PDF(Pubmed)
Abstract：
BACKGROUND: Alpaca (Vicugna pacos), llama (Lama glama), vicugna (Vicugna vicugna) and guanaco (Lama guanicoe), are the camelid species distributed over the Andean high-altitude grasslands, the Altiplano, and the Patagonian arid steppes. Despite the wide interest on these animals, most of the loci under selection are still unknown. Using whole-genome sequencing (WGS) data we investigated the occurrence and the distribution of Runs Of Homozygosity (ROHs) across the South American Camelids (SACs) genome to identify the genetic relationship between the four species and the potential signatures of selection.
RESULTS: A total of 37 WGS samples covering the four species was included in the final analysis. The multi-dimensional scaling approach showed a clear separation between the four species; however, admixture analysis suggested a strong genetic introgression from vicugna and llama to alpaca. Conversely, very low genetic admixture of the guanaco with the other SACs was found. The four species did not show significant differences in the number, length of ROHs (100-500 kb) and genomic inbreeding values. Longer ROHs (> 500 kb) were found almost exclusively in alpaca. Seven overlapping ROHs were shared by alpacas, encompassing nine loci (FGF5, LOC107034918, PRDM8, ANTXR2, LOC102534792, BSN, LOC116284892, DAG1 and RIC8B) while nine overlapping ROHs were found in llama with twenty-five loci annotated (ERC2, FZD9, BAZ1B, BCL7B, LOC116284208, TBL2, MLXIPL, PHF20, TRNAD-AUC, LOC116284365, RBM39, ARFGEF2, DCAF5, EXD2, HSPB11, LRRC42, LDLRAD1, TMEM59, LOC107033213, TCEANC2, LOC102545169, LOC116278408, SMIM15, NDUFAF2 and RCOR1). Four overlapping ROHs, with three annotated loci (DLG1, KAT6B and PDE4D) and three overlapping ROHs, with seven annotated genes (ATP6V1E1, BCL2L13, LOC116276952, BID, KAT6B, LOC116282667 and LOC107034552), were detected for vicugna and guanaco, respectively.
CONCLUSIONS: The signatures of selection revealed genomic areas potentially selected for production traits as well as for natural adaptation to harsh environment. Alpaca and llama hint a selection driven by environment as well as by farming purpose while vicugna and guanaco showed selection signals for adaptation to harsh environment. Interesting, signatures of selection on KAT6B gene were identified for both vicugna and guanaco, suggesting a positive effect on wild populations fitness. Such information may be of interest to further ecological and animal production studies.
RESULTS: A total of 37 WGS samples covering the four species was included in the final analysis. The multi-dimensional scaling approach showed a clear separation between the four species; however, admixture analysis suggested a strong genetic introgression from vicugna and llama to alpaca. Conversely, very low genetic admixture of the guanaco with the other SACs was found. The four species did not show significant differences in the number, length of ROHs (100-500 kb) and genomic inbreeding values. Longer ROHs (> 500 kb) were found almost exclusively in alpaca. Seven overlapping ROHs were shared by alpacas, encompassing nine loci (FGF5, LOC107034918, PRDM8, ANTXR2, LOC102534792, BSN, LOC116284892, DAG1 and RIC8B) while nine overlapping ROHs were found in llama with twenty-five loci annotated (ERC2, FZD9, BAZ1B, BCL7B, LOC116284208, TBL2, MLXIPL, PHF20, TRNAD-AUC, LOC116284365, RBM39, ARFGEF2, DCAF5, EXD2, HSPB11, LRRC42, LDLRAD1, TMEM59, LOC107033213, TCEANC2, LOC102545169, LOC116278408, SMIM15, NDUFAF2 and RCOR1). Four overlapping ROHs, with three annotated loci (DLG1, KAT6B and PDE4D) and three overlapping ROHs, with seven annotated genes (ATP6V1E1, BCL2L13, LOC116276952, BID, KAT6B, LOC116282667 and LOC107034552), were detected for vicugna and guanaco, respectively.
CONCLUSIONS: The signatures of selection revealed genomic areas potentially selected for production traits as well as for natural adaptation to harsh environment. Alpaca and llama hint a selection driven by environment as well as by farming purpose while vicugna and guanaco showed selection signals for adaptation to harsh environment. Interesting, signatures of selection on KAT6B gene were identified for both vicugna and guanaco, suggesting a positive effect on wild populations fitness. Such information may be of interest to further ecological and animal production studies.
