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Exclusion and Genomic Relatedness Methods for Assignment of Parentage Using Genotyping-by-Sequencing Data.

Dodds KG, McEwan JC, Brauning R, van Stijn TC, Rowe SJ, McEwan KM, Clarke SM.

G3 (Bethesda). 2019 Aug 5. pii: g3.400501.2019. doi: 10.1534/g3.119.400501. [Epub ahead of print]


Genetic parameters of plasma and ruminal volatile fatty acids in sheep fed alfalfa pellets and genetic correlations with enteric methane emissions1.

Jonker A, Hickey SM, McEwan JC, Rowe SJ, Janssen PH, MacLean S, Sandoval E, Lewis S, Kjestrup H, Molano G, Agnew M, Young EA, Dodds KG, Knowler K, Pinares-Patiño CS.

J Anim Sci. 2019 Jul 2;97(7):2711-2724. doi: 10.1093/jas/skz162.


Using genotyping-by-sequencing to predict gender in animals.

Bilton TP, Chappell AJ, Clarke SM, Brauning R, Dodds KG, McEwan JC, Rowe SJ.

Anim Genet. 2019 Jun;50(3):307-310. doi: 10.1111/age.12782. Epub 2019 Apr 7.


Population Connectivity and Traces of Mitochondrial Introgression in New Zealand Black-Billed Gulls (Larus bulleri).

Mischler C, Veale A, van Stijn T, Brauning R, McEwan JC, Maloney R, Robertson BC.

Genes (Basel). 2018 Nov 9;9(11). pii: E544. doi: 10.3390/genes9110544.


Heritability of ram mating success in multi-sire breeding situations.

Juengel JL, Hickey SM, Clarke SM, Cullen NG, McEwan JC, Dodds KG.

Animal. 2019 May;13(5):917-923. doi: 10.1017/S1751731118002446. Epub 2018 Oct 22.


Across-Experiment Transcriptomics of Sheep Rumen Identifies Expression of Lipid/Oxo-Acid Metabolism and Muscle Cell Junction Genes Associated With Variation in Methane-Related Phenotypes.

Xiang R, McNally J, Bond J, Tucker D, Cameron M, Donaldson AJ, Austin KL, Rowe S, Jonker A, Pinares-Patino CS, McEwan JC, Vercoe PE, Oddy VH, Dalrymple BP.

Front Genet. 2018 Aug 20;9:330. doi: 10.3389/fgene.2018.00330. eCollection 2018.


Ovine keratome: identification, localisation and genomic organisation of keratin and keratin-associated proteins.

Yu Z, Plowman JE, Maclean P, Wildermoth JE, Brauning R, McEwan JC, Maqbool NJ.

Anim Genet. 2018 Oct;49(5):361-370. doi: 10.1111/age.12694. Epub 2018 Jul 30.


Development of an in situ procedure to evaluate the reticulo-rumen morphology of sheep selected for divergent methane emissions.

Waite SJ, Zhang J, Cater JE, Waghorn GC, Bain WE, McEwan JC, Suresh V.

Animal. 2019 Mar;13(3):542-548. doi: 10.1017/S1751731118001854. Epub 2018 Jul 24.


Genetic parameters of methane emissions determined using portable accumulation chambers in lambs and ewes grazing pasture and genetic correlations with emissions determined in respiration chambers.

Jonker A, Hickey SM, Rowe SJ, Janssen PH, Shackell GH, Elmes S, Bain WE, Wing J, Greer GJ, Bryson B, MacLean S, Dodds KG, Pinares-Patiño CS, Young EA, Knowler K, Pickering NK, McEwan JC.

J Anim Sci. 2018 Jul 28;96(8):3031-3042. doi: 10.1093/jas/sky187.


An entropy-reducing data representation approach for bioinformatic data.

McCulloch AF, Jauregui R, Maclean PH, Ashby RL, Moraga RA, Laugraud A, Brauning R, Dodds KG, McEwan JC.

Database (Oxford). 2018 Jan 1;2018. doi: 10.1093/database/bay029.


Linkage Disequilibrium Estimation in Low Coverage High-Throughput Sequencing Data.

