. While the genetic diversity in the Icelandic horse is acceptable, a critically low genetic diversity was estimated for the Exmoor pony, which requires further validation. Identified signatures of selection highlight the differences in the use of the two breeds as well as their adaptive trait similarities. The results provide insight into genomic regions under selection pressure in a gaited performance horse breed and various adaptive traits in small-sized native horse breeds. This understanding contributes to preserving genetic diversity and population health in these equine populations.
RESULTS: HO was estimated at 0.34 and 0.33 in the Icelandic horse and Exmoor pony, respectively, aligning closely with HE of 0.34 for both breeds. Based on genomic data, the Ne for the last generation was calculated to be 125 individuals for Icelandic horses and 42 for Exmoor ponies. Genomic inbreeding coefficient (FROH) ranged from 0.08 to 0.20 for the Icelandic horse and 0.12 to 0.27 for the Exmoor pony, with the majority of inbreeding attributed to short ROHs in both breeds. Several ROH islands associated with performance were identified in the Icelandic horse, featuring target genes such as DMRT3, DOCK8, EDNRB, SLAIN1, and NEURL1. Shared ROH islands between both breeds were linked to metabolic processes (FOXO1), body size, and the immune system (CYRIB), while private ROH islands in Exmoor ponies were associated with coat colours (ASIP, TBX3, OCA2), immune system (LYG1, LYG2), and fertility (TEX14, SPO11, ADAM20).
CONCLUSIONS: Evaluations of genetic diversity and inbreeding reveal insights into the evolutionary trajectories of both breeds, highlighting the consequences of population bottlenecks. While the genetic diversity in the Icelandic horse is acceptable, a critically low genetic diversity was estimated for the Exmoor pony, which requires further validation. Identified signatures of selection highlight the differences in the use of the two breeds as well as their adaptive trait similarities. The results provide insight into genomic regions under selection pressure in a gaited performance horse breed and various adaptive traits in small-sized native horse breeds. This understanding contributes to preserving genetic diversity and population health in these equine populations.
摘要：
背景：冰岛马和埃克斯穆尔小马很古老，本地品种，适应恶劣的环境条件，他们都经历了严重的历史瓶颈。然而,在现代，这些品种的选择压力大不相同。这项研究的目的是通过预期（HE）和观察到的杂合性（HO）和有效种群大小（Ne）评估两个品种的遗传多样性。此外，我们旨在鉴定纯合性(ROH)序列,以评估和比较品种中基因组近交和选择特征.
结果：在冰岛马和埃克穆尔小马中，HO估计为0.34和0.33，分别,这两个品种的HE都与0.34的HE密切相关。根据基因组数据,经计算，上一代的Ne为冰岛马125个个体，Exmoor小马42个个体。冰岛马的基因组近交系数（FROH）为0.08至0.20，埃克穆尔小马为0.12至0.27，在两个品种中，大多数近亲繁殖都归因于短ROH。在冰岛马匹中发现了几个与性能相关的ROH岛，具有目标基因，如DMRT3，DOCK8，EDNRB，SLAIN1和NEURL1。两个品种之间共享的ROH岛与代谢过程(FOXO1)有关，身体尺寸,和免疫系统（CYRIB），而Exmoor小马的私人ROH岛与外套颜色(ASIP，TBX3,OCA2),免疫系统（LYG1，LYG2），和生育率（TEX14，SPO11，ADAM20）。
结论：对遗传多样性和近亲繁殖的评估揭示了对两个品种的进化轨迹的见解，强调人口瓶颈的后果。虽然冰岛马的遗传多样性是可以接受的，估计埃克斯穆尔小马的遗传多样性极低，这需要进一步验证。选择的识别特征突出了两个品种的使用差异以及它们的适应性特征相似性。结果提供了对成群的性能马品种在选择压力下的基因组区域以及小型本地马品种中的各种适应性特征的见解。这种理解有助于保持这些马种群的遗传多样性和种群健康。
结果：在冰岛马和埃克穆尔小马中，HO估计为0.34和0.33，分别,这两个品种的HE都与0.34的HE密切相关。根据基因组数据,经计算，上一代的Ne为冰岛马125个个体，Exmoor小马42个个体。冰岛马的基因组近交系数（FROH）为0.08至0.20，埃克穆尔小马为0.12至0.27，在两个品种中，大多数近亲繁殖都归因于短ROH。在冰岛马匹中发现了几个与性能相关的ROH岛，具有目标基因，如DMRT3，DOCK8，EDNRB，SLAIN1和NEURL1。两个品种之间共享的ROH岛与代谢过程(FOXO1)有关，身体尺寸,和免疫系统（CYRIB），而Exmoor小马的私人ROH岛与外套颜色(ASIP，TBX3,OCA2),免疫系统（LYG1，LYG2），和生育率（TEX14，SPO11，ADAM20）。
结论：对遗传多样性和近亲繁殖的评估揭示了对两个品种的进化轨迹的见解，强调人口瓶颈的后果。虽然冰岛马的遗传多样性是可以接受的，估计埃克斯穆尔小马的遗传多样性极低，这需要进一步验证。选择的识别特征突出了两个品种的使用差异以及它们的适应性特征相似性。结果提供了对成群的性能马品种在选择压力下的基因组区域以及小型本地马品种中的各种适应性特征的见解。这种理解有助于保持这些马种群的遗传多样性和种群健康。
