In the summer of 2014 we celebrated the achievement of the 200th peer-reviewed publication since the inception of Livestock Gentec as an Alberta Ingenuity Centre in 2010. For an updated list CLICK HERE
One of the global highlights of bovine genomics in 2009 was the publication of two landmark papers in the international journal Science, presenting the genome sequence of cattle and a high-density SNP survey that uncovered the genetic structure of cattle breeds. These ground-breaking studies represent significant efforts by a large number of international researchers. The Alberta Bovine Genomics Program (now Livestock Genomics) research team was well represented among the contributors to both papers.
Click on the researcher's name below to view his or her key publications.
- John Basarab
- Urmila Basu
- Heather Bruce
- Carolyn Fitzsimmons
- Leluo Guan
- Changxi Li
- Stephen Miller
- Graham Plastow
- Paul Stothard
- Zhiquan Wang
- Rong-Cai Yang
Basarab, J.A., Baron, V.S., López-Campos, O., Aalhus, J.L., Haugen-Kozyra, K. and Okine, E.K. 2012. Greenhouse gas emissions from calf-fed and yearling-fed beef production systems, with and without the use of growth promotants. Animals 2012, 2, 1-x manuscripts; doi:10.3390/ani20x000x, in press.
Basarab, J.A., Colazo, M.G., Ambrose, D.J., Novak, S., McCartney, D. and Baron, V.S. 2011. Residual feed intake adjusted for backfat thickness and feeding frequency is independent of fertility in beef heifers. Can. J. Anim. Sci., 91:573-584.
Basarab, J.A., McCartney,D., Okine, E.K., and Baron, V., P. 2007. Relationships between progeny residual feed intake and dam lifetime production efficiency traits. Can. J. Anim. Sci. 87: 489-502.
Basarab, J.A., Mir, P.S., Aalhus, J.L., Shah, M.A., Baron, V.S., Okine, E.K. and Robertson, W.M. 2007. Effect of sunflower seed supplementation on the fatty acid composition of muscle and adipose tissue of pasture-fed and feedlot finished beef. Can. J. Anim. Sci. 87: 71-86.
Basarab, J.A., Price, M.A., Aalhus, J.L., Okine, E.K., Snelling W.M., and Lyle, K.L. 2003. Residual feed intake and body composition in young growing cattle. Can. J. Anim. Sci. 83: 189-204.
Basu U, Romao JM, Guan LL (2012) Adipogenic transcriptome profiling using high throughput technologies. Journal of Genomics 1: 22-28.
Basu U, Zhao YM, Zhou M, Dodson MV, Basarab JA, Guan LL (2010) Proteome differences associated with fat accumulation in the bovine subcutaneous adipose tissues. Proteome Science 8-14.
Jin W, Olson NE, Moore SS, Basarab JA, Basu U, Guan LL (2012) Transcriptome analysis of subcutaneous adipose tissues in beef cattle using 3' digital gene expression-tag profiling. Journal of Animal Science 90:171-183.
Murdoch M, Clawson ML, Yue S, Basu U, McKay S, Settles M, Capoferri R, Laegreid WW, Williams JL, Moore SS (2010) Prion haplotype associated with classical BSE incidence in European Holstein Cattle. PLoS One 5(9): e12786. doi:10.1371/journal.pone.0012786.
Stothard P, Choi JW, Basu U, Sumner-Thomson JM, Meng Y, Liao X, Moore SS (2011) Whole genome resequencing of Black Angus and Holstein cattle for SNP and CNV discovery. BMC genomics 12:559-574.
Girard, I., Aalhus, J. L., Basarab, J. A., Larsen, I. L. and Bruce, H. L. 2012. Modification of beef quality through age at steer age at slaughter, breed cross and growth promotants. Canadian Journal of Animal Science, accepted.
Girard, I., Aalhus, J. L., Basarab, J. A., Larsen, I. L. and Bruce, H. L. 2011. Modification of muscle inherent properties through age at slaughter, growth promotants and breed crosses. Canadian Journal of Animal Science 91: 635-648.
Jia, W., Rogiewicz, A., Bruce, H. L. and Slominski, B. A. 2010. Feeding flaxseed enhances deposition of omega-3 fatty acids in broiler meat portions in different manner. Canadian Journal of Animal Science 90: 203-206.
Jia, W., Slominski, B. A., Bruce, H. L., Nyachoti, C. M. and Jones, R. M. 2009. Enzyme addition facilitates the post-disease compensatory growth of broiler chickens challenged with Clostridium perfringens. Canadian Journal of Animal Science 89: 369-381.
