@article {3672,
	title = {Comparison of associations between estimated breeding values and cow survival in herds being milked once or twice a day},
	journal = {New Zealand Journal of Animal Science and Production},
	volume = {82},
	year = {2022},
	month = {01/2022},
	pages = {93-98},
	address = {Online},
	abstract = {The objective of this study was to investigate the link between estimated breeding values (EBV) for selected traits, including Traits Other than Production (TOP), and cow survival in herds milked once-a-day (OAD), and to contrast with herds milked twice-a-day (TAD). After filtering, data from 234 OAD herds (71,321 cows) and 234 TAD herds (75,123 cows) were extracted from the Dairy Industry Good Animal Database between 2007 and 2021. Cow survival from parities 1 to 2, 2 to 3, 3 to 4, 4 to 5 and 5 to 6 (S12, S23, S34, S45 and S56) were modelled within each milking frequency and age parity group, with trait EBVs fitted as covariables and the fixed effect of herd-year, using a generalised linear model with a gaussian kernel. The survival rate in OAD cows was higher than in TAD cows in S12 and less in S34 to S56. Udder support EBV became important in older cows (S45 and S56) but there were no significant differences between OAD and TAD herds. Compared to OAD herds, Fertility EBV had a greater effect on survival in TAD herds up to S34, as did Body Condition EBV for S12. Conversely, milk Volume, Fat, Protein and Somatic Cell Score EBVs had smaller effects on survival in TAD herds. Our results do not contain evidence that warrant greater selection pressure on functional traits in OAD systems relative to TAD to enhance animal survival. When selecting sires, selection pressure could be reduced on some traits, such as Fertility and Body Condition, in OAD systems, with a greater emphasis placed on production and milk composition.},
	issn = {1176-5283},
	author = {Edwards JP and Zhang X and Stachowicz K and Waters ACL and Amer PR}
}
@article {3672,
	title = {Impact of trait genetic gains on methane emissions from NZ beef and dairy farms},
	journal = {New Zealand Journal of Animal Science and Production},
	volume = {80},
	year = {2020},
	month = {09/2020},
	pages = {76-79},
	address = {Online},
	abstract = {The objective of this study was to provide estimates of the impact of trait genetic gains on methane emissions from NZ dairy and
beef farms. The effect of each trait on gross emissions (GE) and emissions intensity (EI) was modelled by estimating effects of trait
changes on per-animal feed consumption and the associated methane production, per-animal production and numbers of animals in
the system. In dairy, the annual gross emissions per breeding cow associated with genetic change were estimated to increase for all
traits except Residual Survival and Fertility. Conversely, emission intensity values were estimated to decrease for Milk Fat, Milk
Protein, Milk Solids, Residual Survival, Fertility and Body-condition Score (BCS) as genetic merit improves. In beef production,
increases in genetic merit for cow mature weight, cow BCS, cow calving ease and heifer pregnancy were estimated to increase the
annual gross emissions per breeding cow. Conversely, an increase in merit associated with stayability and gestation length reduced
annual gross emissions per breeding cow. The effect of increasing carcase weight on gross emissions depended on whether the
faster growth performance was used to slaughter the animal earlier, or to take the animal through to heavier finishing weights.

Keywords: methane; emissions intensity; gross emissions; dairy; beef},
	issn = {1176-5283},
	author = {Proctor LE and Archer JA and Sise JA and Zhang X and Crowley JJ and Amer PR}
}
@conference {3672,
	title = {Calf and heifer development and the onset of puberty in dairy cows with divergent genetic merit for fertility},
	booktitle = {Proceedings of the New Zealand Society of Animal Production},
	volume = {77},
	year = {2017},
	month = {06/2017},
	pages = {205-210},
	address = {Rotorua},
	abstract = {A research herd with divergent genetic merit for fertility was established to better understand the underlying drivers of fertility in dairy cattle. This paper describes the establishment of this herd, heifer growth and development, and the effect of divergence in fertility breeding value (FBV) on the timing of puberty. The average FBV of the high and low fertility groups of heifers was +5.6 and -4.6, respectively. The heifers were weighed fortnightly, with body condition score (BCS) and stature recorded at six, nine, 12 and 15 months of age. Weight and age at puberty were defined as the first day when plasma progesterone was >1 ng/ml in two of three consecutive once weekly samples. There was no effect of FBV on live weight (LWT), BCS, nor stature by age as the heifers matured. High-fertility heifers attained puberty at a lighter LWT (271 vs. 296 kg; SED 4.3 kg), an earlier age (358 vs. 379 days; SED 6.0 days) and a lower proportion of estimated mature LWT (51 vs. 55\%; SED 0.7\%), compared with Low-fertility heifers. Therefore, the premise that high genetic merit for fertility is positively associated with reaching puberty earlier is supported. Further work is required to support and assess the value of incorporating a puberty trait into the FBV.},
	issn = {1176-5283},
	author = {Meier S and Fisher B and Eketone K and McNaughton LR and Amer PR and Beatson P and Bryant JR and Dodds KG and Spelman R and Roche JR and Burke CR}
}
@conference {3672,
	title = {Analysing hidden patterns of farmers{\textquoteright} preferences for farm performance characteristics that may be related to tail-docking practice decisions},
	booktitle = {Proceedings of the New Zealand Society of Animal Production},
	volume = {75},
	year = {2015},
	month = {07/2015},
	pages = {205-209},
	address = {Dunedin},
	abstract = { We investigated how multivariate statistics can be used to determine the different patterns of preferences that may exist within a
farmer population. As a case study, we used adaptive conjoint analysis to analyse farmers{\textquoteright} preferences for nine farm performance
