Sustainable Livestock Systems Group

Scottish, United Kingdom

Sustainable Livestock Systems Group

Scottish, United Kingdom

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Berry D.P.,Animal and Grassland Research and Innovation Center | Bastiaansen J.W.M.,Wageningen University | Veerkamp R.F.,Animal Breeding and Genomics Center | Wijga S.,Wageningen University | And 3 more authors.
Animal | Year: 2012

Genome-wide association studies for difficult-to-measure traits are generally limited by the sample population size with accurate phenotypic data. The objective of this study was to utilise data on primiparous Holstein-Friesian cows from experimental farms in Ireland, the United Kingdom, the Netherlands and Sweden to identify genomic regions associated with traditional measures of fertility, as well as a fertility phenotype derived from milk progesterone profiles. Traditional fertility measures investigated were days to first heat, days to first service, pregnancy rate to first service, number of services and calving interval (CI); post-partum interval to the commencement of luteal activity (CLA) was derived using routine milk progesterone assays. Phenotypic and genotypic data on 37 590 single nucleotide polymorphisms (SNPs) were available for up to 1570 primiparous cows. Genetic parameters were estimated using linear animal models, and univariate and bivariate genome-wide association analyses were undertaken using Bayesian stochastic search variable selection performed using Gibbs sampling. Heritability estimates of the traditional fertility traits varied from 0.03 to 0.16; the heritability for CLA was 0.13. The posterior quantitative trait locus (QTL) probabilities, across the genome, for the traditional fertility measures were all <0.021. Posterior QTL probabilities of 0.060 and 0.045 were observed for CLA on SNPs each on chromosome 2 and chromosome 21, respectively, in the univariate analyses; these probabilities increased when CLA was included in the bivariate analyses with the traditional fertility traits. For example, in the bivariate analysis with CI, the posterior QTL probability of the two aforementioned SNPs were 0.662 and 0.123. Candidate genes in the vicinity of these SNPs are discussed. The results from this study suggest that the power of genome-wide association studies in cattle may be increased by sharing of data and also possibly by using physiological measures of the trait under investigation. © Copyright The Animal Consortium 2012.


Lovendahl P.,University of Aarhus | Chagunda M.G.G.,Sustainable Livestock Systems Group
Journal of Dairy Science | Year: 2010

Detection of estrus in dairy cattle is effectively aided by electronic activity tags or pedometers. Characterization of estrus intensity and duration is also possible from activity data. This study aimed to develop an algorithm to detect and characterize behavioral estrus from hourly recorded activity data and to apply the algorithm to activity data from an experimental herd. The herd comprised of Holstein (n=211), Jersey (n=126), and Red Dane (n=178) cattle, with virgin heifers (n=132) and lactating cows in the first 4 parities; n=895 cow-parities, with a total of 3,674 activity episodes. The algorithm was based on deviations from exponentially smoothed hourly activity counts and was used to identify onset, duration, and intensity of estrus. Learning data included 461 successful inseminations with activity records over a 2-wk period before and after the artificial insemination. Rates of estrus detection and error rate depended on the chosen threshold level. At a threshold giving 74.6% detection rate, daily error rate was 1.3%. When applied to a subset of the complete data where milk progesterone was also available, concordance of days to first activity-detected estrus with the similar trait based on progesterone was also dependent on the chosen threshold so that, with stricter thresholds, the agreement was closer. A single-trait mixed model was used to determine the effects of systematic factors on the estrus activity traits. In general, an activity episode lasted 9.24. h in heifers and 8.12. h in cows, with the average strength of 1.03 ln units (equivalent to a 2.8-fold increase) in both age groups. Red Danes had significantly fewer days to first episode of high activity than Holsteins and Jerseys (29.4, 33.1, and 33.9 d, respectively). However, Jerseys had significantly shorter duration and less strength of estrus than both Red Danes and Holsteins of comparable age. The random effect of cow affected days to first episode of high activity and strength as well as estrus duration. Days from calving to first episode of high activity correlated negatively with body condition scores in early lactation. The results suggest that data from activity monitors could supply valuable information about fertility traits and could thereby be helpful in management of herd fertility. To establish the complementarities or interdependence between progesterone and activity measurements, further studies with more information from different sources of measuring estrus are needed. © 2010 American Dairy Science Association.


