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Hamilton, New Zealand
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Lee J.M.,DairyNZ Ltd | Roche J.R.,DairyNZ Ltd | Donaghy D.J.,University of Tasmania | Thrush A.,Hoffmann-La Roche | Sathish P.,C O ViaLactia Biosciences NZ Ltd
BMC Molecular Biology | Year: 2010

Background: Perennial ryegrass (Lolium perenne L.) is an important pasture and turf crop. Biotechniques such as gene expression studies are being employed to improve traits in this temperate grass. Quantitative reverse transcription-polymerase chain reaction (qRT-PCR) is among the best methods available for determining changes in gene expression. Before analysis of target gene expression, it is essential to select an appropriate normalisation strategy to control for non-specific variation between samples. Reference genes that have stable expression at different biological and physiological states can be effectively used for normalisation; however, their expression stability must be validated before use.Results: Existing Serial Analysis of Gene Expression data were queried to identify six moderately expressed genes that had relatively stable gene expression throughout the year. These six candidate reference genes (eukaryotic elongation factor 1 alpha, eEF1A; TAT-binding protein homolog 1, TBP-1; eukaryotic translation initiation factor 4 alpha, eIF4A; YT521-B-like protein family protein, YT521-B; histone 3, H3; ubiquitin-conjugating enzyme, E2) were validated for qRT-PCR normalisation in 442 diverse perennial ryegrass (Lolium perenne L.) samples sourced from field- and laboratory-grown plants under a wide range of experimental conditions. Eukaryotic EF1A is encoded by members of a multigene family exhibiting differential expression and necessitated the expression analysis of different eEF1A encoding genes; a highly expressed eEF1A (h), a moderately, but stably expressed eEF1A (s), and combined expression of multigene eEF1A (m). NormFinder identified eEF1A (s) and YT521-B as the best combination of two genes for normalisation of gene expression data in perennial ryegrass following different defoliation management in the field.Conclusions: This study is unique in the magnitude of samples tested with the inclusion of numerous field-grown samples, helping pave the way to conduct gene expression studies in perennial biomass crops under field-conditions. From our study several stably expressed reference genes have been validated. This provides useful candidates for reference gene selection in perennial ryegrass under conditions other than those tested here. © 2010 Lee et al; licensee BioMed Central Ltd.

Sun X.Z.,Agresearch Ltd. | Waghorn G.C.,DairyNZ Ltd | Clark H.,Agresearch Ltd.
Animal Feed Science and Technology | Year: 2010

Perennial ryegrass is the principal component of diets fed to ruminants in New Zealand. Selection for ryegrass improvement should incorporate measures relating to feeding value (i.e. quality × intake) for sheep and cattle. This study was designed to measure the variation in characteristics of nutritive value of three ryegrass cultivars harvested at different stages of regrowth. The cultivars were Grasslands Greenstone (Greenstone; tetraploid), Grasslands Samson (Samson; diploid) and Quartet (tetraploid). They were grown as pure swards with leafy regrowth harvested after 2, 3, 4, 5, 6 and 7 weeks for measurement of chemical composition, physical parameters (i.e. shear force and energy required for mincing), degradation kinetics and distribution of constituents between the immediately degradable (A), potentially degradable (B) and undegradable (C) fractions. Analyses showed that age of regrowth resulted in larger differences in composition and degradation kinetics than cultivar, and emphasised the need to harvest material in a similar condition to that grazed by animals. Cultivar differences were best indicated by chemical composition and ratios of crude protein (CP):neutral detergent fibre (aNDF) in the dry matter (DM), the proportion of CP in the 'A' fraction as well as degradation of DM in the 'B' fraction. The CP:aNDF ratios averaged for the three cultivars at 2, 3, 4, 5, 6, and 7 weeks were 0.82, 0.76, 0.71, 0.55, 0.48 and 0.42, respectively, with averages at weeks 5 and 6 for Greenstone, Samson and Quartet of 0.59, 0.49 and 0.48, respectively. The ratio differed between ages (P<0.001) and across cultivars (P<0.05). The DM fractional degradation rates (k) tended to decline from 0.18 to 0.12/h with maturity (P<0.05) and after weeks 5 and 6 of regrowth averaged 0.17, 0.16 and 0.14/h for the respective cultivars. Both the concentration of lignin(sa) in DM and shear force were weakly associated with regrowth and cultivar and appeared to be less important than chemical composition for indicating nutritive value of leafy ryegrass. © 2009 Elsevier B.V. All rights reserved.

