Text S1. Additional Information About the Horses Studied in This Project

Text S1. Additional information about the horses studied in this project.

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.

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).

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.

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.