Impact of breeding for reduced methane emissions in New Zealand sheep on maternal and health traits.

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 and Nematodirus egg 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 CH4 to dry matter intake (g CH4/kg DMI; CH4/DMI) and the ratio of CH4 to 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.

Genetic variation in skin traits in New Zealand lambs.

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 (h2 = 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. © 2022 The Authors. Journal of The Science of Food and Agriculture published by John Wiley & Sons Ltd on behalf of Society of Chemical Industry.

Across-country genomic predictions in Norwegian and New Zealand Composite sheep populations with similar development history.

The goal of this study was to assess the feasibility of across-country genomic predictions in Norwegian White Sheep (NWS) and New Zealand Composite (NZC) sheep populations with similar development history. Different training populations were evaluated (i.e., including only NWS or NZC, or combining both populations). Predictions were performed using the actual phenotypes (normalized) and the single-step GBLUP via Bayesian inference. Genotyped NWS animals born in 2016 (N = 267) were used to assess the accuracy and bias of genomic estimated breeding values (GEBVs) predicted for birth weight (BW), weaning weight (WW), carcass weight (CW), EUROP carcass classification (EUC), and EUROP fat grading (EUF). The accuracy and bias of GEBVs differed across traits and training population used. For instance, the GEBV accuracies ranged from 0.13 (BW) to 0.44 (EUC) for GEBVs predicted including only NWS, from 0.06 (BW) to 0.15 (CW) when including only NZC, and from 0.10 (BW) to 0.41 (EUC) when including both NWS and NZC animals in the training population. The regression coefficients used to assess the spread of GEBVs (bias) ranged from 0.26 (BW) to 0.64 (EUF) for only NWS, 0.10 (EUC) to 0.52 (CW) for only NZC, and from 0.42 (WW) to 2.23 (EUC) for both NWS and NZC in the training population. Our findings suggest that across-country genomic predictions based on ssGBLUP might be possible for NWS and NZC, especially for novel traits.

Genetic parameters of methane emissions determined using portable accumulation chambers in lambs and ewes grazing pasture and genetic correlations with emissions determined in respiration chambers.

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.

Genetic diversity of a New Zealand multi-breed sheep population and composite breeds' history revealed by a high-density SNP chip.

BACKGROUND: 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. RESULTS: Overall, as expected, levels of pairwise LD decreased with increasing distance between SNP pairs. The mean LD r2 between adjacent SNP was 0.26 ± 0.10. The most recent effective population size for all animals (687) and separately per breed-groups: Primera (974), Lamb Supreme (380), Texel (227) and Dual-Purpose (125) was quite variable. The genotyped animals were outbred or had an average low level of inbreeding. Consistency of gametic phase was higher than 0.94 for all breed pairs at the average distance between SNP on the chip (~4.74 kb). Moreover, there was not a clear separation between the breed-groups based on principal component analysis, suggesting that a mixed-breed training population for calculation of molecular breeding values would be beneficial. CONCLUSIONS: This study reports, for the first time, estimates of linkage disequilibrium, genetic diversity and population structure parameters from a genome-wide perspective in New Zealand Terminal Sire composite sheep breeds. The levels of linkage disequilibrium indicate that genomic selection could be implemented with the high density SNP panel. The moderate to high consistency of gametic phase between breed-groups and overlapping population structure support the pooling of the animals in a mixed training population for genomic predictions. In addition, the moderate to high Ne highlights the need to genotype and phenotype a large training population in order to capture most of the haplotype diversity and increase accuracies of genomic predictions. The results reported herein are a first step toward understanding the genomic architecture of a Terminal Sire composite sheep population and for the optimal implementation of genomic selection and genome-wide association studies in this sheep population.

Prediction of genomic breeding values for growth, carcass and meat quality traits in a multi-breed sheep population using a HD SNP chip.

BACKGROUND: 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. RESULTS: The average observed accuracies (± SD) for traits measured in the live animal, carcass, and, meat quality traits ranged from 0.18 ± 0.07 to 0.33 ± 0.10, 0.28 ± 0.09 to 0.55 ± 0.05 and 0.21 ± 0.07 to 0.36 ± 0.08, respectively, depending on the scenario/method used in the genomic predictions. When accounting for population stratification by adjusting for 2, 4 or 6 principal components (PCs) the observed accuracies of molecular breeding values (mBVs) decreased or kept constant for all traits. The mBVs observed accuracies when fitting both G and A matrices were similar to fitting only G matrix. The lowest accuracies were observed for k-means cross-validation and forward validation performed within each k-means cluster. CONCLUSIONS: The accuracies observed in this study support the feasibility of genomic selection for growth, carcass and meat quality traits in New Zealand Terminal Sire breeds using the Ovine HD SNP chip. There was a clear advantage on using a mixed training population instead of performing analyzes per genomic clusters. In order to perform genomic predictions per breed group, genotyping more animals is recommended to increase the size of the training population within each group and the genetic relationship between training and validation populations. The different scenarios evaluated in this study will help geneticists and breeders to make wiser decisions in their breeding programs.

