Identification of Selection Footprints on the X Chromosome in Pig

Abstract

Identifying footprints of selection can provide a straightforward insight into the mechanism of artificial selection and further dig out the causal genes related to important traits. In this study, three between-population and two within-population approaches, the Cross Population Extend Haplotype Homozygosity Test (XPEHH), the Cross Population Composite Likelihood Ratio (XPCLR), the F-statistics (Fst), the Integrated Haplotype Score (iHS) and the Tajima's D, were implemented to detect the selection footprints on the X chromosome in three pig breeds using Illumina Porcine60K SNP chip. In the detection of selection footprints using between-population methods, 11, 11 and 7 potential selection regions with length of 15.62 Mb, 12.32 Mb and 9.38 Mb were identified in Landrace, Chinese Songliao and Yorkshire by XPEHH, respectively, and 16, 13 and 17 potential selection regions with length of 15.20 Mb, 13.00 Mb and 19.21 Mb by XPCLR, 4, 2 and 4 potential selection regions with length of 3.20 Mb, 1.60 Mb and 3.20 Mb by Fst. For within-population methods, 7, 10 and 9 potential selection regions with length of 8.12 Mb, 8.40 Mb and 9.99 Mb were identified in Landrace, Chinese Songliao and Yorkshire by iHS, and 4, 3 and 2 potential selection regions with length of 3.20 Mb, 2.40 Mb and 1.60 Mb by Tajima's D. Moreover, the selection regions from different methods were partly overlapped, especially the regions around 22 ∼25 Mb were detected under selection in Landrace and Yorkshire while no selection in Chinese Songliao by all three between-population methods. Only quite few overlap of selection regions identified by between-population and within-population methods were found. Bioinformatics analysis showed that the genes relevant with meat quality, reproduction and immune were found in potential selection regions. In addition, three out of five significant SNPs associated with hematological traits reported in our genome-wide association study were harbored in potential selection regions.

Genome‐wide association analysis identifies the genetic basis of fat deposition in the tails of sheep (Ovis aries)

“…Earlier XWAS in humans revealed candidate functional genes associated with height and fasting insulin (Tukiainen et al 2014). In addition, a previous study in swine using the Illumina Porcine 60K SNP chip showed that genes located in potential selective regions on the X chromosome have a significant effect on meat quality, reproduction and the immune system (Ma et al 2014). In sheep, several genes on the X chromosome are involved in fat deposition, reproduction, the immune system and disease-and biosynthesisrelated pathways (Zhang et al 2013;Zhu et al 2015).…”

Signatures of Natural Selection at the FTO (Fat Mass and Obesity Associated) Locus in Human Populations

“…In contrast, other population genetic measures like Tajima’s D, Fu and Li’s D*, and Fu and Li’s F* suggest the signature of balancing selection in FTO on a significant level. Detection of balancing selection might be explained by the fact that whereas Tajima’s D considers the sites themselves in terms of allele frequencies, it does not take into account the surrounding regions of sites through addressing LD (such as iHS) [ 49 , 50 ]. This is interesting when considering that polymorphisms in the third intron showed the strongest association with BMI in the Sorbs from Germany [ 11 ].…”

Genome-wide detection of selective signatures in a Duroc pig population

“…Furthermore, the relative extended haplotype homozygosity (REHH) test overcomes limitations of the heterogeneous recombination among chromosomal regions, which may potentially cause some false positives in EHH detection (Qanbari et al 2010). Many recent studies focused on genome-wide selective signature detection were conducted in various pig breeds, including Chinese indigenous breeds and western commercial breeds (Ai et al 2013(Ai et al , 2014Wilkinson et al 2013;Ma et al 2014Ma et al , 2015Wang et al 2014;Yang et al 2014;Moon et al 2015). Wilkinson et al (2013) reported several genes associated with reproduction, growth, and fat deposition traits in European breeds using F ST tests.…”