Genomic Application in Sheep and Goat Breeding

Auvray, B., J.C. McEwan, S.-A.N. Newman, M. Lee, and K.G. Dodds. (2014). “Genomicprediction of breeding values in the New Zealand sheep industry using a 50K SNP chip”. J. Anim. Sci. 92(10):4375–4389. doi:10.2527/jas.2014-7801.

Badke, Y.M., R.O. Bates, C.W. Ernst, C. Schwab, J.P. Steibel. (2012). “Estimation of linkage disequilibrium in four US pig breeds”. BMC Genomics 13:24. doi:10.1186/1471-2164-13-24

Baloche, G., A. Legarra, G. Sallé, H. Larroque, J.M. Astruc, C. Robert-Granié, and F.Barillet. (2014). “Assessment of accuracy of genomic prediction for French Lacaunedairy sheep”. J. Dairy Sci. 97(2):1107–1116. doi:10.3168/jds.2013-7135.

Barillet, F., D. Mariat, Y. Amigues, R. Faugeras, H. Caillat, K. Moazami-Goudarzi, and R. Rupp. (2009). “Identification of seven haplotypes of the caprine PrP gene at codons 127, 142, 154, 211, 222 and 240 in French Alpine and Saanen breeds and their association with classical scrapie”. J. Gen. Virol. 90(Pt 3):769–776. doi:10.1099/vir.0.006114-0.

Brito, L.F., M. Jafarikia, D.A. Grossi, J.W. Kijas, L.R. Porto-Neto, R.V. Ventura, M. Salgorzaei,and F.S. Schenkel. (2015). “Characterization of linkage disequilibrium, consistencyof gametic phase and admixture in Australian and Canadian goats”. BMC Genet. 16:67. doi:10.1186/s12863-015-0220-1.

Carillier, C., H. Larroque, I. Palhière, V. Clément, R. Rupp, and C. Robert-Granié. (2013). “A first step toward genomic selection in the multi-breed French dairy goat population.” J. Dairy Sci. 96(11):7294–7305. doi:10.3168/jds.2013-6789.

Carillier-Jacquin C., H. Larroque, and C. Robert-Granié. (2015). “Including casein αs1 gene effect on genetic and genomic evaluation of French dairy goats”. In: Proc. 66^th Annual Meeting of the EAAP, Warsaw, Poland, 31 Aug.–4 Sept. 2015.

Carillier, C., H. Larroque, and C. Robert-Granié. (2014). “Comparison of joint versus purebred genomic evaluation in the French multi-breed dairy goat population”. Genet. Sel. Evol. 46:67. doi:10.1186/s12711-014-0067-3.

Clarke, S.M., H.M. Henry, K.G. Dodds, T.W.D. Jowett, T.R. Manley, R.M. Anderson, and J.C. McEwan. (2014). “A high throughput single nucleotide polymorphism multiplex assay for parentage assignment in New Zealand sheep”. PLoS ONE 9 (4):E93392. doi:10.1371/journal.pone.0093392.

Clop, A., F. Marcq, H. Takeda, D. Pirottin, X. Tordoir, B. Bibé, J. Bouix et al. (2006). “A mutation creating a potential illegitimate microRNA target site in the myostatin gene affects muscularity in sheep”. Nat. Genet. 38(7):813–818. doi:10.1038/ng1810.

Daetwyler, H.D., J.M. Hickey, J.M. Henshall, S. Dominik, B. Gredler, J.H.J. vander Werf, and B.J. Hayes. (2010). “Accuracy of estimated genomic breeding values for wool and meat traits in a multi-breed sheep population”. Anim. Prod. SCI.50(12):1004-1010. doi: 10.1071/AN10096.

Daetwyler, H.D., K.E. Kemper, J.H.J. van der Werf, and B.J. Hayes. (2012a). Components of the accuracy of genomic prediction in a multi-breed sheep population. J. Anim. Sci. 90(10):3375–3384. doi:10.2527/jas.2011-4557.

Daetwyler, H.D., A.A. Swan, J.H. van der Werf, and B.J. Hayes. (2012b). “Accuracy of pedigree and genomic predictions of carcass and novel meat quality traits in multi-breed sheep data assessed by cross-validation”. Genet. Sel. Evol. 44:33. doi: 10.1186/1297-9686-44-33.

Demars, J., S. Fabre, J. Sarry, R. Rossetti, H. Gilbert, L. Persani, G. Tosser-Klopp etal. (2013). “Genome-wide association studies identify two novel BMP15 mutations responsible for an atypical hyperprolificacy phenotype in sheep”. PLoS Genet. 9 (4): E1003482. doi:10.1371/journal.pgen.1003482.

