The inclusion of eating quality traits in sheep genetic improvement programmes is desirable. Intramuscular fat (IMF) plays a key role in ensuring consumer satisfaction when eating lamb, but genetic progress for IMF is constrained by a lack of routine data collection. This study investigated the potential for IMF predictor traits to substitute for measured IMF in genetic improvement programmes. Carcass and predicted IMF (near-infrared estimated IMF and marbling score) data were available on 10,113 New Zealand lambs, 1678 of which also had measured chemical IMF on a slice of M. longissimus lumborum on which the predictions of IMF had been made. Genetic antagonisms were observed between carcass lean traits and IMF. The genetic correlation between the predictors and measured IMF approached one, indicating that predictors of IMF can be used in genetic improvement programmes. Through using selection indexes, simultaneous increases in IMF and the existing terminal selection index are possible, provided all traits are measured. This study highlights the importance and potential of predicted IMF to achieve genetic improvement in traits of importance to consumers.

The application of individual spectroscopic techniques for meat analysis has been widely explored. Attempts to fuse data from multiple spectroscopic instruments for meat analysis are still lacking. Comparative assessment of the performance of mid infrared (MIR), near infrared (NIR) and Raman spectroscopy to estimate fatty acid (FA) composition in processed lamb was investigated. The acquired data from these individual techniques were then utilised in estimating similar parameters using a multi-block partial least square data fusion approach. Model performance was assessed with respect to the determination coefficient and ratio of predictive deviation upon cross-validation of the model. The fused data had slight improvements for the prediction of four FA parameters including MUFA, C18:0, C18:1 c9 and C9, t11- CLA), suggesting possible information enhancement with use of multiple instruments. However, MIR offered better predictability (RPD values) across the FA parameters considered.

BACKGROUND This study explored the genetic variability in the New Zealand sheep population for economically important skin traits. Skins were collected at slaughter from two progeny test flocks, resulting in 725 skins evaluated for grain strain, flatness, crust leather strength and overall suitability for shoe leather. DNA profiles collected from skins post-slaughter were matched to individual animals using previously collected high-density genotypes. RESULTS Considerable phenotypic variation for skin traits was observed, with around 40% of the skins being identified as suitable for high-value shoe leather production. Several key traits associated with leather production, including flatness, tear strength, grain strength and grain strain were found to be moderate to highly heritable (h(2) = 0.28-0.82). There were no major significant genome-wide association study (GWAS) peaks associated with many of the traits examined, however, one single-nucleotide polymorphism (SNP) reached significance for the flatness of the skin over the hindquarters. CONCLUSION This research confirms that suitable lamb skins can be bred for use as high-value shoe leather. While moderately to highly heritable, skin traits in New Zealand lambs appear to be polygenic with no genes of major effect underlaying the traits of interest. Given the complex nature of these traits, the identification and selection of animals with higher-value skins may be enabled by geomic selection. (c) 2022 The Authors. Journal of The Science of Food and Agriculture published by John Wiley & Sons Ltd on behalf of Society of Chemical Industry.

Post-slaughter alimentary tract measures were collected from eight-month-old ram lambs during routine culling of sheep divergently selected for methane yield. Measures from 142 and 132 lambs from the high and low methane lines respectively were collected over five years. Low CH4 animals had lighter reticulo-rumen full, empty and contents weights (P<0.05), but tended to have longer rumen papillae (P=0.06). Preliminary heritability estimates for reticulo-rumen components and papillae traits were significantly different from zero, ranging from 0.09 to 0.25. Results validate earlier findings that differences in the anatomical characteristics of the alimentary tract are associated with methane emissions and suggest that there is a significant host genetic component, warranting further investigation.

Enteric methane emissions from ruminants account for ∼35% of New Zealand’s greenhouse gas emissions. This poses a significant threat to the pastoral sector. Breeding has been shown to successfully lower methane emissions, and genomic prediction for lowered methane emissions has been introduced at the national level. The long-term genetic impacts of including low methane in ruminant breeding programs, however, are unknown. The success of the New Zealand sheep industry is currently heavily reliant on the prolificacy, fecundity and survival of adult ewes. The objective of this study was to determine genetic and phenotypic correlations between adult maternal ewe traits (live weight, body condition score, number of lambs born, litter survival to weaning, pregnancy scanning and fleece weight), faecal andNematodirusegg counts and measures of methane in respiration chambers. More than 9,000 records for methane from over 2,200 sheep measured in respiration chambers were collected over 10 years. Sheep were fed on a restricted diet calculated as approximately twice the maintenance. Methane measures were converted to absolute daily emissions of methane measured in g per day (CH4/day). Two measures of methane yield were recorded: the ratio of CH4to dry matter intake (g CH4/kg DMI; CH4/DMI) and the ratio of CH4to total gas emissions (CH4/(CH4+ CO2)). Ewes were maintained in the flocks for at least two parities. Non-methane trait data from over 8,000 female relatives were collated to estimate genetic correlations. Results suggest that breeding for low CH4/DMI is unlikely to negatively affect faecal egg counts, adult ewe fertility and litter survival traits, with no evidence for significant genetic correlations. Fleece weight was unfavourably (favourably) correlated with CH4/DMI (rg= −0.21 ± 0.09). Live weight (rg= 0.3 ± 0.1) and body condition score (rg= 0.2 ± 0.1) were positively correlated with methane yield. Comparing the two estimates of methane yield, CH4/DMI had lower heritability and repeatability. However, correlations of both measures with adult ewe traits were similar. This suggests that breeding is a suitable mitigation strategy for lowering methane yield, but wool, live weight and fat deposition traits may be affected over time and should be monitored.

