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Unraveling genomic associations with feed efficiency and body weight traits in chickens through an integrative approach.

Moreira GCM, Poleti MD, Pértille F, Boschiero C, Cesar ASM, Godoy TF, Ledur MC, Reecy JM, Garrick DJ, Coutinho LL.

BMC Genet. 2019 Nov 6;20(1):83. doi: 10.1186/s12863-019-0783-3.


Increasing the accuracy of genomic prediction in pure-bred Limousin beef cattle by including cross-bred Limousin data and accounting for an F94L variant in MSTN.

Lee J, Kim JM, Garrick DJ.

Anim Genet. 2019 Dec;50(6):621-633. doi: 10.1111/age.12846. Epub 2019 Sep 5.


Strategies for noise reduction and standardization of milk mid-infrared spectra from dairy cattle.

Tiplady KM, Sherlock RG, Littlejohn MD, Pryce JE, Davis SR, Garrick DJ, Spelman RJ, Harris BL.

J Dairy Sci. 2019 Jul;102(7):6357-6372. doi: 10.3168/jds.2018-16144. Epub 2019 Apr 25.


β-Mannosidosis in German Shepherd Dogs.

Jolly RD, Dittmer KE, Garrick DJ, Chernyavtseva A, Hemsley KM, King B, Fietz M, Shackleton NM, Fairley R, Wylie K.

Vet Pathol. 2019 Sep;56(5):743-748. doi: 10.1177/0300985819839239. Epub 2019 Apr 14.


Identification of recombination hotspots and quantitative trait loci for recombination rate in layer chickens.

Weng Z, Wolc A, Su H, Fernando RL, Dekkers JCM, Arango J, Settar P, Fulton JE, O'Sullivan NP, Garrick DJ.

J Anim Sci Biotechnol. 2019 Feb 26;10:20. doi: 10.1186/s40104-019-0332-y. eCollection 2019.


A certain invariance property of BLUE in a whole-genome regression context.

Gianola D, Fernando RL, Garrick DJ.

J Anim Breed Genet. 2019 Mar;136(2):113-117. doi: 10.1111/jbg.12378. Epub 2019 Jan 7.


Variance component estimates for post-thaw sperm variables measured by computer assisted semen analyzer for inbred and non-inbred Hereford bulls.

Tseveenjav B, Blackburn HD, Garrick DJ.

Anim Reprod Sci. 2018 Dec;199:45-50. doi: 10.1016/j.anireprosci.2018.10.005. Epub 2018 Oct 23.


Integration of genome wide association studies and whole genome sequencing provides novel insights into fat deposition in chicken.

Moreira GCM, Boschiero C, Cesar ASM, Reecy JM, Godoy TF, Pértille F, Ledur MC, Moura ASAMT, Garrick DJ, Coutinho LL.

Sci Rep. 2018 Nov 1;8(1):16222. doi: 10.1038/s41598-018-34364-0.


Empirical Comparisons of Different Statistical Models To Identify and Validate Kernel Row Number-Associated Variants from Structured Multi-parent Mapping Populations of Maize.

Yang J, Yeh CE, Ramamurthy RK, Qi X, Fernando RL, Dekkers JCM, Garrick DJ, Nettleton D, Schnable PS.

G3 (Bethesda). 2018 Nov 6;8(11):3567-3575. doi: 10.1534/g3.118.200636.


Meta-analysis of genome-wide association studies for cattle stature identifies common genes that regulate body size in mammals.

Bouwman AC, Daetwyler HD, Chamberlain AJ, Ponce CH, Sargolzaei M, Schenkel FS, Sahana G, Govignon-Gion A, Boitard S, Dolezal M, Pausch H, Brøndum RF, Bowman PJ, Thomsen B, Guldbrandtsen B, Lund MS, Servin B, Garrick DJ, Reecy J, Vilkki J, Bagnato A, Wang M, Hoff JL, Schnabel RD, Taylor JF, Vinkhuyzen AAE, Panitz F, Bendixen C, Holm LE, Gredler B, Hozé C, Boussaha M, Sanchez MP, Rocha D, Capitan A, Tribout T, Barbat A, Croiseau P, Drögemüller C, Jagannathan V, Vander Jagt C, Crowley JJ, Bieber A, Purfield DC, Berry DP, Emmerling R, Götz KU, Frischknecht M, Russ I, Sölkner J, Van Tassell CP, Fries R, Stothard P, Veerkamp RF, Boichard D, Goddard ME, Hayes BJ.

Nat Genet. 2018 Mar;50(3):362-367. doi: 10.1038/s41588-018-0056-5. Epub 2018 Feb 19.


Genomic study and Medical Subject Headings enrichment analysis of early pregnancy rate and antral follicle numbers in Nelore heifers.

