Loci on Bos taurus chromosome 2 and Bos taurus chromosome 26 are linked with bovine respiratory disease and associated with persistent infection of bovine viral diarrhea virus

The objective of this study was to identify loci linked with bovine respiratory disease (BRD) and subsequently to determine if these same loci were associated with bovine viral diarrhea virus persistent infection (BVD-PI) in affected calves or their dams. A genome-wide linkage study using 312 microsatellites was conducted to identify loci linked with BRD in a Brahman × Hereford sire half-sib family. Disease incidence was recorded from birth to slaughter by daily monitoring. Linkage was suggestive for a QTL on BTA2 (F = 7.31, P = 0.007) and BTA26 (F = 10.46, P = 0.001). Six and 7 markers were added and genotyped between 110 and 126 cM on BTA2 and between 42 and 72 cM on BTA26, respectively, in the intervals where linkage was found. These markers were used to reevaluate the Brahman × Hereford family and to evaluate 3 additional crossbred half-sib families. Linkage was found with BRD on BTA2 (F = 4.94, P < 0.01), with a peak at 110 cM, and on BTA26 (F = 4.03, P < 0.05), with peaks at 42 and 52 cM. The same markers were then tested for an association with BVD-PI in 1) BVD-PI calves compared with age-matched unaffected calves from the same herd or 2) dams with BVD-PI compared with age-matched unaffected calves. Sixty commercial beef cow-calf herds were tested for BVD-PI, and 79 calves from 8 ranches had BVD-PI. Four of 6 markers were associated (P = 4.8 × 10(-9) to P = 0.01) with BVD-PI on BTA2, and 4 of 7 markers were associated (P = 0.008 to P = 0.04) with BVD-PI on BTA26 when BVD-PI calves were compared with unaffected calves. The comparison of BVD-PI dams with unaffected calves detected associations with BVD-PI for all markers tested on BTA2 (P = 3 × 10(-9) to P = 0.005) and for 3 of 7 markers on BTA26 (P = 1.4 × 10(-6) to P = 0.006).

A whole genome association analysis identifies loci associated with Mycobacterium avium subsp. paratuberculosis infection status in US holstein cattle

The purpose of this study was to identify loci associated with Mycobacterium avium subspecies paratuberculosis (Map) infection status in US Holsteins using the Illumina BovineSNP50 BeadChip whole genome single nucleotide polymorphism (SNP) assay. Two hundred forty-five cows from dairies in New York, Pennsylvania and Vermont enrolled in longitudinal herd studies between January 1999 and November 2007 were assessed for the presence of Map in both faecal and tissue samples. An animal was considered tissue infected if any sample contained at least one colony forming unit of Map per gram of tissue (CFU/g) and the same definition was employed for faecal samples. Each animal was genotyped with the Illumina BovineSNP50 BeadChip and after quality assurance filtering, 218 animals and 45 683 SNPs remained. We sought to identify loci associated with four different case/control classifications: presence of Map in the tissue, presence of Map in faeces, presence of Map in both tissue and faeces and presence of Map in tissue but not faeces. A case-control genome wide association study was conducted to test the four different classifications of Map infection status (cases) when compared with a Map-negative control group (control). Regions on chromosomes 1, 5, 7, 8, 16, 21 and 23 were identified with moderate significance (P < 5 x 10(-5)). Two regions, one on chromosome 3 (near EDN2) and another on chromosome 9 (no positional gene candidates), were identified with a high level of association to the presence of Map in tissue and both tissue and faeces respectively (P < 5 x 10(-7), genome-wide Bonferonni P < 0.05).