[en] Despite single nucleotide polymorphism (SNP) availability and frequent cost reduction has allowed genome-wide association studies even in complex traits as tick resistance, the use of this information source in SNP by environment interaction context is unknown for many economically important traits in cattle. We aimed at identifying putative genomic regions explaining differences in tick resistance in Hereford and Braford cattle under SNP by environment point of view as well as to identify candidate genes derived from outliers/significant markers. The environment was defined as contemporary group means of tick counts, since they seemed to be the most appropriate entities to describe the environmental gradient in beef cattle. A total of 4363 animals having tick counts (n = 10 673) originated from 197 sires and 3966 dams were used. Genotypes were acquired on 3591 of these cattle.From top 1% SNPs (410) having the greatest effects in each environment, 75 were consistently relevant in all environments, whichindicated SNP by environment interaction. The outliers/significant SNPs were mapped on chromosomes 1, 2, 5, 6, 7, 9, 11, 13, 14, 15, 16, 18, 21, 23, 24, 26 and 28, and potential candidate genes were detected across environments. The presence of SNP by environment interaction for tick resistance indicates that genetic expression of resistance depends upon tick burden. Markers with major portion of genetic variance explained across environments appeared to be close to genes with different direct or indirect functions related to immune system, inflammatory process and mechanisms of tissue destruction/repair, such as energy metabolism and cell differentiation.
Disciplines :
Animal production & animal husbandry
Author, co-author :
REIS MOTA, Rodrigo ; Université de Liège - ULiège > Agronomie, Bio-ingénierie et Chimie (AgroBioChem) > Ingénierie des productions animales et nutrition
Fonseca e Silva, Fabyano; Universidade Federal de Viçosa > Animal Science
Lopes, Paulo Sávio; Universidade Federal de Viçosa > Animal Science
Tempelman, Robert John; Michigan State University > Animal Science
Sollero, Bruna Pena; Embrapa South Livestock, Bagé, Brazil
Aguilar, Ignacio; National Agricultural Research Institute, 90200 Las Brujas, Uruguay
Flores Cardoso, Fernando; Embrapa South Livestock, Bagé, Brazil
Language :
English
Title :
Analyses of reaction norms reveal new chromosome regions associated with tick resistance in cattle
Publication date :
2017
Journal title :
Animal
ISSN :
1751-7311
eISSN :
1751-732X
Publisher :
Cambridge University Press, Cambridge, United Kingdom
Astrup, E., Lekva, T., Davì, G., Otterdal, K., Santilli, F., Øie, E., Halvorsen, B., Vitale, G., A complex interaction between Rickettsia conorii and Dickkopf-1-potential role in immune evasion mechanisms in endothelial cells (2012) PloS One, 7, p. e43638
Bagnall, N., Gough, J., Cadogan, L., Burns, B., Kongsuwan, K., Expression of intracellular calcium signalling genes in cattle skin during tick infestation (2009) Parasite Immunology, 31, pp. 177-187
Biegelmeyer, P., Gulias-Gomes, C.C., Caetano, A.R., Steibel, J.P., Cardoso, F.F., Linkage disequilibrium, persistence of phase and effective population size estimates in Hereford and Braford cattle (2016) BMC Genetics, 17, p. 1
Cardoso, F., Gomes, C., Sollero, B., Oliveira, M., Roso, V., Piccoli, M., Higa, R., Aguilar, I., Genomic prediction for tick resistance in Braford and Hereford cattle (2015) Journal of Animal Science, 93, pp. 2693-2705
Cardoso, F., Tempelman, R., Linear reaction norm models for genetic merit prediction of Angus cattle under genotype by environment interaction (2012) Journal of Animal Science, 90, pp. 2130-2141