Júnior GAO, Perez BC, Cole JB, Santana MHA, Silveira J, Mazzoni G, Ventura RV, Júnior MLS, Kadarmideen HN, Garrick DJ, Ferraz JBS.

J Anim Sci. 2017 Nov;95(11):4796-4812. doi: 10.2527/jas2017.1752.


Familial episodic ataxia in lambs is potentially associated with a mutation in the fibroblast growth factor 14 (FGF14) gene.

Dittmer KE, Jolly RD, Mayhew IG, Ridler AL, Chernyavtseva A, Garrick DJ, Blair HT.

PLoS One. 2017 Dec 18;12(12):e0190030. doi: 10.1371/journal.pone.0190030. eCollection 2017.


Network Analysis Reveals Putative Genes Affecting Meat Quality in Angus Cattle.

Mateescu RG, Garrick DJ, Reecy JM.

Front Genet. 2017 Nov 6;8:171. doi: 10.3389/fgene.2017.00171. eCollection 2017.


Genotype imputation in a tropical crossbred dairy cattle population.

Oliveira Júnior GA, Chud TCS, Ventura RV, Garrick DJ, Cole JB, Munari DP, Ferraz JBS, Mullart E, DeNise S, Smith S, da Silva MVGB.

J Dairy Sci. 2017 Dec;100(12):9623-9634. doi: 10.3168/jds.2017-12732. Epub 2017 Oct 4.


The Accuracy and Bias of Single-Step Genomic Prediction for Populations Under Selection.

Hsu WL, Garrick DJ, Fernando RL.

G3 (Bethesda). 2017 Aug 7;7(8):2685-2694. doi: 10.1534/g3.117.043596.


Genome-wide association study for feed efficiency and growth traits in U.S. beef cattle.

Seabury CM, Oldeschulte DL, Saatchi M, Beever JE, Decker JE, Halley YA, Bhattarai EK, Molaei M, Freetly HC, Hansen SL, Yampara-Iquise H, Johnson KA, Kerley MS, Kim J, Loy DD, Marques E, Neibergs HL, Schnabel RD, Shike DW, Spangler ML, Weaber RL, Garrick DJ, Taylor JF.

BMC Genomics. 2017 May 18;18(1):386. doi: 10.1186/s12864-017-3754-y.


A comparison of identity-by-descent and identity-by-state matrices that are used for genetic evaluation and estimation of variance components.

Fernando RL, Cheng H, Sun X, Garrick DJ.

J Anim Breed Genet. 2017 Jun;134(3):213-223. doi: 10.1111/jbg.12275.


Efficient strategies for leave-one-out cross validation for genomic best linear unbiased prediction.

Cheng H, Garrick DJ, Fernando RL.

J Anim Sci Biotechnol. 2017 May 2;8:38. doi: 10.1186/s40104-017-0164-6. eCollection 2017.


Single nucleotide variants and InDels identified from whole-genome re-sequencing of Guzerat, Gyr, Girolando and Holstein cattle breeds.

Stafuzza NB, Zerlotini A, Lobo FP, Yamagishi ME, Chud TC, Caetano AR, Munari DP, Garrick DJ, Machado MA, Martins MF, Carvalho MR, Cole JB, Barbosa da Silva MV.

PLoS One. 2017 Mar 21;12(3):e0173954. doi: 10.1371/journal.pone.0173954. eCollection 2017.


Erratum to: A FAS-ligand variant associated with autoimmune lymphoproliferative syndrome in cats.

Aberdein D, Munday JS, Gandolfi B, Dittmer KE, Malik R, Garrick DJ, Lyons LA; 99 Lives Consortium.

Mamm Genome. 2017 Apr;28(3-4):152-154. doi: 10.1007/s00335-016-9676-1. No abstract available.


Epistatic interactions associated with fatty acid concentrations of beef from angus sired beef cattle.

Kramer LM, Ghaffar MA, Koltes JE, Fritz-Waters ER, Mayes MS, Sewell AD, Weeks NT, Garrick DJ, Fernando RL, Ma L, Reecy JM.

BMC Genomics. 2016 Nov 8;17(1):891.


A FAS-ligand variant associated with autoimmune lymphoproliferative syndrome in cats.

Aberdein D, Munday JS, Gandolfi B, Dittmer KE, Malik R, Garrick DJ, Lyons LA; 99 Lives Consortium.

Mamm Genome. 2017 Feb;28(1-2):47-55. doi: 10.1007/s00335-016-9668-1. Epub 2016 Oct 21. Erratum in: Mamm Genome. 2017 Apr;28(3-4):152-154.


An Upper Bound for Accuracy of Prediction Using GBLUP.