De Roos, A.P., B.J. Hayes, R.J. Spelman, and M.E. Goddard. (2008). “Linkage disequilibrium and persistence of phase in Holstein-Friesian, Jersey and Angus cattle”. Genetics.179 (3):1503-1512. doi:10.1534/genetics.107.084301.

Dodds, K.G., J. McEwan, R. Brauning, R.M. Anderson, T.C. van Stijn, T. Kristjánsson, and S.M. Clarke. (2015). “Construction of relatedness matrices using genotyping-bysequencing data”. bioRxiv. http://dx.doi.org/10.1101/025379.

Dodds, K.G., M.L. Tate, and J.A. Sise. (2005). “Genetic evaluation using parentage information from genetic markers”. J. Anim. Sci. 83(10):2271–2279.

Dong, Y., M. Xie, Y. Jiang, N. Xiao, X. Du, W. Zhang, G. Tosser-Klopp et al. (2013). “Sequencing and automated whole-genome optical mapping of the genome of a domestic goat (Capra hircus)”. Nat. Biotechnol. 31(2):135–141. doi:10.1038/nbt.2478.

Elsen, J.M., Y. Amigues, et al. (1999). “Genetic susceptibility and transmission factors in scrapie: Detailed analysis of an epidemic in a closed flock of Romanov”. Arch. Virol.144 (3):431-445. doi:10.1007/s007050050516

Eynard, S.E., J.J. Windig, G. Leroy, R. van Binsbergen, and M.P.L. Calus. (2015). “The effect of rare alleles on estimated genomic relationships from whole genome sequence data”. BMC Genet. 16:24. doi:10.1186/s12863-015-0185-0.

Habier, D., J. Tetens, F.R. Seefried, P. Lichtner, and G. Thaller. (2010). “The impact of genetic relationship information on genomic breeding values in German Holstein cattle”. Genet. Sel. Evol. 42:5. doi:10.1186/1297-9686-42-5.

Heaton, M.P., M.L. Clawson, C.G. Chitko-Mckown, K.A. Leymaster, T.P.L. Smith, G.P. Harhay, S.N. White et al. (2012). “Reduced lentivirus susceptibility in sheep with TMEM154 mutations”. PLoS Genet. 8(1):E1002467. doi:10.1371/journal. pgen.1002467.

Heaton, M.P., K.A. Leymaster, T.S. Kalbfleisch, J.W. Kijas, S.M. Clarke, J. McEwan, J.F. Maddox et al. (2014). “SNPs for parentage testing and traceability in globally diverse breeds of sheep”. PLoS ONE. 9(4):E94851. doi:10.1371/journal.pone.0094851.

Jiang, Y., M. Xie, W. Chen, R. Talbot, J.F. Maddox, T. Faraut, C. Wu et al. (2014). “The sheep genome illuminates biology of the rumen and lipid metabolism”. Science. 344 (6188):1168-1173. doi:10.1126/science.1252806.

Kijas, J.W., L. Porto-Neto, S. Dominik, A. Reverter, R. Bunch, R. McCulloch, B.J. Hayes et al. (2014). “Linkage disequilibrium over short physical distances measured in sheep using a high-density SNP chip”. Anim. Genet. 45(5):754–757. doi:10.1111/ age.12197.

Kijas, J.W., D. Townley, B.P. Dalrymple, M.P. Heaton, J.F. Maddox, A. McGrath, P. Wilson et al. (2009). “A genome wide survey of SNP variation reveals the genetic structure of sheep breeds”. PLoS ONE 4(3):E4668. doi:10.1371/journal.pone.0004668.

Larroque, H., F. Barillet, G. Baloche, J-M. Astruc, D. Buisson, F. Shumbusho, V. Clément et al. (2014). “Toward genomic breeding programs in French dairy sheep and goats”. In: Proc. 10th World Congress on Genetics Applied to Livestock Production. http://bit.ly/1OebpGS.

Legarra, A., I. Aguilar, and I. Misztal. (2009). “A relationship matrix including full pedigree and genomic information”. J. Dairy Sci. 92(9):4656–4663. doi:10.3168/jds.2009-2061.

Legarra, A., G. Baloche, F. Barillet, J.M. Astruc, C. Soulas, X. Aguerre, F. Arrese, L. Mintegi, M. Lasarte, F. Maeztu, I. Beltrán de Heredia, and E. Ugarte. (2014). “Within- and across-breed genomic predictions and genomic relationships for Western Pyrenees dairy sheep breeds Latxa, Manech, and Basco-Bearnaise”. J. Dairy Sci.97(5):3200-3212. doi:10.3168/jds.2013-7745.

