Comparison of homogeneity and heterogeneity of residual variance using random regression test-day models for first lactation Japanese Holstein cows

Using a large‐scale data set that included first lactation test day records from 1975 to 2000 for Japanese Holsteins, genetic parameters for milk yield were estimated by using random regression (RR) test‐day models (TDM) with heterogeneous and homogeneous residual variances. It is necessary for the RR‐TDM to include a function that explains the shape of the lactation curve. The RR‐TDM with the LW curve, which combined Wilmink's curve and a Legendre polynomial, was used for fitting the model for milk yield. In recent years, increases in residual variance have been noted for Japanese dairy cattle. Thus, three kinds of heterogeneous residual variance over the calving year were considered: H1, H2 and HG. Linear and quadratic exponential functions for the calving year were used in H1 and H2, respectively. Residual variance of HG was divided into five groups according to calving year. Homogeneous residual variance was HO. All heterogeneous residual variances increased with calving year in an almost linear fashion. Residual variance increased over the study period. However, there is no need to consider heterogeneous residual variances in genetic evaluations, because the heterogeneity of residual variance over the years did not affect the ranking of top sires and cows.     

Development of a genomic tool for breed assignment by comparison of different classification models: Application to three local cattle breeds

Assignment of individual cattle to a specific breed can often not rely on pedigree information. This is especially the case for local breeds for which the development of genomic assignment tools is required to allow individuals of unknown origin to be included to their herd books. A breed assignment model can be based on two specific stages: (a) the selection of breed-informative markers and (b) the assignment of individuals to a breed with a classification method. However, the performance of combination of methods used in these two stages has been rarely studied until now. In this study, the combination of 16 different SNP panels with four classification methods was developed on 562 reference genotypes from 12 cattle breeds. Based on their performances, best models were validated on three local breeds of interest. In cross-validation, 14 models had a global cross-validation accuracy higher than 90%, with a maximum of 98.22%. In validation, best models used 7,153 or 2,005 SNPs, based on a partial least squares-discriminant analysis (PLS-DA) and assigned individuals to breeds based on nearest shrunken centroids. The average validation sensitivity of the first two best models for the three local breeds of interest were 98.33% and 97.5%. Moreover, results reported in this study suggest that further studies should consider the PLS-DA method when selecting breed-informative SNPs.     

A comparison of different models for assessing variations in the sero-prevalence of infectious bovine rhinotracheitis by farm, area and district in Kenya

The relative variability of the sero-prevalence of antibodies to infectious bovine rhinotracheitis (IBR) due to cow, farm, and agroecological area levels were investigated for three contrasting districts in Kenya: Samburu, an arid and pastoral area; Kiambu, a tropical highland area; and Kilifi, a typical tropical coastal area. Cattle were selected by two-stage cluster sampling and visited once between August 1991 and 1992. Data on animal, farm, and area factors were analyzed using Schall's algorithm and MLn (multi-level, n-level), two generalized mixed-model programs suitable for multi-level analysis. Most variation in IBR sero-prevalence was from farm-to-furm. This was reflected by the many farm-level fixed effects (farm size, disease control measures and type of breeding) significant in models both ignoring and accounting for single variance components (clustering) at farm, area, and district levels. Area-to-area and district-to-district variations were noted but the area and district variance components were one-third and one-fifth the size of the farm variance components for both methods. As farm-to-farm variation differed markedly by farm size and district, models in MLn were extended to allow for multiple farm-level variance components by these categories. For each, sero-prevalence of IBR increased with age and was significantly decreased on small-sized zero-grazing farms. These models, particularly the model with different farm variance components by districts, fit the data better and highlighted well that there was considerable farm-to-farm variation—differing by district—and that the available farm-level fixed effects did not predict IBR sero-prevalence well.     

An international comparison of different laboratory tests for the diagnosis of bovine leukosis: suggestions for international standardization

A collaborative study was conducted to compare the detection limit of different laboratory tests for antibodies against bovine leukemia virus (BLV). Serum and milk samples were tested in agar gel immunodiffusion (AGID), different modifications of indirect ELISA, blocking ELISA and ELISA procedures using monoclonal antibodies to BLV gp51 or BLV p24. The detection limit of reference serum E4 diluted 2-fold in negative serum gave a median value of 1:16 in AGID, indirect ELISA, and monoclonal ELISA p24, 1:128 in monoclonal ELISA gp51, and 1:1024 in blocking ELISA. The detection limit of a 4% immunoglobulin preparation of E4 diluted in negative milk showed median values of 1:800 in indirect ELISA, 1:1000 in monoclonal ELISA, and 1:2400 in blocking ELISA. None of the ELISA procedures could detect all the positive individual milk samples diluted 1:50. The AGID test is the official reference test for detection of antibodies against BLV. Reference serum E4 diluted 1:10 in negative serum must be scored positive in the AGID test. It is suggested that an international reference serum standard be established rather than an official recommendation of a particular ELISA test.     