Bilton TP, McEwan JC, Clarke SM, Brauning R, van Stijn TC, Rowe SJ, Dodds KG.

Genetics. 2018 Jun;209(2):389-400. doi: 10.1534/genetics.118.300831. Epub 2018 Mar 27.


Estimation of linkage disequilibrium and effective population size in New Zealand sheep using three different methods to create genetic maps.

Prieur V, Clarke SM, Brito LF, McEwan JC, Lee MA, Brauning R, Dodds KG, Auvray B.

BMC Genet. 2017 Jul 21;18(1):68. doi: 10.1186/s12863-017-0534-2.


An ovine hepatorenal fibrocystic model of a Meckel-like syndrome associated with dysmorphic primary cilia and TMEM67 mutations.

Stayner C, Poole CA, McGlashan SR, Pilanthananond M, Brauning R, Markie D, Lett B, Slobbe L, Chae A, Johnstone AC, Jensen CG, McEwan JC, Dittmer K, Parker K, Wiles A, Blackburne W, Leichter A, Leask M, Pinnapureddy A, Jennings M, Horsfield JA, Walker RJ, Eccles MR.

Sci Rep. 2017 May 9;7(1):1601. doi: 10.1038/s41598-017-01519-4.


Characterization of an X-chromosomal non-mosaic monosomy (59, X0) dairy heifer detected using routinely available single nucleotide polymorphism genotype data.

Berry DP, Wolfe A, O'Donovan J, Byrne N, Sayers RG, Dodds KG, McEwan JC, O'Connor RE, McClure M, Purfield DC.

J Anim Sci. 2017 Mar;95(3):1042-1049. doi: 10.2527/jas.2016.1279.


Genetic diversity of a New Zealand multi-breed sheep population and composite breeds' history revealed by a high-density SNP chip.

Brito LF, McEwan JC, Miller SP, Pickering NK, Bain WE, Dodds KG, Schenkel FS, Clarke SM.

BMC Genet. 2017 Mar 14;18(1):25. doi: 10.1186/s12863-017-0492-8.


Prediction of genomic breeding values for growth, carcass and meat quality traits in a multi-breed sheep population using a HD SNP chip.

Brito LF, Clarke SM, McEwan JC, Miller SP, Pickering NK, Bain WE, Dodds KG, Sargolzaei M, Schenkel FS.

BMC Genet. 2017 Jan 26;18(1):7. doi: 10.1186/s12863-017-0476-8.


Gene network analysis identifies rumen epithelial cell proliferation, differentiation and metabolic pathways perturbed by diet and correlated with methane production.

Xiang R, McNally J, Rowe S, Jonker A, Pinares-Patino CS, Oddy VH, Vercoe PE, McEwan JC, Dalrymple BP.

Sci Rep. 2016 Dec 14;6:39022. doi: 10.1038/srep39022.


Assessing accuracy of imputation using different SNP panel densities in a multi-breed sheep population.

Ventura RV, Miller SP, Dodds KG, Auvray B, Lee M, Bixley M, Clarke SM, McEwan JC.

Genet Sel Evol. 2016 Sep 23;48(1):71.


Copy number variants in the sheep genome detected using multiple approaches.

Jenkins GM, Goddard ME, Black MA, Brauning R, Auvray B, Dodds KG, Kijas JW, Cockett N, McEwan JC.

BMC Genomics. 2016 Jun 8;17:441. doi: 10.1186/s12864-016-2754-7.


Natural variation in methane emission of sheep fed on a lucerne pellet diet is unrelated to rumen ciliate community type.

Kittelmann S, Pinares-Patiño CS, Seedorf H, Kirk MR, McEwan JC, Janssen PH.

Microbiology. 2016 Mar;162(3):459-65. doi: 10.1099/mic.0.000245. Epub 2016 Jan 26.


Construction of relatedness matrices using genotyping-by-sequencing data.

Dodds KG, McEwan JC, Brauning R, Anderson RM, van Stijn TC, Kristjánsson T, Clarke SM.

BMC Genomics. 2015 Dec 9;16:1047. doi: 10.1186/s12864-015-2252-3.


