Genome-wide detection of selection signatures in Chinese indigenous Laiwu pigs revealed candidate genes regulating fat deposition in muscle

BMC Genetics
Minhui ChenJian-Feng Liu

Abstract

Currently, genome-wide scans for positive selection signatures in commercial breed have been investigated. However, few studies have focused on selection footprints of indigenous breeds. Laiwu pig is an invaluable Chinese indigenous pig breed with extremely high proportion of intramuscular fat (IMF), and an excellent model to detect footprint as the result of natural and artificial selection for fat deposition in muscle. In this study, based on GeneSeek Genomic profiler Porcine HD data, three complementary methods, FST, iHS (integrated haplotype homozygosity score) and CLR (composite likelihood ratio), were implemented to detect selection signatures in the whole genome of Laiwu pigs. Totally, 175 candidate selected regions were obtained by at least two of the three methods, which covered 43.75 Mb genomic regions and corresponded to 1.79% of the genome sequence. Gene annotation of the selected regions revealed a list of functionally important genes for feed intake and fat deposition, reproduction, and immune response. Especially, in accordance to the phenotypic features of Laiwu pigs, among the candidate genes, we identified several genes, NPY1R, NPY5R, PIK3R1 and JAKMIP1, involved in the actions of two sets of neurons, which ar...Continue Reading

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Citations

Jun 19, 2019·Animals : an Open Access Journal From MDPI·Shuqi DiaoJiaqi Li
May 28, 2020·Frontiers in Genetics·Nompilo Lucia HlongwaneFarai Catherine Muchadeyi
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
genotyping
Profiler
chip

Software Mentioned

Ensembl
PLINK
CLR
GCTA
iHS
BEAGLE
SweepFinder2
DAVID

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