title: Genetic diversity and signatures of selection in various goat breeds revealed by genome-wide SNP markers.
abstract: The detection of signatures of selection has the potential to elucidate the identities of genes and mutations associated with phenotypic traits important for livestock species. It is also very relevant to investigate the levels of genetic diversity of a population, as genetic diversity represents the raw material essential for breeding and has practical implications for implementation of genomic selection. A total of 1151 animals from nine goat populations selected for different breeding goals and genotyped with the Illumina Goat 50K single nucleotide polymorphisms (SNP) Beadchip were included in this investigation.
  
  
  
  The proportion of polymorphic SNPs ranged from 0.902 (Nubian) to 0.995 (Rangeland). The overall mean HOand HEwas 0.374 ± 0.021 and 0.369 ± 0.023, respectively. The average pairwise genetic distance (D) ranged from 0.263 (Toggenburg) to 0.323 (Rangeland). The overall average for the inbreeding measures FEH, FVR, FLEUT, FROHand FPEDwas 0.129, -0.012, -0.010, 0.038 and 0.030, respectively. Several regions located on 19 chromosomes were potentially under selection in at least one of the goat breeds. The genomic population tree constructed using all SNPs differentiated breeds based on selection purpose, while genomic population tree built using only SNPs in the most significant region showed a great differentiation between LaMancha and the other breeds. We hypothesized that this region is related to ear morphogenesis. Furthermore, we identified genes potentially related to reproduction traits, adult body mass, efficiency of food conversion, abdominal fat deposition, conformation traits, liver fat metabolism, milk fatty acids, somatic cells score, milk protein, thermo-tolerance and ear morphogenesis.
  
  
  
  In general, moderate to high levels of genetic variability were observed for all the breeds and a characterization of runs of homozygosity gave insights into the breeds' development history. The information reported here will be useful for the implementation of genomic selection and other genomic studies in goats. We also identified various genome regions under positive selection using smoothed FSTand hapFLK statistics and suggested genes, which are potentially under selection. These results can now provide a foundation to formulate biological hypotheses related to selection processes in goats.
authors.affiliation: Centre for Genetic Improvement of Livestock, University of Guelph, Guelph, Ontario, Canada. lbrito@uoguelph.ca.
authors.forename: Luiz F
authors.initials: LF
authors.lastname: Brito
authors.affiliation: CSIRO Agriculture & Food, Brisbane, Queensland, Australia.
authors.forename: James W
authors.initials: JW
authors.lastname: Kijas
authors.affiliation: Centre for Genetic Improvement of Livestock, University of Guelph, Guelph, Ontario, Canada.|Beef Improvement Opportunities, Guelph, Ontario, Canada.
authors.forename: Ricardo V
authors.initials: RV
authors.lastname: Ventura
authors.affiliation: Centre for Genetic Improvement of Livestock, University of Guelph, Guelph, Ontario, Canada.|The Semex Alliance, Guelph, Ontario, Canada.
authors.forename: Mehdi
authors.initials: M
authors.lastname: Sargolzaei
authors.affiliation: CSIRO Agriculture & Food, Brisbane, Queensland, Australia.
authors.forename: Laercio R
authors.initials: LR
authors.lastname: Porto-Neto
authors.affiliation: Centre for Genetic Improvement of Livestock, University of Guelph, Guelph, Ontario, Canada.
authors.forename: Angela
authors.initials: A
authors.lastname: Cánovas
authors.affiliation: Department of Mathematics and Statistics, University of Guelph, Guelph, Ontario, Canada.
authors.forename: Zeny
authors.initials: Z
authors.lastname: Feng
authors.affiliation: Centre for Genetic Improvement of Livestock, University of Guelph, Guelph, Ontario, Canada.|Canadian Centre for Swine Improvement Inc., Ottawa, Ontario, Canada.
authors.forename: Mohsen
authors.initials: M
authors.lastname: Jafarikia
authors.affiliation: Centre for Genetic Improvement of Livestock, University of Guelph, Guelph, Ontario, Canada.
authors.forename: Flávio S
authors.initials: FS
authors.lastname: Schenkel
mesh_terms: D000818:Animals; D004423:Ear / Q000033:anatomy & histology / Q000502:physiology; D005787:Gene Frequency; D014644:Genetic Variation; D016678:Genome; D055106:Genome-Wide Association Study; D005838:Genotype; D006041:Goats / Q000235:genetics*; D006579:Heterozygote; D006720:Homozygote; D010641:Phenotype; D020641:Polymorphism, Single Nucleotide; D012641:Selection, Genetic
keywords: Capra hircus; F-statistics; SNP; Selective sweep; hapFLK