Selection signatures in goats reveal copy number variants underlying breed-defining coat color phenotypes

Autoři: Jan Henkel aff001;  Rashid Saif aff001;  Vidhya Jagannathan aff001;  Corinne Schmocker aff001;  Flurina Zeindler aff004;  Erika Bangerter aff005;  Ursula Herren aff005;  Dimitris Posantzis aff006;  Zafer Bulut aff007;  Philippe Ammann aff008;  Cord Drögemüller aff001;  Christine Flury aff004;  Tosso Leeb aff001
Působiště autorů: Institute of Genetics, Vetsuisse Faculty, University of Bern, Bern, Switzerland aff001;  DermFocus, University of Bern, Bern, Switzerland aff002;  Institute of Biotechnology, Gulab Devi Educational Complex, Lahore, Pakistan aff003;  School of Agricultural, Forest and Food Sciences, Bern University of Applied Sciences, Zollikofen, Switzerland aff004;  Swiss Goat Breeding Association, Zollikofen, Switzerland aff005;  Attica Zoological Park, Spata, Greece aff006;  Department of Biochemistry, Faculty of Veterinary Medicine, Selcuk University, Konya, Turkey aff007;  ProSpecieRara, Basel, Switzerland aff008
Vyšlo v časopise: Selection signatures in goats reveal copy number variants underlying breed-defining coat color phenotypes. PLoS Genet 15(12): e32767. doi:10.1371/journal.pgen.1008536
Kategorie: Research Article
doi: 10.1371/journal.pgen.1008536


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.

Klíčová slova:

Animal sexual behavior – Antigen-presenting cells – Domestic animals – Gene pool – Genetic loci – Genome analysis – Goats – Species diversity


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