Carvalho, W.A., Domingues, R., De Azevedo Prata, M.C., Da Silva, M.V.G., De Oliveira, G.C., Guimarães, S.E.F., Machado, M.A., Microarray analysis of tick-infested skin in resistant and susceptible cattle confirms the role of inflammatory pathways in immune activation and larval rejection (2014) Veterinary Parasitology, 205, pp. 307-317
Choi, S.-C., Titov, A.A., Sivakumar, R., Li, W., Morel, L., Immune cell metabolism in systemic lupus erythematosus (2016) Current Rheumatology Reports, 18, p. 66
Ellis, S.A., Codner, G., The impact of MHC diversity on cattle T cell responses (2012) Veterinary Immunology and Immunopathology, 148, pp. 74-77
Fernández, J., Toro, M., A new method to estimate relatedness from molecular markers (2006) Molecular Ecology, 15, pp. 1657-1667
Fischer, D., Laiho, A., Gyenesei, A., Sironen, A., Identification of reproduction-related gene polymorphisms using whole transcriptome sequencing in the large white pig population (2015) G3: Genes, Genomes, Genetics, 5, pp. 1351-1360
Flandez, M., Cendrowski, J., Cañamero, M., Salas, A., Del Pozo, N., Schoonjans, K., Real, F.X., Nr5a2 heterozygosity sensitises to, and cooperates with, inflammation in KRasG12V-driven pancreatic tumourigenesis (2014) Gut, 63, pp. 647-655
Forristal, C., Henley, S.A., MacDonald, J.I., Bush, J.R., Ort, C., Passos, D.T., Talluri, S., Norley, C.J., Loss of the mammalian DREAM complex deregulates chondrocyte proliferation (2014) Molecular and Cellular Biology, 34, pp. 2221-2234
Gasparin, G., Miyata, M., Coutinho, L., Martinez, M., Teodoro, R., Furlong, J., Machado, M., Regitano, L., Mapping of quantitative trait loci controlling tick [Riphicephalus (Boophilus) microplus] resistance on bovine chromosomes 5, 7 and 14 (2007) Animal Genetics, 38, pp. 453-459
Gras, R., Almonacid, L., Ortega, P., Serramia, M.J., Gomez, R., De La Mata, F.J., Lopez-Fernandez, L.A., Muñoz-Fernandez, M.A., Changes in gene expression pattern of human primary macrophages induced by carbosilane dendrimer 2G-NN16 (2009) Pharmaceutical Research, 26, pp. 577-586
Hanna, L.L.H., Riley, D.G., Mapping genomic markers to closest feature using the R package Map2NCBI (2014) Livestock Science, 162, pp. 59-65
Kariuki, S.N., Ghodke-Puranik, Y., Dorschner, J.M., Chrabot, B.S., Kelly, J.A., Tsao, B.P., Kimberly, R.P., Criswell, L.A., Genetic analysis of the pathogenic molecular sub-phenotype interferon-alpha identifies multiple novel loci involved in systemic lupus erythematosus (2015) Genes and Immunity, 16, pp. 15-23
Lee, H.-C., Chang, D.-E., Yeom, M., Kim, G.-H., Choi, K.-D., Shim, I., Lee, H.-J., Hahm, D.-H., Gene expression profiling in hypothalamus of immobilization-stressed mouse using cDNA microarray (2005) Molecular Brain Research, 135, pp. 293-300
Lee, H.-J., Su, Y., Yin, P.-H., Lee, H.-C., Chi, C.-W., PPAR?/PGC-1? Pathway in E-cadherin expression and motility of HepG2 cells (2009) Anticancer Research, 29, pp. 5057-5063
Lemos, M.V., Chiaia, H.L.J., Berton, M.P., Feitosa, F.L., Aboujaoud, C., Camargo, G.M., Pereira, A.S., Mueller, L.F., Genome-wide association between single nucleotide polymorphisms with beef fatty acid profile in Nellore cattle using the single step procedure (2016) BMC Genomics, 17, p. 213
Liao, Y.-W., Wu, X.-M., Jia, J., Wu, X.-L., Hong, T., Meng, L.-X., Wu, X.-Y., Myosin VI contributes to maintaining epithelial barrier function (2013) Journal of Biomedical Science, 20, p. 68
Machado, M.A., Azevedo, A.L.S., Teodoro, R.L., Pires, M.A., Peixoto, M.G.C., De Freitas, C., Prata, M.C.A., Guimarães, S.E., Genome wide scan for quantitative trait loci affecting tick resistance in cattle (Bos taurus × Bos indicus) (2010) BMC Genomics, 11, p. 1
Mapholi, N., Maiwashe, A., Matika, O., Riggio, V., Bishop, S., MacNeil, M., Banga, C., Dzama, K., Genome-wide association study of tick resistance in South African Nguni cattle (2016) Ticks and Tick-Borne Diseases, 7, pp. 487-497
Martinez, M., Machado, M., Nascimento, C., Silva, M., Teodoro, R., Furlong, J., Prata, M., Azevedo, A., Association of BoLA-DRB3. 2 alleles with tick (boophilus microplus) resistance in cattle (2006) Genetics and Molecular Research, 5, pp. 513-524
