Research publications

Our scientists contribute to a wide range of well-respected scientific journals and reports.

The types of research our scientists publish falls into four broad categories:

  1. Genomics and molecular biology.
  2. Reproduction and artificial insemination.
  3. Quantitative genetics and animal evaluation.
  4. Animal health and welfare.

DISCOVERY OF BREED SPECIFIC GENOMIC CONTENT IN BEEF AND DAIRY BREEDS
Reynolds, E.; Couldrey, C.; Keehan, M.; Tiplady, K.; Johnson, T.; Garrick, D.; Littlejohn, M.
11th World Congress of Genetics Applied to Livestock Production 5p. 2018

FROM RNA TO MILK: USING MOLECULAR PHENOTYPES TO STUDY LACTATION IN CATTLE: poster
Lopdell, T.; Littlejohn, M.; Snell, R. 2018

GWAS OF NOVEL PROTEIN CODING VARIANTS DISCOVERED THROUGH WHOLE GENOME SEQUENCING OF DAIRY CATTLE
Burborough, K.; Spelman, R.; Snell, R.; Littlejohn, M.
11th World Congress of Genetics Applied to Livestock Production 5p. 2018

GERMLINE MUTATIONS IN BOS TAURUS. PhD thesis
Harland, Chad Simeon. University Of Liege Faculty Of Veterinary Medicine Dept of Animal Production, Animal Genomics Unit, 2018 

MATN3 UNDERLIES A QTL FOR STATURE IN CATTLE
Lopdell, T.; Littlejohn, M.
New Zealand journal of animal science and production v.78 p.51-55 2018

RATE OF DE NOVO MUTATION IN DAIRY CATTLE AND POTENTIAL IMPACT OF REPRODUCTIVE TECHNOLOGIES
Harland, C.; Durkin, K.; Artesi, M.; Karim, L.; Cambisano, M.;Deckers, M.; Tamma, N.; Mullaart, E.; Coppieters, W.; Charlier, C.; Georges, M.
11th World Congress of Genetics Applied to Livestock Production 5p. 2018

THE USE OF SEQUENCE SNP IN A MARKER MODEL FOR AN ACROSS-BREED DAIRY CATTLE GENOMIC EVALUATION
Harris, B.L.; Sherlock, R.G.; Couldrey, C.; Keeham, M.D.; Tiplady, K.M.
11th World Congress of Genetics Applied to Livestock Production 9p. 2018 

USING RNA SEQ DATA TO IMPROVE GENOMIC SELECTION IN DAIRY CATTLE
Lopdell, T.; Tiplady, K.; Littlejohn, M.
11th World Congress of Genetics Applied to Livestock Production 5p. 2018

BOVINE MAMMARY GLAND X CHROMOSOME INACTIVATION
Couldrey, C.; Johnson, T.; Lopdell, T.; Zhang, I.L.; Littlejohn, M.D.; Keehan, M.; Sherlock, R.G.; Tiplady, K.; Scott, A.; Davis, S.R.; Spelman, R.J.
Journal of dairy science v.100 no.7 p.5491-5500 2017

INTEGRATION OF LARGE-SCALE DNA AND RNA SEQUENCE DATASETS HIGHLIGHTS MEMBRANE-TRANSPORT GENES AS KEY MODULATORS OF MILK LACTOSE CONTENT
Lopdell, T.; Tiplady, K.; Struchalin, M.; Davis, S.R.; Snell, R.; Spelman, R.J.; Littlejohn, M.
PlosOne (submitted) 17p. 2017

FUNCTIONAL CONFIRMATION OF PLAG1 AS THE CANDIDATE CAUSATIVE GENE UNDERLYING MAJOR
PLEIOTROPIC EFFECTS ON BODY WEIGHT AND MILK CHARACTERISTICS

Fink, T.; Tiplady, K.; Lopdell, T.; Snell, R.G.; Spelman, R.J.; Davis, S.R.; Littlejohn, M.D.
Scientific reports no.7 no.44793 2017

BREEDING HEAT TOLERANT DAIRY CATTLE: THE CASE FOR INTROGRESSION OF THE “SLICK” PROLACTIN RECEPTOR VARIANT INTO BOS TAURUS DAIRY BREEDS
Davis, S.R.; Spelman, R.J.; Littlejohn, M.D.
Journal of animal science Breeding and Genetics Symposium 2017

