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* Sustainable Livestock Systems Group, Scottish Agricultural College, Edinburgh, EH9 3JG, United Kingdom
Institute of Evolutionary Biology, University of Edinburgh, West Mains Road, Edinburgh, EH9 3JT, United Kingdom
1 Corresponding author: marie.haskell{at}sac.ac.uk
| ABSTRACT |
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Key Words: genotype x environment interaction life span herd environment
| INTRODUCTION |
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Investigating the extent of GxE, particularly those for which reranking occurs, is important for a number of reasons. Quantifying the degree of environmental sensitivity shown by individual sires provides information on the performance of their daughters in different FE and allows us to identify sires as specialists (those ranking highly in certain FE) or generalists (those ranking similarly across FE). For the individual farmer, breeding decisions could be improved if information were available on the suitability of sires for particular FE. Identifying genotypes that are unsuitable for specific FE is important in terms of health and welfare. Additionally, international bull evaluations currently treat each country as a single entity in terms of FE (Schaeffer, 1994; Banos and Sigurdsson, 1996), despite large countries having great variation in the production systems used and small neighboring countries having similar FE (Weigel and Rekaya, 2000; Zwald et al., 2003). If FE or management system could be used in bull evaluations rather than geographical boundaries, it would improve the accuracy of calculating international breeding values.
To assess the extent of environmental sensitivity, environmental factors must be quantified (possibly on a continuous scale), and then the relationship between FE and the trait or traits of interest can be explored. A number of methods for quantifying the FE exist. In some studies, a single aspect of the FE has been used (Cromie et al., 1998; Ravagnolo and Misztal, 2000; Mulder et al., 2004), whereas others have incorporated multiple environmental factors, such as cows per herd, milk production, and rainfall, into a single environmental score (e.g., Weigel and Rekaya, 2000; Zwald et al., 2003; Bryant et al., 2005; Windig et al., 2005).
Random regression models have often been used to investigate environmental sensitivity in production and fertility traits (e.g., Kolmodin et al., 2002; Calus and Veerkamp, 2003; Hayes et al., 2003; Bryant et al., 2006; Windig et al., 2006). However, the effect of FE on the health of dairy cattle is also important to investigate, because it may indicate that some FE are unsuitable for particular genotypes. Using the bulk tank SCS as a measure of FE, Calus et al. (2006) found significant GxE when SCS during early lactation were assessed. Health- and welfare-related traits, such as longevity, often appear to show lower genetic correlations across countries in international evaluations than do production traits, suggesting that these traits may be more sensitive to differences in FE (Mark, 2004).
The aims of this study were 1) to derive a useful categorization of herds in the United Kingdom by obtaining detailed information from farmers on their management and feeding systems, 2) to relate this fine-scale, farm-level data to information available at the national level to provide a definition of FE, and 3) to assess the effect of FE on life span.
| MATERIALS AND METHODS |
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A total of 1,273 questionnaires from across Great Britain were returned. Of the surveys returned, 6.7% were from farms with a majority of cows that were not Holstein, Holstein-Friesian, or British Friesian. These farms were excluded from further analyses. A question on the number of acres the farm covered was included, but the range of answers returned indicated that the question was not framed correctly to obtain the information required or that the question had been misunderstood. Tables 1
and 2
show the means, ranges, and scales for the responses to the questionnaire. A number of relevant variables, such as length of the housing period (month cows in to month cows out to pasture), and the length of the calving period (1 season vs. 2 seasons vs. all year round) were calculated from the answers. To calculate values when the farmers answer was categorical, such as the ratio of cows to staff members, the midpoint of the category was used. Because a number of farmers had not entered answers to some of the questions, the analyses were based on 778 complete questionnaires.
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Analysis of the Farmer Questionnaire
A principal components analysis (PCA) with a correlation matrix was used to analyze the data (Jobson, 1992). The results of these analyses are often represented in graphs showing the position (or loading) of each of the input variables with respect to the principal components, which are drawn as the axes. For our study, the response to each question was entered as a separate input variable into the PCA, as were the land class of the farm and the weather variables for the nearest weather station. An initial analysis of the weather variables showed that the air temperature, soil temperature, and hours of sunshine were closely associated, and the mean summer, mean winter, and yearly mean figures for each variable were very similar. Therefore, only the mean temperature and mean rainfall were used in subsequent analyses. No other clusters of data were found. Examination of the eigenvalues indicated that 2 of the components explained more of the variation in the data than did the others, so interpretation of the results focused on these 2 components.
Data from the National MRO
Traits chosen to describe the FE at the national level were herd averages for milk, fat, and protein yields; average age at first calving; and average herd size. In addition, we used farm postal codes recorded on the MRO databases to locate the meteorological station nearest the farm and so obtain the relevant average annual temperature and average annual rainfall.
