Abstract
Structural variants (SVs) represent essential forms of genetic variation, and they are associated with various phenotypic traits in a wide range of important livestock species. However, the distribution of SVs in the pig genome has not been fully characterized, and the function of SVs in the economic traits of pig has rarely been studied, especially for most domestic pig breeds. Meishan pig is one of the most famous Chinese domestic pig breeds, with excellent reproductive performance. Here, to explore the genome characters of Meishan pig, we construct an SV map of porcine using whole-genome sequencing data and report 33,698 SVs in 305 individuals of 55 globally distributed pig breeds. We perform selective signature analysis using these SVs, and a number of candidate variants are successfully identified. Especially for the Meishan pig, 64 novel significant selection regions are detected in its genome. A 140-bp deletion in the Indoleamine 2,3-Dioxygenase 2 (IDO2) gene, is shown to be associated with reproduction traits in Meishan pig. In addition, we detect two duplications only existing in Meishan pig. Moreover, the two duplications are separately located in cytochrome P450 family 2 subfamily J member 2 (CYP2J2) gene and phospholipase A2 group IVA (PLA2G4A) gene, which are related to the reproduction trait. Our study provides new insights into the role of selection in SVs' evolution and how SVs contribute to phenotypic variation in pigs.
Highlights
Structural variants (SVs) are significant contributors to genetic diversity, and it includes insertions/deletions (InDels), inversions, translocations and copy number variations (CNVs) (Alkan et al, 2011; Tattini et al, 2015)
We randomly validated eight SVs with Polymerase Chain Reaction (PCR) amplification, and they existed in Meishan pig and Tibetan wild boars, respectively
Among all the SVs detected in Meishan pig, there were 18,690 indels (17,690 deletions and 1,000 insertions), 112 inversions, 8 translocations, and 1,960 CNVs
Summary
Structural variants (SVs) are significant contributors to genetic diversity, and it includes insertions/deletions (InDels), inversions, translocations and copy number variations (CNVs) (Alkan et al, 2011; Tattini et al, 2015). “Balanced” SVs refer to rearrangements hardly causing major gain or loss of genomic DNA, including inversions and translocations. “Unbalanced” SVs, containing deletions, insertions of novel sequences and duplications, which can result in differences in the numbers of base pairs (bp) among individual genomes (Escaramís et al, 2015; Collins et al, 2017). Structural Variants Reveal Selective Regions in phenotypic traits; previous studies have indicated that SVs were more significantly related to phenotypic diversity than single nucleotide polymorphisms (SNPs) (Chiang et al, 2017). The study of SVs can improve our understanding of the evolution of populations, phenotypic polymorphisms, and the functional genome
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