Admixture mapping of tuberculosis and pigmentation-related traits in an Africanâ€“European hybrid cattle population

Kassahun, Yonas; Mattiangeli, Valeria; Ameni, Gobena; Hailu, Elena; Aseffa, Abraham; Young, Douglas B.; Hewinson, R. Glyn; Vordermeier, H. Martin; Bradley, Daniel G.

doi:10.3389/fgene.2015.00210

Cited by 12 publications

(19 citation statements)

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“…The present study did not confirm QTL identified in previous association studies on bTB susceptibility [17–21], which further supports the notion of a polygenic trait controlled by multiple genes. The closest GWA results on BTA 23 were reported by Richardson et al [18] who identified a QTL about 28 Mb downstream on the same chromosome for Irish dairy cattle.…”

Section: Discussioncontrasting

confidence: 91%

“…Tsairidou et al [20] applied RHM to perform a meta-analysis using the datasets from previous studies in the Republic of Ireland [17] and Northern Ireland [19], and identified a new region on BTA 6. Furthermore, Kassahun et al [21] also identified a SNP on BTA 6 associated with bTB in a mixed breed cattle population in Ethiopia; however, this region was distinct from that of Tsairidou et al [20]. In general, genomic studies performed to date have not revealed any major common QTL; therefore further studies with independent populations are required.…”

Section: Introductionmentioning

confidence: 99%

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Genomic regions underlying susceptibility to bovine tuberculosis in Holstein-Friesian cattle

et al. 2017

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BackgroundThe significant social and economic loss as a result of bovine tuberculosis (bTB) presents a continuous challenge to cattle industries in the UK and worldwide. However, host genetic variation in cattle susceptibility to bTB provides an opportunity to select for resistant animals and further understand the genetic mechanisms underlying disease dynamics.MethodsThe present study identified genomic regions associated with susceptibility to bTB using genome-wide association (GWA), regional heritability mapping (RHM) and chromosome association approaches. Phenotypes comprised de-regressed estimated breeding values of 804 Holstein-Friesian sires and pertained to three bTB indicator traits: i) positive reactors to the skin test with positive post-mortem examination results (phenotype 1); ii) positive reactors to the skin test regardless of post-mortem examination results (phenotype 2) and iii) as in (ii) plus non-reactors and inconclusive reactors to the skin tests with positive post-mortem examination results (phenotype 3). Genotypes based on the 50 K SNP DNA array were available and a total of 34,874 SNPs remained per animal after quality control.ResultsThe estimated polygenic heritability for susceptibility to bTB was 0.26, 0.37 and 0.34 for phenotypes 1, 2 and 3, respectively. GWA analysis identified a putative SNP on Bos taurus autosomes (BTA) 2 associated with phenotype 1, and another on BTA 23 associated with phenotype 2. Genomic regions encompassing these SNPs were found to harbour potentially relevant annotated genes. RHM confirmed the effect of these genomic regions and identified new regions on BTA 18 for phenotype 1 and BTA 3 for phenotypes 2 and 3. Heritabilities of the genomic regions ranged between 0.05 and 0.08 across the three phenotypes. Chromosome association analysis indicated a major role of BTA 23 on susceptibility to bTB.ConclusionGenomic regions and candidate genes identified in the present study provide an opportunity to further understand pathways critical to cattle susceptibility to bTB and enhance genetic improvement programmes aiming at controlling and eradicating the disease.Electronic supplementary materialThe online version of this article (doi:10.1186/s12863-017-0493-7) contains supplementary material, which is available to authorized users.