Ovine rumen papillae biopsy via oral endoscopy; a rapid and repeatable method for serial sampling.

McRae KM, Schultz M, Mackintosh CG, Shackell GH, Martinez MF, Knowler KJ, Williams M, Ho C, Elmes SN, McEwan JC.

N Z Vet J. 2016 May;64(3):174-8. doi: 10.1080/00480169.2015.1121845. Epub 2016 Jan 14.


Genomic prediction and genome-wide association study for dagginess and host internal parasite resistance in New Zealand sheep.

Pickering NK, Auvray B, Dodds KG, McEwan JC.

BMC Genomics. 2015 Nov 17;16:958. doi: 10.1186/s12864-015-2148-2.


Anaesthesia-associated hypersensitivity reactions: seven years' data from a British bi-specialty clinic.

Low AE, McEwan JC, Karanam S, North J, Kong KL.

Anaesthesia. 2016 Jan;71(1):76-84. doi: 10.1111/anae.13273. Epub 2015 Nov 13.


Gremlin1 induces anterior-posterior limb bifurcations in developing Xenopus limbs but does not enhance limb regeneration.

Wang YH, Keenan SR, Lynn J, McEwan JC, Beck CW.

Mech Dev. 2015 Nov;138 Pt 3:256-67. doi: 10.1016/j.mod.2015.10.003. Epub 2015 Oct 23.


Genetic analysis and genomic selection of stayability and productive life in New Zealand ewes.

Lee MA, Cullen NG, Newman SA, Dodds KG, McEwan JC, Shackell GH.

J Anim Sci. 2015 Jul;93(7):3268-77. doi: 10.2527/jas.2014-8259.


Animal board invited review: genetic possibilities to reduce enteric methane emissions from ruminants.

Pickering NK, Oddy VH, Basarab J, Cammack K, Hayes B, Hegarty RS, Lassen J, McEwan JC, Miller S, Pinares-Patiño CS, de Haas Y.

Animal. 2015 Sep;9(9):1431-40. doi: 10.1017/S1751731115000968. Epub 2015 Jun 9. Review.


Coordinated international action to accelerate genome-to-phenome with FAANG, the Functional Annotation of Animal Genomes project.

Andersson L, Archibald AL, Bottema CD, Brauning R, Burgess SC, Burt DW, Casas E, Cheng HH, Clarke L, Couldrey C, Dalrymple BP, Elsik CG, Foissac S, Giuffra E, Groenen MA, Hayes BJ, Huang LS, Khatib H, Kijas JW, Kim H, Lunney JK, McCarthy FM, McEwan JC, Moore S, Nanduri B, Notredame C, Palti Y, Plastow GS, Reecy JM, Rohrer GA, Sarropoulou E, Schmidt CJ, Silverstein J, Tellam RL, Tixier-Boichard M, Tosser-Klopp G, Tuggle CK, Vilkki J, White SN, Zhao S, Zhou H; FAANG Consortium.

Genome Biol. 2015 Mar 25;16:57. doi: 10.1186/s13059-015-0622-4.


Genome-wide DNA methylation analysis: no evidence for stable hemimethylation in the sheep muscle genome.

Couldrey C, Brauning R, Henderson HV, McEwan JC.

Anim Genet. 2015 Apr;46(2):185-9. doi: 10.1111/age.12268. Epub 2015 Feb 6.


Genetic parameters for predicted methane production and laser methane detector measurements.

Pickering NK, Chagunda MG, Banos G, Mrode R, McEwan JC, Wall E.

J Anim Sci. 2015 Jan;93(1):11-20. doi: 10.2527/jas.2014-8302. Epub 2014 Nov 17.


Genomic breed prediction in New Zealand sheep.

Dodds KG, Auvray B, Newman SA, McEwan JC.

BMC Genet. 2014 Sep 16;15:92. doi: 10.1186/s12863-014-0092-9.


Estimates of genetic parameters for breech strike and potential indirect indicators in sheep.

Pickering NK, Blair HT, Hickson RE, Johnson PL, Dodds KG, McEwan JC.