DETECTION AND ASSESSMENT OF COPY NUMBER VARIATION USING PACBIO LONG READ SEQUENCING IN NEW ZEALAND DAIRY CATTLE
Couldrey, C.; Keehan, M.; Johnson, T.; Tiplady, K.; Winkelman, A.; Thresher, C.; Littlejohn, M.D.; Scott, A.; Kemper, K.; Hayes, B.; Davis, S.R.; Spelman, R.J.
AAABG proceedings 2017 

USING GENOTYPIC INFORMATION TO DETERMINE SEX IN DAIRY CATTLE
Zhang, I.L.; Couldrey, C.; Sherlock, R.
New Zealand Society of Animal Production proceedings v.76 p.26-30 2016 
 
SEQUENCE-BASED ASSOCIATION ANALYSIS REVEALS AN MGST1 EQTL WITH PLEIOTROPIC EFFECTS ON BOVINE MILK COMPOSITION
Littlejohn, M.; Tiplady, K.; Fink, T.A.; Lehnert, K.; Lopdell, T.; Johnson, T.; Couldrey, C.; Keehan, M.; Sherlock, R.G.; Harland, C.; Scott, A.; Snell, R.; Davis, S.R.; Spelman, R.J.
Scientific reports 6:25376 2016 
 
NGS-BASED REVERSE GENETIC SCREEN FOR COMMON EMBRYONIC LETHAL MUTATIONS COMPROMISING FERTILITY IN LIVESTOCK
Charlier, C.; Li, W.; Harland, C.; Littlejohn, M.; Coppieters, W.; Creagh, F.; Davis, S.; Druet, T.; Faux, P.; Guillaume, F.; Karim, L.; Keehan, M.; Kadri, N.K.; Tamma, N.; Spelman, R.J.; Georges, M.
Genome research v.26 p.1333-1341 2016 
 
LEVERAGING GENETICALLY SIMPLE TRAITS TO IDENTIFY SMALL-EFFECT VARIANTS FOR COMPLEX PHENOTYPES
Kemper, K.E.; Littlejohn, M.D.; Lopdell, T.; Hayes, B.J.; Bennett, L.E.; Williams, R.P.; Xu, X.Q.; Visscher, P.M.; Carrick, M.J.; Goddard, M.E
BMC genomics 17:858 9p. 2016 
 
FUNCTIONAL CONFIRMATION OF PLAG1 AS THE CAUSATIVE GENE UNDERLYING MAJOR PLEIOTROPIC EFFECTS ON STATURE AND MILK CHARACTERISTICS
Fink, T.; Tiplady, K.; Lopdell, T.; Snell, R.G.; Spelman, R.J.; Davis, S.R.; Littlejohn, M.D.
Scientific reports (submitted) 2016 
 
DETECTING COPY NUMBER VARIATION FROM PACBIO LONG SEQUENCE READS IN NEW ZEALAND DAIRY CATTLE
Couldrey, C.; Keehan, M.; Johnson, T.; Tiplady, K.; Winkelman, A.; Littlejohn, M.D.; Scott, A.; Kemper, K.; Hayes, B.; Davis, S.R.; Spelman, R.J.
Journal of dairy science (submitted) 2016 
 
CODING AND NONCODING VARIANTS IN HFM1, MLH3, MSH4, MSH5, RNF212 AND RNF212B AFFECT RECOMBINATION RATE IN CATTLE
Kadri, N.K.; Harland, C.; Faux, P.; Cambisano, N.; Karim, L.; Coppieters, W.; Fritz, S.; Mullaart, E.; Baurain, D.; Boichard, D.; Spelman, R.J.; Charlier, C.; Georges, M.; Druet, T.
Genome research v.26 no.10 p.1323-1332 2016 
 
THE CD4+ T CELL METHYLOME CONTRIBUTES TO A DISTINCT CD4+ T CELL TRANSCRIPTIONAL SIGNATURE IN MYCOBACTERIUM BOVIS-INFECTED CATTLE
Doherty, R.; Whiston, R.; Cormican, P.; Couldrey, C.; Brady, C.; O'Farrelly, C.; Meade, K.G.
Scientific reports 6:31014 15p. 2016 
 
BOVINE MAMMARY GLAND X CHROMOSOME INACTIVATION
Couldrey, C.; Johnson, T.; Lopdell, T.; Zhang, I.L.; Littlejohn, M.D.; Keehan, M.; Sherlock, R.G.; Tiplady, K.; Scott, A.; Davis, S.R.; Spelman, R.J.
Journal of dairy science (submitted) 2016
 
GENE DISCOVERY, GENOMICS AND DAIRY CATTLE IMPROVEMENT, 2015.
Davis, S.R. Proceedings of the Society of Dairy Cattle Veterinarians of the NZVA Annual Conference p.81-92
 
