Haplotypes that include the integrin alpha 11 gene are associated with tick burden in cattle

Background: Infestations on cattle by the ectoparasite Boophilus (Rhipicephalus) microplus (cattle tick) impact negatively on animal production systems. Host resistance to tick infestation has a low to moderate heritability in the range 0.13 - 0.64 in Australia. Previous studies identified a QTL on bovine chromosome 10 (BTA10) linked to tick burden in cattle.Results: To confirm these associations, we collected genotypes of 17 SNP from BTA10, including three obtained by sequencing part of the ITGA11 (Integrin alpha 11) gene. Initially, we genotyped 1,055 dairy cattle for the 17 SNP, and then genotyped 557 Brahman and 216 Tropical Composite beef cattle for 11 of the 17 SNP. In total, 7 of the SNP were significantly (P < 0.05) associated with tick burden tested in any of the samples. One SNP, ss161109814, was significantly (P < 0.05) associated with tick burden in both the taurine and the Brahman sample, but the favourable allele was different. Haplotypes for three and for 10 SNP were more significantly (P < 0.001) associated with tick burden than SNP analysed individually. Some of the common haplotypes with the largest sample sizes explained between 1.3% and 1.5% of the residual variance in tick burden.Conclusions: These analyses confirm the location of a QTL affecting tick burden on BTA10 and position it close to the ITGA11 gene. The presence of a significant association in such widely divergent animals suggests that further SNP discovery in this region to detect causal mutations would be warranted

The Genetic Architecture of Climatic Adaptation of Tropical Cattle

Adaptation of global food systems to climate change is essential to feed the world. Tropical cattle production, a mainstay of profitability for farmers in the developing world, is dominated by heat, lack of water, poor quality feedstuffs, parasites, and tropical diseases. In these systems European cattle suffer significant stock loss, and the cross breeding of taurine x indicine cattle is unpredictable due to the dilution of adaptation to heat and tropical diseases. We explored the genetic architecture of ten traits of tropical cattle production using genome wide association studies of 4,662 animals varying from 0% to 100% indicine. We show that nine of the ten have genetic architectures that include genes of major effect, and in one case, a single location that accounted for more than 71% of the genetic variation. One genetic region in particular had effects on parasite resistance, yearling weight, body condition score, coat colour and penile sheath score. This region, extending 20 Mb on BTA5, appeared to be under genetic selection possibly through maintenance of haplotypes by breeders. We found that the amount of genetic variation and the genetic correlations between traits did not depend upon the degree of indicine content in the animals. Climate change is expected to expand some conditions of the tropics to more temperate environments, which may impact negatively on global livestock health and production. Our results point to several important genes that have large effects on adaptation that could be introduced into more temperate cattle without detrimental effects on productivity

The Genetic Architecture of Climatic Adaptation of Tropical Cattle

Adaptation of global food systems to climate change is essential to feed the world. Tropical cattle production, a mainstay of profitability for farmers in the developing world, is dominated by heat, lack of water, poor quality feedstuffs, parasites, and tropical diseases. In these systems European cattle suffer significant stock loss, and the cross breeding of taurine x indicine cattle is unpredictable due to the dilution of adaptation to heat and tropical diseases. We explored the genetic architecture of ten traits of tropical cattle production using genome wide association studies of 4,662 animals varying from 0% to 100% indicine. We show that nine of the ten have genetic architectures that include genes of major effect, and in one case, a single location that accounted for more than 71% of the genetic variation. One genetic region in particular had effects on parasite resistance, yearling weight, body condition score, coat colour and penile sheath score. This region, extending 20 Mb on BTA5, appeared to be under genetic selection possibly through maintenance of haplotypes by breeders. We found that the amount of genetic variation and the genetic correlations between traits did not depend upon the degree of indicine content in the animals. Climate change is expected to expand some conditions of the tropics to more temperate environments, which may impact negatively on global livestock health and production. Our results point to several important genes that have large effects on adaptation that could be introduced into more temperate cattle without detrimental effects on productivity

The use of anaesthesia and analgesia during dehorning and their effects on the welfare of Bos indicus cattle

In northern Australia, cattle genotypes are predominantly Bos indicus-derived and the extensive nature of the production systems mean they are commonly dehorned at 5-9 months of age. Dehorning at this age is permitted without the use of anaesthetics or analgesics. To adopt pain relief management, producers must be convinced it is effective and practical. We examined the effects on welfare of the administration of a local anaesthetic and/or a non-steroidal anti-inflammatory drug (NSAID) during the dehorning of Brahman heifers (animal ethics approval RH245/08). Weaners, 5-7 months-old, were allocated to four treatments (n=15/group): Sham dehorn (S); Dehorn only (D); Dehorn + local anaesthetic (cornual block) + NSAID (LA/NSAID); and Dehorn + NSAID (NSAID). Blood samples were taken, via jugular venipuncture, 20min before treatment then 0.5, 1, 1.5, 2, 3, 5, 7, 9, 24, 48 and 72 hours and 2, 4 and 6 weeks post-dehorning. Liveweights were recorded fortnightly for 8 weeks. Counts of behaviour during dehorning showed LA/NSAID vocalised (mean±s.e; 1.6±0.9) and struggled (1.9±0.9) less (GLM,

