Genome-wide SNP profiling of worldwide goat populations reveals strong partitioning of diversity and highlights post-domestication migration routes.
Genome-wide SNP profiling of worldwide goat populations reveals strong partitioning of diversity and highlights post-domestication migration routes.
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DOI：
10.1186/s12711-018-0422-x
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发表时间：
2018-11-19
期刊：
影响因子：
--
通讯作者：
AdaptMap Consortium
中科院分区：
文献类型：
--
作者：
Colli L;Milanesi M;Talenti A;Bertolini F;Chen M;Crisà A;Daly KG;Del Corvo M;Guldbrandtsen B;Lenstra JA;Rosen BD;Vajana E;Catillo G;Joost S;Nicolazzi EL;Rochat E;Rothschild MF;Servin B;Sonstegard TS;Steri R;Van Tassell CP;Ajmone-Marsan P;Crepaldi P;Stella A;AdaptMap Consortium
AdaptMap项目中描述的山羊种群覆盖了该物种在全球分布的很大一部分，并为在全球范围内评估其多样性提供了机会。我们分析了144个群体的全基因组50kK单核苷酸多态(SNP)数据，以描述分子变异的全球模式，将它们与在其他牲畜物种中观察到的模式进行比较，并确定导致山羊当前分布的驱动因素。在所研究的山羊群体中，存在高度的遗传变异。我们的结果突显了大陆之间和大陆内分子多样性的强烈分割。三个主要基因库对应于来自欧洲、非洲和西亚的山羊。对亚结构的剖析揭示了区域基因库，反映了主要的后驯化迁徙路线。我们还确定了几个主要在非洲种群中的交流，这些交流经常涉及混血和世界性品种。在特定地区(如南欧、摩洛哥和马里-布基纳法索-尼日利亚)发生了广泛的基因流动，而在其他地方，由于地理障碍(如海洋或山脉)或人类管理而导致的隔离减少了当地的基因流动。在新石器时代早期(约12000年前)在肥沃的新月地区驯化后，已经携带有分化基因库的家养山羊传播到欧洲、非洲和亚洲。这些种群的扩散决定了大陆种群的主要基因组背景，目前大陆种群的细分比在其他反刍动物物种中观察到的更明显。随后，由于地理和生殖隔离，区域一级出现了进一步的多样化，伴随而来的是更多的移徙和/或输入，其痕迹至今仍可察觉。品种形成的影响很明显，特别是在中欧和北欧。总体而言，我们的结果突出了在全球范围内发生的显著多样性，并且是局部分割的，经常受到来自世界性品种的导入的影响。这些发现支持了长期保存山羊多样性的重要性，并为研究适应性导入、指导遗传改良和选择育种目标提供了有用的框架。本文的在线版本(10.1186/s12711-0180422-x)包含向授权用户提供的补充材料。
Goat populations that are characterized within the AdaptMap project cover a large part of the worldwide distribution of this species and provide the opportunity to assess their diversity at a global scale. We analysed genome-wide 50 K single nucleotide polymorphism (SNP) data from 144 populations to describe the global patterns of molecular variation, compare them to those observed in other livestock species, and identify the drivers that led to the current distribution of goats. A high degree of genetic variability exists among the goat populations studied. Our results highlight a strong partitioning of molecular diversity between and within continents. Three major gene pools correspond to goats from Europe, Africa and West Asia. Dissection of sub-structures disclosed regional gene pools, which reflect the main post-domestication migration routes. We also identified several exchanges, mainly in African populations, and which often involve admixed and cosmopolitan breeds. Extensive gene flow has taken place within specific areas (e.g., south Europe, Morocco and Mali-Burkina Faso-Nigeria), whereas elsewhere isolation due to geographical barriers (e.g., seas or mountains) or human management has decreased local gene flows. After domestication in the Fertile Crescent in the early Neolithic era (ca. 12,000 YBP), domestic goats that already carried differentiated gene pools spread to Europe, Africa and Asia. The spread of these populations determined the major genomic background of the continental populations, which currently have a more marked subdivision than that observed in other ruminant livestock species. Subsequently, further diversification occurred at the regional level due to geographical and reproductive isolation, which was accompanied by additional migrations and/or importations, the traces of which are still detectable today. The effects of breed formation were clearly detected, particularly in Central and North Europe. Overall, our results highlight a remarkable diversity that occurs at the global scale and is locally partitioned and often affected by introgression from cosmopolitan breeds. These findings support the importance of long-term preservation of goat diversity, and provide a useful framework for investigating adaptive introgression, directing genetic improvement and choosing breeding targets. The online version of this article (10.1186/s12711-018-0422-x) contains supplementary material, which is available to authorized users.
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DOI：
10.1186/s12711-018-0425-7
发表时间：
2018-11-19
期刊：
Genetics, selection, evolution : GSE
影响因子：
--
作者：
Cardoso TF;Amills M;Bertolini F;Rothschild M;Marras G;Boink G;Jordana J;Capote J;Carolan S;Hallsson JH;Kantanen J;Pons A;Lenstra JA;AdaptMap Consortium
通讯作者：
AdaptMap Consortium
影响因子：
9.2
作者：
Chang CC;Chow CC;Tellier LC;Vattikuti S;Purcell SM;Lee JJ
通讯作者：
Lee JJ
影响因子：
56.9
作者：
Daly, Kevin G.;Delser, Pierpaolo Maisano;Bradley, Daniel G.
通讯作者：
Bradley, Daniel G.
影响因子：
4.4
作者：
Colli L;Lancioni H;Cardinali I;Olivieri A;Capodiferro MR;Pellecchia M;Rzepus M;Zamani W;Naderi S;Gandini F;Vahidi SM;Agha S;Randi E;Battaglia V;Sardina MT;Portolano B;Rezaei HR;Lymberakis P;Boyer F;Coissac E;Pompanon F;Taberlet P;Ajmone Marsan P;Achilli A
通讯作者：
Achilli A
影响因子：
2.4
作者：
Amills, M.;Ramirez, O.;Capote, J.
通讯作者：
Capote, J.