@article {3672,
	title = {MATN3 underlies a QTL for stature in cattle},
	journal = {New Zealand Journal of Animal Science and Production},
	volume = {78},
	year = {2018},
	month = {07/2018},
	pages = {51-55},
	address = {Lincoln},
	abstract = {Live weight (LWT) in dairy cattle is associated with milk production efficiency, and also has a high genetic correlation with
stature. To identify genetic regions impacting stature and LWT, we conducted a genome-wide association study using 65,500
mixed-breed NZ dairy cattle and 16,243,015 imputed genotypes. We identified a quantitative trait locus (QTL) at BTA11:78-
79Mbp for stature that was significant at a genome-wide level (β=3.98mm {\textpm} 0.56; P=1.6{\texttimes}10-12) but not significant for LWT
(β=1.253 {\textpm} 0.393 kg; P=1.4{\texttimes}10-3). Ensembl{\textquoteright}s Variant Effect Predictor was used to search for coding variants to attempt to identify
a candidate causative gene for this QTL, and gene expression from RNA sequence data representing 373 cows were analysed for
16 genes and 3,640 markers to highlight expression QTL (eQTL) in this region. The gene with the most significant eQTL was
MATN3 (ENSBTAG00000020893; P=2.5{\texttimes}10-38), encoding a protein which is involved in bone development. The correlation
between variant effects (-log p-values) was calculated for the stature QTL and MATN3 eQTL (r=0.584), with the same variant
(rs475277351) most significant for both QTL. This suggests a common genetic signal underlying both QTL, supporting the
hypothesis that the MATN3 gene underlies the stature QTL.},
	issn = {1176-5283},
	author = {Lopdell TJ and Littlejohn MD}
}
@conference {3672,
	title = {More dairy heifers are achieving liveweight targets},
	booktitle = {Proceedings of the New Zealand Society of Animal Production},
	volume = {76},
	year = {2016},
	month = {07/2016},
	pages = {3-7},
	address = {Adelaide},
	abstract = {Dairy heifers should reach industry liveweight targets that are set to ensure heifers achieve good reproductive performance and
milk production. The aim of this study was to determine if more dairy heifers born between the 2011-12 and 2014-15 dairy seasons
(current) in New Zealand are achieving liveweight targets since a study on heifers born between the 2006-07 and 2010-11 dairy
seasons (historic). In all age groups the mean live weight of current heifers was heavier than that of historic heifers. There were
also a greater percentage of the current heifers at or above their target live weight compared with the historic heifers (P<0.001),
suggesting that the rearing of dairy heifers has improved. The greatest improvement was seen at 15 months of age (mating) when
25\% of historic heifers were at or above target compared with 56\% of current heifers. Despite the improvement, 44\% of current
heifers were below target at mating and 65\% were below target pre-calving (22 months of age). At 22 months of age, current
heifers were on average nearly 42 kg below target live weight. By failing to achieve targets near calving, farmers are not capturing
potential milk production benefits.},
	issn = {1176-5283},
	author = {Handcock RC and Lopdell TJ and McNaughton LR}
}
@conference {78999,
	title = {Are dairy heifers achieving liveweight targets?},
	booktitle = {Proceedings of the New Zealand Society of Animal Production},
	volume = {72},
	year = {2012},
	month = {Jan},
	pages = {120-122},
	publisher = {New Zealand Society of Animal Production},
	organization = {New Zealand Society of Animal Production},
	address = {Christchurch},
	abstract = {The reproductive performance of the national dairy herd has declined (Harris et al. 2006). Heifer rearing is one of eight "ingredients" for achieving good reproductive performance identified by the InCalf project (Burke et al. 2007). Many New Zealand dairy farmers graze their heifers on a run-off or pay a grazier to grow the heifers, with heifers commonly leaving the dairy farm at weaning, or nine months of age and returning at around 22 months of age.},
	issn = {1176-5283},
	author = {McNaughton LR and Lopdell TJ}
}
@conference {79027,
	title = {Effect of resolving a sub-clinical uterine infection on plasma and follicular fluid steroid concentrations in early lactation dairy cows},
	booktitle = {Proceedings of the New Zealand Society of Animal Production},
	volume = {72},
	year = {2012},
	month = {Jan},
	pages = {231-235},
	publisher = {New Zealand Society of Animal Production},
	organization = {New Zealand Society of Animal Production},
	address = {Christchurch},
	abstract = {Sub-clinical endometritis (scEndo) in early lactation affects ovarian follicle dynamics, delays a return to cyclicity, with changes in plasma and follicular fluid (FF) amino acid concentrations around the time of rebreeding. This study examined the effect of resolving scEndo in early lactation on plasma and FF oestrogen, progestagen, androgen and corticosteroid concentrations at the time of rebreeding in 46 dairy cattle. On D42 postpartum, cows were classified as having scEndo, clean or having resolved scEndo cased on uterine cytology on D21 of > 18\% polymorphonuclear (PMN) cells amongst uterine nucleated cells. On D42 and D63 follicular and plasma samples were collected and steroid concentrations analysed. On D21 and D42, 35\% and 7\% of cows respectively were classified as having scEndo, with 81\% of scEndo cows having self-resolved the infection by D42. In those cows that resolved scEndo, none of the plasma or FF steroid concentrations changed between D42 and D63, except for plasma progesterone (P = 0.08). Using a low (4\%PMN) threshold to classify scEndo did not identify any significant changes in steroid concentrations. In contrast to previously described changes in plasma and FF amino acid concentrations, there were no significant effects on steroid concentrations when cows self-resolved a sub-clinical uterine infection.},
	issn = {1176-5283},
	author = {Lopdell TJ and Berg MC and Green MP and Back PJ}
}
@conference {69460,
	title = {Automatic reading of Kamars for heat detection in dairy herds},
	booktitle = {Proceedings of the New Zealand Society of Animal Production},
	volume = {70},
	year = {2010},
	month = {Jun},
	pages = {8-12},
	publisher = {New Zealand Society of Animal Production},
	organization = {New Zealand Society of Animal Production},
	address = {Palmerston North},
	abstract = {Most existing heat detection systems for dairy cattle are labour-intensive requiring manual inspection of 
every animal to maximise submission rates. Our solution is to automate heat detection using Kamar HeatMount 
Detectors and a camera-based recognition system. The goal of our system is to obtain 99\% sensitivity and 
specificity, ensuring that cows that are on heat are rarely missed and over-drafts are kept to a minimum. Trials 
of various camera prototypes have been undertaken over the past three years, most recently during the artificial 
breeding period in the Spring of 2009. Over 70,000 images from four farms were taken during the latest trials; 
these photographs were used to assess the system. When considering photo observations, the fully automated 
system had an error rate less than 1\% across all sites in the latest trial, and reaches our goal of 99\% sensitivity 
and specificity. },
	issn = {1176-5283},
	author = {Hempstalk K and Harris BL and Lopdell TJ}
}