characteristics that may be related to tail docking practice decisions. As expected, at the whole population level, farmers{\textquoteright}
preferences for these traits were found to be highly heterogeneous, with only the most important issues and least important issues
being able to be statistically differentiated. Using Cluster Analysis and Principal Components Analysis we found some hidden
relationships and identified the existence of four groups of farmers that had greater preferences for different characteristics; group
one preferred having less dags and less costs associated with dagging and crutching, group two preferred to reduce euthanasia
from uterine prolapse and rectal prolapse, group three preferred to avoid stressing lambs at the time of docking and group four
preferred to have less fly-strike and greater weaning weights. We discuss how the use of multivariate statistics allowed a deeper
interpretation of preference studies in a context of importance to NZ farmers.},
	issn = {1176-5283},
	author = {Martin-Collado D and Byrne TK and Amer PR and Behrent MJ and Maclennan G and Kerslake JI}
}
@conference {3672,
	title = {Transfers of genetic merit through multiple-tiered breeding structures into trait expressions for commercial sheep production},
	booktitle = {Proceedings of the New Zealand Society of Animal Production},
	volume = {75},
	year = {2015},
	month = {07/2015},
	pages = {97-100},
	address = {Dunedin},
	abstract = { In New Zealand, selection of both replacement females and sires based on performance is typically highly rudimentary in
multiplier and commercial flocks. Selection of ewes and rams in these tiers is frequently driven by soundness and overall condition
of selected animals and sometimes, based on whether or not the replacement candidate was born in a multiple litter. In breeder
flocks, selection is usually supported by knowledge of the genetic merit of candidates. In multi-tiered breeding schemes, genetic
progress is disseminated from the nucleus to the commercial tier through the transfer of males. Gene-flow principles can be applied
in the optimization of multi-tiered breeding schemes, particularly to define the proportion of genetic superiority expressed in an
individual, which also gets expressed in its descendants, in time, across tiers. The opportunity to increase the rate of progress
and reduce the genetic lag between tiers in integrated production systems might be exploited by selecting candidates from which
performance of the progeny can be predicted. The results of this simulation study demonstrate the long time delays of up to 25
years for genetic expressions to fully flow through a multiple-tiered breeding scheme. There was long time delay before genetic
progress realised in the nucleus was achieved in the commercial flocks. For example, it was approximately fourteen years until
70\% of benefits of genetic improvement in lambing and slaughter traits were captured in the commercial flocks. This delay was
mitigated when performance recording was implemented in the multiplier flock. This gain however, does not have the permanent
and cumulative properties of genetic progress achieved in the nucleus flock, and so needs to be continued each year for the benefits
to be maintained.},
	issn = {1176-5283},
	author = {Santos BFS and Byrne TJ and Amer PR and Gibson JP and Van der Werf JHJ}
}
@conference {3672,
	title = {Uncovering genetic variation in cow fertility using simulation},
	booktitle = {Proceedings of the New Zealand Society of Animal Production},
	volume = {75},
	year = {2015},
	month = {07/2015},
	pages = {42-47},
	address = {Dunedin},
	abstract = { Dairy cow fertility is currently measured using two traits: the proportion of cows mated within 21 days of the start of mating
(PM21) and the proportion of cows that calve within 42 days of the start of calving (CR42). These traits indirectly measure a cow{\textquoteright}s
genetic propensity to return to a fertile state after calving. Both PM21 and CR42 have low heritability (0.05 and 0.03, respectively)
and fertility is suspected to have much stronger genetic drivers than indicated by these lowly heritable components. The purpose
of this study was to explore genetic and environmental factors that contribute to dairy cow fertility using a stochastic simulation
model. The model traces the reproductive life of cows from birth until their second calving date using environmental and genetic
variables to simulate fertility phenotypes. The model demonstrated that even when significant genetic variation was simulated
in underlying fertility traits, this variation appears only weakly as genetic effects using the current fertility traits evaluated for
genetic selection purposes. Potential alternative traits (e.g. gestation length, heifer puberty trait, strength of oestrus expression or
post-partum anoestrous interval) were shown to have potential to add value when identifying sires whose daughters calve earlier
in the season.},
	issn = {1176-5283},
	author = {Dennis NA and Stachowicz K and Visser B and Hely FS and Amer PR and Meier S and Burke CR}
}
@conference {3678,
	title = {BRIEF COMMUNICATION: Predicting the impact of climate change on the risk of facial eczema outbreaks throughout New Zealand},
	booktitle = {Proceedings of the New Zealand Society of Animal Production},
	volume = {74},
	year = {2014},
	month = {06/2014},
	pages = {161-163},
	address = {Napier},
	abstract = {Facial eczema (FE) is caused by the sporidesmin toxin, which is produced by the spores of the fungus, Pithomyces chartarum (PC). Sporidesmin causes damage to the gut, liver and bile ducts in ruminants. This can result in weight loss, decreased production and skin photosensitivity which characterise clinical FE cases (Sheath et al. 1987; Towers \& Smith 1978). Production losses also occur in sub-clinical cases, which may go undetected under normal farm management.},
	issn = {1176-5283},
	author = {Dennis NA and Amer PR and Meier S}
}
@conference {79026,
	title = {Chinook salmon (Oncorhynchus tshawytscha) feed conversion efficiency: evaluation and potential for selection},
	booktitle = {Proceedings of the New Zealand Society of Animal Production},
