Abstract
Pigs have experienced long-term selections, resulting in dramatic phenotypic changes. Structural variants (SVs) are reported to exert extensive impacts on phenotypic changes. We built a high resolution and informative SV map based on high-depth sequencing data from 66 Chinese domestic and wild pigs. We inferred the SV formation mechanisms in the pig genome and used SVs as materials to perform a population-level analysis. We detected the selection signals on chromosome X for northern Chinese domestic pigs, as well as the differentiated loci across the whole genome. Analysis showed that these loci differ between southern and northern Chinese domestic pigs. Our results based on SVs provide new insights into genetic differences in Chinese pigs.
Highlights
Structural variants (SVs), including deletions, duplications, and inversions, widely exist in the genome
We created a precise set of SVs of which SVs were less than 60 kb from the merged set, and with the breakpoints refined at single-nucleotide resolution via local de novo assembly (Table 2 and S3 Table)
We investigated the differentiated loci between southern domestic Chinese pigs (SCPG) and northern domestic Chinese pigs (NCPG) as well (S11 Table), Gene Ontology (GO) enrichment analysis showed over-representation of functional categories related to the local adaptation to hot and cold temperatures in low- and high-latitude areas (S14 Fig and Table 3), including sprouting angiogenesis (TEK, KLF4, EFNB2, E2F8 and PARVA; p = 0.0031), cardiac septum development (SMAD6, SAV1, PITX2, ADAMTS6 and PARVA; p = 0.0136), kidney development enriched category (SMAD6, EFNB2, ARID5B, ADAMTS6, WT1, KLHL3, CALB1, TFAP2A, PKD2 and CENPF; p = 0.0053), and transmission of nerve impulse (GRM7, GLRA1, SCN3A and SCN8A)
Summary
Structural variants (SVs), including deletions, duplications, and inversions, widely exist in the genome. It has been estimated that the occurrence rate of deletions is 0.113 deletions per haploid genome per generation in humans [1,2]. Current advances in genome sequencing techniques have enabled the high-throughput and accurate detection of SVs. For example, the recent releases of a high-resolution deletion map of 1,092 human genomes which contains 8,943 high-quality deletions and an SV map of 2,504 individuals provided a comprehensive survey of 68,818 SVs in the human genome [2,3]. It has been widely reported that SVs cause various phenotype changes. A 900-kb inversion polymorphism enriched in the European population was discovered to be associated with increased fecundity in humans [4]. An inversion on chicken chromosome 7 causes the transient ectopic expression of MNR2, resulting in the rose-comb phenotype [5]. The white coat color in goats and pigs was found to be caused by duplications of ASIP [6] and KIT [7,8], respectively
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