Karaman E, Cheng H, Firat MZ, Garrick DJ, Fernando RL.

PLoS One. 2016 Aug 16;11(8):e0161054. doi: 10.1371/journal.pone.0161054. eCollection 2016.


Deriving Gene Networks from SNP Associated with Triacylglycerol and Phospholipid Fatty Acid Fractions from Ribeyes of Angus Cattle.

Buchanan JW, Reecy JM, Garrick DJ, Duan Q, Beitz DC, Koltes JE, Saatchi M, Koesterke L, Mateescu RG.

Front Genet. 2016 Jun 20;7:116. doi: 10.3389/fgene.2016.00116. eCollection 2016.


Impact of fitting dominance and additive effects on accuracy of genomic prediction of breeding values in layers.

Heidaritabar M, Wolc A, Arango J, Zeng J, Settar P, Fulton JE, O'Sullivan NP, Bastiaansen JW, Fernando RL, Garrick DJ, Dekkers JC.

J Anim Breed Genet. 2016 Oct;133(5):334-46. doi: 10.1111/jbg.12225. Epub 2016 Jun 30.


Effects of number of training generations on genomic prediction for various traits in a layer chicken population.

Weng Z, Wolc A, Shen X, Fernando RL, Dekkers JC, Arango J, Settar P, Fulton JE, O'Sullivan NP, Garrick DJ.

Genet Sel Evol. 2016 Mar 19;48:22. doi: 10.1186/s12711-016-0198-9.


The Effect of Calf Gender on Milk Production in Seasonal Calving Cows and Its Impact on Genetic Evaluations.

Hess MK, Hess AS, Garrick DJ.

PLoS One. 2016 Mar 14;11(3):e0151236. doi: 10.1371/journal.pone.0151236. eCollection 2016.


Mixture models detect large effect QTL better than GBLUP and result in more accurate and persistent predictions.

Wolc A, Arango J, Settar P, Fulton JE, O'Sullivan NP, Dekkers JC, Fernando R, Garrick DJ.

J Anim Sci Biotechnol. 2016 Feb 11;7:7. doi: 10.1186/s40104-016-0066-z. eCollection 2016.


A fast and efficient Gibbs sampler for BayesB in whole-genome analyses.

Cheng H, Qu L, Garrick DJ, Fernando RL.

Genet Sel Evol. 2015 Oct 14;47:80. doi: 10.1186/s12711-015-0157-x.


Response and inbreeding from a genomic selection experiment in layer chickens.

Wolc A, Zhao HH, Arango J, Settar P, Fulton JE, O'Sullivan NP, Preisinger R, Stricker C, Habier D, Fernando RL, Garrick DJ, Lamont SJ, Dekkers JC.

Genet Sel Evol. 2015 Jul 7;47:59. doi: 10.1186/s12711-015-0133-5.


Genetic parameters and genetic correlations among triacylglycerol and phospholipid fractions in Angus cattle.

Buchanan JW, Reecy JM, Garrick DJ, Duan Q, Beitz DC, Mateescu RG.

J Anim Sci. 2015 Feb;93(2):522-8. doi: 10.2527/jas.2014-8418.


Comparison of Bayesian models to estimate direct genomic values in multi-breed commercial beef cattle.

Rolf MM, Garrick DJ, Fountain T, Ramey HR, Weaber RL, Decker JE, Pollak EJ, Schnabel RD, Taylor JF.

Genet Sel Evol. 2015 Apr 1;47:23. doi: 10.1186/s12711-015-0106-8.


Functionally reciprocal mutations of the prolactin signalling pathway define hairy and slick cattle.

Littlejohn MD, Henty KM, Tiplady K, Johnson T, Harland C, Lopdell T, Sherlock RG, Li W, Lukefahr SD, Shanks BC, Garrick DJ, Snell RG, Spelman RJ, Davis SR.

Nat Commun. 2014 Dec 18;5:5861. doi: 10.1038/ncomms6861.


Comparison of breeding value prediction for two traits in a Nellore-Angus crossbred population using different Bayesian modeling methodologies.

Hulsman Hanna LL, Garrick DJ, Gill CA, Herring AD, Sanders JO, Riley DG.

Genet Mol Biol. 2014 Oct;37(4):631-7. doi: 10.1590/S1415-47572014005000021. Epub 2014 Nov 14.


Genetic parameters for sensory traits in longissimus muscle and their associations with tenderness, marbling score, and intramuscular fat in Angus cattle.

Mateescu RG, Garrick DJ, Garmyn AJ, VanOverbeke DL, Mafi GG, Reecy JM.

J Anim Sci. 2015 Jan;93(1):21-7. doi: 10.2527/jas.2014-8405. Epub 2014 Nov 20.