	volume = {72},
	year = {2012},
	month = {Jan},
	pages = {227-230},
	publisher = {New Zealand Society of Animal Production},
	organization = {New Zealand Society of Animal Production},
	address = {Christchurch},
	abstract = {Improving performance through selective breeding is a key priority for the New Zealand Chinook salmon (Oncorhynchus tshawytscha) aquaculture industry. The family selective breeding programme operated by The New Zealand King Salmon Company has successfully improved growth and quality after six generations of selection. However, feed conversion efficiency is not currently a direct breeding goal. Research was established to analyse daily feed intake and feed conversion ratio, a measure of feed efficiency, in 160 families over two spawning year classes. Daily feed intake assessment methodology employing digital X-radiography was validated and used to obtain repeated measurements of daily feed intake. Measurements of growth, and feed conversion ratio up to harvest size were also obtained. Genetic parameter estimates for daily feed intake and feed conversion ratio indicated that there are family differences for these traits. As a result the continued measurement of feed conversion ratio in The New Zealand King Salmon families and incorporation of the traits into The New Zealand King Salmon breeding programme is being considered.},
	issn = {1176-5283},
	author = {Walker SP and Ingram M and J Bailey and Dodds KG and Fisher PJ and Amer PR and Symonds JE}
}
@conference {79009,
	title = {A comparative analysis of genetic trends within the New Zealand sheep industry},
	booktitle = {Proceedings of the New Zealand Society of Animal Production},
	volume = {72},
	year = {2012},
	month = {Jan},
	pages = {159-162},
	publisher = {New Zealand Society of Animal Production},
	organization = {New Zealand Society of Animal Production},
	address = {Christchurch},
	abstract = {Rates of genetic progress made by Dual Purpose and Terminal Sire flocks in the New Zealand sheep industry between 1990 and 2007 have previously been examined (Amer 2009) and showed substantial gains in the rate of progress since the introduction of Sheep Improvement Ltd. (SIL) and SIL-ACE (Advanced Central Evaluation). Key findings from this earlier study showed that the rates of genetic progress doubled following the introduction of SIL, and increased by a further 50\% after the introduction of the Beef + Lamb New Zealand Central Progeny test (CPT), which effectively evaluates the performance of key industry sires, providing the ... continued},
	issn = {1176-5283},
	author = {Sise JA and Byrne TJ and Jopson NB and Young MJ and Amer PR}
}
@conference {75919,
	title = {Predicting the benefits of two stage genomic selection in young breeding rams},
	booktitle = {Proceedings of the New Zealand Society of Animal Production},
	volume = {71},
	year = {2011},
	month = {Jan},
	pages = {266-269},
	publisher = {New Zealand Society of Animal Production},
	organization = {New Zealand Society of Animal Production},
	address = {Invercargill},
	abstract = {A two stage selection index model was developed to assess the cost effectiveness of using genomic technologies to assist in selection decisions for retention of ram lambs for breeding within a ram breeder flock. The principle of two stage selection is that many of the benefits of an expensive, but more accurate, measure of genetic merit can be captured while drastically reducing measurement costs. This paper describes the two stage model used, and some of the potential benefits of testing the top 6{\textendash}50\% of selection candidates ranked according to estimated breeding values, prior to ranking on a combined score using genomic breeding values. The model assumes a hypothetical panel of markers and trait predictive accuracies to explore the benefits of selection using both types of breeding values. The value of genetic progress is assessed using selection index theory to predict trait changes according to a selection index recently revised for implementation as the recommended index for dual purpose sheep in New Zealand. Results suggest that maximum benefits were obtained when the top 10-20\% of selection candidates were tested, with the level of benefits dependent on both the prediction accuracy and price of the test.},
	issn = {1176-5283},
	author = {Sise JA and Linscott EM and Amer PR}
}
@conference {75896,
	title = {The role of breeding in reducing sheep GHG intensity},
	booktitle = {Proceedings of the New Zealand Society of Animal Production},
	volume = {71},
	year = {2011},
	month = {Jan},
	pages = {162-167},
	publisher = {New Zealand Society of Animal Production},
	organization = {New Zealand Society of Animal Production},
	address = {Invercargill},
	abstract = {Historic and potential future greenhouse gas (GHG) emission reductions resulting from genetic selection decisions in sheep have been quantified. Historic genetic trends in number of lambs born in maternal breeds and growth in terminal sire breeds were estimated to have reduced GHG emissions per kilogram of lamb carcass weight by 0.45\% and 0.09\% per year of genetic change, respectively. The implications of future selection using different indexes were also examined. Selection based solely on farm profits could lead to emission reductions per unit of product by 0.185 kg CO2-e/kg carcass weight, or a 0.59\% reduction in lamb carcass weight emissions per annum. Selection of sheep ignoring profit and solely targeting reduced GHG emissions per kilogram of lamb carcass weight could lead to emission reductions of 0.242 kg CO2-e/kg lamb carcass weight, equivalent to a 0.77\% reduction in total emissions per annum. However, doing this would come at a cost of 26.6 cents per breeding ewe reduction of 23.7\% per annum in annual genetic progress. An alternative index that provides a balance between reducing GHG emissions and improving farm profits was estimated to produce an annual 0.193 kg CO2-e/kg carcass weight or a reduction of 0.62\% reduction in emissions per annum in GHG emissions with minimal sacrifice in genetic improvement of farm profitability.