Pacheco D.,Agresearch Ltd. | Waghorn G.,DairyNZ Ltd | Janssen P.H.,Agresearch Ltd.
Animal Production Science | Year: 2014

Ruminants contribute to human food supply and also anthropogenic greenhouse gas (GHG) emissions. An understanding of production systems and information on animal populations has enabled global inventories of ruminant GHG emissions (methane and nitrous oxide), and dietary strategies are being developed to reduce GHG emissions from ruminants. Mitigation strategies need to consider the management/feeding systems used to ensure that these strategies will be readily accepted and adopted by farmers. Housed systems allow diets to be formulated in ways that may reduce GHG production, but the challenge is much greater for systems where animals graze outdoors for long periods. A methane mitigation option in the form of fresh forage would be desirable in livestock production systems with high reliance on grazing. A brief summary of New Zealand research, carried out on fresh grasses, legumes, herbs and crops, suggest that we have an incomplete understanding of the feed characteristics that define a 'high' or a 'low' methane feed. The variation in methane emissions measured between feeds, individual animals and experiment is large, even in controlled conditions, and the dynamic nature of sward-animal interactions will only exacerbate this variation, creating challenges beyond the identification of mitigants. Furthermore, implementation of knowledge gained from controlled studies requires validation under grazing systems to identify any trade-offs between methane reduction and animal productivity or emission of other pollutants. Therefore, investment and research should be targeted at mitigation options that can and will be adopted on-farm, and the characteristics of temperate grasslands farming suggest that these options may differ from those for intensive (high input/output) or extensive (low input/output) systems. © CSIRO 2014.

Bryant R.H.,Lincoln University at Christchurch | Gregorini P.,DairyNZ Ltd. | Edwards G.R.,Lincoln University at Christchurch
Animal Feed Science and Technology | Year: 2012

New Zealand dairy systems are based on Lolium perenne pastures with low nitrogen use efficiency (NUE) and high urinary N losses. Modelling attempts to provide solutions to improve NUE are limited due to lack of data on pasture N fractions under a range of management situations. The effects of N application (0 or 25. kg. N/ha), cultivar (standard and high sugar cultivars), regrowth interval (leaf appearance of 2, 3 and 4 leaf) and time of day (morning or afternoon) on chemical composition and N fractionation of L. perenne were investigated in a field study in early spring. Leaf appearance interval and time of day had the greatest influence on chemical composition and fractionation. Both fraction A (non-protein N) and water soluble carbohydrates increased by 60% between second and fourth leaf appearance (P<0.001) and by 20% between morning and afternoon (P<0.001). Total N and fractions B1 and B2 (soluble true protein) declined during the day and with leaf appearance. Addition of low fertiliser N rates did not alter N fractionation or chemical composition but improved herbage yield. The effects of using a high sugar cultivar were small and inconsistent and differences between cultivars were more closely linked with flowering date. Generally, the relative proportions of N fractions could be altered with management strategies but the overall solubility of N remained high at over 0.85. While management factors play an important role in influencing the quality of herbage and total N relative to carbohydrate, there is little scope to improve NUE by reducing the proportions of soluble N fractions. © 2012 Elsevier B.V..

Berry D.P.,Moorepark Dairy Production Research Center | Kearney J.F.,Irish Cattle Breeding Federation | Roche J.R.,DairyNZ Ltd.
Theriogenology | Year: 2011

There is a paucity of estimates of genetic variation for secondary sex ratio (i.e., sex ratio at birth) in dairy cattle. The objective of this study was to estimate the direct and maternal genetic variance as well as maternal permanent environmental variance for offspring sex in dairy herds. The data consisted of 77,508 births from 61,963 dams and 2,859 sires in 1,369 Irish dairy herds across the years 2003 to 2008, inclusive. Mixed models were used to estimate all parameters. Significant genetic variation in sex ratio existed, with a heritability for secondary sex ratio estimated at 0.02; the genetic standard deviation was 0.07 percentage units. No maternal genetic effects on secondary sex ratio were identified but the proportion of phenotypic variance in secondary sex ratio attributable to maternal permanent environmental effects was similar to that attributable to the additive genetic variance (i.e., 0.02). These results, therefore, suggest that the paternal (genetic) influence on secondary sex ratio is just as large as the maternal (non-genetic) influence, both of which are biologically substantial. The results from this study will be useful in generating a sample population of divergent animals for inclusion in a controlled experiment to elucidate the physiological mechanism underpinning differences in secondary sex ratio. © 2011 Elsevier Inc.