SUSPENSION OF MILKING IN DAIRY COWS PRODUCES A TRANSIENT INCREASE IN MILK LACTOFERRIN CONCENTRATION AND YIELD AFTER RESUMPTION OF MILKING 2015.
Davis, S.R. South, C.R. Journal of dairy science v.98 no.11 p.7823-7830
 
LACTATION TRAITS ASSOCIATED WITH SHORT AND LONG TERM ONCE-DAILY MILKING PERFORMANCE IN NEW ZEALAND CROSSBRED DAIRY CATTLE, 2015.
Davis, S.R. Turner, S.-A. Obolonkin, V. Tiplady, K. Spelman, R.J.  Phyn, C.V.C. Journal of dairy science v.98 p.1–14
 
APPLICATION OF GENOMIC EVALUATION TO DAIRY CATTLE IN NEW ZEALAND, 2015.
Winkelman, A.M. Johnson, D.L. Harris, B.L. Journal of dairy science v.98 p.659–675
 
FUNCTIONALLY RECIPROCAL MUTATIONS OF THE PROLACTIN SIGNALLING PATHWAY  DEFINE HAIRY AND SLICK CATTLE
Littlejohn, M.; Henty, K.; Tiplady, K.; Johnson, T.; Harland, C.; Lopdell, T.; Sherlock, R.; Li, W.; Lukefahr, S.D.; Shanks, B.C.; Garrick, D.J.; Snell, R.G.; Spelman, R.J.; Davis, S.R.; Snell, R. 2014.
 
STATISTICAL ANALYSES OF MILK TRAITS IN THE NEW ZEALAND DAIRY CATTLE POPULATION: MASTERS THESIS
Hayr, Melanie Kate.  Ames: Iowa State University, 2014.
 
EXPRESSION VARIANTS OF THE LIPOGENIC AGPAT6 GENE AFFECT DIVERSE MILK COMPOSITION PHENOTYPES IN BOS TAURUS
Littlejohn, M.; Tiplady, K.; Lopdell, T.; Law, T.A.; Scott, A.; Harland, C.; Sherlock, R.; Henty, K.; Obolonkin, V.; Lehnert, K.; MacGibbin, A.; Spelman, R.J.; Davis, S.R.; Snell, R. 2014.
 
PRENATAL MATERNAL, DAM PERMANENT ENVIRONMENTAL AND PATERNAL EPIGENETIC EFFECTS IN NEW ZEALAND DAIRY CATTLE
Gudex, B.; Johnson, D.L.; Gondro, C.; Singh, K. 2014. 
 
SINGLE GENE DYNAMICS UNDER CONTROLLED MATING  
Obolonkin, V.; Zherelo, A.; Krylov, G.; Jorgensen, M.; Spelman, R.J. 2014.
 
PRENATAL MATERNAL AND POSSIBLE TRANSGENERATIONAL EPIGENETIC EFFECTS ON MILK PRODUCTION IN NEW ZEALAND DAIRY CATTLE
Gudex, B.; Johnson, D.L.; Singh, K. 2014.
 
VARIANTS MODULATING THE EXPRESSION OF A CHROMOSOME DOMAIN ENCOMPASSING PLAG1 INFLUENCE BOVINE STATURE
Karim, L.; Takeda, H.; Druet, T.; Arias, J.A.C.; Baurain, D.; Cambisano, N.; Davis, S.R.; Farnir, F.; Grisart, B.; Harris, B.L.; Keehan, M.D.; Littlejohn, M.D.; Spelman, R.J.; Georges, M.; Coppieters, W. 2011.

APPLICATION OF LIQUID SEMEN TECHNOLOGY UNDER THE SEASONAL DAIRY PRODUCTION SYSTEM IN NEW ZEALAND
Yang, D.; McMillan, G.; Standley, N.; Xu, Z.
Animal reproduction science 2018 

MATING STRATEGIES TO MAXIMIZE GENETIC MERIT IN DAIRY CATTLE HERDS
Johnson, T.; Eketone, K.; McNaughton, L.; Tiplady, K.; Voogt, J.; Sherlock, R.; Anderson, G.; Keehan, M.; Davis, S.R.; Spelman, R.J.; Chin, D.; Couldrey, C.
Journal of dairy science v.101 no.5 p. 4650-4659 2018