Müller, W., Bruce, H. L., Tume, R. J., Beilken, S., Barnes, J. A. and Greenfield, H. 2009. National sampling and gross composition of Australian retail pork cuts. Meat Science 81: 626-631.
Anand-Ivell R., Hiendleder S., Viñoles C., Martin G.B., Fitzsimmons C., Eurich A., Hafen B. & Ivell R. (2011) INSL3 in the Ruminant: A Powerful Indicator of Gender- and Genetic-Specific Feto-Maternal Dialogue. PLoS One 6, e19821.
Fitzsimmons C., Whisnant S., Wettemann B. and Basarab J. Interactions with other Traits: Reproduction and Fertility. In Hill R. (Ed.), Feed Efficiency in the Beef Industry (Submitted Dec 2011). Hoboken, NJ: Wiley-Blackwell.
The Bovine Genome Sequencing and Analysis Consortium, C. G. Elsik, R. L. Tellam, K. C. Worley, et al. (2009) The Genome Sequence of Taurine Cattle: A Window to Ruminant Biology and Evolution. Science 324, 522-528.
S. Ka, J. Lindberg, L. Stömstedt, C. J. Fitzsimmons, N. Lindqvist, J. Lundeberg, P.B. Siegel, L. Andersson, and F. Hallböök. (2009) Extremely different behaviours in high and low body weight lines of chicken are involved in differential expression of genes involved in neuronal plasticity. J Neuroendocrinol 21, 208-216.
G. Rosengren-Pielberg, A. Golovko, E. Sundström, I. Curik, J. Lennartsson, M. H. Seltenhammer, T. Druml, M. Binns, C. Fitzsimmons, G. Lindgren, K. Sandberg, R. Baumung, M. Vetterlein, S. Strömberg, M. Grabherr, C. Wade, K. Lindblad-Toh1, F. Pontén, C. Heldin, J. Sölkner and L. Andersson. (2008) A cis-acting regulatory mutation causes premature hair greying and susceptibility to melanoma in the horse. Nature Genetics 40, 1004-1009.
Josue Moura Romao1, Weiwu Jin1, Maolong He2, Tim McAllister2, Le Luo Guan. Altered MicroRNA Expression in Bovine Subcutaneous and Visceral Adipose Tissues from Cattle under Different Diet. 2012. PLoS One. 7:e40605.
Yanhong Chen, Gregory B. Penner, Meiju Li, Masahito Oba, and Le Luo Guan. 2011. The Epithelial Tissue Associated Bacterial Diversity Changes in the Rumen of Beef Cattle During Dietary Transition to High Grain Diets. Appl Environ Microbiol. 77(16):5770-81
Hernandez-Sanabria E, Guan LL, Goonewardene LA, Li M, Fujibi D, Stothard P, Moore SS & Leon-Quintero MC 2010. Association Between Microbial Diversity and Microbial Fermentation Parameters in the Bovine Rumen and Host's Feed Efficiency Traits. Appl Environ Microbiol 76: 6338 – 6350
Zhou M, E. Hernandez-Sanabria, and L. L. Guan. 2009. Assessment of Microbial Ecology of Ruminal Methane Producers and Cattle's High Feed Efficiency and Low Methane Production Activities. Applied and Environmental Microbiology 75: 6524-6533.
Jin W., J. Grant, P. Stothard, S. S. Moore, L. L. Guan. 2009. Characterization of bovine miRNAs by sequencing and bioinformatics. BMC Molecular Biology. 11:29.
Li, C., Aldai, N., Vinsky, M.D., Dugan, M.E.R, and McAllister, T.A. (2012). "Association analyses of single nucleotide polymorphisms in bovine stearoyl-CoA desaturase and fatty acid synthase genes with fatty acid composition in commercial crossbred beef steers.", Animal Genetics. 43, 94-97.
Nalaila, S.M., Stothard, P., Moore, S.S., Wang, Z., and Li, C. (2011). "Whole genome fine mapping of QTL for ultrasound and carcass merit traits in beef cattle.", Canadian Journal of Animal Science, 91(1), pp. 61-73.
Li, C., Vinsky, M.D., Aldai, N., Osoro, K., and Dugan, M.E.R. (2010). "Associations of a bovine SCD1 SNP with fatty acid composition in concentrate-finished yearling bulls of different muscular hypertrophy genotypes", Proc. 9th World Congress on Genetics Applied to Livestock Production (WCGALP). 505.