Global agreements in place to reduce methane emissions in livestock are a potential threat to food security. Successful but independent breeding strategies for improved production and lower methane are in place. The unanswered questions are whether these strategies can be combined and how they impact one another, physically and economically. The New Zealand economy is largely dependent on pastoral agriculture from grazing ruminants. The sheep industry produces ∼20 million lamb carcasses for export each year primarily from grass. Methane emitted from the fermentation of forage by grazing ruminants accounts for one-third of all New Zealand’s greenhouse gas emissions. Here, we use sheep selection lines bred for divergent methane production and large numbers of their relatives to determine the genetic and phenotypic correlations between enteric methane emissions, carcass yield, and meat quality. The primary objectives were to determine whether previously shown physiological differences between methane selection lines (differing by ∼12% in methane) result in a negative impact on meat production and quality by measuring close relatives. The results show no negative effects of breeding for lowered methane on meat and carcass quality. Gross methane emissions were highly correlated with liveweight and measures of carcass weight and negatively correlated with dressing-out percentage and fat yield (GR). Trends were similar but not significant for methane yield (g CH4/kg DMI). Preliminary evidence, to date, shows that breeding for low methane may result in animals with higher lean yields that are economically favorable even before carbon costs and environmental benefits are taken into account. These benefits were seen in animals measured for methane on fixed intakes and require validation on intakes that are allowed to vary.

The implementation of Raman and infrared spectroscopy with three data fusion strategies to predict pH and % IMF content of red meat was investigated. Raman and FTIR systems were utilized to assess quality parameters of intact red meat. Quantitative models were built using PLS, with model performances assessed with respect to the determination coefficient (R2), root mean square error and normalized root mean square error (NRMSEP). Results obtained on validation against an independent test set show that the high-level fusion strategy had the best performance in predicting the observed pH; with R2P and NRMSEP values of 0.73 and 12.9% respectively, whereas low-level fusion strategy showed promise in predicting % IMF (NRMSEP = 8.5%). The fusion of data from more than one technique at low and high level resulted in improvement in the model performances; highlighting the possibility of information enhancement.

With increasing demand for fast and reliable techniques for intact meat discrimination, we explore the potential of Raman spectroscopy in combination with three chemometric techniques to discriminate beef, lamb and venison meat samples. Ninety (90) intact red meat samples were measured using Raman spectroscopy, with the acquired spectral data preprocessed using a combination of rubber-band baseline correction, Savitzky-Golay smoothing and standard normal variate transformation. PLSDA and SVM classification were utilized in building classification models for the meat discrimination, whereas PCA was used for exploratory studies. Results obtained using linear and non-linear kernel SVM models yielded sensitivities of over 87 and 90 % respectively, with the corresponding specificities above 88 % on validation against a test set. The PLSDA model yielded over 80 % accuracy in classifying each of the meat specie. PLSDA and SVM classification models in combination with Raman spectroscopy posit an effective technique for red meat discrimination.

Published studies have shown that methane yield (g CH4/kg dry matter) from sheep is positively correlated with the size (volume and surface area) of the reticulo-rumen (RR) and the weight of its contents. However, the relationship between CH4 yield and RR shape has not been investigated. In this work, shape analysis has been performed on a data set of computerised tomography (CT) scans of the RR from sheep having high and low CH4 yields (n=20 and n=17, respectively). The three-dimensional geometries of the RRs were reconstructed from segmented scan data and split into three anatomical regions. An iterative fitting technique combining radial basis functions and principal component (PC) fitting was used to create a set of consistent landmarks which were then used as variables in a PC analysis to identify shape variation within the data. Significant size differences were detected for regions corresponding to the dorsal and ventral compartments between sheep with high and low CH4 yields. When the analysis was repeated after scaling the geometries to remove the effect of size, there was no significant shape variation correlating with CH4 yield. The results have demonstrated the feasibility of CT-based computational shape determination for studying the morphological characteristics of the RR and indicate that size, but not shape correlates with CH4 yield in sheep.

