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* Facultad de Zootecnia, Universidad Autónoma de Chihuahua, Chihuahua, Chih. 31031, México
Campus Montecillo, Colegio de Postgraduados, 56230 Montecillo, Texcoco, Edo. de México, México
Asociación Mexicana de Criadores de Ganado Romosinuano y Lechero Tropical, Tuxpan, Veracruz 92801, México
Department of Dairy Science, University of Wisconsin-Madison, Madison 53706
# Departamento de Zootecnia, Universidad Autónoma Chapingo, Chapingo 56230, México
1 Corresponding author: esantellano{at}uach.mx
| ABSTRACT |
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Key Words: random regression lactation genetic parameter Tropical Milking Criollo
| INTRODUCTION |
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Use of test-day yields instead of 305-d lactation production has become common in genetic evaluation of dairy animals (Jensen, 2001). Test-day models have several advantages over traditional lactation models. These include the ability to account for environmental effects on each test day (thus accounting for environmental signals that change over time), as well as the possibility of modeling individual cow lactations (Jensen, 2001; Strabel et al., 2005). Although the use of test-day models implies analysis of larger data sets and possibly more parameters than for a traditional 305-d lactation model, they have already been developed and utilized in many countries (Strabel et al., 2005).
Random regression test-day models (RRTDM), suggested by Schaeffer and Dekkers (1994), are appealing because all test-day records of an animal are utilized and genetic evaluation of persistency is a direct byproduct given that breeding values can be predicted at any point of lactation (Jamrozik et al., 1997). In addition, test-day records can be used to derive early predictors of genetic merit (Jaffrézic and Minini, 2003). In tropical areas, where data on milk production are generally scarce, efficient use of all information available is especially important (Carvalheira et al., 1998; Ilatsia et al., 2007).
Different functions have been applied in RRTDM. Lactation functions, such as Wilminks function (Wilmink, 1987), are common choices because their parameters can be easily related to the characteristics of the lactation curve shape (Druet et al., 2003; Cobuci et al., 2005; Ilatsia et al., 2007). On the other hand, orthogonal polynomials are appealing in RRTDM, because covariance structures derived from orthogonal polynomials do not involve assumptions about the shape of the trajectory other than those implicit in the choice of order of approximation (Meyer and Kirkpatrick, 2005). Legendre polynomials, proposed by Kirkpatrick et al. (1990), have been used extensively in RRTDM analyses. Legendre polynomials have several attractive features, such as the following: 1) the polynomials are orthogonal, which is useful for analyzing patterns of genetic variation (Kirkpatrick et al., 1990); 2) covariates have small magnitudes (standardized unit of time, from –1 to +1), which decrease problems with rounding errors (Schaeffer, 2004); 3) missing records can be predicted with an acceptable accuracy (Pool and Meuwissen, 1999); and 4) a higher-order regression is often estimable when conventional polynomials fail because of properties that allow for improved convergence in iterative algorithms (Pool and Meuwissen, 1999). The objectives of this research were to infer genetic parameters of lactation in TMC cattle and to compare 5 different random regression functions for test-day analyses.
| MATERIALS AND METHODS |
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The initial database contained 2,026 lactations from 588 TMC cows that calved between 1974 and 2006. Records were discarded if they fell in either of the following cases: lactations with fewer than 3 test-day records, observations under disease status, lactations in which the calf was not used to induce let-down, the records of a cow for the same lactation were in 2 different herds, and records before 6 or after 400 DIM. After these edits, 15,377 test-day records from 1,438 multilactations (356 first lactation, 282 second, 238 third, and 562
fourth lactation), of 467 cows were used for the analysis. There were 119 sires and 602 dams in the pedigree. The 11.8% of sires had daughters with records simultaneously in Mexico and Nicaragua, and the 34.5% of the Mexican cows with records were connected directly with at least 1 Nicaraguan cow with records by means of a common parent (i.e., paternal half-sister). The proportion of sires to cows was large because of the importance to avoid mating-related animals and consanguinity, given that this population was small. Moreover, we had eliminated several cows from the original database because they did not have the test-day records (in many cases, the only information available was the total production by lactation). A common practice in TMC is to continue to milk the cow beyond 305 d, because small amounts of milk per cow are still valuable in the tropical dairy unit. Figure 1
shows the distribution of number of test-day records and mean milk yield along lactation. The numbers of test-day records after 305 DIM was smaller than for other stages of lactation.
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where yijklq:t = the qth observation on the lth animal at time t; HYSi, TSj, and Parityk = the fixed effects of herd-year-calving season i, test-day season j, and parity k; fk (t) = a fixed regression function on time that accounts for an average trajectory of yield across all animals within parity k;
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2 that was assumed to be a constant in the interval from 6 to 400 DIM. All random effects were assumed to be normally distributed.
The fixed effects were the same for all RRTDM and included the following: herd-year-calving season with 165 levels, test-day season with 4 levels (December to February, March to May, June to August, and September to November), and parity with 4 levels (1, 2, 3, and
4). Because of the limited number of test-day records available for TMC cattle, all available lactations for each cow were considered.