},
	issn = {1176-5283},
	author = {Ludemann CI and Byrne TJ and Sise JA and Amer PR}
}
@conference {60956,
	title = {Background effects on ewe lambing and weaning performance in well recorded breeding flocks},
	booktitle = {Proceedings of the New Zealand Society of Animal Production},
	volume = {69},
	year = {2009},
	month = {Jun},
	pages = {115-117},
	publisher = {New Zealand Society of Animal Production},
	organization = {New Zealand Society of Animal Production},
	address = {Christchurch},
	abstract = {Results of analyses of Sheep Improvement Ltd. (SIL) data (27 flocks and 128,203 lambings) showed a substantial impact of ewes being scanned pregnant but failing to rear a lamb (wet-dry), on weight of lamb weaned at the next lambing. Compared to ewes that reared a lamb at the previous lambing, {\textquoteright}wet-dry{\textquoteright} ewes had 0.3 to 0.5 less lambs born per ewe lambing, lamb survival rates were lower by 60 to 70 percentage points and weaning weights up to 0.5 kg lighter per lamb weaned. These effects compounded into 30 to 40 kg less weight of lamb weaned per ewe. The failure to rear part of a litter, such as one lamb of a set of twins, had less effect on performance at next lambing and weaning, than loss of the whole litter. Those ewes that previously gave birth to three lambs weaned 4 kg less lamb weight than ewes that previously gave birth to singles, after allowing for their higher genetic drive for prolificacy. A modest but significant effect of previous litter size was observed on weight of lamb weaned within each litter size category. Lamb survival was observed to be 2\% lower (P <0.01) for twin ewes that had failed to rear one of their two lambs, compared with those that had reared both in their previous lambing. },
	issn = {1176-5283},
	author = {Amer PR and Sise JA and Jopson NB and Bray AR}
}
@conference {60966,
	title = {Rates of genetic progress being achieved throughout the New Zealand ram breeding industry},
	booktitle = {Proceedings of the New Zealand Society of Animal Production},
	volume = {69},
	year = {2009},
	month = {Jun},
	pages = {155-157},
	publisher = {New Zealand Society of Animal Production},
	organization = {New Zealand Society of Animal Production},
	address = {Christchurch},
	abstract = {Changes in the rate of genetic progress in the New Zealand sheep industry since 1990 are linked to structural aspects of breeding scheme design and to major industry sheep breeding initiatives. Data was sourced from the December 2007 SIL-ACE genetic evaluation for 140 recorded Dual Purpose flocks and 62 recorded Terminal Sire flocks. Genetic trends in both of these flock types approximately doubled after the introduction of Sheep Improvement Ltd. and there was a further incremental increase of similar magnitude after the introduction of the Central Progeny Test and SIL ACE. Substantial variation in the magnitude of genetic trends was observed across flocks within and between breeds. Large numbers of flocks average less than 50 cents gain in index per year, while significant numbers of flocks are achieving in excess of 150 cents gain per year. Flocks with higher rates of genetic gain tended to be using superior rams introduced from other flocks, while flocks with lower rates of genetic gain tended to be repeatedly using older sires of lower genetic merit. The implications of these results for industry sheep genetic improvement initiatives are discussed. },
	issn = {1176-5283},
	author = {Amer PR}
}
@conference {60981,
	title = {A simulation model to partition ewe efficiency into component traits for genetic analysis},
	booktitle = {Proceedings of the New Zealand Society of Animal Production},
	volume = {69},
	year = {2009},
	month = {Jun},
	pages = {223-227},
	publisher = {New Zealand Society of Animal Production},
	organization = {New Zealand Society of Animal Production},
	address = {Christchurch},
	abstract = {Ewe efficiency is extremely topical in the New Zealand sheep industry. This paper describes a stochastic simulation model which facilitates partitioning of a defined ewe efficiency equation into its component genetic traits. It accounts for, and simplifies, the complex and sometimes unfavorable interactions among components of ewe efficiency. The model tracks simulated genetic effects, inherited from the ewe{\textquoteright}s sires, in breeding ewes and their lambs for key performance recorded traits. The traits simulated are weaning weight, mature weight, number of lambs born, lamb survival, and longevity. Ewe efficiency is defined as the difference between value of lambs weaned and ewe and lamb costs, rather than as a ratio. Output value in NZ$ for the efficiency equation is computed on a ewe by ewe basis, as a function of number of lambs born, lamb survival and weight of lamb weaned, with each of these components partly influenced by one or more genetic effects inherited from simulated sires of the breeding ewes. Preliminary results from the model have identified litter size, ewe longevity, maternal lamb survival, and maternal weaning weight as being important drivers of ewe efficiency. The relative balance of their importance is influenced by farm production levels and environment. },
	issn = {1176-5283},
	author = {Sise JA and Shackell GH and Byrne TJ and Glennie SF and Amer PR}
}
@conference {41782,
	title = {SNiP and cut: Quantifying the potential benefits of genomic selection tools for genetic fault elimination in sheep},
	booktitle = {Proceedings of the New Zealand Society of Animal Production},
	volume = {68},
	year = {2008},
	month = {Jan},
	pages = {33-36},
	publisher = {New Zealand Society of Animal Production},
	organization = {New Zealand Society of Animal Production},