Marufu, M.C., Qokweni, L., Chimonyo, M., Dzama, K., Relationships between tick counts and coat characteristics in Nguni and Bonsmara cattle reared on semiarid rangelands in South Africa (2011) Ticks and Tick-Borne Diseases, 2, pp. 172-177
Melo, T.P., Takada, L., Baldi, F., Oliveira, H.N., Dias, M.M., Neves, H.H., Schenkel, F.S., Carvalheiro, R., Assessing the value of phenotypic information from non-genotyped animals for QTL mapping of complex traits in real and simulated populations (2016) BMC Genetics, 17, p. 89
Moore, K.J., Rosen, E.D., Fitzgerald, M.L., Randow, F., Andersson, L.P., Altshuler, D., Milstone, D.S., Freeman, M.W., The role of PPAR-? In macrophage differentiation and cholesterol uptake (2001) Nature Medicine, 7, pp. 41-47
Morota, G., Beissinger, T.M., Peñagaricano, F., MeSH-informed enrichment analysis and MeSH-guided semantic similarity among functional terms and gene products in chicken (2016) G3: Genes, Genomes, Genetics, 6, pp. 2447-2453
Morota, G., Peñagaricano, F., Petersen, J., Ciobanu, D.C., Tsuyuzaki, K., Nikaido, I., An application of MeSH enrichment analysis in livestock (2015) Animal Genetics, 46, pp. 381-387
Mota, R., Lopes, P., Tempelman, R., Silva, F., Aguilar, I., Gomes, C., Cardoso, F., Genome-enabled prediction for tick resistance in Hereford and Braford beef cattle via reaction norm models (2016) Journal of Animal Science, 94, pp. 1834-1843
Mota, R.R., Tempelman, R.J., Lopes, P.S., Aguilar, I., Silva, F.F., Cardoso, F.F., Genotype by environment interaction for tick resistance of Hereford and Braford beef cattle using reaction norm models (2016) Genetics Selection Evolution, 48, p. 1
Mulenga, A., Sugino, M., Nakajima, M., Sugimoto, C., Onuma, M., Tickencoded serine proteinase inhibitors (serpins)
Potential target antigens for tick vaccine development (2001) Journal of Veterinary Medical Science, 63, pp. 1063-1069
Neels, J.G., Grimaldi, P.A., Physiological functions of peroxisome proliferator-activated receptor ? (2014) Physiological Reviews, 94, pp. 795-858
Nelson, S.J., Schopen, M., Savage, A.G., Schulman, J.-L., Arluk, N., The MeSH translation maintenance system: Structure, interface design, and implementation (2004) Medinfo, 11, pp. 67-69
Perry, D.J., Yin, Y., Telarico, T., Baker, H.V., Dozmorov, I., Perl, A., Morel, L., Murine lupus susceptibility locus Sle1c2 mediates CD4+ T cell activation and maps to estrogen-related receptor ? (2012) The Journal of Immunology, 189, pp. 793-803
Porto Neto, L., Bunch, R., Harrison, B., Barendse, W., DNA variation in the gene ELTD1 is associated with tick burden in cattle (2011) Nimal Genetics, 42, pp. 50-55
Porto Neto, L.R., Bunch, R.J., Harrison, B.E., Prayaga, K.C., Barendse, W., Haplotypes that include the integrin alpha 11 gene are associated with tick burden in cattle (2010) BMC Genetics, 11, p. 55
Porto Neto, L.R., Jonsson, N.N., Ingham, A., Bunch, R.J., Harrison, B.E., Barendse, W., The RIPK2 gene: A positional candidate for tick burden supported by genetic associations in cattle and immunological response of knockout mouse (2012) Immunogenetics, 64, pp. 379-388. , Technologies CRCfBG
Porto Neto, L.R., Jonsson, N.N., Michael, J., Barendse, W., Molecular genetic approaches for identifying the basis of variation in resistance to tick infestation in cattle (2011) Veterinary Parasitology, 180, pp. 165-172
Porto-Neto, L.R., Sonstegard, T.S., Liu, G.E., Bickhart, D.M., Da Silva, M.V., Machado, M.A., Utsunomiya, Y.T., Van Tassell, C.P., Genomic divergence of zebu and taurine cattle identified through high-density SNP genotyping (2013) BMC Genomics, 14, p. 876
Prayaga, K., Henshall, J., Adaptability in tropical beef cattle: Genetic parameters of growth, adaptive and temperament traits in a crossbred population (2005) Animal Production Science, 45, pp. 971-983
