Identification of "selection signatures" in pigs and wild boars (review)

The pig is one of the few species that has living wild ancestors, which provides a unique opportunity to track the evolutionary history of mammals and determine the “selection signatures” caused by both domestication and natural selection (K. Chen et al., 2007). Animal selection leads to changes in certain regions in the genome associated with economically significant traits, adaptation to climate and stress conditions, immune response and resistance to diseases, and as a result of its pressure, traces are formed in the genome of animals (S.R. Keller et al., 2008), known as selection signatures (M. Kreitman, 2000). Identification of selection prints attracts special attention of evolutionary geneticists, since it can serve as a source of information, ranging from basic knowledge about evolutionary processes to functional information about genes/genomic regions (C. Schlötterer, 2003; C. Horscroft et al.). The purpose of this review is to summarize approaches used to identify “selection signatures”, as well as to analyze the detected traces of selection in domestic pigs and wild boar. The development of modern methods of full-scale research has significantly expanded the arsenal of tools that allow searching for regions subjected to selection pressure at a fundamentally new level. Analysis of data obtained using full-genome resequencing (C.J. Rubin et al., 2012; X. Li et al., 2017), full-genome genotyping on biochips of different densities (M. Huang et al., 2020; M. Muñoz et al., 2019), RADseq (Y. Li et al., 2017), RNA-seq (M. Li et al., 2017; Y. Yang et al., 2018), GBS (Y. Ma et al., 2018; K. Wang et al., 2018) is used to search for selection prints in Sus scrofa . Methods are based on scanning areas of homozygosity, as well as evaluating differences in the frequency of alleles or haplotypes between populations or generations within a population. The most commonly used statistical methods for identifying selection prints are extended haplotypic homozygosity (EHH) (P.C. Sabeti et al., 2002), integrated haplotype estimation (iHS) (B.F. Voight et al., 2006), runs of homozygous segments (ROH) (J. Gibson et al., 2006), FST-statistics (R.C. Lewontin, J. Krakauer, 1973), haplotype-based analysis (hapFLK) (M.I. Fariello et al., 2013), composite selection signal method (CSS) (I.A. Randhawa et al., 2014), and a combination of these methods. Breeding models in pig breeds differ depending on their evolution and breeding history, so studying the “selection signatures” of a large number of different breeds will help to better understand the genetic variations underlying the traits of interest. Based on these methods, large-scale fingerprint scans of diversifying selection have been successfully applied to domestic pigs. In most cases, the research was aimed at studying the evolutionary and selection mechanisms of the genome of Chinese pigs (X. Li et al., 2017; M. Chen et al., 2018). The research found genomic regions that contribute to adaptation to various climatic conditions (R.J. Cesconeto et al., 2017), as well as candidate genes associated with growth, development (K. Wang et al., 2018), reproductive traits (Z. Zhang et al., 2018) and certain aspects of the immune response (S. Yang et al., 2014). Full-genomic research of domestic resources (A. Traspov et al., 2016) showed that pig populations bred on the territory of the Russian Federation, including local ones, are a cultural achievement of domestic animal science and have their own unique structure, even though they originated with the participation of imported breeds. This may be due to several factors, including differences in origin, long periods of genetic isolation, and differences in climate and food resources. However, domestic breeding resources remain poorly studied at the moment. Thus, the proposed approaches designed to identify “selection signatures” in pigs bred on the territory of the Russian Federation and wild boar can be used to search and analyze the detected traces of selection in domestic pigs and wild boar of domestic origin.