Table S1. Animal phenotypic data.

Animal / Sire / Dam / Sex / DOB / Resistance Type / Mean EPG / Serum Pepsinogen (M)
20041438 / 20011295 / 19961129 / F / 9/15/2004 / Susceptible/High / 65 / 546.1
20041439 / 20011295 / 19961129 / F / 9/15/2004 / Resistant/Low / 7 / 754.8
20041441 / 20011303 / 19971163 / M / 9/15/2004 / Susceptible/High / 45 / 2900.8
20041445 / 20011295 / 19981200 / M / 9/19/2004 / Resistant/Low / 15 / 858.4
20041451 / 20011303 / 19991226 / M / 9/23/2004 / Susceptible/High / 113 / 1805.6

For 44 Angus cattle born in 2004, the average EPG with standard deviation is 28.2 ± 24.0 and the average serum pepsinogen with standard deviation is 1010.7 ± 462.9 M. Similar overall distributions were observed in a larger group (n=~500) within this Angus population. The five selected animals (Susceptible/High or Resistant/Low) are within the top or bottom 1/3 portion of the phenotype distributions, respectively.

Table S2. Coefficients of relationships among the selected animals.

Animal / 19991210 / 19991230 / 19991238 / 19991242 / 19991218 / 19991224 / 19991229 / 19991233 / 20041438 / 20041439 / 20041441 / 20041445 / 20041451
19991210(R) / 0.0437 / 0.0718 / 0.1132 / 0.3318 / 0.1034 / 0.0872 / 0.0576 / 0.0985 / 0.0985 / 0.0856 / 0.1057 / 0.1140
19991230(R) / 0.0464 / 0.0413 / 0.0623 / 0.0493 / 0.0453 / 0.0403 / 0.0637 / 0.0637 / 0.0475 / 0.0579 / 0.0476
19991238(R) / 0.1813 / 0.0623 / 0.0527 / 0.2681 / 0.0858 / 0.1071 / 0.1071 / 0.0480 / 0.0892 / 0.0569
19991242(R) / 0.1439 / 0.0815 / 0.0667 / 0.0602 / 0.1062 / 0.1062 / 0.0643 / 0.0861 / 0.0824
19991218(S) / 0.1599 / 0.0503 / 0.0657 / 0.1471 / 0.1471 / 0.1798 / 0.1370 / 0.1659
19991224(S) / 0.0503 / 0.0645 / 0.1346 / 0.1346 / 0.1072 / 0.1395 / 0.2401
19991229(S) / 0.0880 / 0.1556 / 0.1556 / 0.0433 / 0.1182 / 0.0770
19991233(S) / 0.1188 / 0.1188 / 0.0319 / 0.1827 / 0.0586
20041438(S) / 0.6078 / 0.1097 / 0.3854 / 0.1249
20041439(R) / 0.1097 / 0.3854 / 0.1249
20041441(S) / 0.0997 / 0.3384
20041445(R) / 0.1151
20041451(S)

We examined the pedigree (Figure S1) and calculated the coefficients of relationship among the selected animals (Table S2). For mRNA expression by candidate gene array hybridization (Araujo et al., 2009), the resistant pool included 19991210, 19991230, 19991238, and 19991242 and the susceptible pool included 19991218, 19991224, 19991229, and 19991233. For array CGH samples in this study, resistant samples included 20041439 and 20041445, while susceptible samples included 20041438, 20041441, and 20041451. The average with standard deviation of coefficients of relationship between 1999 and 2004 animals was 0.1057 ± 0.0453. The biological relationship between these 2 groups of animals was similar to second to first cousins.

The covariance coefficient or coefficient of relationship between individuals X and Y was calculated using the SAS INBREED procedure: Cov(X,Y) = 2fXY where fXY is the coancestry between X and Y (Falconer and Mackay 1996, p.153; Crow and Kimura 1970, p.134). The coancestry is defined as the probability that the alleles at a particular locus chosen at random from two individuals are identical by descent.
Table S3. Array CGH plan.

