Domestication and the subsequent selection of animals for either economic or morphological features can leave a variety of imprints on the genome of a population. Genomic regions subjected to high selective pressures often show reduced genetic diversity and frequent runs of homozygosity (ROH). Therefore, the objective of the present study was to use 42,182 autosomal SNPs to identify genomic regions in 3,191 sheep from six commercial breeds subjected to selection pressure and to quantify the genetic diversity within each breed using ROH. In addition, the historical effective population size of each breed was also estimated and, in conjunction with ROH, was used to elucidate the demographic history of the six breeds. ROH were common in the autosomes of animals in the present study, but the observed breed differences in patterns of ROH length and burden suggested differences in breed effective population size and recent management. ROH provided a sufficient predictor of the pedigree inbreeding coefficient, with an estimated correlation between both measures of 0.62. Genomic regions under putative selection were identified using two complementary algorithms; the fixation index and hapFLK. The identified regions under putative selection included candidate genes associated with skin pigmentation, body size and muscle formation; such characteristics are often sought after in modern-day breeding programs. These regions of selection frequently overlapped with high ROH regions both within and across breeds. Multiple yet uncharacterised genes also resided within putative regions of selection. This further substantiates the need for a more comprehensive annotation of the sheep genome as these uncharacterised genes may contribute to traits of interest in the animal sciences. Despite this, the regions identified as under putative selection in the current study provide an insight into the mechanisms leading to breed differentiation and genetic variation in meat production.

The objective of this study was to examine whether there was genotype by environment interaction (G x E) for female fertility traits for various environmental descriptors used in the United Kingdom. Records on days to first service (DFS), nonreturn rate at 56 d (NR56), calving interval (CI), and number of inseminations (NINS) on approximately 200,000 first-lactation Holstein cows in 3,192 herds and from 1,147 sires were analyzed using both random regression reaction norm models and multiple-trait models. The environmental descriptors were herd averages of DFS, CI, and NR56, and herd production and intensity indices, the latter based on 305-d milk, fat, and protein yields, age at first calving, temperature, and rainfall. No GxE was found for NR56 and NINS. There was an indication of G x E for DFS and CI with respect to the herd average of that trait, but only from the reaction norm model. Genotype by environment interaction existed for DFS and CI with respect to both production and intensity indexes-genetic correlations between top and bottom quartiles ranged from 0.73 to 0.84, with similar results from both models, indicating reranking of bulls. Part of this G x E might be explained by low production and intensity herds also having more concentrated spring calving.

This is a PDF file of an article that has undergone enhancements after acceptance, such as the addition of a cover page and metadata, and formatting for readability, but it is not yet the definitive version of record. This version will undergo additional copyediting, typesetting and review before it is published in its final form, but we are providing this version to give early visibility of the article. Please note that, during the production process, errors may be discovered which could affect the content, and all legal disclaimers that apply to the journal pertain.

This is a PDF file of an unedited manuscript that has been accepted for publication. As a service to our customers we are providing this early version of the manuscript. The manuscript will undergo copyediting, typesetting, and review of the resulting proof before it is published in its final form. Please note that during the production process errors may be discovered which could affect the content, and all legal disclaimers that apply to the journal pertain. Highlights Economic values are widely used in the development of breeding objectives internationally. The economic value of a trait in a breeding objective can be defined as the change in profit value of a unit change in an individual trait, while keeping all other traits constant. A total of fourteen traits of economic importance representing maternal, lambing, production and health characteristics were calculated within a whole farm bioeconomic model. Results from this study will enable the implementation of new economic values within the national terminal and maternal Irish sheep breeding objectives which highlights the traits of importance for increasing overall farm profitability.

Body condition score (BCS) is a subjective assessment of the proportion of body fat an animal possesses and is independent of frame size. There is a growing awareness of the importance of mature animal live-weight given its contribution to the overall costs of production of a sector. Because of the known relationship between BCS and live-weight, strategies to reduce live-weight could contribute to the favouring of animals with lesser body condition. The objective of the present study was to estimate the average difference in live-weight per incremental change in BCS, measured subjectively on a scale of 1 to 5. The data used consisted of 19 033 BCS and live-weight observations recorded on the same day from 7556 ewes on commercial and research flocks; the breeds represented included purebred Belclare (540 ewes), Charollais (1484 ewes), Suffolk (885 ewes), Texel (1695 ewes), Vendeen (140 ewes), as well as, crossbreds (2812 ewes). All associations were quantified using linear mixed models with the dependent variable of live-weight; ewe parity was included as a random effect. The independent variables were BCS, breed (n=6), stage of the inter-lambing interval (n=6; pregnancy, lambing, pre-weaning, at weaning, post-weaning and mating) and parity (1, 2, 3, 4 and 5+). In addition, two-way interactions were used to investigate whether the association between BCS and live-weight differed by parity, a period of the inter-lambing interval or breed. The association between BCS and live-weight differed by parity, by a period of the inter-lambing interval and by breed. Across all data, a one-unit difference in BCS was associated with 4.82 (SE=0.08) kg live-weight, but this differed by parity from 4.23 kg in parity 1 ewes to 5.82 kg in parity 5+ ewes. The correlation between BCS and live-weight across all data was 0.48 (0.47 when adjusted for nuisance factors in the statistical model), but this varied from 0.48 to 0.53 by parity, from 0.36 to 0.63 by stage of the inter-lambing interval and from 0.41 to 0.62 by breed. Results demonstrate that consideration should be taken of differences in BCS when comparing ewes on live-weight as differences in BCS contribute quite substantially to differences in live-weight; moreover, adjustments for differences in BCS should consider the population stratum, especially breed.