	address = {Brisbane, Australia},
	abstract = {Whole genome single nucleotide polymorphism marker (SNP) technologies are rapidly being developed and could well play a role in the future selection of farmed animals. In sheep, work is being carried out to identify SNP{\textquoteleft}s associated with economically important production traits and disease resistance. Stud sheep breeders routinely cull up to 30\% of lambs born due to a variety of faults. Despite this culling pressure, the faults keep occurring, suggesting low heritability, recessive inheritance or incomplete penetration of fault causing genes. The objective of this paper was to identify the potential of SNP fault detection and elimination in sheep. Simulation was used to predict changes in gene frequencies and in an index of genetic merit of production traits over time when between two and 30 SNPs were used to aid selection. The SNPs are assumed to predict the presence of deleterious recessive genes. As selection pressure applied to individual or combination SNPs increased, the rate of increase in production trait genetic merit slowed down. Thus, a balance would be required between the emphasis on SNPs actively used to select against genetic faults, relative to emphasis on genetic merit. This work identified scope for substantial economic benefits from application of SNP technology for removal of faults to both stud breeders and commercial sheep farmers. },
	issn = {1176-5283},
	author = {Sise JA and Auvray B and Dodds KG and Amer PR}
}
@conference {41698,
	title = {Impact of early age litter size on subsequent litter output in ewes},
	booktitle = {Proceedings of the New Zealand Society of Animal Production},
	volume = {67},
	year = {2007},
	month = {Jan},
	pages = {39-43},
	publisher = {New Zealand Society of Animal Production},
	organization = {New Zealand Society of Animal Production},
	address = {Wanaka},
	abstract = {Data from 28 performance recorded sheep flocks were evaluated to test for effects of litter size early in a ewe{\textquoteright}s life, on subsequent litter sizes. Ewes lambing twins at 2, 3 or 4 years of age had litters with on average 0.04 to 0.08 more lambs at each subsequent lambing than ewes lambing singles. The corresponding increases for ewes lambing triplets versus singles ranged from 0.23 to 0.26, with retention of the effect through successive litters. When data were adjusted to accountfor a ewe{\textquoteright}s lifetime genetic potential for prolificacy, evidence for an antagonistic environmental effecton litter size following a previous large litter was identified. This effect was approximately twice as high for triplets relative to singles (-0.19 to -0.32) when compared with twins relative to singles (-0.09 to -0.18), and declined in its effect on lambings more than one year later. It suggests that preferential treatment ofewes based on their previouslambing performance might improve their subsequent lambing performance. Culling two tooth ewes based on a single lambing record is unlikely to be economically viable, but there may be situations where reduced flushing of two tooth ewes prior to mating might be justified in prolific commercial flocks. The power and limitations of using data from performance recorded flocks to make recommendations relating to management decisions in commercial flocks is discussed.},
	issn = {1176-5283},
	author = {Amer PR and Jopson NB and Cocks J and Scarlet AL}
}
@conference {41973,
	title = {Prospects for genome wide selection in the New Zealand livestock industries},
	booktitle = {Proceedings of the New Zealand Society of Animal Production},
	volume = {67},
	year = {2007},
	month = {Jan},
	pages = {162-168},
	publisher = {New Zealand Society of Animal Production},
	organization = {New Zealand Society of Animal Production},
	address = {Wanaka},
	abstract = {A number of DNA marker applications aid genetic selection within subpopulations of New Zealand{\textquoteright}s livestock farming industries. Advances in genomic tools have opened the possibility of genotyping individuals for a large set of markers, enough to have a large proportion of the genome {\textquoteleft}tagged{\textquoteright} with at least one of these markers. This creates opportunities for genome wide selection (GWS) {\textendash} the selection of breeding animals based on very large numbers of marker genotypes. There are a number of requirements for GWS to work, including the existence of genotyping technology to provide genotypes at a sufficient density, tractable statistical methods for estimating marker  effects to use in prediction models and suitably phenotyped populations which when genotyped allow estimation of relationships between markers and traits. Additional phenotyped populations are required to validate their predictive ability and demonstrate economic benefits to breeders and to the commercial tier. A high density genotyping platform is available for cattle, but may need further developments. Plans are underway for a similar platform for sheep, but not for deer. The dairy industry is well placed to implement GWS, as there is a large bank of DNA samples of industry sires representing most of the genome variation present. Genotyping these animals will allow marker effects to be estimated and the reduced generation interval arising from selecting young sires should easily overcome any decrease in selection accuracy compared with progeny testing. Industry structures are likely to evolve to allow a return to entities undertaking GWS. GWS will be mostbeneficial for traits with low heritability, that cannot be measured on selected parents and/or that are expensive to measure. Genes of known effect may continue to be accounted for individually, particularly if they exhibit non-additive effects.},
