Whole-genome genotype data for French Large White pigs from two distinct sampling times

Genotype data at plink binary format for 36 pigs from the french Large White breed: 13 animals from the female line born in 2014 and 2015, 13 animals from the male line born between 2012 and 2016, and 10 animals from a common ancestral line, born in 1977. These genotypes were obtained from individual whole genome sequencing (WGS) data, whiwh are available at https://www.ebi.ac.uk/ena under the accession number PRJEB51909.

Two different genotype datasets were obtained from the raw WGS:

1) snp20_auto_cr (.bed/bim/fam): High quality autosomal SNPs, called by 3 different software, with a call rate of at least 90%

2) all10_auto (.bed/bim/fam): All SNPs or indels called by at least one of 3 different software.

More details about these datasets and their use can be found in the following study:

Boitard et al (under revision): Whole-genome sequencing of cryo-preserved resources from French Large White pigs at two distinct sampling times reveals strong signatures of convergent and divergent selection between the dam and sire lines.