Methane (CH4) emission traits were previously found to be heritable and repeatable in sheep fed alfalfa pellets in respiration chambers (RC). More rapid screening methods are, however, required to increase genetic progress and to provide a cost-effective method to the farming industry for maintaining the generation of breeding values in the future. The objective of the current study was to determine CH4 and carbon dioxide (CO2) emissions using several 1-h portable accumulation chamber (PAC) measurements from lambs and again as ewes while grazing ryegrass-based pasture. Many animals with PAC measurements were also measured in RC while fed alfalfa pellets at 2.0 × maintenance metabolizable energy requirements (MEm). Heritability estimates from mixed models for CH4 and CO2 production (g/d) were 0.19 and 0.16, respectively, when measured using PAC with lambs; 0.20 and 0.27, respectively, when measured using PAC with ewes; and 0.23 and 0.34, respectively, when measured using RC with lambs. For measured gas traits, repeatabilities of measurements collected 14 d apart ranged from 0.33 to 0.55 for PAC (combined lambs and ewes) and were greater at 0.65 to 0.76 for the same traits measured using RC. Genetic correlations (rg) between PAC in lambs and ewes were 0.99 for CH4, 0.93 for CH4 + CO2, and 0.85 for CH4/(CH4 + CO2), suggesting that CH4 emissions in lambs and ewes are the same trait. Genetic correlations between PAC and RC measurements were lower, at 0.62 to 0.67 for CH4 and 0.41 to 0.42 for CH4 + CO2, likely reflecting different environmental conditions associated with the protocols used with the 2 measurement methods. The CH4/(CH4 + CO2) ratio was the most similar genetic trait measured using PAC (both lambs and ewes, 63% and 66% selection efficiency, respectively) compared with CH4 yield (g/kg DMI) measured using RC. These results suggest that PAC measurements have considerable value as a rapid low-cost method to estimate breeding values for CH4 emissions in sheep.

Knowledge about the genetic diversity of a population is a crucial parameter for the implementation of successful genomic selection and conservation of genetic resources. The aim of this research was to establish the scientific basis for the implementation of genomic selection in a composite Terminal sheep breeding scheme by providing consolidated linkage disequilibrium (LD) measures across SNP markers, estimating consistency of gametic phase between breed-groups, and assessing genetic diversity measures, such as effective population size (Ne), and population structure parameters, using a large number of animals (n = 14,845) genotyped with a high density SNP chip (606,006 markers). Information generated in this research will be useful for optimizing molecular breeding values predictions and managing the available genetic resources.

New Zealand has some unique Terminal Sire composite sheep breeds, which were developed in the last three decades to meet commercial needs. These composite breeds were developed based on crossing various Terminal Sire and Maternal breeds and, therefore, present high genetic diversity compared to other sheep breeds. Their breeding programs are focused on improving carcass and meat quality traits. There is an interest from the industry to implement genomic selection in this population to increase the rates of genetic gain. Therefore, the main objectives of this study were to determine the accuracy of predicted genomic breeding values for various growth, carcass and meat quality traits using a HD SNP chip and to evaluate alternative genomic relationship matrices, validation designs and genomic prediction scenarios. A large multi-breed population (n = 14,845) was genotyped with the HD SNP chip (600 K) and phenotypes were collected for a variety of traits.

Meat quality and carcass characteristics are becoming more relevant for the sheep breeding programs because of their economic value. Understanding the genetic basis for these traits and its relationship with standard traits is necessary for this to be accomplished. Genetic and phenotypic parameters were estimated for 33 growth, carcass and meat quality traits using a large and unique data set from a variety of terminal sire sheep breeds and composites. This is the most comprehensive study to date of genetic parameter estimates for carcass and meat quality traits in New Zealand sheep and includes many traits that are difficult or expensive to measure and novel traits such as number of rib pairs. Heritability estimates ranged from 0.01 for meat redness at 168 h after display to 0.44 for ultrasonic eye muscle depth. Most genetic correlations among growth and carcass traits were favourable and moderate to high. However, some genetic antagonisms such as those between carcass fatness and carcass weight were observed indicating that selection to produce heavier carcasses would also result in fatter carcasses. The genetic correlations among meat quality traits were quite variable. Marbling and tenderness were favourably but weakly genetically correlated, indicating that indirect selection gains by selecting only for traditional traits (i.e. growth and carcass traits) would be small and it is recommended that both be included in a breeding program in order to make greater genetic progress in these traits. The genetic correlations among growth/carcass and eating quality traits were moderate to low; however, some genetic antagonisms were observed, such as carcass fatness with marbling and meat redness, indicating that a stronger emphasis on selection for leanness could affect meat quality traits and consequently consumer eating satisfaction. The heritability estimates and phenotypic variances for the carcass and meat quality traits of New Zealand sheep populations suggest that most traits, apart from pH and meat yellowness, have sufficient phenotypic and genetic variation to enable substantial genetic gains to be achieved through selection. The genetic parameters presented in this study provide a valuable reference to design and/or update a terminal sire breeding program emphasizing meat quality traits. It is important to note that unfavourable genetic correlations identified in this study were low to moderate in magnitude, making it practical to select for favourable genetic progress in all traits or at least to maintain commercially acceptable levels for some traits, if they are measured and balanced in a selection index.