	issn = {1176-5283},
	author = {Dodds KG and Amer PR and Spelman RJ and Archer JA and Auvray B}
}
@conference {41939,
	title = {Quantitative genetic selection for twinning rate in ewes},
	booktitle = {Proceedings of the New Zealand Society of Animal Production},
	volume = {66},
	year = {2006},
	month = {Jan},
	pages = {429-433},
	publisher = {New Zealand Society of Animal Production},
	organization = {New Zealand Society of Animal Production},
	address = {Napier},
	abstract = {Data from 19 recorded sheep flocks were included in this study involving 324 thousand lambings from the 1970{\textquoteright}s up until the 2004 lambing season. The genetic correlation between number of lambs born, and a triplet trait coded as 1 for ewes lambing triplets or higher multiples, and 0 for ewes lambing singles or twins was estimated separately over 13 data sets. Genetic correlation estimates ranged between 0.78 and 0.95 with all but two dataset estimates differing from 1.00 by two or more standard error intervals. Flock differences in the relationship between mean NLB and the proportion of ewes lambing twins were also investigated through an analysis of sire mean results. Strong evidence was found for within flock genetic variation in twinning incidence that is independent of mean NLB. This is different to the clear relationship that exists between mean litter size of a group of ewes and the proportion that lamb twins. There were also meaningful differences across-flocks in the proportions of ewes lambing twins after accounting for the effects on twinning percent of flock mean litter size. Our analyses suggest that simple selection strategies such as screening in twin lambing ewes from a commercial flock, and/or, only using twin-born rams in the breeding flock, will be relatively ineffective for improving twinning rates. A recommendation arising from the study is that genetic evaluation tools for twinning be made available to New Zealand sheep breeders. These tools would allow breeders to select for decreased triplets without compromising genetic progress in other traits including mean number of lambs born. },
	issn = {1176-5283},
	author = {Amer PR and Bodin L}
}
@conference {41507,
	title = {Comparison of two-stage selection breeding programmes for terminal sire sheep},
	booktitle = {Proceedings of the New Zealand Society of Animal Production},
	volume = {64},
	year = {2004},
	month = {Jan},
	pages = {212-216},
	publisher = {New Zealand Society of Animal Production},
	organization = {New Zealand Society of Animal Production},
	address = {Hamilton},
	abstract = {Two-stage selection is a technique used in animal breeding to make the use of expensive measurements economically viable in a breeding programme. Selection candidates are first screened using inexpensive, but imperfect, predictors of their genetic merit. A selected subset are then evaluated using more accurate, but expensive, measurements and the final selection is made. This study compared the assessment of carcass composition traits using either computed tomography (CT) scanning or progeny testing (with 10 or 20 progeny per sire; PT10 and PT20, respectively) in the second stage of two stage selection systems using quantitative genetic theory. Stage 1 selection was assumed to be based on live weight and ultrasonic predictions of carcass merit. For a genetic correlation of 0.7 between ultrasonic and CT/PT measures, the economic return peaked for progeny test at $2.70 and $2.38 per commercial ewe when 10 and 5\% of the male selection candidates were evaluated in PT10 and PT20, respectively. CT had a greater return at $3.52 per commercial ewe when 20\% of the male selection candidates were evaluated using CT. The results show that given the moderate heritability of carcass composition traits, the reduction in generation interval and the lower cost of evaluation of CT outweighs the increased accuracy of selection and higher mating ratios associated with progeny testing. },
	issn = {1176-5283},
	author = {Jopson NB and Amer PR and McEwan JC}
}
@conference {41440,
	title = {Genetics of lamb survival},
	booktitle = {Proceedings of the New Zealand Society of Animal Production},
	volume = {63},
	year = {2003},
	month = {Jan},
	pages = {201-203},
	publisher = {New Zealand Society of Animal Production},
	organization = {New Zealand Society of Animal Production},
	address = {Queenstown},
	abstract = {Data from seven commercial New Zealand sheep flocks were analysed to quantify the extent to which lamb survival in New Zealand sheep is influenced by genetic factors. Estimates of direct and maternal genetic variance components, and the effects of inbreeding in either the lamb or the dam on lamb survival, were found to vary significantly across flocks. Direct heritability estimates ranged from 0.008 to 0.070, while maternal heritability estimates ranged from 0.002 to 0.075. Inbreeding in the lamb showed a statistically significant (P<0.05) effect on survival in three of the seven flocks, ranging in value from -0.17 to -0.29\% reduction in lamb survival for a 1\% increase in inbreeding coefficient. Inbreeding of the lamb{\textquoteright}s dam had a statistically significant effect (P<0.05) on survival in two of the seven flocks, taking values of -0.32 to -0.71\% reduction in lamb survival for a 1\% increase in the dam{\textquoteright}s inbreeding coefficient. It is recommended that lamb survival records be transformed to a constant variance within flock and year prior to estimation of breeding values, but that no transformation to either a logit or probit scale within the statistical analysis is required. Inbreeding coefficients for both the lamb and the lamb{\textquoteright}s dam should be included as linear covariates in the mixedmodel analysis of lamb survival breeding values. },