The lactation curve in TMC data seems to be flatter (with an earlier or null peak) than for breeds from temperate conditions. The scatterplots for individual and groups of cows were reviewed, and an earlier examination of lactation curve shapes was carried out using local regression (LOESS), a nonparametric approach (Cleveland and Loader, 1996), in which first- and second-order polynomials (with span = 0.4) seemed to fit the data well. In this form, we decided to decrease the order of polynomials in the random regression models, and 5 random regression functions were chosen for this study. The first model used random regression covariables as in Wilminks function (Wilmink, 1987), and the other 4 used covariables defined through Legendre polynomials (Kirkpatrick et al., 1990). In brief: WI = Wilminks function for both additive genetic and permanent environmental effects; L11 = La(1) + Lp(1); L12 = La(1) + Lp(2); L21 = La(2) + Lp(1); and L22 = La(2) + Lp(2), where the number in parentheses gives the order of the Legendre polynomial for the additive genetic effect (La) or permanent environmental effect (Lp). Fixed regression functions were Wilminks function for WI (β0 + β1 x W1 + β2 x W2, where W1 = DIM/10 and W2 = e–0.05W1) and second-order Legendre polynomial for models L11, L12, L21, and L22 (β0 + β1 x L1 + β2 x L2). The jth-order Legendre polynomials at time t were calculated as:

where [j/2] denotes that fractional values are rounded down to the nearest integer, k involves regression coefficients, and qt is standardized days at time t, ranging from –1 to 1 (Kirkpatrick et al., 1990). The standardized days qt were computed as
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where tmin and tmax = the smallest and largest values of time (tmin = 6, tmax = 400). Fixed regressions were fitted (nested) within parity for each cow.
The residual variance (VR) and Akaike information criterion (AIC; Akaike, 1973) were used for model comparison. In addition, the likelihood ratio test was used to compare nested models using Legendre polynomials. The shapes of estimated variances along lactation and correlations among different DIM were examined. Variance components, solutions of location effects, and likelihoods were estimated using the AIREMLF90 package for Legendre polynomial models. The Wilmink function estimations were obtained from the REMLF90 package, because the model did not converge when using AIREMLF90 (Misztal et al., 2002).
Estimates of the (co)variance matrices among random regression coefficients for the additive genetic effects (
a) were utilized to calculate additive genetic (co) variances along lactation from the covariance function f (ti, ti') = z(ti)'
a z(ti'), where z(ti) and z(ti') = the vectors of covariates evaluated at times ti and ti'. An equivalent procedure was applied to calculate the permanent environmental (co)variances.
| RESULTS |
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Heritability and Repeatability
As a consequence of different estimates of VG and VPE, estimated heritabilities and repeatabilities were different between models. In general, heritability of test-day milk yield ranged from 0.18 to 0.45 across lactation. Differences in estimated heritabilities among Legendre polynomials models were observed at the edges of the lactation, which were similar to those in VG. Standard errors for heritability in the model using first-order Legendre polynomials for additive genetic effect and second-order polynomials for permanent environmental effect (L12) were smaller at the beginning of lactation (0.027 to 0.030) and larger at the ends (0.045 to 0.048). The WI model had a different shape in heritabilities along lactation, and it gave larger heritability estimates. Figure 3
showed the heritabilities and repeatabilities for models WI and L12.
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Genetic and Phenotypic Correlations
Genetic and phenotypic correlations among DIM for most models were, as expected, near unity for adjacent DIM and decreased as the time-lag between the test days increased. Figure 4
displays the genetic correlations between all pairs of DIM throughout lactation for L12 and WI models.
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The trends of phenotypic correlations among DIM were similar to those of genetic correlations. Estimates of phenotypic correlations were greater than genetic correlations, and there was less variation among models. An exception was model L11, and it produced a gentler decay pattern in early and midlactation. Model L11 also gave lower phenotypic correlations in the early and later DIM. Overall, the phenotypic correlations ranged between 0.64 and 0.99 across lactation for most models. Both genetic and phenotypic correlations were positive for all models studied.
Model Comparison
The VR, AIC (Akaike, 1973), and –2 log likelihood for all models are given in Table 1
. Model L12 had the smallest –2 log likelihood value among models using Legendre polynomials. The likelihood ratio tests among nested Legendre polynomials models favored L12 (P < 0.01). In addition, model L12 had the smallest AIC and VR values among the 5 competing models.
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| DISCUSSION |
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Several studies have discussed levels and patterns of daily milk yield heritability obtained using RRTDM (Misztal et al., 2000; Strabel et al., 2005). We observed different trends between the models studied. Models L11 and L22 had less variation throughout lactation, whereas model L12 had smaller estimates at the beginning and then a monotonically increasing trend until the final part of the lactation. Models L21 yielded greater estimates at the edges of lactation and smaller estimates in the middle of lactation. The latter was also reported in Canadian Holsteins under intensive dairy systems (Jamrozik and Schaeffer, 1997). However, this pattern is opposite to other studies with greater heritability in the middle of lactation and lower at the edges (Rekaya et al., 1999; Druet et al., 2003) in Holsteins. On the other hand, the Wilmink model in this study produced a contrasting pattern compared with model L12, which had larger values at the beginning of the lactation and smaller at the end. Behavior of daily milk yield heritabilities with lower values at the beginning of lactation, as in model L12, seem more acceptable, because the first lactation period is influenced by non-genetic effects cumulated before calving.
