<p>Text S1. Additional information about the horses studied in this project. </p><p>All eight horses that contributed sequences to this study were screened for microsatellite alleles at 11 intra-MHC loci (Table S1). With the exception of horse #3474, the BAC library DNA donor, and horse 2446, all were homozygous at each microsatellite locus (Table 1, Table S1). Tseng and colleagues reported three microsatellite haplotypes associated with the ELA-A3 serotype (Table S1); horse #3474 is heterozygous for the -A3b and -A3c types (Tseng et al., 2010). Horse 3729 is homozygous for the -A3a type. Horse 2446 is homozygous by serology for the ELA-A10 serotype but shows minor variation in the microsatellite typing at the distal end of Class II (Table 1, Table S1) which are reported as ELA-A10 a & b microsatellite haplotypes. </p><p>The ELA-A2 line founder was horse #0834. He was the product of mating an ELA-A2/-A3 stallion (#0002) to an ELA–A2/A3 mare (#0051). #0834 was determined to be homozygous for -A2 by serology and then later, microsatellite analysis. He is the donor of several early MHC Class I and Class II alleles in the public domain (GenBank accession #s M95409, M95410, L33909, L33910), and he produced a single sequence at every Class II locus investigated in this study. His son, #3475, is currently serving as our ELA-A2 homozygous stallion. Like his father, #0834, he is homozygous for ELA, and his DNA was used for Next Generation Sequencing (NGS) (Table 1).</p><p>The ELA-A3 line (Figure S1) was founded by two unrelated Thoroughbreds, stallion #2505 and mare #1535, who were both homozygous by serology for ELA–A3, and produced negative results in MLC assays when tested against each other. This sire/dam combination produced four homozygous offspring, including stallion #3105. #3105 is the sire of both #3474, the stallion whose DNA was used for the horse BAC library, and #3729, the mare whose DNA was used for the horse whole genome sequence (WGS). Sire #3105 was bred to his full sister, #2885, to produce stallion #3474. Prior to that mating, mare #2885 was bred back to her sire, #2505, resulting in mare #3157. Finally, mare #3157 was bred to stallion #3105 resulting in mare #3729. </p><p>Tseng, C.T., D. Miller, J. Cassano, E. Bailey, and D.F. Antczak. 2010. Identification of equine major histocompatibility complex haplotypes using polymorphic microsatellites. Anim Genet 41 Suppl 2:150-153. </p>