N Z Vet J. 2015 Mar;63(2):98-103. doi: 10.1080/00480169.2014.961582. Epub 2015 Jan 19.


Genomic prediction of breeding values in the New Zealand sheep industry using a 50K SNP chip.

Auvray B, McEwan JC, Newman SA, Lee M, Dodds KG.

J Anim Sci. 2014 Oct;92(10):4375-89. doi: 10.2527/jas.2014-7801. Epub 2014 Aug 22.


Two different bacterial community types are linked with the low-methane emission trait in sheep.

Kittelmann S, Pinares-Patiño CS, Seedorf H, Kirk MR, Ganesh S, McEwan JC, Janssen PH.

PLoS One. 2014 Jul 31;9(7):e103171. doi: 10.1371/journal.pone.0103171. eCollection 2014.


Signatures of selection in sheep bred for resistance or susceptibility to gastrointestinal nematodes.

McRae KM, McEwan JC, Dodds KG, Gemmell NJ.

BMC Genomics. 2014 Jul 30;15:637. doi: 10.1186/1471-2164-15-637.


Genome-wide DNA methylation patterns and transcription analysis in sheep muscle.

Couldrey C, Brauning R, Bracegirdle J, Maclean P, Henderson HV, McEwan JC.

PLoS One. 2014 Jul 10;9(7):e101853. doi: 10.1371/journal.pone.0101853. eCollection 2014.


Methane yield phenotypes linked to differential gene expression in the sheep rumen microbiome.

Shi W, Moon CD, Leahy SC, Kang D, Froula J, Kittelmann S, Fan C, Deutsch S, Gagic D, Seedorf H, Kelly WJ, Atua R, Sang C, Soni P, Li D, Pinares-Patiño CS, McEwan JC, Janssen PH, Chen F, Visel A, Wang Z, Attwood GT, Rubin EM.

Genome Res. 2014 Sep;24(9):1517-25. doi: 10.1101/gr.168245.113. Epub 2014 Jun 6.


The sheep genome illuminates biology of the rumen and lipid metabolism.

Jiang Y, Xie M, Chen W, Talbot R, Maddox JF, Faraut T, Wu C, Muzny DM, Li Y, Zhang W, Stanton JA, Brauning R, Barris WC, Hourlier T, Aken BL, Searle SMJ, Adelson DL, Bian C, Cam GR, Chen Y, Cheng S, DeSilva U, Dixen K, Dong Y, Fan G, Franklin IR, Fu S, Guan R, Highland MA, Holder ME, Huang G, Ingham AB, Jhangiani SN, Kalra D, Kovar CL, Lee SL, Liu W, Liu X, Lu C, Lv T, Mathew T, McWilliam S, Menzies M, Pan S, Robelin D, Servin B, Townley D, Wang W, Wei B, White SN, Yang X, Ye C, Yue Y, Zeng P, Zhou Q, Hansen JB, Kristensen K, Gibbs RA, Flicek P, Warkup CC, Jones HE, Oddy VH, Nicholas FW, McEwan JC, Kijas J, Wang J, Worley KC, Archibald AL, Cockett N, Xu X, Wang W, Dalrymple BP.

Science. 2014 Jun 6;344(6188):1168-1173. doi: 10.1126/science.1252806.


Towards genomic selection for facial eczema disease tolerance in the New Zealand sheep industry.

Phua SH, Hyndman DL, Baird HJ, Auvray B, McEwan JC, Lee MA, Dodds KG.

Anim Genet. 2014 Aug;45(4):559-64. doi: 10.1111/age.12167. Epub 2014 May 7.


A high throughput single nucleotide polymorphism multiplex assay for parentage assignment in New Zealand sheep.

Clarke SM, Henry HM, Dodds KG, Jowett TW, Manley TR, Anderson RM, McEwan JC.

PLoS One. 2014 Apr 16;9(4):e93392. doi: 10.1371/journal.pone.0093392. eCollection 2014.


Accuracy of genomic predictions in Bos indicus (Nellore) cattle.

