@article {3672,
	title = {BRIEF COMMUNICATION: Reproductive performance of herds milked once a day all season compared with herds milked twice a day all season},
	journal = {New Zealand Journal of Animal Science and Production},
	volume = {78},
	year = {2018},
	month = {07/2018},
	pages = {170-172},
	address = {Lincoln},
	abstract = {The objective of this study was to compare the reproductive performance of herds milked once a day (OAD) for the whole season
with that of herds milked twice a day (TAD) for the whole season. Herds were classified as OAD or TAD if they herd tested >=
three times a season and >90\% of animals had the same milking regime (OAD or TAD) at each test. Once the OAD herds were
identified, the closest geographical TAD herd was identified and included in the dataset for the 2014 to 2016 seasons. Only herds
with a Detailed InCalf Fertility Focus report were analysed (OAD n=75, TAD n=76). The means of five key reproduction measures
were analysed and the means were significantly different for all measures (P<0.001). The OAD herds had a 7.7\% higher mean herd
3-week submission rate (OAD=84.6\%, TAD=76.9\%), 7.9\% higher mean conception rate (OAD=60.1\%, TAD=52.2\%), 10.4\%
higher mean 6-week in-calf rate (OAD=74.8\%, TAD=64.4\%), 4.8\% lower mean not-in-calf rate (OAD=12.8\%, TAD=17.6\%), and
4.3\% more of the herd calved by week six of calving (OAD=88.2\%, TAD=83.9\%) than TAD herds. These results indicate that
herds milking OAD for the whole season have, on average, better reproductive performance than those milked TAD the whole
season.},
	issn = {1176-5283},
	author = {Hemming NV and McNaughton LR and Couldrey C}
}
@conference {3672,
	title = {Using genomic information to predict sex in dairy cattle},
	booktitle = {Proceedings of the New Zealand Society of Animal Production},
	volume = {76},
	year = {2016},
	month = {07/2016},
	pages = {26-30},
	address = {Adelaide},
	abstract = {Sex misassignment of animals in breeding programmes can arise from sources such as misidentification and data-entry errors. The
objective of this study was to develop a test for checking sex using Single Nucleotide Polymorphism (SNP) chip genotypes on
chromosome X. All animals in this study were genotyped using the GeneSeek Genomic Profiler LD v3 (GGPv3) SNP chip. After
filtering, 16478 sex-verified animals (15703 cows and 775 bulls) were available in the training set. The proportion of heterozygous
SNPs on chromosome X was used to predict sex. The distribution of heterozygosity was bimodal in the training population with
a clear gap between 0.01 and 0.03. Using the heterozygosity cutoff of 0.02 resulted in 100\% and 99.6\% prediction accuracy for
males and females, respectively. Additional analysis determined that four incorrectly classified females were either XO or inbred.
The test was validated on an independent set of 2212 animals, which resulted in seven animals for which the predicted sex differed
to the recorded sex. Physical examination of these animals revealed that the predicted sex was correct in all cases. The method
developed is a useful addition to quality control of genotypes obtained as part of a genomic selection programme.},
	issn = {1176-5283},
	author = {Zhang IL and Couldrey C and Sherlock RG}
}
@conference {89266,
	title = {The effect of milking frequency in early lactation on gene expression in the bovine mammary gland},
	booktitle = {Proceedings of the New Zealand Society of Animal Production},
	volume = {73},
	year = {2013},
	month = {Jan},
	pages = {45-47},
	publisher = {New Zealand Society of Animal Production},
	organization = {New Zealand Society of Animal Production},
	address = {Hamilton},
	abstract = {<p>In ruminants, altered milking frequency influences milk production due to either an increase in the number of secretory mammary epithelial cells and/or the activity of these cells (Stelwagen 2001). Microarray studies examining the response of mammary epithelial cells to either increased (Connor et al. 2008) or decreased (Littlejohn et al. 2010) milking frequency, reportedaltered gene expression in several regulatory pathways. These changes would appear to be locally regulated within the mammary gland, as milk production is different in different glands within the same udder depending on the milking frequency of individual glands (Stelwagen 2001). Therefore, the udder lends itself well as a model system to study the effect of different milking frequencies by comparing the response in adjacent udder halves (Murney et al. 2012).</p>
},
	issn = {1176-5283},
	author = {MacLean PH and Stelwagen K and Maqbool N and Oden K and Murney R and Couldrey C and Singh K}
}
@conference {89264,
	title = {Genome wide DNA methylation patterns and transcription analysis in sheep muscle},
	booktitle = {Proceedings of the New Zealand Society of Animal Production},
	volume = {73},
	year = {2013},
	month = {Jan},
	pages = {37-40},
	publisher = {New Zealand Society of Animal Production},