Lovendahl P.,University of Aarhus | Chagunda M.G.G.,Sustainable Livestock Systems Group
Journal of Dairy Science | Year: 2011

Automatic milking systems allow cows voluntary access to milking and concentrates within set limits. This leads to large variation in milking intervals, both within and between cows, which further affects yield per milking and composition of milk. This study aimed to describe the degree to which differences in milking interval were attributable to individual cows, and how this correlated to individual differences in yield and composition of milk throughout lactation. Data from 288,366 milkings from 664 cow-lactations were used, of which 229,020 milkings had milk composition results. Cows were Holsteins, Red Danes, and Jerseys in parities 1, 2, and 3. Data were analyzed using a linear mixed model, with cow-lactation as a random effect and assuming heterogeneous residual variance over the lactation. Cow-lactation variance was fitted using linear spline functions with 5 knot-points. Residual variance was generally greatest in early lactation and declined thereafter. Accordingly, animal-related variance tended to increase with progression of lactation. Milking frequency (the reverse of milking interval) was found to be moderately repeatable throughout lactation. Daily milk yield expressed per milking was found to be highly repeatable in all breeds, with the highest values occurring by the end of lactation. Fat percentage had only moderate repeatability in early to mid lactation but increased toward the end of lactation. Individual level correlations showed that cows with higher milking frequency also had greater yields, but had lower fat percentage. Correlations were slightly weaker in very early lactation than in the remaining parts of lactation. We concluded that individual differences exist among cows milked automatically. Cows with higher yields are milked more often and have lower fat content in their milk. © 2011 American Dairy Science Association.


Banos G.,Aristotle University of Thessaloniki | Coffey M.P.,Sustainable Livestock Systems Group
Animal | Year: 2010

The objective of this study was to quantify the genetic association of body energy assessed throughout lactation with a cows fertility. Nine direct and indirect body energy traits were defined at different stages of lactation. Four were daily records of energy balance, energy content, cumulative effective energy (CEE) and body condition score (BCS) calculated between lactation days 4 and 311. The other five traits included duration of negative energy balance (DNEB), rate of recovery during DNEB (RNEB), sum of negative energy balance (SNEB), nadir of energy content (NEC) and number of days from calving to NEC. Of these traits, energy balance, DNEB, RNEB and SNEB were primarily based on individual cow feed intake and milk yield, and considered direct measures of body energy. The other traits were calculated from body lipid and protein changes, predicted from BCS and live weight profiles, and were considered indirect measures of body energy. Fertility was defined by number of days between calving and commencement of luteal activity (DLA), first observed oestrus (DH) and conception (DC), and number of services per conception. A total of 957 cows in their first four lactations were considered in the study. Genetic models fitted cubic splines to define longitudinal traits (energy balance, energy content, CEE and BCS) and calculate heritability and genetic correlation with fertility. Daily heritability estimate ranges were 0.10 to 0.34, 0.35 to 0.61, 0.32 to 0.53 and 0.24 to 0.56 for energy balance, energy content, CEE and BCS, respectively, and, in most cases, tended to increase towards the middle of lactation and remain relatively stable thereafter. Of the other body energy traits, heritability of NEC (0.44) was the most notable. Statistically significant (P < 0.05) genetic correlations of DH with daily energy balance, energy content, CEE and BCS ranged from 0.16 to 0.28, 0.35 to 0.48, 0.16 to 0.26 and 0.37 to 0.44, respectively. For DC, respective estimates were 0.28 to 0.64, 0.37 to 0.60, 0.30 to 0.48 and 0.29 to 0.53. For DLA, they ranged from 0.47 to 0.56 with energy content and from 0.50 to 0.74 with BCS. Of special interest was the genetic correlation of NEC with DH (0.54) and DC (0.48). Results suggest that indirect measures of body energy have the strongest genetic association with cow fertility. NEC and early lactation (circa day 50) BCS and energy content are the most useful traits for selection in terms of the correlated improvement in a cows capacity to resume her reproductive activity post partum. © 2009 The Animal Consortium.