Lactation 1 to lactation 5 305-d production records of calvings between 1998 and 2004 were extracted from the national database. This time period was chosen to reflect the current dairy cattle breeding population. After deleting first-lactation records when the age at calving was less than 17 mo or greater than 40 mo and deleting herds with fewer than 5 first-lactation cows, 1,221,475 production records from 3,886 herds remained.
For each herd, the average age at first calving and herd size were calculated. Herd solutions for milk, fat, and protein yields were obtained by using the following fixed effects model:
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where y is the milk, fat, or protein yield of the ith cow, µ is the overall mean, lac is the effect of the jth lactation(j = 1, 2, . . . 5), ßj is the regression coefficient associated with age at calving within lactation j, ymk is the effect of the kth year-month of calving, herdl is the effect of the lth herd, and e is the random residual error. Age at calving was expressed as a within-lactation deviation from the mean ages of 30 mo (lactation 1), 44 mo (lactation 2), 58 mo (lactation 3), 72 mo (lactation 4), and 86 mo (lactation 5), and herd solutions were adjusted to lactation 2 equivalents.
Canonical Correlation Analysis of Questionnaire and National Data
Our aim was to assess the relationship between variables from the questionnaire data and variables from national data. A canonical correlation analysis is a generalization of multiple regression that allows one to investigate the relationship between 2 sets of variables. Given a set of G-variables and a set of F-variables, one can calculate the correlation between any given linear combination of the G-variables with a given linear combination of the F-variables. The maximum value of this correlation (because the coefficients of the linear combinations are allowed to vary) is the first canonical correlation, and the corresponding linear combinations of G and F are the first canonical variables. The second canonical correlation and variables are defined as the set of variables, uncorrelated with the first set, that have the maximum correlation, and so on.
The G-variables in this analysis were available for all farms and comprised herd solutions for milk, fat, and protein yields; age at first calving; herd size; temperature; and rainfall. The F-variables, specific to the farms in the survey, were chosen because they had high loadings on the first dimension of the PCA analysis, and were further refined by consultation with farm experts to reflect the different farming systems. The variables were months outside, number of cows, regular veterinary visits (0 = no, 1 = yes), and amount of concentrates fed (t/cow per yr).
Farms in the survey were matched to the national data by using herd numbers. Many herd numbers were incorrectly specified on the survey forms, and national data were obtained on only 419 of the possible 778 survey farms. The canonical correlation analysis was therefore based on G- and F-variables from these 419 herds.
Life Span Analysis
The life span of a cow can be considered an overall indicator of the health of the animal in a specific FE and, to some extent, is a measure of how well the animal is matched to her FE. Life span data (Brotherstone et al., 1997) were extracted for daughters of approximately 11,000 sires in 3,879 national herds calving between 1998 and 2004. Because this created an extremely sparse sire x herd (SxH) incidence table, the data were reduced to records of daughters of the 1,000 most widespread sires. After this reduction, the number of herds per sire varied from 26 to more than 1,000, and the total number of daughters with data was
400,000. To avoid the consequences of length-biased sampling, the life span of each cow was measured from the year she entered the data window of 1998 to 2004. For example, a cow calving for the first time in 1996 and dying in 2000 was credited with lactations only during or after 1998.
We fitted 2 models to the data. Model [1] fitted sire, herd, and SxH as random effects:
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where Yijk is the life span score for the kth daughter of sire i in herd j. Model [2] was obtained from model [1] by adding
Gj and (si –
)Gj, where Gj is the FE score for herd j, and si is the sensitivity for the ith sire. The herd and SxH terms remain, and in model [2] represent residual effects (herd or SxH effects unexplained by overall regression on Gj or variation in the slope of that regression). Retaining these terms is important in preserving the correct variance-covariance structure in the mixed model. Omitting them would create an inhomogeneous residual variance and possibly biased tests of other fixed and random effects in the model.
Model [2] is a random regression model (Schaeffer and Dekkers, 1994) with a random intercept and slope for each sire. The covariance between intercept and slope was included in the model.
| RESULTS |
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The corresponding canonical correlation between F and G was 0.62. The first canonical F-variate could be interpreted as a measure of system input, with large values corresponding to high-input farms (high concentrate usage, frequent veterinary visits, a large number of cows that spend a lower than average time out at grass). The corresponding G-variate could be used for the same purpose with the larger sample of farms selected from the MRO databases.
Life Span Analysis
Table 3
shows the estimated variance components for the model omitting environmental sensitivity (model [1]) and for the model including environmental sensitivity (model [2]). The sire variance was the same for both models. The reduction in the herd term for model [2] represents the contribution of the overall regression to the herd variance. Similarly, the reduction in the SxH term represents the contribution of the variation in the slope of the regression to the SxH variance. This explained about 4.5% of the SxH interaction.