Kamphuis C.,DairyNZ Ltd. | DelaRue B.,DairyNZ Ltd. | Burke C.R.,DairyNZ Ltd. | Jago J.,DairyNZ Ltd.
Journal of Dairy Science | Year: 2012

This study tested the hypothesis that a commercially available system for detecting estrus based on cow activity would perform similarly to that of typical, visual assessment of mounting indicators placed on the tail head of the cow. The hypothesis was applied to a large, pasture-grazed, seasonal-calving dairy herd, and the technology was tested as a stand-alone system. One of 2 types of commercially available collar-mounted activity meters was fitted to 635 cows, and the activity data collected during the 37-d artificial breeding period were analyzed. The first collar-mounted activity meter monitored activity only (AO collars), whereas the second meter measured activity and rumination characteristics (AR collars). Only activity data were used in the current study. Activity-based estrus alerts were initially identified using the default activity threshold value recommended by the manufacturer, but a range of activity threshold values was then analyzed to determine their effect on estrus detection performance. Milk progesterone data and insemination records were used to identify gold standard positive (n = 835) and negative (n = 22,660) estrus dates, to which activity alerts were compared. Visual assessment of mounting indicators resulted in a manual detection performance of 91.3% sensitivity (SN), 99.8% specificity (SP), and 94.5% positive predictive value (PPV). The AR collars achieved 76.9, 99.4, and 82.4% for SN, SP, and PPV, whereas the AO collars achieved 62.4, 99.3, and 76.6% for SN, SP, and PPV, respectively. The observed performance of the activity systems may be underestimated due to test design and applied assumptions, including determining the date of estrus. Lowering the activity threshold from the default value improved sensitivity but the number of false positive alerts was considered to become unmanageable from a practical perspective as sensitivity reached peak values. Time window analysis, receiver operating characteristic curves, and curves of SN and PPV were found to be useful in the analysis and interpretation of results. They generate relevant performance data that allow for meaningful comparisons between similar studies. Although the 2 activity systems tested did not perform to the high level of manual estrus detection found in this study, the potential exists for these systems to be a valuable tool on farms with lower estrus detection performance or for farmers managing larger herds. © 2012 American Dairy Science Association.

The New Zealand (NZ) economy and its dairy industry are sensitive to global consumer perception of farming practices used to generate milk products because milk exports account for > 25% of national export earnings and > 90% of milk produced is exported as products. Astute management of product image and market risk is, therefore, important for the viability of the industry and country. More than 95% of milk produced in NZ comes from strictly seasonal, pasture-based systems, with associated constraints on reproductive performance. Increasing herd sizes, operational changes and genetic selection priorities have further challenged dairy farmers to achieve optimal levels of herd fertility. Reproductive management practices have developed to address the need to maintain a 365-day inter-calving interval, essentially through maximizing the number of cyclic cows during the breeding period and minimizing the duration of the seasonal calving period. Aspects of the hormonal interventions developed and routinely used to achieve these objectives have been the subject of product quality and market risk concerns forcing the industry to explore alternative ways of achieving reproductive performance goals. One approach has been to exploit the inherently high level of fertility in NZ dairy herds. This approach has seen the inclusion of fertility-related traits in the national genetic evaluation system to prevent further decline in genetic fertility. More recently, a nationally coordinated extension program has been adopted to support farmers and their advisors to identify, prioritize and improve on key management areas for incremental gains in herd reproductive performance. Advances in automation and bio-sensing are yet to make a significant impact, but remain potentially valuable additions in supporting the dairy farmer to manage the areas having the largest effects on reproductive performance.

Walker C.G.,DairyNZ Ltd | Mitchell M.D.,University of Queensland
Animal Production Science | Year: 2013

Epigenetic mechanisms, such as DNA methylation, regulate gene expression and, subsequently, phenotype, without changing the underlying DNA sequence. It is well established that the environment and nutrition can regulate methylation and, therefore, modify phenotype. In this review, regulation of DNA methylation and in particular, the influence of B-vitamin on one-carbon metabolism is outlined, and how deficiency or supplementation with B-vitamins, such as folate, can influence disease. Evidence is provided for the roles of B-vitamin in regulating reproduction and how deficiency of B-vitamin may be impacting dairy cattle fertility. Results from our laboratory provide evidence for an association between DNA methylation and gene expression in the endometrium during early pregnancy. It is, therefore, hypothesised that DNA methylation may regulate the uterine response to the embryo during early pregnancy and that aberrant DNA methylation during this time may jeopardise pregnancy success. Further research is required to establish if B-vitamin supplementation can improve reproductive success and if this effect is via changes to DNA methylation and gene expression in the endometrium, or via positive effects on oocyte and embryo development. © CSIRO 2013.

