Identification of Signatures of Selection by Whole-Genome Resequencing of a Chinese Native Pig

Abstract

Identification of genomic signatures of selection that help reveal genetic mechanisms underlying traits in domesticated pigs is of importance. Anqing six-end-white pig (ASP), a representative of the native breeds in China, has many distinguishing phenotypic characteristics. To identify the genomic signatures of selection of the ASP, wholegenome sequencing of 20 ASPs produced 469.01 Gb of sequence data and more than 26 million single-nucleotide polymorphisms. Combining these data with the available whole genomes of 13 Chinese wild boars, 157 selected regions harboring 48 protein-coding genes were identified by applying the polymorphism levels (θπ) and genetic differentiation (F ST) based cross approaches. The genes found to be positively selected in ASP are involved in crucial biological processes such as coat color (MC1R), salivary secretion (STATH), reproduction (SPIRE2, OSBP2, LIMK2, FANCA, and CABS1), olfactory transduction (OR5K4), and growth (NPY1R, NPY5R, and SELENOM). Our research increased the knowledge of ASP phenotype-related genes and help to improve our understanding of the underlying biological mechanisms and provide valuable genetic resources that enable effective use of pigs in agricultural production.

Population genomic, olfactory, dietary, and gut microbiota analyses demonstrate the unique evolutionary trajectory of feral pigs

“…Interestingly, feral pigs also possess some regions with F ST values exceeding the threshold and hosting genes involved in meat quality (MYOT and FRMD8: Kim et al, 2020; Velez‐Irizarry et al, 2019), feed efficiency (VPR1 and PFKFB4: Hao et al, 2016; Hou et al, 2018; Yun et al, 2012), uptake and carbohydrate metabolism (SLC16A1 and LNPEP: Bosse et al, 2015; Ghareeb et al, 2015; Liu et al, 2015), obesity and fat deposition (AGBL4 and NR2C2: Locke et al, 2015; Ramayo‐Caldas et al, 2014) spermatogenesis and reproduction (WT1, HSPA4, HSPA9 OSBP2: Dun et al, 2012; Hashemitabar et al, 2015; Lahbib‐Mansais et al, 1997; Zhang, Yang, et al, 2020), brain development (DAB1: Long et al, 2011) and immunity (SH2D2A, ANKRD34B, ERAP2, BHLHE40, MASP1: Al‐Shaibi & Ghosh, 2004; Andrés et al, 2010; Berge et al, 2012; Boldt et al, 2016; Lin et al, 2014). Some regions under selection have been identified in the wild form as well, although they only slightly exceed the threshold value.…”

Assessing Genomic Diversity and Selective Pressures in Bohai Black Cattle Using Whole-Genome Sequencing Data

“…All of these pathways had p -values less than 0.05. In particular, some overlapped candidate genes were strongly selected in Bohai Black cattle and related to muscle development ( ITGA9 , ENAH , CAPG , ABI2 , and ISLR ) [ 39 , 40 ], fat deposition ( TBC1D1 , CYB5R4 , TUSC3 , and EPS8 ) [ 41 , 42 , 43 ], reproduction traits ( SPIRE2 , KHDRBS2 , and FANCA ) [ 44 , 45 ], and immune system ( CD84 , SLAMF6 , SLAMF1 , and CDK10 ) [ 46 , 47 , 48 ] in Bohai Black cattle ( Tables S9 and S10 , Figure 4 a). Interestingly, the selection signal was found on BTA3 (3:9070076-9175511) and contained the CD84 and SLAMF6 genes from the two tests ( Figure 4 b,c).…”

“…The KHDRBS2 gene has been found to be possibly associated with reproduction traits under positive selection in goats using a genome-wide association study (GWAS) [ 44 ]. The SPIRE2 and FANCA genes were identified as candidate genes related to reproduction in indigenous Chinese pigs [ 45 ]. Therefore, we boldly speculate that these genes are associated with reproductive performance in Bohai Black cattle.…”

Mining livestock genome datasets for an unconventional characterization of animal DNA viromes

“…A total of 3.2% of the pig datasets contained reads from Porcine cytomegalovirus (Suid betaherpesvirus 2) demonstrating that it would be possible to use WGS as diagnostic method to identify pigs infected with this immunosuppressive virus that raises a specific attention in xenotransplantation [95]. The identification of Porcine polyomavirus 2 in a WGS datasets of a Chinese pig generated in 2020 [72] indicates that this virus has been recently expanded in another continent from the original identification in 2018 in USA [71]. This result demonstrates in practice the usefulness of our approach to monitor the diffusion of potential harmful viruses.…”

“…Porcine polyomavirus (NCBI:NC_040714; Fig. 3), recently described for the first time by a metagenomic sequencing of pooled nasal swabs from pre-weaned pigs with unexplained respiratory disease raised in a Minnesota farm [71], was identified within the unmapped reads of a Chinese Anqing Six-end-white pig [72].…”