Kapell D.N.R.G.,Sustainable Livestock Systems Group | Ashworth C.J.,Sustainable Livestock Systems Group | Ashworth C.J.,Roslin Institute | Knap P.W.,PIC Germany GmbH | Roehe R.,Sustainable Livestock Systems Group
Livestock Science | Year: 2011

Genetic parameters for survival at birth, litter size, birth weight and its variation within litter have been estimated in dam (D1, D2 and D3) and sire lines (S1 and S2) and genetic associations among these traits were examined. Genetic parameters, calculated as posterior means, were estimated at piglet (D1 and D2; 23,565 piglets) and litter level (all lines; 3497 litters) using a Bayesian approach. Posterior means of heritabilities for survival at piglet level (SVBP) were consistently low at 0.01, 0.06 to 0.07 and 0.04 to 0.06 for direct (h2d), maternal (h2m) and total (h2t) genetic effects, respectively, with positive posterior means of correlations between the direct and maternal effect (rg-dm). For survival at litter level (SVBL) heritabilities were between 0.05 and 0.20, with highest estimates in lines with lowest birth weight. For individual piglet birth weight (IBW) heritabilities were substantially higher than for SVBP, ranging from 0.13 to 0.19 (h2d), 0.16 to 0.28 (h2m) and 0.08 to 0.28 (h2t). Heritabilities for average litter birth weight (ALBW) ranged from 0.23 to 0.34, while heritabilities for variation of birth weight within litter (STD) ranged from 0.10 to 0.27. Heritabilities for number born in total (NBT) ranged from 0.11 to 0.16. Genetic associations between SVBL and NBT varied from favourable at 0.39 (D1) to unfavourable at -0.22 (D2). Genetic correlations of SVBL with ALBW and STD were mostly favourable (0.22 to 0.55 and -0.18 to -0.52, respectively) except for SVBL-ALBW in D1 (-0.50) and SVBL-STD in S2 (0.48). In D1 favourable genetic correlations were estimated between direct or maternal effects of SVBP and IBW whereas those for D2 were unfavourable. Consistently negative correlations were estimated between direct effects of SVBP and maternal effects of IBW. Adjustment for NBT resulted in slightly higher h2d and h2m for SVBP, with unfavourable rg-dm.Selection for survival is expected to be successful because all lines showed considerable variation for this trait and relatively high heritabilities, in particular in lines with low ALBW. Maternal heritabilities of IBW were mostly at moderate magnitude and thus of interest for selection. For most lines, the correlations between traits indicate that selection on either IBW or ALBW is indirectly increasing survival at birth. The variation in heritabilities among lines indicates that the strategy of selection for an optimal birth weight with lowest variation within litter should be considered per line individually to maximise overall genetic improvement in piglet survival and growth. © 2010 Elsevier B.V.


Masri A.Y.,Sustainable Livestock Systems Group | Lambe N.R.,Sustainable Livestock Systems Group | Macfarlane J.M.,Sustainable Livestock Systems Group | Brotherstone S.,University of Edinburgh | And 2 more authors.
Meat Science | Year: 2011

This study evaluated the effects of the ovine c.*1232. G > A myostatin mutation (MM) on carcass traits in heterozygous crossbred lambs sired by Texel and Poll Dorset rams using ultrasound, CT scanning, carcass classification and VIA. In experiment 1, MM was associated with increased loin depth (+. 2.8%) and area (+. 3.2%). MM-carriers had significantly higher CT-estimated lean weight and proportion (2 to 4%) and muscle to bone ratio (by ~. 3%), in both experiments, and muscle to fat ratio (28%) in experiment 2. Muscle areas in three cross-sectional CT scans, were higher (2 to 5%) in MM-carriers. In experiment 2, fat-related measurements were significantly lower in MM-carrier lambs but this was not seen in experiment 1. A significant increase in muscle density, indicative of lower intramuscular fat, in MM-carriers shows that meat quality characteristics need attention. Carrying MM significantly decreased carcass fat scores. VIA did not detect any significant MM effects. © 2010 The American Meat Science Association.


Wall E.,Sustainable Livestock Systems Group | Simm G.,Sustainable Livestock Systems Group | Moran D.,Land economics and Environmental Research Group
Animal | Year: 2010

Genetic improvement of livestock is a particularly effective technology, producing permanent and cumulative changes in performance. This paper highlights some of the options for including mitigation in livestock breeding schemes, focusing on ruminant species, and details three routes through which genetic improvement can help to reduce emissions per kg product via: (i) improving productivity and efficiency, (ii) reducing wastage in the farming system and (iii) directly selecting on emissions, if or when these are measurable. Selecting on traits that improve the efficiency of the system (e.g. residual feed intake, longevity) will have a favourable effect on the overall emissions from the system. Specific examples of how genetic selection will have a favourable effect on emissions for UK dairy systems are described. The development of breeding schemes that incorporate environmental concerns is both desirable and possible. An example of how economic valuation of public good outcomes can be incorporated into UK dairy selection indices is given. This paper focuses on genetic selection tools using, on the whole, currently available traits and tools. However, new direct and indirect measurement techniques for emissions will improve the potential to reduce emissions by genetic selection. The complexities of global forces on defining selection objectives are also highlighted.© 2010 The Animal Consortium.


