Maps of homozygosity status for the three pigs lines SLA bb, SLA cc and SLA dd. Each figure shows a snapshot of the level of homozygosity for a given chromosome.

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Maps of homozygosity status for the three pigs lines SLA bb, SLA cc and SLA dd. Each figure shows a snapshot of the level of homozygosity for a given chromosome. Each row contains one individual’s colour- coded SNP genotype. Locations of SNPs within each chromosome run in ascending numerical order from left to right. S1 Figure

Chromosome 1 SLA bb (n=5) SLA cc (n=27) SLA dd (n=11) Homozygous for major alleleHomozygous for minor alleleHeterozygous

Chromosome 2 Homozygous for major alleleHomozygous for minor alleleHeterozygous SLA bb (n=5) SLA cc (n=27) SLA dd (n=11)

Chromosome 3 Homozygous for major alleleHomozygous for minor alleleHeterozygous SLA bb (n=5) SLA cc (n=27) SLA dd (n=11)

Chromosome 4 SLA bb (n=5) SLA cc (n=27) SLA dd (n=11) Homozygous for major alleleHomozygous for minor alleleHeterozygous

Chromosome 5 SLA bb (n=5) SLA cc (n=27) SLA dd (n=11) Homozygous for major alleleHomozygous for minor alleleHeterozygous

Chromosome 6 SLA bb (n=5) SLA cc (n=27) SLA dd (n=11) Homozygous for major alleleHomozygous for minor alleleHeterozygous

Chromosome 7 * SLA bb (n=5) SLA cc (n=27) SLA dd (n=11) * Approximate position of the MHC Homozygous for major alleleHomozygous for minor alleleHeterozygous

Chromosome 8 SLA bb (n=5) SLA cc (n=27) SLA dd (n=11) Homozygous for major alleleHomozygous for minor alleleHeterozygous

Chromosome 9 SLA bb (n=5) SLA cc (n=27) SLA dd (n=11) Homozygous for major alleleHomozygous for minor alleleHeterozygous

Chromosome 10 SLA bb (n=5) SLA cc (n=27) SLA dd (n=11) Homozygous for major alleleHomozygous for minor alleleHeterozygous

Chromosome 11 SLA bb (n=5) SLA cc (n=27) SLA dd (n=11) Homozygous for major alleleHomozygous for minor alleleHeterozygous

Chromosome 12 SLA bb (n=5) SLA cc (n=27) SLA dd (n=11) Homozygous for major alleleHomozygous for minor alleleHeterozygous

Chromosome 13 SLA bb (n=5) SLA cc (n=27) SLA dd (n=11) Homozygous for major alleleHomozygous for minor alleleHeterozygous

Chromosome 14 SLA bb (n=5) SLA cc (n=27) SLA dd (n=11) Homozygous for major alleleHomozygous for minor alleleHeterozygous

Chromosome 15 SLA bb (n=5) SLA cc (n=27) SLA dd (n=11) Homozygous for major alleleHomozygous for minor alleleHeterozygous

Chromosome 16 SLA bb (n=5) SLA cc (n=27) SLA dd (n=11) Homozygous for major alleleHomozygous for minor alleleHeterozygous

Chromosome 17 SLA bb (n=5) SLA cc (n=27) SLA dd (n=11) Homozygous for major alleleHomozygous for minor alleleHeterozygous

Chromosome 18 SLA bb (n=5) SLA cc (n=27) SLA dd (n=11) Homozygous for major alleleHomozygous for minor alleleHeterozygous