Streptothricosis in cattle on the coastal plains of Ghana: A comparison of the disease in animals reared under two different management systems

The prevalence of streptothricosis in selected cattle herds under two different management systems was investigated and related to the presence of various factors which the literature suggests may play a role in its development. The disease was more prevalent on farms with traditional management compared to that on farms with improved management.     

Breeding versus survival: proximate causes of abrupt population decline under environmental change in a desert rodent,the midday gerbil (Meriones meridianus)

Studying abrupt ecological shifts under gradual environmental change caused, in particular, by human activity is important for understanding the fundamental aspects and underlying mechanisms of ecological resilience. One of the rare well‐documented examples of an abrupt ecological shift is the delayed step transition of the population of a desert rodent, the midday gerbil (Meriones meridianus), from high‐abundance (1994–2002) to low‐abundance (2003–2017) regimes. This was in response to landscape transformation from desert to steppe caused by the drastic reduction of livestock in the rangelands of southern Russia after the collapse of the USSR in the early 1990s. In this study, we tested whether demographic parameters were correlated with the observed abrupt downward population shift. We found that reproductive activity (the percentage of breeding females, the number of litters, fecundity and the number of young recruited per female) showed no trend over time and did not differ between periods of high and low abundance. In contrast, the adult sex ratio (SR = males: females) decreased significantly with time and was as much as twice more female‐biased for the low‐abundance population regime. However, SR was not related to any reproductive parameter, including the percentage of breeding females. We conclude that proximate reasons for an abrupt population decline in M. meridianus are not associated with the changes in breeding patterns or mate limitation caused by the Allee effect but relate to the increased mortality as a result of the desert landscape being fragmented by steppezation. The mortality is expected to be higher for males as the mobile and dispersing sex.     

Surgical arthrodesis for the treatment of osteoarthrosis of the proximal intertarsal, distal intertarsal and tarsometatarsal joints in 30 horses: a comparison of four different techniques

Over a period of seven years, 30 horses were treated by surgical arthrodesis for lameness resulting from osteoarthrosis of the proximal intertarsal, distal intertarsal and tarsometatarsal joints (bone and occult spavin). Twenty-five horses were affected in one hock only and five were affected bilaterally. Four different techniques for achieving arthrodesis were used. Fourteen out of 18 horses (78 per cent) with involvement of the distal intertarsal and tarsometatarsal joints only and six out of 11 horses (55 per cent) in which the proximal intertarsal joint was also involved became sound following surgery. The status of one other horse, with involvement of the proximal intertarsal joint, is not known.     

Prediction of crude fat content of longissimus muscle of beef using the ratio of fat area calculated from computer image analysis: comparison of regression equations for prediction using different input devices at different stations

Crude fat content of longissimus (ribeye) muscle of beef cattle was predicted from a ratio of fat area (RFA) to area of ribeye muscle calculated from computer image analysis (CIA). Cross sections of 64 ribeyes taken from the 6-7th rib from cattle at experiment station A and cross sections of 94 ribeyes taken from the 6-7th rib from cattle at Experiment Station B were used in this study. Slices (1 to 1.5 cm in thickness) of just the Longissimus dorsi were homogenized and sampled for chemical estimation of crude fat content using petroleum ether. Crude fat content as determined from chemical analysis was used as the true estimate of fat content. A CCD (charge-coupled device) camera was used as the input device at Experiment Station A, and a single-lens reflex camera was used at Experiment Station B to photograph ribeyes for CIA. The contour comparison method, which assigns a threshold value for each marbling particle, was used to obtain accurate binarization in this study. Minimum and maximum of chemical measurements of crude fat were 2.1 and 39.8%, and for CIA calculation of the RFA were 6.1 and 56.8%, respectively. This range covered almost the complete range of the beef marbling standard used in carcass grading in Japan. The equation for the regression of the crude fat content (Y) on RFA (X) calculated from CIA for all of the data was Y = .793X-3.04 with r2 = .96. Regression equations for prediction of crude fat percentage from RFA taking into consideration the effect of experiment station were Y = .741X-2.22 with r2 = .91 for Experiment Station A, and Y = .782X-2.54 with r2 = .91 for Experiment Station B. Analysis of covariance showed that the effects of experiment stations on intercepts and slopes were not significant (P > .10). The ranges of differences between actual and predicted crude fat content from the prediction equation that was calculated without consideration of the effect of station were -6.4 to 4.0%. CIA of cross sections of the ribeye muscle seems to have potential for prediction of crude fat content.