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| DISCUSSION |
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The survey farms provided data that could be used to measure system input directly. The purpose of the canonical correlation analysis was to find a way to measure system input on national farms. Because data on key variables, such as months outside and veterinary visits, were not available, this had to be indirect. The signs of the coefficients of the first canonical F-variable (from survey data) were such that the F-variable could be interpreted as a direct measure of system input. High concentrate use, frequent veterinary visits, large herd size, and a short time out on grass all contributed to a large F-variable, and vice versa. There was no simple interpretation for the corresponding first canonical G-variable (from national data). Nevertheless, the substantial correlation of 0.62 between the 2 variables suggests G as a potentially useful indirect measure of system input.
In the life span analysis, the variance components from model [1] imply a heritability for life span of 0.08 ± 0.005. This across-herd heritability is consistent with the value used in the national genetic evaluations (Brotherstone et al., 1997) and is similar to other estimates (Harris et al., 1992; Short and Lawlor, 1992). The genetic correlation between life span in 2 randomly chosen herds was estimated from model [1] as the ratio of the sire variance component to the sum of the sire plus SxH components (see equation [22.12b] on page 671 of Lynch and Walsh, 1998). The correlation of 0.44 ± 0.018 was clearly significantly less than 1.0. With model [2], the genetic correlation between life span in 2 herds depended on the FE score (x, y) in those herds. A contour plot over the region –3 < (x, y) < +3 (corresponding roughly to the range of G in the data) showed that the correlation is fairly constant at approximately 0.4 to 0.5 when x = y, but that it falls away to approximately 0.1 to 0.2 as x – y
± 3 (and x + y = 0). In other words, model [2] predicts relatively low genetic correlations between 2 herds when each is at opposite extremes on the scale of G, whereas model [1] predicts the same correlation whatever the values of G.
The regression on G explained a small but statistically significant proportion of the SxH variance. Despite the small proportion of variance explained, we were able to identify sires showing evidence of contrasting sensitivities. Both specialist and generalist sires were observed. Kolmodin et al. (2002) also found significant variation between sires in their sensitivity to the FE; they observed that sires with high genetic merit for production were more sensitive to changes in the production FE than sires that had lower genetic merit for production. The presence of environmental sensitivity presents an opportunity for farmers to choose sires based on their own farm type. This may improve dairy cow welfare, because farmers would be able to choose animals that perform well, in terms of health and production, on their own type of farm. Variation among sires has also been shown in production traits (Hayes et al., 2003) and in fertility (Oseni et al., 2004).
The results also suggest that the daughters of some sires live longer in low-input FE than in high-intensity production FE, suggesting that these sires are producing daughters suited to low-input FE. Other studies have shown that health and production varies with FE, but low-intensity FE are not always favored. There is also variation in performance within a herd. For instance, Windig et al. (2005) found that herds with a high level of production had lower average SCC than herds with a low level of production. However, the highest producing cows within these herds had greater SCC. Calus et al. (2005) also showed that herds with high average protein production had lower levels of mastitis, lower SCC, and higher BCS than herds with low average protein, but high-producing animals in these herds had slightly poorer fertility.
If certain FE have adverse affects on health, this raises an animal welfare issue. It would appear that the daughters of certain sires can cope with poorer FE, and this would assist the breeding decisions of farmers. However, further assessment of these animals is necessary to ensure that the apparent coping has no other, as yet unquantified, health or welfare costs. When considering production traits, many authors have concluded that GxE effects need not be considered in the implementation of a breeding program (Boettcher et al., 2003; Calus and Veerkamp, 2003; Kearney et al., 2004). However, the results from the present study and from one assessing SCC (Calus et al., 2006) suggest that environmental information might be taken into account when considering health traits.
Throughout the paper, we have left open the question of how to select sires. There are several possibilities. One could ignore the sensitivity and select in the usual way on the average performance over all FE. As a theoretical possibility, one could also ignore the average performance and select based purely on sensitivity, although it is hard to envisage circumstances under which this would be sensible. Most likely, one would take both aspects of performance into account. One way to do this would be to plot the sensitivity BLUP (y) against average performance BLUP (x) for each candidate bull, and select from a desired subset (e.g., top right). This has long been a common practice among plant breeders (Finlay and Wilkinson, 1963). If selecting for a particular type of FE (with score G), one would select on the basis of x + G x y.
| CONCLUSIONS |
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| ACKNOWLEDGEMENTS |
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Received for publication December 20, 2006. Accepted for publication June 28, 2007.
| REFERENCES |
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