A Genome Scan for Selection Signatures in Pigs

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 Mb, were greater than those of Yorkshire and Rongchang. Meanwhile, the overlaps between Landrace and Songliao were greater than those of Landrace and Rongchang but less than those of Songliao and Ronchang. Bioinformatics analysis showed that the genes/QTLs relevant to fertility, coat color, and ear morphology were found in candidate selection regions. Some genes, such as LEMD3, MC1R, KIT, TRHR etc. that were reported under selection, were confirmed in our study, and this analysis also demonstrated the diversity of breeds.

Selection signature analysis reveals genes associated with tail type in Chinese indigenous sheep

“…Using only a single method to scan for selection signatures may suffer from some unknown bias (Ma et al . ); therefore, F ST was also implemented in this study.…”

Genome‐wide scan reveals divergent selection among taurine and zebu cattle populations from different regions

“…The identification of genomic regions associated with environmental and human selective pressures offers insights into the evolutionary pressures that have shaped genetic diversity (Biswas & Akey ) and can help identify causal genes underlying observed phenotypic variation and adaptation (Ma et al . ). More importantly, the identification of environment‐mediated selective signatures could shed light on the genetic basis of local adaptation in response to climate change (Joost et al .…”

Comparing genomic signatures of domestication in two Atlantic salmon (Salmo salar L.) populations with different geographical origins

“…Detecting genomic signatures of selection is a major goal of modern population genetics (Fariello et al, 2014;Nielsen, Hellmann, Hubisz, Bustamante, & Clark, 2007) as it enhances our knowledge of the molecular mechanisms shaping the genome as well as providing functional information on specific genes/genomic regions that would be of interest for breeding programs (Qanbari & Simianer, 2014). Recently, the progress of high-throughput and cost-effective genotyping techniques has offered a unique opportunity to analyze large datasets of domesticated species to study genome changes in response to domestication events (Druet, Pérez-Pardal, Charlier, & Gautier, 2013;Ma et al, 2015). In livestock species, genomewide analyses have already shown promising results in mapping traits of economic interest, such as genomic regions related to milk production in cattle (Bos tourus) (Qanbari et al, 2011), muscle development in pig (Sus scrofa) (Amaral et al, 2011), coat pigmentation and skeletal morphology in sheep (Ovis aries) (Kijas et al, 2012), or gait and size in horses (Equus caballus) (Petersen et al, 2013).…”

“…Recently, methods such as whole genome sequencing or genomewide SNP arrays have enabled the screening of a large part of the genome to detect signatures of selection in domestic and natural populations (Druet et al, 2013;Fuentes-Pardo & Ruzzante, 2017;Ma et al, 2015). Moreover, new genome scan approaches have been developed with the goal of efficiently and accurately identifying genomic footprints of selection out of the thousands of markers screened (Jensen, Foll, & Bernatchez, 2016).…”