Array No. / Chip / Test Animal / Reference Animal
1 / 6867002 / 20041438 / 20041439
2 / 7327702 / 20041441 / 20041445
3 / 7533902 / 20041451 / 20041445

Table S4. qPCR primer and probe sequence information.

Name / Btau_4.0 / Btau_3.1
Chr / Strand / Start / End / Chr / Strand / Start / End
chr9NR0B1_R / chrUn.004.21 / + / 218225 / 218244 / chr9 / + / 57344683 / 57344702
chr9NR0B1_L / chrUn.004.21 / - / 218411 / 218430 / chr9 / - / 57344869 / 57344888
chr25MAD1L1_L / chr25 / + / 43115297 / 43115316 / chr25 / + / 40025825 / 40025844
chr25MAD1L1_R / chr25 / - / 43115516 / 43115535 / chr25 / - / 40026044 / 40026063
chrUn.003.251_L / chrUn.004.111 / + / 261781 / 261800 / chrUn.003.251 / + / 261781 / 261800
chrUn.003.251_R / chrUn.004.111 / - / 261919 / 261938 / chrUn.003.251 / - / 261875 / 261894
chrUn.003.1186_L / chrUn.004.531 / + / 64569 / 64588 / chrUn.003.1186 / + / 64569 / 64588
chrUn.003.1186_R / chrUn.004.531 / - / 64782 / 64801 / chrUn.003.1186 / - / 64782 / 64801

Table S5. Enrichment of PANTHER molecular function, biological process, and pathway terms.

Genome (23415) / CNV (95) / Expected / Enrichment / P-value
Molecular Function
Defense/immunity protein / 706 / 33 / 2.86 / + / 1.14E-24
Immunoglobulin receptor family member / 271 / 23 / 1.1 / + / 1.36E-21
Receptor / 2862 / 48 / 11.61 / + / 3.59E-18
Other defense and immunity protein / 137 / 10 / 0.56 / + / 4.87E-08
ATP-binding cassette (ABC) transporter / 104 / 9 / 0.42 / + / 9.02E-08
Other receptor / 366 / 10 / 1.48 / + / 4.22E-04
Transporter / 838 / 11 / 3.4 / + / 1.75E-02
Biological Process
Immunity and defense / 1912 / 43 / 7.76 / + / 1.44E-20
T-cellmediated immunity / 349 / 24 / 1.42 / + / 1.48E-20
Oncogenesis / 531 / 22 / 2.15 / + / 8.58E-15
Natural killer cell-mediated immunity / 120 / 10 / 0.49 / + / 1.23E-08
Other oncogenesis / 103 / 9 / 0.42 / + / 7.47E-08
Detoxification / 130 / 9 / 0.53 / + / 5.56E-07
Cytokine/chemokine-mediated immunity / 146 / 9 / 0.59 / + / 1.50E-06
Extracellular transport and import / 159 / 9 / 0.65 / + / 3.09E-06
Small molecule transport / 218 / 9 / 0.88 / + / 4.35E-05
Chemosensory perception / 1073 / 14 / 4.35 / + / 1.60E-02
Olfaction / 1063 / 14 / 4.31 / + / 1.98E-02
Pathway
Tcell activation / 244 / 23 / 0.99 / + / 1.36E-22

Figure S1. Pedigree of the Angus population.

Figure S2. FISH confirmation. Examples of interphase 2-color FISH include 3 new BAC clones. Clones 481N5, 28A8, and 466B6 (red) were identified in CNV2, 3, and 4, corresponding to CLEC5A, DYNLL1DYNLL2, and ULBP17, respectively. Increased signal intensity was confirmed using cohybridization with a unique control BAC clone (297K6, green) in the same nucleus. The first 2 BACs produced variable signal count and/or intensity, 481N5: 1 & 2, 1, and 2 and 28A8: 1 & 2, 1 & 2, and 2. The third BAC 466B6 was not variable: 2, 2, and 2 in these 3 cell lines, respectively. For other BACs, FISH results are also available online at or see Table S8 and Figure S5 in Liu et al. (2010).

Figure S3. Pathway analyses: KEGG (Kyoto Encyclopedia of Genes and Genomes) antigen processing and presentation reference pathway in which CIITA is involved.