Dataset Information

Genome-Wide Signatures of Selection Reveal Genes Associated With Performance in American Quarter Horse Subpopulations.

ABSTRACT: Selective breeding for athletic performance in various disciplines has resulted in population stratification within the American Quarter Horse (QH) breed. The goals of this study were to utilize high density genotype data to: (1) identify genomic regions undergoing positive selection within and among QH subpopulations; (2) investigate haplotype structure within each QH subpopulation; and (3) identify candidate genes within genomic regions of interest (ROI), as well as biological pathways, predicted to play a role in elite performance in each group. For that, 65K SNP genotyping data on 143 elite individuals from 6 QH subpopulations (cutting, halter, racing, reining, western pleasure, and working cow) were imputed to 2M SNPs. Signatures of selection were identified using FST-based (di ) and haplotype-based (hapFLK) analyses, accompanied by identification of local haplotype structure and sharing within subpopulations (hapQTL). Regions undergoing positive selection were identified on all 31 autosomes, and ROI on 2 chromosomes were identified by all 3 methods combined. Genes within each ROI were retrieved and used to identify pathways and genes that might contribute to performance in each subpopulation. These included, among others, candidate genes associated with skeletal muscle development, metabolism, and central nervous system development. This work improves our understanding of equine breed development, and provides breeders with a better understanding of how selective breeding impacts the performance of QH populations.

SUBMITTER: Avila F

PROVIDER: S-EPMC6060370 | biostudies-literature | 2018

REPOSITORIES: biostudies-literature

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Genome-Wide Signatures of Selection Reveal Genes Associated With Performance in American Quarter Horse Subpopulations.

Avila Felipe F Mickelson James R JR Schaefer Robert J RJ McCue Molly E ME

Frontiers in genetics 20180719

Selective breeding for athletic performance in various disciplines has resulted in population stratification within the American Quarter Horse (QH) breed. The goals of this study were to utilize high density genotype data to: (1) identify genomic regions undergoing positive selection within and among QH subpopulations; (2) investigate haplotype structure within each QH subpopulation; and (3) identify candidate genes within genomic regions of interest (ROI), as well as biological pathways, predic ...[more]

PMID: 30105047

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Project description:The genetic differentiation of the current horse population was evolutionarily created by natural or artificial selection which shaped the genomes of individual breeds in several unique ways. The availability of high throughput genotyping methods created the opportunity to study this genetic variation on a genome-wide level allowing detection of genome regions divergently selected between separate breeds as well as among different horse types sharing similar phenotypic features. In this study, we used the population differentiation index (FST) that is generally used for measuring locus-specific allele frequencies variation between populations, to detect selection signatures among six horse breeds maintained in Poland. These breeds can be classified into three major categories, including light, draft and primitive horses, selected mainly in terms of type (utility), exterior, performance, size, coat color and appearance. The analysis of the most pronounced selection signals found in this study allowed us to detect several genomic regions and genes connected with processes potentially important for breed phenotypic differentiation and associated with energy homeostasis during physical effort, heart functioning, fertility, disease resistance and motor coordination. Our results also confirmed previously described association of loci on ECA3 (spanning LCORL and NCAPG genes) and ECA11 (spanning LASP1 gene) with the regulation of body size in our draft and primitive (small size) horses. The efficiency of the applied FST-based approach was also confirmed by the identification of a robust selection signal in the blue dun colored Polish Konik horses at the locus of TBX3 gene, which was previously shown to be responsible for dun coat color dilution in other horse breeds. FST-based method showed to be efficient in detection of diversifying selection signatures in the analyzed horse breeds. Especially pronounced signals were observed at the loci responsible for fixed breed-specific features. Several candidate genes under selection were proposed in this study for traits selected in separate breeds and horse types, however, further functional and comparative studies are needed to confirm and explain their effect on the observed genetic diversity of the horse breeds.

Project description:Plants and their pathogens are engaged in continuous evolutionary battles, with pathogens evolving to circumvent plant defense mechanisms and plants responding through enhanced protection to prevent or mitigate damage induced by pathogen attack. Managed ecosystems are composed of genetically identical populations of crop plants with few changes from year to year. These environments are highly conducive to the emergence and dissemination of pathogens and they exert selective pressure for both qualitative virulence factors responsible for fungal pathogenicity, and quantitative traits linked to pathogen fitness, such as aggressiveness. In this study, we used a comparative genome-wide approach to investigate the genomic basis underlying the pathogenicity and aggressiveness of the fungal coffee pathogen Colletotrichum kahawae infecting green coffee berries. The pathogenicity was investigated by comparing genomic variation between C. kahawae and its non-pathogenic sibling species, while the aggressiveness was studied by a genome-wide association approach with groups of isolates with different phenotypic profiles. High genetic differentiation was observed between C. kahawae and the most closely related species with 5,560 diagnostic SNPs identified, in which a significant enrichment of non-synonymous mutations was detected. Functional annotation of these non-synonymous mutations revealed a significant enrichment mainly in two gene ontology categories, "oxidation-reduction process" and "integral component of membrane." Finally, the annotation of several genes potentially under-selection revealed that C. kahawae's pathogenicity may be a complex biological process, in which important biological functions, such as, detoxification and transport, regulation of host and pathogen gene expression, and signaling are involved. On the other hand, the genome-wide association analyses for aggressiveness were able to identify 10 SNPs and 15 SNPs of small effect in single and multi-association analysis, respectively, from which 7 were common, giving in total 18 SNPs potentially associated. The annotation of these genomic regions allowed the identification of four candidate genes encoding F-box domain-containing, nitrosoguanidine resistance, Fungal specific transcription factor domain-containing and C6 transcription factor that could be associated with aggressiveness. This study shed light, for the first time, on the genetic mechanisms of C. kahawae host specialization.

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Dataset Information

Genome-Wide Signatures of Selection Reveal Genes Associated With Performance in American Quarter Horse Subpopulations.

Publications

Genome-Wide Signatures of Selection Reveal Genes Associated With Performance in American Quarter Horse Subpopulations.

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