QTLs associated with dry matter intake, metabolic mid-test weight, growth and feed efficiency have little overlap across 4 beef cattle studies.

Saatchi M, Beever JE, Decker JE, Faulkner DB, Freetly HC, Hansen SL, Yampara-Iquise H, Johnson KA, Kachman SD, Kerley MS, Kim J, Loy DD, Marques E, Neibergs HL, Pollak EJ, Schnabel RD, Seabury CM, Shike DW, Snelling WM, Spangler ML, Weaber RL, Garrick DJ, Taylor JF.

BMC Genomics. 2014 Nov 20;15:1004. doi: 10.1186/1471-2164-15-1004.


Evaluation of variant identification methods for whole genome sequencing data in dairy cattle.

Baes CF, Dolezal MA, Koltes JE, Bapst B, Fritz-Waters E, Jansen S, Flury C, Signer-Hasler H, Stricker C, Fernando R, Fries R, Moll J, Garrick DJ, Reecy JM, Gredler B.

BMC Genomics. 2014 Nov 1;15:948. doi: 10.1186/1471-2164-15-948.


Polymorphisms in lipogenic genes and milk fatty acid composition in Holstein dairy cattle.

Nafikov RA, Schoonmaker JP, Korn KT, Noack K, Garrick DJ, Koehler KJ, Minick-Bormann J, Reecy JM, Spurlock DE, Beitz DC.

Genomics. 2014 Dec;104(6 Pt B):572-81. doi: 10.1016/j.ygeno.2014.10.001. Epub 2014 Oct 8.


Identification of genomic regions associated with feed efficiency in Nelore cattle.

de Oliveira PS, Cesar AS, do Nascimento ML, Chaves AS, Tizioto PC, Tullio RR, Lanna DP, Rosa AN, Sonstegard TS, Mourao GB, Reecy JM, Garrick DJ, Mudadu MA, Coutinho LL, Regitano LC.

BMC Genet. 2014 Sep 26;15:100. doi: 10.1186/s12863-014-0100-0.


A class of Bayesian methods to combine large numbers of genotyped and non-genotyped animals for whole-genome analyses.

Fernando RL, Dekkers JC, Garrick DJ.

Genet Sel Evol. 2014 Sep 22;46:50. doi: 10.1186/1297-9686-46-50.


Reduction in accuracy of genomic prediction for ordered categorical data compared to continuous observations.

Kizilkaya K, Fernando RL, Garrick DJ.

Genet Sel Evol. 2014 Jun 9;46:37. doi: 10.1186/1297-9686-46-37.


Large-effect pleiotropic or closely linked QTL segregate within and across ten US cattle breeds.

Saatchi M, Schnabel RD, Taylor JF, Garrick DJ.

BMC Genomics. 2014 Jun 6;15:442. doi: 10.1186/1471-2164-15-442.


Recombination locations and rates in beef cattle assessed from parent-offspring pairs.

Weng ZQ, Saatchi M, Schnabel RD, Taylor JF, Garrick DJ.

Genet Sel Evol. 2014 May 29;46:34. doi: 10.1186/1297-9686-46-34.


Use of robust multivariate linear mixed models for estimation of genetic parameters for carcass traits in beef cattle.

Peters SO, Kizilkaya K, Garrick DJ, Fernando RL, Pollak EJ, Enns RM, De Donato M, Ajayi OO, Imumorin IG.

J Anim Breed Genet. 2014 Dec;131(6):504-12. doi: 10.1111/jbg.12093. Epub 2014 May 17.


Estimating the impact of somatic cell count on the value of milk utilising parameters obtained from the published literature.

Geary U, Lopez-Villalobos N, O'Brien B, Garrick DJ, Shalloo L.

J Dairy Res. 2014 May;81(2):223-32. doi: 10.1017/S0022029914000053. Epub 2014 Mar 26.


Genome-wide association study for intramuscular fat deposition and composition in Nellore cattle.

Cesar AS, Regitano LC, Mourão GB, Tullio RR, Lanna DP, Nassu RT, Mudado MA, Oliveira PS, do Nascimento ML, Chaves AS, Alencar MM, Sonstegard TS, Garrick DJ, Reecy JM, Coutinho LL.

BMC Genet. 2014 Mar 25;15:39. doi: 10.1186/1471-2156-15-39.


Genome-wide association study for egg production and quality in layer chickens.

Wolc A, Arango J, Jankowski T, Dunn I, Settar P, Fulton JE, O'Sullivan NP, Preisinger R, Fernando RL, Garrick DJ, Dekkers JC.

J Anim Breed Genet. 2014 Jun;131(3):173-82. doi: 10.1111/jbg.12086. Epub 2014 Mar 17.


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