	issn = {1176-5283},
	author = {Amer PR and Jopson NB}
}
@conference {41437,
	title = {Ram Focus - matching rams to buyer flocks},
	booktitle = {Proceedings of the New Zealand Society of Animal Production},
	volume = {63},
	year = {2003},
	month = {Jan},
	pages = {190-193},
	publisher = {New Zealand Society of Animal Production},
	organization = {New Zealand Society of Animal Production},
	address = {Queenstown},
	abstract = {A new software package has been developed to assist ram breeders to target rams to buyers{\textquoteleft} flocks. "Ram Focus" leads the potential buyer through a short series of questions relating to the buyer{\textquoteright}s current levels of animal performance, aims and future expectations. The answers to these questions are used to calculate economic values for individual traits, which are subsequently combined into an index customised for the buyer. The end result is that Ram Focus reranks the suitability of rams for alternative commercial flocks. Examples are presented of how the suitability of rams changes between commercial flocks, first using examples of differing reproductive performance, and second, differences in expectations of a drench failure.},
	issn = {1176-5283},
	author = {Jopson NB and Amer PR}
}
@conference {41436,
	title = {What is a better ram worth?},
	booktitle = {Proceedings of the New Zealand Society of Animal Production},
	volume = {63},
	year = {2003},
	month = {Jan},
	pages = {187-189},
	publisher = {New Zealand Society of Animal Production},
	organization = {New Zealand Society of Animal Production},
	address = {Queenstown},
	abstract = {This paper presents equations that can be used to quantify the differences in value to a commercial farmer among rams available for purchase from a single ram breeder. The same approach can be taken for a group of breeders for which across-flock genetic evaluation results are available. Separate equations are presented in detail for buyers of both dual-purpose and terminal sire rams. A working version of the terminal sire equation incorporates the difference in the terminal sire index value between two rams, the number of years, and the number of ewes per year, to which the ram is to be mated and the tailing percentage in the commercial flock as variables. A working version of the dual-purpose sire equation incorporates the same variables as the terminal sire equation, but with the percentage of the ram{\textquoteleft}s daughters to be kept as replacement ewes also added. },
	issn = {1176-5283},
	author = {Meikle A and Amer PR}
}
@conference {41346,
	title = {Dynamic selection for sheep genetic improvement},
	booktitle = {Proceedings of the New Zealand Society of Animal Production},
	volume = {62},
	year = {2002},
	month = {Jan},
	pages = {188-190},
	publisher = {New Zealand Society of Animal Production},
	organization = {New Zealand Society of Animal Production},
	address = {Palmerston North},
	abstract = {Dynamic selection is a process used in livestock improvement programmes to maximise genetic progress while constraining the long term rate of inbreeding. An optimisation algorithm identifies proportions of genes each selection candidate should contribute to the next generation. Application of dynamic selection procedures to select cull and replacement ewes, and then subsequently to select a ram team, was demonstrated using data from a Romney sheep breeder. When compared with selection based on an index of breeding values alone, dynamic selection of cull and replacement ewes reduced the accumulation of relatedness by approximately 85\% of the average annual accumulation from 1994 to 2000. To achieve this, approximately 33\% of the average annual genetic progress in average index value was sacrificed. Using dynamic selection to identify a ram team to be mated to selected ewes resulted in a saving in relatedness by an amount equal to the average annual accumulation from 1994 to 2000 with only a very modest drop in genetic progress of 9\% of the average annual genetic progress in average index value. This study has demonstrated that dynamic selection tools could, when practically applied to sheep breeding populations, provide a transparent and efficient means of managing the tradeoff between rate of genetic progress and rate of accumulation of relatedness. },
	issn = {1176-5283},
	author = {Amer PR and Jopson NB and McEwan JC}
}
@conference {41239,
	title = {Optimal utilization of genetic resources in aquaculture},
	booktitle = {Proceedings of the New Zealand Society of Animal Production},
	volume = {61},
	year = {2001},
	month = {Jan},
	pages = {35-37},
	publisher = {New Zealand Society of Animal Production},
	organization = {New Zealand Society of Animal Production},
	address = {Christchurch},
	abstract = {This paper uses a vertically integrated salmon farming company as a case study to describe how quantitative genetics  and decision support optimisation tools have been used in an aquaculture breeding programme. The complex tasks of  maximising genetic progress while managing genetic diversity and avoiding inbreeding are considered at two levels. The  first level relates to the management of a nucleus breeding structure for which long term genetic progress and management  of genetic diversity are the primary objectives. The second level relates to the tactical selection among available broodstock  candidates and their mating to avoid inbreeding. The importance of both effective data management systems and practical implementation of theoretical genetic principles is emphasised.},