Islam, K. K., Vinsk, M., Crews, R., Okine, E., Moore, S. S., Crews Jr. D. H., and Li, C. (2009). Association analyses of a SNP in the promoter of IGF1 with fat deposition and carcass merit traits in hybrid, Angus and Charolais beef cattle. Animal Genetics, 40, 766-769.
Sherman, E. L., J. D. Nkrumah, C. Li, R. Bartusiak, B. Murdoch, and S. S. Moore. (2009). Fine mapping quantitative trait loci for feed intake and feed efficiency in beef cattle . J. Anim Sci. 87:37-45.
Sherman, E. L., Nkrumah, J. D., Murdoch, B. M., Li, C., Wang, Z., Fu, A., and Moore, S. S. (2008). Polymorphisms and haplotypes in the bovine neuropeptide Y, growth hormone receptor, ghrelin, insulin-like growth factor 2, and uncoupling proteins 2 and 3 genes and their associations with measures of growth, performance, feed efficiency, and carcass merit in beef cattle. J. Anim. Sci. 86: 1-16.
Nkrumah, J. D., Sherman, E. L., Li, C., Marques, E., Crews, D. H., Bartusiak, R., Murdoch, B., Wang, Z., Basarab, J. A., and Moore. S. S., 2007. Primary genome scan to identify putative quantitative trait loci for feedlot growth rate, feed intake, and feed efficiency of beef cattle, J. Anim. Sci. 85:.3170-3181.
Li, C., J.D. Nkrumah, R. Bartusiak, A. Fu, B.M. Murdoch, E.L. Sherman, S.D. McKay, Z. Wang, D.H. Crews, Jr., and S.S. Moore. 2006. "A genome-wise scan for quantitative trait affecting ultrasound and carcass backfat thickness in beef cattle." Proc. 8th World Congress on Genetics Applied to Animal Production. Communication 03-53.
Montanholi, Y.R., K.C. Swanson, R. Palme, F.S. Schenkel, B.W. McBride, D. Lu and S.P. Miller. 2010. Assessing feed efficiency in beef steers through feeding behavior, infrared thermography and glucocorticoids. Animal 4(5):692-701.
Montanholi, Y.R., K.C. Swanson, F.S. Schenkel, B.W. McBride, T.R. Caldwell and S.P. Miller. 2009. On the determination of residual feed intake and associations of infrared thermography with efficiency and ultrasound traits in beef bulls. Livest. Sci. 125:22-30.
Core, S., S. Miller, T. Widowski and G. Mason. 2009. Eye white percentage as a predictor of temperament in beef cattle. J. Anim. Sci. 87:2168-2174.
Montanholi, Y.R., N.E. Odongo, K.C. Swanson, F.S. Schenkel, B.W. McBride and S.P. Miller. 2008. Application of infrared thermography as an indicator of heat and methane production and its use in the study of skin temperature in response to physiological events in dairy cattle (Bos taurus). J. Thermal Biol. 33:468-475.
Carvalheiro, R., F.S. Schenkel, L.A. Fries, S.A. de Queiroz and S.P.Miller. 2007. Empirical properties of solutions from Henderson's mixed model equations when sires are non-randomly used across contemporary group. Rev. Bras. Biom., Sao Paula 25(3):7-21.
Carvalheiro, R.S., F.S. Schenkel, L.A. Fries, S.A. de Queiroz and S.P. Miller. 2007. Alternative genetic evaluation models under parental selection. Brazil. J. Math. Stat. 25(2) :41-57.
Roso, V.M., F.S. Schenkel and S.P. Miller. 2004. Degree of connectedness among groups of centrally tested beef bulls. Can. J. Anim. Sci. 84:37-47.
B.J. Hayes and S.P. Miller. 2000. Mating selection strategies to exploit across- and within-breed dominance variation. J. Anim. Breed. Genet. 117:347-359. P.G. Sullivan, J.W. Wilton, S.P. Miller and L.R. Banks. 1999. Genetic trends and breed overlap derived from multiple-breed genetic evaluations of beef cattle for growth traits. J. Anim. Sci. 77:2019-2027.
S.P. Miller and J.W. Wilton. 1999. Genetic relationships among direct and maternal components of milk yield and maternal weaning gain in a multibreed beef herd. J. Anim. Sci. 77:1155-1161.
S.P. Miller, J.W. Wilton and W.C. Pfeiffer. 1999. Effects of milk yield on biological efficiency and profit of beef production from birth to slaughter. J. Anim. Sci. 77:344-352.