Sharma, N., Jeong, D.K., Stem cell research: A novel boulevard towards improved bovine mastitis management (2013) International Journal of Biological Science, 9, pp. 818-829
Silva, F., Mulder, H., Knol, E., Lopes, M., Guimarães, S., Lopes, P., Mathur, P., Bastiaansen, J., Sire evaluation for total number born in pigs using a genomic reaction norms approach (2014) Journal of Animal Science, 92, pp. 3825-3834
Silva-García, O., Valdez-Alarcón, J.J., Baizabal-Aguirre, V.M., The Wnt/ ?-catenin signaling pathway controls the inflammatory response in infections caused by pathogenic bacteria (2014) Mediators of Inflammation, 2014, pp. 1-7
Singh, S.K., Girschick, H.J., Tick-host interactions and their immunological implications in tick-borne diseases (2003) Current Science, 85, pp. 1284-1298
Stear, M., Bishop, S., Mallard, B., Raadsma, H., The sustainability, feasibility and desirability of breeding livestock for disease resistance (2001) Research in Veterinary Science, 71, pp. 1-7
Streit, M., Wellmann, R., Reinhardt, F., Thaller, G., Piepho, H.-P., Bennewitz, J., Using genome-wide association analysis to characterize environmental sensitivity of milk traits in dairy cattle (2013) G3: Genes, Genomes, Genetics, 3, pp. 1085-1093
Theilgaard-Mönch, K., Knudsen, S., Follin, P., Borregaard, N., The transcriptional activation program of human neutrophils in skin lesions supports their important role in wound healing (2004) The Journal of Immunology, 172, pp. 7684-7693
Thompson-Crispi, K.A., Sargolzaei, M., Ventura, R., Abo-Ismail, M., Miglior, F., Schenkel, F., Mallard, B.A., A genome-wide association study of immune response traits in Canadian Holstein cattle (2014) BMC Genomics, 15, p. 559
Utsunomiya, Y.T., Carmo, A.S., Neves, H.H., Carvalheiro, R., Matos, M.C., Zavarez, L.B., Ito, P.K., Porto-Neto, L.R., Genome-wide mapping of loci explaining variance in scrotal circumference in Nellore cattle (2014) PLoS One, 9, p. e88561
Valente, T.S., Baldi, F., Sant'Anna, A.C., Albuquerque, L.G., Da Costa, M.J.R.P., Genome-wide association study between single nucleotide polymorphisms and flight speed in Nellore cattle (2016) PloS One, 11, p. e0156956
Verardo, L., Lopes, M., Wijga, S., Madsen, O., Silva, F., Groenen, M., Knol, E., Guimarães, S., After genome-wide association studies: Gene networks elucidating candidate genes divergences for number of teats across two pig populations (2016) Journal of Animal Science, 94, pp. 1446-1458
Vivier, E., Tomasello, E., Baratin, M., Walzer, T., Ugolini, S., Functions of natural killer cells (2008) Nature Immunology, 9, pp. 503-510
Wambura, P., Gwakisa, P., Silayo, R., Rugaimukamu, E., Breed-associated resistance to tick infestation in Bos indicus and their crosses with Bos taurus (1998) Veterinary Parasitology, 77, pp. 63-70
Wang, H., Misztal, I., Aguilar, I., Legarra, A., Muir, W., Genome-wide association mapping including phenotypes from relatives without genotypes (2012) Genetics Research, 94, pp. 73-83
Wei, J., Wang, H., Yang, X., Dong, M., Wang, Z., Altered gene profile of placenta from women with intrahepatic cholestasis of pregnancy (2010) Archives of Gynecology and Obstetrics, 281, pp. 801-810
Wiggans, G., Sonstegard, T., VanRaden, P., Matukumalli, L., Schnabel, R., Taylor, J., Schenkel, F., Van Tassell, C., Selection of single-nucleotide polymorphisms and quality of genotypes used in genomic evaluation of dairy cattle in the United States and Canada (2009) Journal of Dairy Science, 92, pp. 3431-3436
Wikel, S., Allen, J., Acquired resistance to ticksI. Passive transfer of resistance (1976) Immunology, 30, pp. 311-316
Zhang, X., Lourenco, D., Aguilar, I., Legarra, A., Misztal, I., Weighting strategies for single-step genomic BLUP: An iterative approach for accurate calculation of GEBV and GWAS (2016) Frontiers in Genetics, 7, pp. 1-14
