Genome-Wide Characterization of Selection Signatures and Runs of Homozygosity in Ugandan Goat Breeds

Frontiers in Genetics
R B OnzimaRichard P M A Crooijmans

Abstract

Both natural and artificial selection are among the main driving forces shaping genetic variation across the genome of livestock species. Selection typically leaves signatures in the genome, which are often characterized by high genetic differentiation across breeds and/or a strong reduction in genetic diversity in regions associated with traits under intense selection pressure. In this study, we evaluated selection signatures and genomic inbreeding coefficients, FROH, based on runs of homozygosity (ROH), in six Ugandan goat breeds: Boer (n = 13), and the indigenous breeds Karamojong (n = 15), Kigezi (n = 29), Mubende (n = 29), Small East African (n = 29), and Sebei (n = 29). After genotyping quality control, 45,294 autosomal single nucleotide polymorphisms (SNPs) remained for further analyses. A total of 394 and 6 breed-specific putative selection signatures were identified across all breeds, based on marker-specific fixation index (FST-values) and haplotype differentiation (hapFLK), respectively. These regions were enriched with genes involved in signaling pathways associated directly or indirectly with environmental adaptation, such as immune response (e.g., IL10RB and IL23A), growth and fatty acid composition (e.g., FGF9 an...Continue Reading

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Citations

Oct 17, 2019·BMC Genomics·Zaira M Estrada-ReyesRaluca G Mateescu
Jun 20, 2019·Frontiers in Genetics·Wilson NandoloJohann Sölkner
Nov 14, 2019·Animals : an Open Access Journal From MDPI·Richard Osei-AmponsahFrank R Dunshea
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Mar 29, 2020·Journal of Animal Breeding and Genetics = Zeitschrift Für Tierzüchtung Und Züchtungsbiologie·Salvatore MastrangeloMartino Cassandro
Apr 11, 2020·Frontiers in Genetics·Jun-Jie WangChu-Zhao Lei
May 6, 2020·Genes·Grazyella M YoshidaJosé M Yáñez
Oct 21, 2020·G3 : Genes - Genomes - Genetics·Reza TalebiSaber Qanbari
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Jun 3, 2021·Animals : an Open Access Journal From MDPI·Salvatore MastrangeloBaldassare Portolano
Sep 11, 2021·Genetics, Selection, Evolution : GSE·Elaheh Rostamzadeh MahdabiMasood Asadi Fozi
Nov 3, 2021·Scientific Reports·Bruno SerranitoAnne Da Silva

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Methods Mentioned

BETA
environmental stress
chip

Software Mentioned

PLINK
Database for Annotation , Visualization , and Integrated Disco...
hapFLK
DAVID
fastPHASE
house

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