Jago J.,DairyNZ Ltd. | Kerrisk K.,DairyNZ Ltd.
Applied Animal Behaviour Science | Year: 2011

Training cows to use an automatic milking system (AMS) is an important process as this method of milking depends on cows voluntarily using the AMS. This study examined two levels of training before calving on the behaviour of cows and heifers in an extensive pasture-based AMS. Animals received either no training (NIL), training which included handling, in the AMS and on-farm gating system (MINIMAL) or training in the AMS including exposure to typical noises and mechanical movements, plus on-farm gating system (EXTRA). Training was carried out over four sessions on four non-consecutive days. Training improved ease of entry into the AMS at the first assisted milking (NIL=17.9. s, MIN=1.4. s, EXTRA=6.7. s, P<0.05). The additional exposure to the noises and sounds of the AMS had no effect (P>0.05) on behaviour during milking. Voluntary milkings were achieved by 92% of heifers and 81% of cows within 6. days following their first assisted milking. Irrespective of the level of training, heifers learned to use the on-farm gating system and achieved their first voluntary milking quicker than cows (Time to milking: Heifers=1.88. d, Cows=2.55. d, SED=0.18, P<0.001). Pre-calving training improved aspects of the behaviour required for successful adaptation to automatic milking but had little impact on time to achieve a voluntary milking. Heifers adapted quicker than cows to automatic milking in a pasture-based farming environment. © 2011 Elsevier B.V.

Beukes P.C.,DairyNZ Ltd. | Gregorini P.,DairyNZ Ltd. | Romera A.J.,DairyNZ Ltd.
Animal Feed Science and Technology | Year: 2011

The strategy for New Zealand dairy farming (DairyNZ, 2009) formulates targets for increased national milk production and a reduction in greenhouse gas (GHG) emissions, but acknowledges these two targets conflict because GHG typically increase with increased milk output. Our objective was to determine if both targets could be achieved by implementing combinations of five mitigations. A farm scale computer model, which includes a mechanistic cow model, was used to model a typical pasture based New Zealand dairy farm as the baseline farm. The five mitigations were: (1) improved reproductive performance of the herd resulting in lower replacement rates, (2) increased genetic merit of the cows combined with lower stocking rate and longer lactations, (3) keeping lactating cows on a loafing pad for 12h/day for 2 mo during autumn, (4) growing low protein crops of grains and/or silages of maize, barley and oats on a portion of the farm and feeding this to lactating cows, (5) reducing fertilizer N use and replacing some of this with nitrification inhibitors and the plant growth stimulant gibberellins. No single mitigation strategy achieved both targets of increasing production by 10-15% and reducing GHG emissions by 20%, but when all were simultaneously implemented in the baseline farm, milk production increased by 15-20% to 1200kg milk fat+protein/ha, and absolute GHG emissions decreased by 15-20% to 0.8kg CO2-equivalents (CO2-e)/kg fat and protein corrected milk (FPCM), which is equivalent to a decrease from 11.7 to 8.2kg CO2-e/kg fat+protein. The synergies of the mitigations resulted in reduced dry matter intake and enteric CH4 emissions, a reduction in N input and N dilution in feed, and, therefore, reduced urinary N excretion onto pastures, and an increase in feed conversion efficiency (i.e., more feed was used for production and less for maintenance). Mechanistic CH4 models as part of farm scale models are important because current GHG inventory methodology cannot properly evaluate CH4 emissions for a range of potential mitigation strategies. There is also a need to develop capabilities in farm scale models to accurately simulate urine patches and N2O emissions from these patches.This paper is part of the special issue entitled: Greenhouse Gases in Animal Agriculture - Finding a Balance between Food and Emissions, Guest Edited by T.A. McAllister, Section Guest Editors: K.A. Beauchemin, X. Hao, S. McGinn and Editor for Animal Feed Science and Technology, P.H. Robinson. © 2011 Elsevier B.V.

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