One of the earliest studies with test-day milk yield records was that of Van Vleck and Henderson (1961) for Holstein cows in the United States. Their estimates of heritability for monthly records were 0.11, 0.17, 0.22, 0.19, 0.19, 0.15, 0.14, 0.14, 0.12, and 0.08 for mo 1 to 10, respectively. Our estimates were larger, and the declining pattern at the end of lactation detected by Van Vleck and Henderson (1961) was different from what we have found in TMC cattle (with the exception of model WI). Estimated heritability of TMC in the midlactation (ranged between 0.20 and 0.25) was similar to that found with RRTDM by López-Romero and Carabaño (2003) for Holstein in the Andalusia and Navarre regions of Spain, and our estimates were smaller than those in the Holsteins in Catalonia in the same study (ranged between 0.35 and 0.40).
Studies of lactation under tropical conditions and using RRTDM are scarce. Carvalheira et al. (1998) used a first-order autoregressive process within and across lactations to account for effects of repeated observations (within cow) in a test-day animal model. Estimates of heritability were 0.13, 0.11, and 0.09 for first, second, and third lactations in Lucerna cattle, a synthetic dual-purpose breed (about 40% of its genes come from Holstein, 30% from Milking Shorthorn, and 30% from Hartón del Valle Creole cattle). According to the authors, 45% of the records were from cows with unknown sires, and the resulting sparse relationship coefficient matrix hampered their estimation of heritability. Morales et al. (1989) reported heritability estimates of 0.12 for 305-d milk yield for the Venezuelan Carora breed (developed from Amarillo de Quebrada Arriba Creole and Brown Swiss). Mackinnon et al. (1996) reported a heritability estimate of 0.09 for 305-d equivalent mature milk yield in a crossbred dairy herd in Kenya (different percentages of Sahiwal, Brown Swiss, and Ayrshire genes). Ilatsia et al. (2007) estimated heritability between 0.28 and 0.52 for Sahiwal cows in Kenya using both univariate and multitrait fixed regression test-day models.
In earlier research conducted in Turrialba, Costa Rica, using Latin American Milking Criollo, Jersey, and their reciprocal F1 crosses and backcrosses, de Alba and Kennedy (1985) found estimates of heritability and repeatability for 305-d milk yield of 0.28 and 0.53, respectively. Later on, de Alba and Kennedy (1994) studied TMC and their crosses with several breeds (Holstein, Canadienne, Brown Swiss, Jersey, and native Mexican cows) in Tamaulipas, Mexico, and reported a heritability of 0.17 for 305-d milk yield and a repeatability of 0.44. Recently, Rosendo-Ponce and Becerril-Pérez (2002) reported heritability and repeatability for 305-d milk yield at 0.17 and 0.50, respectively, for purebred TMC herds in Mexico.
From previous studies, heritability estimates of milk yield from cows in the tropics tend to be smaller than those in temperate regions. However, our estimates for TMC cattle under tropical environments do not differ greatly from other breeds in temperate conditions. This may be attributed to random regression models that better account for variation between environmental conditions in tropical grazing dairy systems.
In our study, model L12 had the greatest genetic correlations between DIM far apart and produced the largest correlations among DIM at the end of lactation. A similar pattern in genetic correlations has been reported in other studies (Van Vleck and Henderson, 1961; Jakobsen et al., 2002; Cobuci et al., 2005). However, our estimates are larger than those reported by Van Vleck and Henderson (1961) and Cobuci et al. (2005) for Holsteins in the United States and Brazil and are similar in magnitudes to those obtained by Jakobsen et al. (2002) in Danish Holsteins. Genetic correlations obtained in this study are much greater than those reported by Ilatsia et al. (2007) for Sahiwals in Kenya. Large and moderate correlations between initial and final DIM suggest that selection for increased milk yield in early lactation will have a positive effect on yield in late lactation.
Although models using higher-order polynomials have been widely used under temperate environments, because they generally improve the model plausibility, authors mention several problems associated with them. The VG follows more oscillatory patterns, which leads to extreme values at the peripheries of lactation and a negative correlation for the extremes of lactation (Pool et al., 2000; López-Romero and Carabaño, 2003; Strabel et al., 2005). Moreover, the more parameters are used, the less accurately they are estimated, because fewer records are available for each estimate. Unrealistically large estimates of genetic variance for some parts of the lactation may lead to overestimation of the average genetic variance across the whole lactation, and the accuracy in genetic evaluations may be overestimated (Strabel et al., 2005). In this sense, results obtained here for TMC cattle, based on an early exploration of a data set and statistically valid comparison criteria, imply an important first step for alternative RRTDM for tropical dairy conditions in Mexico and Central America.
| CONCLUSIONS |
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| ACKNOWLEDGEMENTS |
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| FOOTNOTES |
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Received for publication May 8, 2007. Accepted for publication June 27, 2008.
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