摘要：
背景：羊驼（Vicugnapacos），美洲驼（Lamaglama），vicugna(vicugnavicugna)和guanaco(lamaguanicoe)，是分布在安第斯高海拔草原上的骆驼物种，高原,还有巴塔哥尼亚干旱的草原.尽管人们对这些动物有广泛的兴趣，选择的大多数基因座仍然未知。使用全基因组测序（WGS）数据，我们调查了南美骆驼科动物（SAC）基因组中纯合性运行（ROHs）的发生和分布，以确定四个物种之间的遗传关系和潜在的选择特征。
结果：最终分析中包括了涵盖这四个物种的总共37个WGS样品。多维缩放方法显示了四个物种之间的明显分离；然而，混合物分析表明，从维古纳和美洲驼到羊驼有强烈的遗传渗入。相反，发现了guanaco与其他SAC的极低遗传混合物。这四个物种在数量上没有显示出显著差异，ROHs的长度（100-500kb）和基因组近交值。较长的ROHs(>500kb)几乎只在羊驼中发现。七个重叠的ROH由羊驼共享，包含9个基因座(FGF5,LOC107034918,PRDM8,ANTXR2,LOC102534792,BSN,LOC116284892，DAG1和RIC8B），而在美洲驼中发现了9个重叠的ROH，注释了25个基因座（ERC2，FZD9，BAZ1B，BCL7B,LOC116284208,TBL2,MLXIPL,PHF20,TRNAD-AUC,LOC116284365,RBM39,ARFGEF2,DCAF5,EXD2,HSPB11,LRRC42,LDLRAD1,TMEM59,LOC107033213,TCEANC2,LOC102545169,LOC116278408,SMIM15,NFADUF2和RCOR1)。四个重叠的ROHs，具有三个注释基因座（DLG1，KAT6B和PDE4D）和三个重叠的ROH，具有七个注释基因(ATP6V1E1，BCL2L13，LOC116276952，BID，KAT6B,LOC116282667和LOC107034552),被检测到了维库尼亚和瓜纳科，分别。
结论：选择的特征揭示了可能被选择用于生产性状以及对恶劣环境的自然适应的基因组区域。羊驼和美洲驼暗示了由环境和耕作目的驱动的选择，而vicugna和guanaco则显示了适应恶劣环境的选择信号。有趣,KAT6B基因的选择特征被鉴定为vicugna和guanaco，表明对野生种群适应性有积极影响。此类信息可能对进一步的生态和动物生产研究感兴趣。
结果：最终分析中包括了涵盖这四个物种的总共37个WGS样品。多维缩放方法显示了四个物种之间的明显分离；然而，混合物分析表明，从维古纳和美洲驼到羊驼有强烈的遗传渗入。相反，发现了guanaco与其他SAC的极低遗传混合物。这四个物种在数量上没有显示出显著差异，ROHs的长度（100-500kb）和基因组近交值。较长的ROHs(>500kb)几乎只在羊驼中发现。七个重叠的ROH由羊驼共享，包含9个基因座(FGF5,LOC107034918,PRDM8,ANTXR2,LOC102534792,BSN,LOC116284892，DAG1和RIC8B），而在美洲驼中发现了9个重叠的ROH，注释了25个基因座（ERC2，FZD9，BAZ1B，BCL7B,LOC116284208,TBL2,MLXIPL,PHF20,TRNAD-AUC,LOC116284365,RBM39,ARFGEF2,DCAF5,EXD2,HSPB11,LRRC42,LDLRAD1,TMEM59,LOC107033213,TCEANC2,LOC102545169,LOC116278408,SMIM15,NFADUF2和RCOR1)。四个重叠的ROHs，具有三个注释基因座（DLG1，KAT6B和PDE4D）和三个重叠的ROH，具有七个注释基因(ATP6V1E1，BCL2L13，LOC116276952，BID，KAT6B,LOC116282667和LOC107034552),被检测到了维库尼亚和瓜纳科，分别。
结论：选择的特征揭示了可能被选择用于生产性状以及对恶劣环境的自然适应的基因组区域。羊驼和美洲驼暗示了由环境和耕作目的驱动的选择，而vicugna和guanaco则显示了适应恶劣环境的选择信号。有趣,KAT6B基因的选择特征被鉴定为vicugna和guanaco，表明对野生种群适应性有积极影响。此类信息可能对进一步的生态和动物生产研究感兴趣。