Genomic prediction and genome-wide association study for dagginess and host internal parasite resistance in New Zealand sheep.

BACKGROUND: Dagginess (faecal soiling of the perineum region) and host nematode parasite resistance are important animal welfare traits in New Zealand sheep. Genomic prediction (GP) estimates the genetic merit, as a molecular breeding value (mBV), for each trait based on many SNPs. The additional information the mBV provides (as determined by its accuracy) has led to its incorporation into breeding schemes. Some GP methods give SNP effects, which provide additional information to identify genome-wide associations (GWAS) for a trait of interest. Here we report results from a GP and GWAS study for dagginess and host nematode parasite resistance in a New Zealand sheep industry resource. RESULTS: Genomic prediction analysis was performed using 50K SNP chip data and parent average-removed, de-regressed BVs for five traits, from a resource of 8705 pedigree recorded animals. The five traits were dag score at three and eight months (DAG3, DAG8) and nematode faecal egg count in summer (FEC1), autumn (FEC2) and as an adult (AFEC). The resource consisted of Romney, Coopworth, Perendale, Texel and various breed crosses (designated: CompRCP, CompRCPT and CompCRP). The pure breeds, apart from Texel, plus CompRCP were used to develop the GP. The resulting SNP effects were used to identify genetic regions associated with dagginess and parasite resistance. Accuracies of the weighted correlation between mBV and true BV ranged between -0.07 (Texel) and 0.56 (Coopworth) for DAG3 and DAG8. For FEC1, FEC2 and AFEC accuracies ranged between -0.22 (CompRCPT) and 0.69 (Coopworth). The weighted average individual accuracy (calculated from theory) ranges were 0.13 (Texel) to 0.52 (Coopworth) and 0.11 (Texel) to 0.55 (Coopworth) respectively, for dagginess and parasite traits. There was one SNP for DAG8 that reached Bonferroni significance threshold (P < 1 × 10(-6)) on OAR15, the same two SNPs for each of the parasite traits (OAR26) and none for DAG3. A notable peak was also observed on OAR7 for all the parasite traits, however, it did not reach the Bonferroni significance threshold. CONCLUSIONS: This study presents the first results of a GWAS on dagginess and faecal egg count traits in New Zealand sheep. The results suggest that there are quantitative trait loci on OAR 15 for dagginess and on OAR26 and seven for faecal egg count.

Genome-wide association mapping identifies the genetic basis of discrete and quantitative variation in sexual weaponry in a wild sheep population.

Understanding the genetic architecture of phenotypic variation in natural populations is a fundamental goal of evolutionary genetics. Wild Soay sheep (Ovis aries) have an inherited polymorphism for horn morphology in both sexes, controlled by a single autosomal locus, Horns. The majority of males have large normal horns, but a small number have vestigial, deformed horns, known as scurs; females have either normal horns, scurs or no horns (polled). Given that scurred males and polled females have reduced fitness within each sex, it is counterintuitive that the polymorphism persists within the population. Therefore, identifying the genetic basis of horn type will provide a vital foundation for understanding why the different morphs are maintained in the face of natural selection. We conducted a genome-wide association study using ∼36000 single nucleotide polymorphisms (SNPs) and determined the main candidate for Horns as RXFP2, an autosomal gene with a known involvement in determining primary sex characters in humans and mice. Evidence from additional SNPs in and around RXFP2 supports a new model of horn-type inheritance in Soay sheep, and for the first time, sheep with the same horn phenotype but different underlying genotypes can be identified. In addition, RXFP2 was shown to be an additive quantitative trait locus (QTL) for horn size in normal-horned males, accounting for up to 76% of additive genetic variation in this trait. This finding contrasts markedly from genome-wide association studies of quantitative traits in humans and some model species, where it is often observed that mapped loci only explain a modest proportion of the overall genetic variation.