A genome scan for selection signatures in pigs

PloS One
Yun-Long MaXiang-Dong Ding

Abstract

Identifying signatures of selection can provide a straightforward insight into the mechanism of artificial selection and further uncover the causal genes related to the phenotypic variation. Based on Illumina Porcine60KSNP chip data, four complementary methods, Long-Range Haplotype (LRH), Tajima's D, Cross Population Extend Haplotype Homozygosity Test (XPEHH) and FST, were implemented in this study to detect the selection signatures in the whole genome of one typical Chinese indigenous breed, Rongchang, one Chinese cultivated breed, Songliao, and two western breeds, Landrace and Yorkshire. False Discovery Rate (FDR) was implemented to control the false positive rates. In our study, a total of 159, 127, 179 and 159 candidate selection regions with average length of 0.80 Mb, 0.73 Mb, 0.78 Mb and 0.73 Mb were identified in Landrace, Rongchang, Songliao and Yorkshire, respectively, that span approximately 128.00 Mb, 92.38 Mb, 130.30 Mb and 115.40 Mb and account for approximately 3.74-5.33% of genome across all autosomes. The selection regions of 11.52 Mb shared by Landrace and Yorkshire were the longest when chosen pairs from the pool of the four breeds were examined. The overlaps between Yorkshire and Songliao, approximately 9.20 ...Continue Reading

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Citations

Jul 11, 2018·Animal : an International Journal of Animal Bioscience·Z WangY Pan
Jun 5, 2019·Animals : an Open Access Journal From MDPI·Ligang WangShutang Feng
Aug 30, 2018·Frontiers in Genetics·Robert B OnzimaRichard P M A Crooijmans
Oct 22, 2020·Animals : an Open Access Journal From MDPI·Meilin JinCaihong Wei

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Methods Mentioned

BETA
genotyping
electrophoresis
chip

Software Mentioned

BeadStudio
XPEHH
BEAGLE
Sweep
HAPLOVIEW

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