A deep catalog of autosomal single nucleotide variation in the pig

PloS One
Erica BiancoM Pérez-Enciso

Abstract

A comprehensive catalog of variability in a given species is useful for many important purposes, e.g., designing high density arrays or pinpointing potential mutations of economic or physiological interest. Here we provide a genomewide, worldwide catalog of single nucleotide variants by simultaneously analyzing the shotgun sequence of 128 pigs and five suid outgroups. Despite the high SNP missing rate of some individuals (up to 88%), we retrieved over 48 million high quality variants. Of them, we were able to assess the ancestral allele of more than 39M biallelic SNPs. We found SNPs in 21,455 out of the 25,322 annotated genes in pig assembly 10.2. The annotation showed that more than 40% of the variants were novel variants, not present in dbSNP. Surprisingly, we found a large variability in transition / transversion rate along the genome, which is very well explained (R2=0.79) primarily by genome differences in in CpG content and recombination rate. The number of SNPs per window also varied but was less dependent of known factors such as gene density, missing rate or recombination (R2=0.48). When we divided the samples in four groups, Asian wild boar (ASWB), Asian domestics (ASDM), European wild boar (EUWB) and European domesti...Continue Reading

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Citations

Dec 8, 2015·Frontiers in Genetics·Amanda WarrMick Watson
Aug 10, 2017·Molecular Reproduction and Development·Louisa J ZakEgbert F Knol
Dec 14, 2019·Genes & Genomics·Da-Hye SonYong-Min Kim
Sep 15, 2016·Molecular Reproduction and Development·Jiaxue CaoHongping Zhang
May 14, 2017·G3 : Genes - Genomes - Genetics·Jordi Leno-ColoradoMiguel Pérez-Enciso
Mar 16, 2019·PLoS Genetics·Martijn F L DerksHendrik-Jan Megens
Dec 4, 2016·Genetics·Miguel Pérez-EncisoAndrés Legarra
Apr 19, 2019·Genetics, Selection, Evolution : GSE·Martin JohnssonJohn M Hickey
Feb 10, 2021·BMC Genomics·Maulana M NajiGábor Mészáros
Feb 4, 2021·Molecular Ecology Resources·Sara Guirao-Rico, Josefa González

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Methods Mentioned

BETA
genotyping

Software Mentioned

gplots R library
SIFT
Ensembl
samtools
venn
IndelRealigner
mstatspop
varFilter
VeP
MaCS

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