Selection signatures in goats reveal copy number variants underlying breed-defining coat color phenotypes.,PLOS Genetics

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Selection signatures in goats reveal copy number variants underlying breed-defining coat color phenotypes.
PLOS Genetics ( IF 4.0 ) Pub Date : 2019-12-16 , DOI: 10.1371/journal.pgen.1008536
Jan Henkel _{1,

2} , Rashid Saif _{1,

3} , Vidhya Jagannathan _{1,

2} , Corinne Schmocker ₁ , Flurina Zeindler ₄ , Erika Bangerter ₅ , Ursula Herren ₅ , Dimitris Posantzis ₆ , Zafer Bulut ₇ , Philippe Ammann ₈ , Cord Drögemüller _{1,

2} , Christine Flury ₄ , Tosso Leeb _{1,

2}

Affiliation

Domestication and human selection have formed diverse goat breeds with characteristic phenotypes. This process correlated with the fixation of causative genetic variants controlling breed-specific traits within regions of reduced genetic diversity, so called selection signatures or selective sweeps. Using whole genome sequencing of DNA pools (pool-seq) from 20 genetically diverse modern goat breeds and bezoars, we identified 2,239 putative selection signatures. In two Pakistani goat breeds, Pak Angora and Barbari, we found selection signatures in a region harboring KIT, a gene involved in melanoblast development, migration, and survival. The search for candidate causative variants responsible for these selective sweeps revealed two different copy number variants (CNVs) downstream of KIT that were exclusively present in white Pak Angora and white-spotted Barbari goats. Several Swiss goat breeds selected for specific coat colors showed selection signatures at the ASIP locus encoding the agouti signaling protein. Analysis of these selective sweeps revealed four different CNVs associated with the white or tan (AWt), Swiss markings (Asm), badgerface (Ab), and the newly proposed peacock (Apc) allele. RNA-seq analyses on skin samples from goats with the different CNV alleles suggest that the identified structural variants lead to an altered expression of ASIP between eumelanistic and pheomelanistic body areas. Our study yields novel insights into the genetic control of pigmentation by identifying six functionally relevant CNVs. It illustrates how structural changes of the genome have contributed to phenotypic evolution in domestic goats.

中文翻译：

山羊中的选择签名揭示了定义品种的毛色表型的拷贝数变异。

驯化和人类选择已形成具有特征表型的多种山羊品种。这个过程与控制遗传多样性降低的区域内控制品种特定性状的致病性遗传变异的固定有关，即所谓的选择特征或选择性清除。使用来自20个遗传多样的现代山羊品种和牛黄的DNA池（pool-seq）的全基因组测序，我们确定了2239个推定的选择标记。在两个巴基斯坦山羊品种Pak Angora和Barbari中，我们在一个带有KIT的区域发现了选择签名，该基因与黑素细胞的发育，迁移和存活有关。对负责这些选择性清除的候选致病性变种的搜索揭示了在KIT下游的两个不同的拷贝数变体（CNV），它们仅存在于白朴安哥拉和白色斑点的Barbari山羊中。选择用于特定毛色的几种瑞士山羊品种在编码刺豚鼠信号蛋白的ASIP基因座上显示出选择特征。对这些选择性扫描的分析揭示了与白色或棕褐色（AWt），瑞士标记（Asm），badge面部（Ab）和新提出的孔雀（Apc）等位基因相关的四种不同的CNV。对来自具有不同CNV等位基因的山羊皮肤样品的RNA-seq分析表明，鉴定出的结构变体导致在Eumelanistic和pheomelanistic身体区域之间ASIP的表达发生了变化。我们的研究通过鉴定六个功能相关的CNV，为色素沉着的遗传控制提供了新颖的见解。它说明了基因组的结构变化如何促进了家山羊的表型进化。

更新日期：2019-12-17

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