	organization = {New Zealand Society of Animal Production},
	address = {Hamilton},
	abstract = {<p>The Carwell phenotype is a desirable inherited muscular hypertrophy of the Longissimus dorsimuscle in Poll Dorset sheep that does not have any detrimental effect on eating quality, fat deposition or detectable meat tenderness. The Carwell haplotype has been localized to a 350kb region on the distal end of OAR18 near the Callipyge locus (Nicoll et al. 1998) containing three known genes. However, in spite of considerable effort in sequencing and resequencing, the causative mutation has not been identified. Although unsuccessful in identifying the causative mutation, these studies have revealed that the Carwell phenotype displays an imprinted inheritance pattern, with increased muscling associated with inheritance from the sire but not the dam.</p>
},
	issn = {1176-5283},
	author = {Couldrey C and Brauning R and MacLean PH and Henderson HV and McEwan JC}
}
@conference {79010,
	title = {Development of epigenomic analysis in agricultural animals},
	booktitle = {Proceedings of the New Zealand Society of Animal Production},
	volume = {72},
	year = {2012},
	month = {Jan},
	pages = {163-165},
	publisher = {New Zealand Society of Animal Production},
	organization = {New Zealand Society of Animal Production},
	address = {Christchurch},
	abstract = {Advances made in DNA sequencing technologies over the past 15 years (Zhao \& Grant 2011) have resulted in genome wide selection for production traits becoming a reality. Soon all sequence variations in each individual in closed breeding schemes will be known. What is not currently known is how to rank these variations, especially those that involve changes in gene expression rather than amino acid sequence. In order to continue making genetic progress we will need an understanding of how epigenetics affects gene expression and ultimately phenotype.},
	issn = {1176-5283},
	author = {Couldrey C and Brauning R and Retzel EF and McEwan JC}
}
@conference {78990,
	title = {DNA methylation events in the {\'a}S1-casein-encoding gene associated with involution and re-initiation of lactation in dairy cows},
	booktitle = {Proceedings of the New Zealand Society of Animal Production},
	volume = {72},
	year = {2012},
	month = {Jan},
	pages = {73-75},
	publisher = {New Zealand Society of Animal Production},
	organization = {New Zealand Society of Animal Production},
	address = {Christchurch},
	abstract = {During lactation, prolactin activates STAT5 (Signal Transducer and Activator of Transcription5), which binds to conserved DNA sequence motifs in promoters of milk protein genes to stimulate their expression (Liu et al. 1997). Mammary gland involution induced by termination of milking is characterised by a rapid decrease in milk protein gene expression (Singh et al. 2008). Whereas milk production can be fully restored after seven days of ... continued},
	issn = {1176-5283},
	author = {Pryor S and Swanson K and Couldrey C and Henderson H and Singh K}
}
@conference {75885,
	title = {BRIEF COMMUNICATION: DNA methylation patterns in bovine blastocysts suggest that only limited epigenetic reprogramming has occurred in the early embryo},
	booktitle = {Proceedings of the New Zealand Society of Animal Production},
	volume = {71},
	year = {2011},
	month = {Jan},
	pages = {114-116},
	publisher = {New Zealand Society of Animal Production},
	organization = {New Zealand Society of Animal Production},
	address = {Invercargill},
	abstract = {Epigenetics is the study of changes in phenotype caused by mechanisms other than changes in the underlying DNA sequence. In agriculture, epigenetics largely resides in the environment component of the equation; Phenotype = Genotype + Environment. Epigenetic mechanisms include but are not limited to, DNA methylation, acetylation and... Continued},
	issn = {1176-5283},
	author = {Couldrey C and Wells DN and Lee RSF}
}
@conference {60942,
	title = {DNA methylation events associated with the suppression of milk protein gene expression during involution of the bovine mammary gland : Brief Communication},
	booktitle = {Proceedings of the New Zealand Society of Animal Production},
	volume = {69},
	year = {2009},
	month = {Jun},
	pages = {57-59},
	publisher = {New Zealand Society of Animal Production},
	organization = {New Zealand Society of Animal Production},
	address = {Christchurch},
	abstract = {During lactation, prolactin activates STAT5 (Signal Transducer and Activator of Transcription), which binds to conserved DNA sequence motifs in promoters of milk protein genes to stimulate their expression (Liu et al., 1997). At drying-off, mammary involution is characterised by a rapid decrease in milk protein gene expression (Goodman \& Schanbacher, 1991), including ?S1-casein (Singh et al., 2008). The ?S1-casein promoter features... Continued },
	issn = {1176-5283},
	author = {Singh K and Swanson K and Couldrey C and Seyfert H-M and Stelwagen K}
}