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Section: Discussioncontrasting

confidence: 91%

Section: Introductionmentioning

confidence: 99%

Genomic regions underlying susceptibility to bovine tuberculosis in Holstein-Friesian cattle

et al. 2017

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“…Our results demonstrate that some of the breeds studied have distinct genetic profiles (e.g., Kholmogory, Yakut, Yaroslavl) making them priority targets for deeper studies to reveal signatures of selection and adaptations related to local environments and for conservation purposes. We also observed that a large group of breeds had both old and recent influence from commercial European breeds (e.g., Kostroma, Kazakh Whiteheaded, Istoben) meaning that their genomes could potentially contain only a small fraction of ancestral alleles, but these could be important for surviving local conditions and can be used for admixture mapping programs aiming at economically important traits (Kassahun et al 2015). The links between the Russian breeds and breeds from other countries presented in this study form a basis for future work on contrasting their genomes to reveal causative alleles or haplotypes using a right set of related and outgroup populations for the comparison to avoid 'signal dilution' or false positive signals.…”

Section: Discussionmentioning

confidence: 83%

Genome-wide genotyping uncovers genetic profiles and history of the Russian cattle breeds

et al. 2017

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One of the most economically important areas within the Russian agricultural sector is dairy and beef cattle farming contributing about $11 billion to the Russian economy annually. Trade connections, selection and breeding have resulted in the establishment of a number of breeds that are presumably adapted to local climatic conditions. Little however is known about the ancestry and history of Russian native cattle. To address this question, we genotyped 274 individuals from 18 breeds bred in Russia and compared them to 135 additional breeds from around the world that had been genotyped previously. Our results suggest a shared ancestry between most of the Russian cattle and European taurine breeds, apart from a few breeds that shared ancestry with the Asian taurines. The Yakut cattle, belonging to the latter group, was found to be the most diverged breed in the whole combined dataset according to structure results. Haplotype sharing further suggests that the Russian cattle can be divided into four major clusters reflecting ancestral relations with other breeds. Herein, we therefore shed light on to the history of Russian cattle and identified closely related breeds to those from Russia. Our results will facilitate future research on detecting signatures of selection in cattle genomes and eventually inform future genetics-assisted livestock breeding programs in Russia and in other countries.

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“…Although the reasons for low across-study consistency are likely manifold and include different criteria to classify phenotypes and different statistical procedures, these results suggest that loci with a major effect on Johne's disease do not exist, at least in these breeds. Likewise, GWASs for susceptibility to bovine tuberculosis (caused by Mycobacterium bovis) yielded inconsistent results (Bermingham et al, 2014;Finlay et al, 2012;Kassahun et al, 2015;Richardson et al, 2016). Efforts to identify susceptibility alleles for other infectious diseases detected small-effect loci with poor replicability (reviewed in (Raszek et al, 2016)).…”

Section: Gwass In Cattle and Swinementioning

confidence: 99%

Genetic susceptibility to infectious diseases: Current status and future perspectives from genome-wide approaches

Mozzi

Pontremoli

Sironi

2018

Infection, Genetics and Evolution

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Genome-wide association studies (GWASs) have been widely applied to identify genetic factors that affect complex diseases or traits. Presently, the GWAS Catalog includes >2800 human studies. Of these, only a minority have investigated the susceptibility to infectious diseases or the response to therapies for the treatment or prevention of infections. Despite their limited application in the field, GWASs have provided valuable insights by pinpointing associations to both innate and adaptive immune response loci, as well as novel unexpected risk factors for infection susceptibility. Herein, we discuss some issues and caveats of GWASs for infectious diseases, we review the most recent findings ensuing from these studies, and we provide a brief summary of selected GWASs for infections in non-human mammals. We conclude that, although the general trend in the field of complex traits is to shift from GWAS to next-generation sequencing, important knowledge on infectious disease-related traits can be still gained by GWASs, especially for those conditions that have never been investigated using this approach. We suggest that future studies will benefit from the leveraging of information from the host's and pathogen's genomes, as well as from the exploration of models that incorporate heterogeneity across populations and phenotypes. Interactions within HLA genes or among HLA variants and polymorphisms located outside the major histocompatibility complex may also play an important role in shaping the susceptibility and response to invading pathogens.

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Admixture mapping of tuberculosis and pigmentation-related traits in an Africanâ€“European hybrid cattle population

Cited by 12 publications

References 57 publications

Genomic regions underlying susceptibility to bovine tuberculosis in Holstein-Friesian cattle

Genomic regions underlying susceptibility to bovine tuberculosis in Holstein-Friesian cattle

Genome-wide genotyping uncovers genetic profiles and history of the Russian cattle breeds

Genetic susceptibility to infectious diseases: Current status and future perspectives from genome-wide approaches

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