Miedema H.M.,Roslin Institute | Cockram M.S.,University of Prince Edward Island | Dwyer C.M.,Sustainable Livestock Systems Group | Macrae A.I.,Roslin Institute
Applied Animal Behaviour Science | Year: 2011

Dairy cows require individual monitoring around the time of calving to identify any calving difficulties or health problems as early as possible. To assist with the monitoring of parturition, it would be beneficial to understand the behaviour of dairy cows that is associated with normal calving. This study systematically quantified the behaviour of cows to identify what changes in behaviour occur during the 24. h before normal calving compared with that quantified during pre-calving observations during late pregnancy. The behaviour of twenty Holstein-Friesian cows was recorded for 24. h prior to the calf being expelled and for a 24-hour control period during late pregnancy. Continuous focal observations from video recordings were used to quantify daily frequencies and durations of behaviours. Comparisons were made between daily totals recorded in the 24. h before calving and during the control period and each observation was also divided into four six-hour periods to help determine the time when changes occurred before calving. Segmented regression lines were also fitted to identify the point when behaviour changed before calving.The frequencies of lying and tail raising showed consistent increases in the final six-hour period before calving and a significant break point in their segmented regressions. Durations of lying, walking, eating and ground-licking, and number of walking bouts, did not show consistent changes at the time of calving. This study has shown that counting tail raises or transitions between standing and lying could potentially be useful predictors of calving within the following six hours. © 2011 Elsevier B.V.


Miedema H.M.,Roslin Institute | Cockram M.S.,University of Prince Edward Island | Dwyer C.M.,Sustainable Livestock Systems Group | Macrae A.I.,Roslin Institute
Applied Animal Behaviour Science | Year: 2011

The individual monitoring of dairy cows around the time of calving is important to identify calving difficulties or health problems as early as possible. This study aims to identify whether there are differences in the behaviour before calving, between heifers and cows, and between those that are assisted at calving and those that are not. Behavioural recordings of Holstein-Friesian cows and heifers were made before and during calving. Video recordings from 12 cows and 12 heifers were selected so that half of each group were observed to have calved without assistance and the other half were identified as having been assisted at calving. To compare the 12. h prior to the calf being expelled with a 12-h control period during late pregnancy, continuous focal observations were made from the video recordings to quantify frequencies and durations of behaviours during 2-h periods. An increased duration of tail raising was observed before calving and this was seen earlier in heifers, from 4. h before calving, compared with only 2. h before calving in cows. Lying frequency increased as calving approached from 6. h before calving in unassisted animals, but only during the final 2. h before calving in assisted animals. These results show important differences between heifers and cows in their pre-calving behaviour which must be taken into account when predicting the time of calving from behaviour. However, for those animals that subsequently required assistance, no behavioural early-warning signs of a difficult calving were identified. © 2011 Elsevier B.V.


Doeschl-Wilson A.B.,Sustainable Livestock Systems Group | Doeschl-Wilson A.B.,Roslin Institute | Davidson R.,Animal Health Group | Conington J.,Sustainable Livestock Systems Group | And 3 more authors.
Genetics | Year: 2011

Previous studies have shown that host genetic heterogeneity in the response to infectious challenge can affect the emergence risk and the severity of diseases transmitted through direct contact between individuals. However, there is substantial uncertainty about the degree and direction of influence owing to different definitions of genetic variation, most of which are not in line with the current understanding of the genetic architecture of disease traits. Also, the relevance of previous results for diseases transmitted through environmental sources is unclear. In this article a compartmental genetic-epidemiological model was developed to quantify the impact of host genetic diversity on epidemiological characteristics of diseases transmitted through a contaminated environment. The model was parameterized for footrot in sheep. Genetic variation was defined through continuous distributions with varying shape and degree of dispersion for different disease traits. The model predicts a strong impact of genetic heterogeneity on the disease risk and its progression and severity, as well as on observable host phenotypes, when dispersion in key epidemiological parameters is high. The impact of host variation depends on the disease trait for which variation occurs and on environmental conditions affecting pathogen survival. In particular, compared to homogeneous populations with the same average susceptibility, disease risk and severity are substantially higher in populations containing a large proportion of highly susceptible individuals, and the differences are strongest when environmental contamination is low. The implications of our results for the recording and analysis of disease data and for predicting response to selection are discussed. © 2011 by the Genetics Society of America.

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