	issn = {1176-5283},
	author = {Amer PR and Jopson NB and Dodds KG and Symonds JE and Hills J}
}
@conference {41154,
	title = {Economic benefit of using a major gene in a nucleus selection programme with limits on inbreeding},
	booktitle = {Proceedings of the New Zealand Society of Animal Production},
	volume = {60},
	year = {2000},
	month = {Jan},
	pages = {41-43},
	publisher = {New Zealand Society of Animal Production},
	organization = {New Zealand Society of Animal Production},
	address = {Hamilton},
	abstract = {This study investigates the commercial benefit of including information on an identified major gene in the estimation of breeding values for a breeding nucleus. Two types of selection (dynamic selection to maximise response with controlled inbreeding versus standard truncation selection) and two types of breeding value estimation (using versus ignoring information on a major gene) were compared over 15 generations. Selection strategies based on dynamic rules were commercially superior to strategies using truncation selection under comparable circumstances. Correction of the breeding values of selection candidates for the major gene resulted in extra genotype testing but was commercially superior to ignoring the major gene unless only small numbers of commercial males were sold. Small commercial breeding schemes adopting major gene selection will benefit from the application of selection algorithms that control inbreeding.},
	issn = {1176-5283},
	author = {Amer PR and Villanueva B}
}
@conference {41194,
	title = {Trait economic weights for genetic improvement with SIL},
	booktitle = {Proceedings of the New Zealand Society of Animal Production},
	volume = {60},
	year = {2000},
	month = {Jan},
	pages = {189-191},
	publisher = {New Zealand Society of Animal Production},
	organization = {New Zealand Society of Animal Production},
	address = {Hamilton},
	abstract = {This paper outlines the construction of industry selection indexes for the SIL sheep genetic evaluation process. Traits of direct economic importance in New Zealand sheep production form goal trait groups with each goal trait assigned an economic weight for use in selection indexes. Goal trait group indexes are calculated as the sum of breeding values for each goal trait within the relevant group after multiplication by the relevant economic weight. Three overall indexes can also be calculated by combining goal trait group indexes. The three overall indexes include a Dual Purpose (DP) index, a Terminal Sire (TS) index and a Fine Wool (FW) index. Flexibility is offered to users through the ability to choose overall and goal trait group indexes presented in their results, and the ability to add new indexes to the system. },
	issn = {1176-5283},
	author = {Amer PR}
}
@conference {41016,
	title = {Cost-benefit analysis of commercial use of the Inverdale prolificacy gene},
	booktitle = {Proceedings of the New Zealand Society of Animal Production},
	volume = {58},
	year = {1998},
	month = {Jan},
	pages = {157-160},
	publisher = {New Zealand Society of Animal Production},
	organization = {New Zealand Society of Animal Production},
	abstract = {The Inverdale prolificacy gene is one of several potential major genes currently being explored for commercial application to the New Zealand sheep industry. We calculated economic benefits of two strategies to breed Inverdale carrier stud rams using gene flow methodology. Strategy 1 involves continuous transition matings from a conventional stud flock to generate Inverdale carrier ewes while Inverdale carrier ewes are self replacing in Strategy 2. Strategy 1 involved less DNA testing per ram sold, resulting in a $140 saving in testing costs at $50 per test. Reduction in conventional genetic response was also lower for Strategy 1 (<5\% as opposed to 24\% for Strategy 2) although Strategy 1 requires closer monitoring of animal identification and some Inverdale rams must be kept to produce carrier ewes. Commercial Inverdale use was shown to be highly beneficial in an existing terminal sire mating system with an added value over a normal ram of $3350 per Inverdale ram purchased. This was also highly cost effective with an expected DNA test price of $50 to $75 per sheep genotyped. },
	issn = {1176-5283},
	author = {Amer PR and McEwan JC and Dodds KG and Davis GH}
}
@conference {41013,
	title = {Examination of selection index weights for lamb production},
	booktitle = {Proceedings of the New Zealand Society of Animal Production},
	volume = {58},
	year = {1998},
	month = {Jan},
	pages = {146-149},
	publisher = {New Zealand Society of Animal Production},
	organization = {New Zealand Society of Animal Production},
	abstract = {Economic values for lamb production have historically been derived with the assumption that lambs are slaughtered at a constant age. However, Landcorp Farming Limited slaughters lambs when they reach a set carcass weight. After weaning, heavier lambs are given preferential feeding and slaughtered when they reach a predicted carcass weight of 15kg. In this study index weights for weight of fat (FAT) and weight of lean (LEAN) in the carcass are calculated based on the different costs and returns associated with finishing lambs at a set weight. The nonlinear profit function was responsible for a positive index weight being derived for FAT. This result highlights the problems with using FAT and LEAN as selection criteria for lamb production. It is pointed out that FAT and LEAN are not breeding objectives for sheep production, and that it may be possible to use selection criteria better related to the profit function. },
	issn = {1176-5283},
	author = {Skerritt JW and Amer PR and Nicoll GB}
}