Neves HH, Carvalheiro R, O'Brien AM, Utsunomiya YT, do Carmo AS, Schenkel FS, Sölkner J, McEwan JC, Van Tassell CP, Cole JB, da Silva MV, Queiroz SA, Sonstegard TS, Garcia JF.

Genet Sel Evol. 2014 Feb 27;46:17. doi: 10.1186/1297-9686-46-17.


Accuracy of genotype imputation in Nelore cattle.

Carvalheiro R, Boison SA, Neves HH, Sargolzaei M, Schenkel FS, Utsunomiya YT, O'Brien AM, Sölkner J, McEwan JC, Van Tassell CP, Sonstegard TS, Garcia JF.

Genet Sel Evol. 2014 Oct 10;46:69. doi: 10.1186/s12711-014-0069-1.


Imputation of microsatellite alleles from dense SNP genotypes for parentage verification across multiple Bos taurus and Bos indicus breeds.

McClure MC, Sonstegard TS, Wiggans GR, Van Eenennaam AL, Weber KL, Penedo CT, Berry DP, Flynn J, Garcia JF, Carmo AS, Regitano LC, Albuquerque M, Silva MV, Machado MA, Coffey M, Moore K, Boscher MY, Genestout L, Mazza R, Taylor JF, Schnabel RD, Simpson B, Marques E, McEwan JC, Cromie A, Coutinho LL, Kuehn LA, Keele JW, Piper EK, Cook J, Williams R; Bovine HapMap Consortium, Van Tassell CP.

Front Genet. 2013 Sep 18;4:176. doi: 10.3389/fgene.2013.00176. eCollection 2013.


Genetic relationships between dagginess, breech bareness, and wool traits in New Zealand dual-purpose sheep.

Pickering NK, Blair HT, Hickson RE, Dodds KG, Johnson PL, McEwan JC.

J Anim Sci. 2013 Oct;91(10):4578-88. doi: 10.2527/jas.2013-6741. Epub 2013 Jul 26.


Genome-wide association study for birth weight in Nellore cattle points to previously described orthologous genes affecting human and bovine height.

Utsunomiya YT, do Carmo AS, Carvalheiro R, Neves HH, Matos MC, Zavarez LB, Pérez O'Brien AM, Sölkner J, McEwan JC, Cole JB, Van Tassell CP, Schenkel FS, da Silva MV, Porto Neto LR, Sonstegard TS, Garcia JF.

BMC Genet. 2013 Jun 13;14:52. doi: 10.1186/1471-2156-14-52.


Heritability estimates of methane emissions from sheep.

Pinares-Patiño CS, Hickey SM, Young EA, Dodds KG, MacLean S, Molano G, Sandoval E, Kjestrup H, Harland R, Hunt C, Pickering NK, McEwan JC.

Animal. 2013 Jun;7 Suppl 2:316-21. doi: 10.1017/S1751731113000864.


Consistent divergence times and allele sharing measured from cross-species application of SNP chips developed for three domestic species.

Miller JM, Kijas JW, Heaton MP, McEwan JC, Coltman DW.

Mol Ecol Resour. 2012 Nov;12(6):1145-50. doi: 10.1111/1755-0998.12017. Epub 2012 Sep 21.


The locus for an inherited cataract in sheep maps to ovine chromosome 6.

Wilson GR, Morton JD, Palmer DN, McEwan JC, Gately K, Anderson RM, Dodds KG.

Mol Vis. 2012;18:1384-94. Epub 2012 May 31.


Genomic scan of selective sweeps in thin and fat tail sheep breeds for identifying of candidate regions associated with fat deposition.

Moradi MH, Nejati-Javaremi A, Moradi-Shahrbabak M, Dodds KG, McEwan JC.

BMC Genet. 2012 Feb 26;13:10. doi: 10.1186/1471-2156-13-10.


Genetic parameters for production traits in New Zealand dual-purpose sheep, with an emphasis on dagginess.

Pickering NK, Dodds KG, Blair HT, Hickson RE, Johnson PL, McEwan JC.

J Anim Sci. 2012 May;90(5):1411-20. doi: 10.2527/jas.2011-4163. Epub 2011 Nov 18.


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