S.P. Miller and M.E. Goddard. 1998. The super-breed approach to modelling additive and non-additive genetic effects between and within breeds in multi-breed evaluations. Proc. 6th World Congr. Genet. Appl. Livest. Prod. 23:97-100.
Hu X-S, Simila J, Platz SS, Moore SS, Plastow G, Meghen, C.N. (2012) Estimating Animal Abundance in Ground Beef Batches Assayed with Molecular Markers. PLoS ONE 7(3): e34191. doi:10.1371/journal.pone.0034191
Wei, W.H., Skinner, T.M., Anderson, J.A., Southwood, O.I., Plastow, G., Archibald, A.L., Haley, C.S. (2011) Mapping QTL in the porcine MHC region affecting fatness and growth traits in a Meishan/Large White composite population. Animal Genetics 42: 83-85
Suzuki, K., Matsumoto, T., Kobayashi, E., Uenishi, H., Churkina, I., Plastow, G., Yamashita, H., Hamasima, N., Mitsuhashi, T. (2010) Genotypes of Chicken MHC-B Locus Associated with Regression of Rous Sarcoma Virus J-strain Tumors. Poultry Science 89: 651-657.
Fan, B., Onteru, S.K., Plastow, G.S., and Rothschild, M.F. (2009) Detailed Characterization of the porcine MC4R gene in relation to fatness and growth. Animal Genetics 40: 401-409.
Rothschild, M.F. and Plastow, G.S. (2008) Impact of genomics on animal agriculture and opportunities for animal health. Trends in Biotechnology 26:21-25.
Grant JR, Arantes AS, Stothard P (2012) Comparing thousands of circular genomes using the CGView Comparison Tool. BMC Genomics 13:202.
Stothard P, Choi J, Basu U, Sumner-Thomson JM, Meng Y, Liao X, Moore SS (2011) Whole genome resequencing of Black Angus and Holstein cattle for SNP and CNV discovery. BMC Genomics 12:559.
Grant JR, Arantes AS, Xiaoping L, Stothard P (2011) In-depth annotation of SNPs arising from resequencing projects using NGS-SNP. Bioinformatics 27:2300-2301.
Jin W, Grant JR, Stothard P, Moore SS, Guan LL (2009) Characterization of bovine miRNAs by sequencing and bioinformatics analysis. BMC Mol Biol 10:90.
The Bovine Genome Sequencing and Analysis Consortium (2009) The genome sequence of taurine cattle: a window to ruminant biology and evolution. Science 324:522-528.
Hernandez-Sanabria, E., L.A. Goonewardene, Z. Wang, O.N. Durunna, S.S. Moore, L. L. Guan. 2012. Impact of Feed Efficiency and Diet on the Adaptive Variations in the Bacterial Community in the rumen Fluid of Cattle Identified by PCR-Denaturing Gradient Gel Electrophoresis. Appl. Environ. Microbiol. 78:1203-1214.
Durunna, O.N., S.S. Moore, J.A. Basarab, E.K. Okine and Z, Wang. 2011. Genetic parameters and genotype by environment interaction for feed efficiency traits in steers fed grower and finisher diets. J. Anim. Sci. 89: 3394-3340.
Tang, G., X. Li, G. Plastow, S.S. Moore and Z. Wang. 2011. Developing marker assisted models for evaluating growth traits in Canadian beef cattle genetic improvement. Livest.Sci. 138: 62–68.
X-S., Hu, F.C. Yeh and Z. Wang. 2011. Structural Genomics: Correlation Blocks, Population Structure, and Genome Architecture. Current Genomics. 12:55-70.
The Bovine Genome Sequencing and Analysis Consortium. 2009. The genome sequence of taurine cattle: a window to ruminant biology and evolution. Science. 324: 522-528.
Jiang, Q., Z. Wang, S. S. Moore and R.-C. Yang. 2012. Genome-wide analysis of zygotic linkage disequilibrium and its components in crossbred cattle. BMC Genetics (submitted).
Álvarez-Castro J and R.-C.Yang 2012. Clarifying the relationship between average excesses and average effects of allele substitutions. Front. Gene. 3:30. doi: 10.3389/fgene.2012.00030
Alvarez-Castro, J.M. and R.-C. Yang. 2011. Multiallelic models of genetic effects and variance decomposition in non-equilibrium populations. Genetica 139: 1119-1134.
Yang, R.-C., and J. M. Álvarez-Castro. 2008. Functional and statistical genetic effects with multiple alleles. Current Topics in Genetics 3:49-62.
Yang, R.-C. 2004. Epistasis of quantitative trait loci under different gene action models. Genetics 167: 1493-1505.