THE PERCENTAGE OF SPRING-CALVING CARRYOVER COWS IN NEW ZEALAND DAIRY HERDS AND THEIR MILK PRODUCTION, COMPARED TO HEIFERS, AGE-MATCHED AND LACTATION-MATCHED NON- CARRYOVER COWS
Gardner, R.R.; Back, P.J.; Lopez-Villalobos, N.; McNaughton, L.R.
Proceedings of the New Zealand Society of Animal Production v.77 p.3-7 2017

REPRODUCTIVE PERFORMANCE OF HERDS MILKED ONCE A DAY ALL SEASON COMPARED WITH HERDS MILKED TWICE A DAY ALL SEASON
Hemming, N.V.; McNaughton, L.; Couldrey, C.
New Zealand journal of animal science and production v.78 p.170-172 2018

EFFECT OF TIME OF ARTIFICIAL INSEMINATION AFTER OESTRUS DETECTION ON NON-RETURN RATE OF LACTATING DAIRY COWS ON PASTURE
Xu, Z.Z. New Zealand veterinary journal v.65 no.3 p.119-123 2017

EFFECT OF TIME OF ARTIFICIAL INSEMINATION AFTER OESTRUS DETECTION ON NON-RETURN RATE OF LACTATING DAIRY COWS ON PASTURE
Xu, Z.Z. New Zealand veterinary journal (accepted manuscript) 2016

MORE DAIRY HEIFERS ARE ACHIEVING LIVEWEIGHT TARGETS
Handcock, R.C.; Lopdell, T.J.; McNaughton, L.R.
Proceedings of the New Zealand Society of Animal Production v.76 p.3-7 2016 

MACHINE LEARNING ALGORITHMS FOR THE PREDICTION OF CONCEPTION SUCCESS TO A GIVEN INSEMINATION IN LACTATING DAIRY COWS 2015.
Hempstalk, K. McParland, S. Berry, D.P. Journal of dairy science v.98 p.5262–5273

BIRTH WEIGHT OF CALVES BORN TO DAIRY COWS IN NEW ZEALAND (brief communication) 
Hickson, R.E.; Zhang, I.L.; McNaughton, L.R. New Zealand Society of Animal Production proceedings v.75 p.257-259 2015

APPLICATION OF LIQUID SEMEN TECHNOLOGY IMPROVES CONCEPTION RATE OF SEX-SORTED SEMEN IN LACTATING DAIRY COWS
Xu, Z.Z  Journal of dairy science v.97 p.7298–7304 2014 

DIFFERENCE IN SPERM DNA FRAGMENTATION BETWEEN BULLS OF HIGH VERSUS LOW NON-RETURN RATE
Standley, N.; Yang, D. 2014.

EXPERIENCES SOLVING LARGE SCALE SINGLE STEP MARKER BEST LINEAR UNBIASED MODELS
Harris, B.L. Interbull meeting: Tallinn, Estonia 2017

COMPARISON OF RECORDS FROM IN-LINE MILK METERS AND CONVENTIONAL HERD TESTING FOR MANAGEMENT AND GENETIC EVALUATION OF DAIRY COWS 
Anderson, G.P.S.; Zhang, I.L.; Winkelman, A.M.; Harris, B.L. Interbull annual meeting: Puerto Varas 2016

THE EFFECT OF CALF GENDER ON MILK PRODUCTION IN SEASONAL CALVING COWS AND ITS IMPACT ON GENETIC EVALUATIONS
Hess, M.K.; Hess, A.S.; Garrick, D.J. PLOS one v.11 no.3 e0151236 2016

ESTIMATION OF GENETIC PARAMETERS FOR MILK YIELD TRAITS AT DIFFERENT HERD PRODUCTION LEVELS IN COWS MILKED ONCE- OR TWICE-DAILY IN NEW ZEALAND
Lembeye, F.; Lopez-Villalobos, N.; Burke, J.L.; Davis, S.R.
Proceedings of the New Zealand Society of Animal Production v.76 p.49-53 2016

FIXED-LENGTH HAPLOTYPES CAN IMPROVE GENOMIC PREDICTION ACCURACY IN AN ADMIXED DAIRY CATTLE POPULATION
Hess, M.K.; Druet, T.; Hess, A.S.; Garrick, D.J
Genetics selection evolution (submitted) 2016

SUPPLY CURVES FOR YIELDS OF DAIRY PRODUCTS FROM FIRST-LACTATION HOLSTEIN FRIESIAN, JERSEY AND HOLSTEIN FRIESIAN-JERSEY CROSSBRED COWS ACCOUNTING FOR SEASONALITY OF MILK COMPOSITION AND PRODUCTION
Sneddon, N.W.; Lopez-Villalobos, N.; Davis, S.R.; Hickson, R.E.; Shalloo, L.; Garrick, D.J.
Proceedings of the New Zealand Society of Animal Production v.76 p.139-143 2016 