Fine-mapping the POLL locus in Brahman cattle yields the diagnostic marker CSAFG29

The POLL locus has been mapped to the centromeric region of bovine chromosome 1 (BTA1) in both taurine breeds and taurine-indicine crosses in an interval of approximately 1 Mb. It has not yet been mapped in pure-bred zebu cattle. Despite several efforts, neither causative mutations in candidate genes nor a singular diagnostic DNA marker has been identified. In this study, we genotyped a total of 68 Brahman cattle and 20 Hereford cattle informative for the POLL locus for 33 DNA microsatellites, 16 of which we identified de novo from the bovine genome sequence, mapping the POLL locus to the region of the genes IFNAR2 and SYNJ1. The 303-bp allele of the new microsatellite, CSAFG29, showed strong association with the POLL allele. We then genotyped 855 Brahman cattle for CSAFG29 and confirmed the association between the 303-bp allele and POLL. To determine whether the same association was found in taurine breeds, we genotyped 334 animals of the Angus, Hereford and Limousin breeds and 376 animals of the Brangus, Droughtmaster and Santa Gertrudis composite taurine-zebu breeds. The association between the 303-bp allele and POLL was confirmed in these breeds; however, an additional allele (305 bp) was also associated but not fully predictive of POLL. Across the data, CSAFG29 was in sufficient linkage disequilibrium to the POLL allele in Australian Brahman cattle that it could potentially be used as a diagnostic marker in that breed, but this may not be the case in other breeds. Further, we provide confirmatory evidence that the scur phenotype generally occurs in animals that are heterozygous for the POLL allele. © 2012 Commonwealth of Australia, Animal Genetic

The Genetic Architecture of Climatic Adaptation of Tropical Cattle

<div><p>Adaptation of global food systems to climate change is essential to feed the world. Tropical cattle production, a mainstay of profitability for farmers in the developing world, is dominated by heat, lack of water, poor quality feedstuffs, parasites, and tropical diseases. In these systems European cattle suffer significant stock loss, and the cross breeding of taurine x indicine cattle is unpredictable due to the dilution of adaptation to heat and tropical diseases. We explored the genetic architecture of ten traits of tropical cattle production using genome wide association studies of 4,662 animals varying from 0% to 100% indicine. We show that nine of the ten have genetic architectures that include genes of major effect, and in one case, a single location that accounted for more than 71% of the genetic variation. One genetic region in particular had effects on parasite resistance, yearling weight, body condition score, coat colour and penile sheath score. This region, extending 20 Mb on BTA5, appeared to be under genetic selection possibly through maintenance of haplotypes by breeders. We found that the amount of genetic variation and the genetic correlations between traits did not depend upon the degree of indicine content in the animals. Climate change is expected to expand some conditions of the tropics to more temperate environments, which may impact negatively on global livestock health and production. Our results point to several important genes that have large effects on adaptation that could be introduced into more temperate cattle without detrimental effects on productivity.</p></div

Estimated effect of indicine content (indicine%).

A<p>The observation of the empirical density having a clear mode at ∼30% of indicine% (<a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0113284#pone-0113284-g001" target="_blank">Figure 1b</a>) encouraged the exploration of the effect of indicine content separate for each group.</p><p>Estimated effect of indicine content (indicine%).</p

Heritabilities (diagonal), genetic (top) and phenotypic (bottom) correlations.

<p>Heritabilities (diagonal), genetic (top) and phenotypic (bottom) correlations.</p

Selected positional-candidate genes (P<0.01 both breeds) and its different-expression (P<0.05) in muscle before and after undernutrition period^*.

<p>*BRM – Brahman; COMP – Tropical Composite; DE – fold change in gene-expression; Ref trait – trait for which the gene was significantly associated: C – COND, Y – YWT; a – estimated SNP effect; LogP BRM and LogP COMP – -log(p-value) in Brahman and Tropical Composite. If a gene had more than one SNP associated to the trait, the SNP with lower p-value combined in both breeds was selected to represent the gene. REML estimates of genetic variance: COND BRM  = 0.175, COND COMP  = 0.110, YWT BRM 157.30, YWT COMP 348.14.</p><p>Selected positional-candidate genes (P<0.01 both breeds) and its different-expression (P<0.05) in muscle before and after undernutrition period^{<a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0113284#nt105" target="_blank">*</a>}.</p

Cattle genetic differences: (a) a Tropical Composite (left) and a Brahman bull (right).

<p>(b) Distribution of indicine% across the two samples showing a mode at ∼30% for Tropical Composite (red) and ∼95% for Brahman (blue) cattle. (c) Multi-dimensional scaling plot showing a clustering of the Brahman (blue) and Tropical Composite (red) cattle relative to the reference samples of Angus (black) and Nelore (green). (d) Genetic relationship matrices based on genotype similarity among individuals for Tropical Composite (left) and Brahman (right) samples where the diagonal blocks show paternal half-sib families.</p