Genomic Analysis To Identify Signatures of Artificial Selection and Loci Associated with Important Economic Traits in Duroc Pigs

G3 : Genes - Genomes - Genetics
Yunlong MaShuhong Zhao

Abstract

Identifying genetic basis of domestication and improvement in livestock contributes to our understanding of the role of artificial selection in shaping the genome. Here we used whole-genome sequencing and the genotyping by sequencing approach to detect artificial selection signatures and identify the associated SNPs of two economic traits in Duroc pigs. A total of 38 candidate selection regions were detected by combining the fixation index and the Composite Likelihood Ratio methods. Further genome-wide association study revealed seven associated SNPs that were related with intramuscular fat content and feed conversion ratio traits, respectively. Enrichment analysis suggested that the artificial selection regions harbored genes, such as MSTN, SOD2, MC5R and CD83, which are responsible for economic traits including lean muscle mass, fertility and immunization. Overall, this study found a series of candidate genes putatively associated with the breeding improvement of Duroc pigs and the polygenic basis of adaptive evolution, which can provide important references and fundamental information for future breeding programs.

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Citations

Jun 3, 2021·Animals : an Open Access Journal From MDPI·Vivien J ChebiiJean-Baka Domelevo Entfellner

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Datasets Mentioned

BETA
SRP158574

Methods Mentioned

BETA
Illumina
genotyping
PCR

Software Mentioned

SweepFinder
ANNOVAR
- Aligner ( BWA )
PLINK
Beagle
SAMtools
CreateSequenceDictionary
GATK
Burrows
HaplotypeCaller

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