Legarra, A., and Z. Vitezica. (2015). “Genetic evaluation with major genes and polygenic inheritance when some animals are not genotyped using gene content multiple-trait BLUP. Genet. Sel. Evol. 17;47(1):89. doi: 10.1186/s12711-015-0165-x.

Leroux, C., P. Martin, M.-F. Mahé, H. Levéziel, and J.-C. Mercier. (1990). “Restriction fragment length polymorphism identification of goat alpha s1-casein alleles: A potential tool in selection of individuals carrying alleles associated with a high level protein synthesis”. Anim. Genet. 21(4):341–351. doi:10.1111/j.1365-2052.1990.tb01979.x.

Martin, P., J. Raoul, and L. Bodin. (2014). “Effects of the FecL major gene in the Lacaune meat sheep population”. Genet. Sel. Evol. 46:48. doi:10.1186/1297-9686-46-48.

Misztal, I., A. Legarra, and I. Aguilar. (2009). “Computing procedures for genetic evaluation including phenotypic, full pedigree, and genomic information”. J. Dairy Sci. 98(11):8201-8208. doi:10.3168/jds.2009-2064.

Mucha, S., R. Mrode, I. MacLaren-Lee, M. Coffey, and J. Conington. (2015). “Estimation of genomic breeding values for milk yield in UK dairy goats”. J. Dairy Sci. doi:10.3168/jds.2015-9682.

Mucha, S., and J.J. Windig. (2009). “Effects of incomplete pedigree on genetic management of the Dutch Landrace goat. J. Anim. Breed”. Genet. 126(3):250–256. doi:10.1111/j.1439-0388.2008.00757.x.

Pailhoux, E., Vigier, B., Chaffaux, S., Servel, N., Taourit, S., Furet, J. P., Fellous, M., Grosclaude, F., Cribiu, E.P., Cotinot, C. and Vaiman, D. (2001). A 11.7-kb deletion triggers intersexuality and polledness in goats. Nature genetics, 29(4), 453.

Phua, S.H., D.L. Hyndman, H.J. Baird, B. Auvray, J.C. McEwan, M.A. Lee, and K.G. Dodds. (2014). “Towards genomic selection for facial eczema disease tolerance in the New Zealand sheep industry”. Anim. Genet. 45(4):559–564. doi:10.1111/age.12167.

Pickering, N.K., V.H. Oddy, J. Basarab, K. Cammack, B. Hayes, R.S. Hegarty, J. Lassen, J.C. McEwan, S. Miller, C.S. Pinares-Patiño, and Y. de Haas. (2015). “Animal board.invited review: Genetic possibilities to reduce enteric methane emissions from ruminants”. Animal 9(9):1431-1440. doi:10.1017/S1751731115000968.

Rupp, R., P. Senin, J. Sarry, C. Allain, C. Tasca, L. Ligat, D. Portes, F. Woloszyn, O. Bouchez, G. Tabouret, M. Lebastard, C. Caubet, G. Foucras, and G. Tosser- Klopp. (2015). “A point Mutation in Suppressor Of Cytokine Signalling 2 (Socs2) increases the Susceptibility to Inflammation of the Mammary Gland while as- sociated with higher Body Weight and Size and higher Milk Production in a Sheep Model”. Plos Genetics, in press.

Shumbusho, F., J. Raoul, J.M. Astruc, I. Palhiere, and J.M. Elsen. (2013). “Potential ben- efits of genomic selection on genetic gain of small ruminant breeding programs”. J. Anim. Sci. 91(8):3644-3657. doi:10.2527/jas.2012-6205.

Shumbusho, F., J. Raoul, J. M. Astruc, I. Palhiere, S. Lemarié, A. Fugeray-Scarbel and J. M. Elsen. (2015). “Economic evaluation of genomic selection in small ruminants: A sheep meat breeding program”. Animal. Doi: 10.1017/S1751731115002049.

Tortereau, F., C. Moreno, G. Tosser-Klopp, L. Barbotte, L. Genestout, and J. Raoul. (2015). “Development of a SNP parentage assignment panel for French sheep breeds”. In: Proc. 66th Annual Meeting of the EAAP, Warsaw, Poland, 31 Aug.-4 Sept. 2015.

Tosser-Klopp, G., P. Bardou, O. Bouchez, C. Cabau, R. Crooijmans, Y. Dong, C. Don- nadieu-Tonon et al. (2014). “Design and characterization of a 52K SNP chip for goats”. PLoS ONE. 9(1):E86227.doi:10.1371/journal.pone.0086227.

Vage, D.I., and I.A. Boman. (2010). “A nonsense mutation in the beta-carotene oxygenase 2 (BCO2) gene is tightly associated with accumulation of carotenoids in adipose tissue in sheep (Ovis aries)”. BMC Genet. 11:10. doi:10.1186/1471-2156-11-10.