The objective of the present study was to quantify the extent of genetic variation in three health-related traits namely dagginess, lameness and mastitis, in an Irish sheep population. Each of the health traits investigated pose substantial welfare implications as well as considerable economic costs to producers. Data were also available on four body-related traits, namely body condition score (BCS), live weight, muscle depth and fat depth. Animals were categorised as lambs (<365 days old) or ewes (⩾365 days old) and were analysed both separately and combined. After edits, 39 315 records from 264 flocks between the years 2009 and 2015 inclusive were analysed. Variance components were estimated using animal linear mixed models. Fixed effects included contemporary group, represented as a three-way interaction between flock, date of inspection and animal type (i.e. lamb, yearling ewe (i.e. females ⩾365 days but <730 days old that have not yet had a recorded lambing) or ewe), animal breed proportion, coefficients of heterosis and recombination, animal gender (lambs only), animal parity (ewes only; lambs were assigned a separate 'parity') and the difference in age of the animal from the median of the respective parity/age group. An additive genetic effect and residual effect were both fitted as random terms with maternal genetic and non-genetic components also considered for traits of the lambs. The direct heritability of dagginess was similar across age groups (0.14 to 0.15), whereas the direct heritability of lameness ranged from 0.06 (ewes) to 0.12 (lambs). The direct heritability of mastitis was 0.04. For dagginess, 13% of the phenotypic variation was explained by dam litter, whereas the maternal heritability of dagginess was 0.05. The genetic correlation between ewe and lamb dagginess was 0.38; the correlation between ewe and lamb lameness was close to zero but was associated with a large standard error. Direct genetic correlations were evident between dagginess and BCS in ewes and between lameness and BCS in lambs. The present study has demonstrated that ample genetic variation exists for all three health traits investigated indicating that genetic improvement is indeed possible.

The objective of the present study was to quantify the impact of the systematic environmental effects of both birth and rearing type on pre-weaning lamb live weight, and to evaluate the repercussions of inaccurate recording of birth and rearing type on subsequent genetic evaluations. A total of 32,548 birth weight records, 35,770 forty-day weight records and 32,548 records for average daily gain (ADG) between birth and 40-day weight from the Irish national sheep database were used. For each lamb, a new variable, birth-rearing type, reflecting both the birth and rearing type of a lamb was generated by concatenating both parameters. The association between birth-rearing type and birth weight, 40-day weight, and ADG was estimated using linear mixed models. The repercussions of inaccurate recording of birth type were determined by quantifying the impact on sire estimated breeding value (EBV; with an accuracy of ≥ 35%), where one of the lambs born in a selection of twin litter births was assumed to have died at birth but the farmer recorded the birth and rearing type as a singleton. The heaviest mean birth weight was associated with lambs born and subsequently reared as singles (5.47 kg); the lightest mean birth weight was associated with lambs born and reared as triplets (4.10 kg). The association between birth-rearing type and 40-day weight differed by dam parity (P &lt; 0.001). Lambs reared by first parity dams as singles, irrespective of birth type were, on average, heavier at 40-day weighing than lambs reared as multiples, but as parity number increased, single-born lambs reared as twins outperformed triplet-born lambs reared as singles. Irrespective of the trait evaluated, the correlation between sire EBV estimated from the accurately recorded data and sire EBV estimated from the data with recording errors was strong ranging from 0.93 (birth weight) to 0.97 (ADG). The EBV for sires with progeny data manipulated were 0.14 kg, 0.34 kg and 5.56 g/d less for birth weight, 40-day weight and ADG, respectively, compared to their equivalent EBV calculated using accurately recorded data. Results from this study highlight the importance of precise recording of birth-rearing type by producers for the generation of accurate genetic evaluations.

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