PHENOTYPE POPULATION SCREEN IDENTIFIES A NEW MUTATION IN BOVINE DGAT1 RESPONSIBLE FOR UNSATURATED MILK FAT. 2015.
Lehnert, K. Ward, H.E. Berry, S.D. Ankersmit-Udy, A.E. Burrett, A. Beattie, E.M. Thomas, N.L. Harris, B.L. Ford, C.A. Browning, S.R. Rawson, P. Verkerk, G.A. van der Does, Y. Adams, L.F. Davis, S.R. Jordan, T.W. MacGibbon, A.K.H. Spelman, R.J. Snell, R.G. Nature scientific reports v.5 p.1-6

ESTIMATION OF BREED AND HETEROSIS EFFECTS FOR MILK TRAITS AND SOMATIC CELL SCORES IN COWS MILKED ONCE AND TWICE DAILY IN NEW ZEALAND, 2015. 
Lembeye, F. Lopez-Villalobos, N. Burke, J.L. Davis, S.R. Proceedings of the New Zealand Society of Animal Production v.75 p.60-63

METABOLITE PROFILING IN NEW ZEALAND MILK 2015.
Davis, S.R. Jaine, J. Obolonkin, V. Braggins, T.J. Cooney, T.P. Scott, A. Spelman, R.J. Proceedings of the New Zealand Society of Animal Production v.75 p.39-41

GENETIC PARAMETERS FOR MILK COMPONENTS INCLUDING LACTOSE FROM TEST DAY RECORDS IN THE NEW ZEALAND DAIRY HERD. 2015.
Sneddon, N.W. Lopez-Villalobos, N. Davis, S.R. Hickson, R.E.Shalloo, L. New Zealand journal of agricultural research v.58 no.2 p.97-107

POSITIVE RELATIONSHIP BETWEEN LIVE WEIGHT AT FIRST CALVING AND FIRST LACTATION MILK
PRODUCTION 
Handcock, R.C.; Lopez-Villalobos, N.; McNaughton, L.R.; Edwards, G.R.;Hickson, R.E. 
11th World Congress of Genetics Applied to Livestock Production 5p. 2018

MAMMARY GROWTH DURING PREGNANCY AND LACTATION AND ITS RELATIONSHIP WITH MILK YIELD
Davis, S.R. Journal of animal science v.95 no.12 p.5675-5688 2017

GROWTH CURVES OF NEW ZEALAND HOLSTEIN-FRIESIAN, JERSEY AND HOLSTEIN-FRIESIAN-JERSEYCROSSBRED HEIFERS

https://www.researchgate.net/publication/317953423_Growth_curves_of_New_Zealand_Holstein-Friesian_Jersey_and_Holstein-Friesian-Jersey_crossbred_heifers


Handcock, R.C.; Lopez-Villalobos, N.; McNaughton, L.R.; Edwards, G.R.; Hickson, R.E.
Proceedings of the New Zealand Society of Animal Production v.77 p.64-68 2017

CALF AND HEIFER DEVELOPMENT AND THE ONSET OF PUBERTY IN DAIRY COWS WITH DIVERGENT GENETIC MERIT FOR FERTILITY
Meier, S.; Fisher, B.; Eketone, K.; McNaughton, L.R.; Amer, P.R.; Beatson, P.; Bryant, J.R.; Dodds, K.G.; Spelman, R.J.; Roche, J.R.; Burke, C.R.
Proceedings of the New Zealand Society of Animal Production v.77 p.205-210 2017

COMPARING STRATEGIES FOR IMPUTING INFORMATIVE SEQUENCE VARIANTS INTO A WIDER POPULATION OF GENOTYPED DAIRY CATTLE
Tiplady, K.M.; Sherlock, R.G. 11th World Congress of Genetics Applied to Livestock Production 5p. 2018

IDENTIFICATION AND VALIDATION OF COPY NUMBER VARIATION IN NEW ZEALAND DAIRY CATTLE USING (SYNTHETIC) LONG READ AND SHORT READ DNA SEQUENCING
Couldrey, C.; Johnson, T.; Keehan, M. 11th World Congress of Genetics Applied to Livestock Production 5p. 2018

VALIDATION OF SYNTHETIC LONG READS FOR USE IN CONSTRUCTING VARIANT GRAPHS FOR DAIRY CATTLE BREEDING
Keehan, M.; Couldrey, C. 11th World Congress of Genetics Applied to Livestock Production 7p. 2018