Effect of transgenerational environmental condition on genetics parameters of Italian Brown Swiss.

The aim of this study was to infer the effects of heat stress (HS) of dams during late gestation on direct and maternal genetic parameters for traits related to milk production and milk quality parameters (90,558 records) in Italian Brown Swiss cattle (12,072 cows in 617 herds). Daily average temperature-humidity indices (THI) during the last 56 d of pregnancy were calculated, using the climate data from the nearest public weather station for each herd. Heat load effects were considered as the average across the entire periods considering a thermoneutrality condition for data below the THI 60. For parameter estimation a random regression model using the second-order Legendre polynomial regression coefficient for THI considering both animal and maternal effect for heat load. Direct heritability increased sharply from THI 60 to 65, then decreased gradually up to THI ∼72, and sharply thereafter. Maternal heritability showed a different trend, with values close to 0 up until to THI 65 and slightly increasing toward extreme THI values. The study suggests a lower threshold of THI 60 for the onset of HS. Higher heritability values indicate greater selective efficiency in the THI range of 65 to 70, even if a higher standard deviation value have been detected. The effects of high THI during intrauterine life varied among traits with different heritability levels. Genetic correlations for milk, fat, and protein content at 60 THI with increasing value of environmental variable, remained constant (∼0.90) until THI >75, where they slightly decreased (∼0.85). Fat and protein yields, as well as milk and energy-corrected milk, showed correlations dropping to 0.80 around THI 67 to 68 and stabilizing between 0.75 and 0.85 at extreme THI values. Maternal component correlations dropped close to zero, with negative values for protein content at THI 65 to 70. Antagonism between direct and maternal components was stronger for intermediate THI values but less divergent for extremes. Genotype by environment interaction was observed, indicating the selection of resilient animals would be theoretically possible. In the future, the application of climate variables in selection schemes first should take into account the dimensions of the genetic correlations to be able to decide between the simple inclusion of the environmental effect in the statistical models, rather than a real parallel genetic evaluation.

Genotype by environment interaction due to heat stress in Brown Swiss cattle.

Due to its geographical position and a highly variable orography, Italy is characterized by several climatic areas and thus, by many different dairy cow farming systems. Brown Swiss cattle, in this context, are a very appreciated genetic resource for their adaptability and low metabolic requirement. The significant heterogeneity in farming systems may consist of genotype by environment (G × E) interactions with neglected changes in animals' rank position. The objective of this study was to investigate G × E for heat tolerance in Brown Swiss cattle for several production traits (milk, fat, and protein yield in kilograms; fat, protein, and cheese yield in percentage) and 2 derivate traits (fat-corrected milk and energy-corrected milk). We used the daily maximum temperature-humidity index (THI) range, calculated according to weather stations' data from 2008 to 2018 in Italy, and 202,776 test-day records from 23,396 Brown Swiss cows from 639 herds. Two different methodologies were applied to estimate the effect of the environmental variable (THI) on genetic parameters: (1) the reaction norm model, which uses a continuous random covariate to estimate the animal additive effect, and (2) the multitrait model, which splits each production pattern as a distinct and correlated trait according to the first (a thermal comfort condition), third (a moderate heat stress condition), and fifth (a severe heat stress condition) mean THI value quintile. The results from the reaction norm model showed a descending trend of the additive genetic effect until THI reached the value of 80. Then we recorded an increase with high extreme THI values (THI 90). Permanent environmental variance at increasing THI values revealed an opposite trend: The plot of heritability and the ratio of animal permanent environmental variance to phenotypic variance showed that when the environmental condition worsens, the additive genetic and permanent environmental component for production traits play a growing role. The negative additive genetic correlation between slope and linear random coefficient indicates no linear relationship between the production traits or under heat stress conditions, except for milk yield and protein yield. In tridimensional wireframe plots, the extreme margin decreases until a minimum of ∼0.90 of genetic correlation in the ECM trait, showing that the magnitude of G × E interaction is greater than the other traits. Genetic correlation values in Brown Swiss suggest the possibility of moderate changes in animals' estimated breeding value in heat stress conditions. Results indicated a moderate G × E interaction but significant variability in sire response related to their production level.

Short communication: Genetic aspects of milk urea nitrogen and new indicators of nitrogen efficiency in dairy cows.

Milk urea nitrogen (MUN), a trait routinely measured in the national milk recording system, is a useful indicator of nitrogen utilization efficiency of dairy cows, and selection for MUN and MUN-derived traits could be a valid strategy to produce better animals with regard to efficiency of nitrogen utilization. Therefore, the aim of the present study was to explore the genetic aspects of MUN and new potential indicators of nitrogen efficiency, namely ratios of protein to MUN, casein to MUN, and whey protein to MUN, in the Italian Brown Swiss population. A total of 153,175 test-day records of 10,827 cows in 500 herds were used for genetic analysis. Variance components and heritability of the investigated traits were estimated using single-trait repeatability animal models, whereas genetic and phenotypic correlations between the traits were estimated through bivariate repeatability animal models, including fixed effects of herd-test-date, stage of lactation, parity, calving year, and calving season, and the random effects of additive genetic animal, cow permanent environment, and the residual. Heritability estimates for MUN (0.20 ± 0.01) and the 3 new indicators of nitrogen utilization efficiency (0.15 ± 0.01 for protein-to-MUN and casein-to-MUN ratios, and 0.12 ± 0.01 for ratio of whey protein to MUN) suggested that additive genetic variation exists for these traits, and thus there is potential to select for greater organic nitrogen and lower inorganic nitrogen in milk. Genetic association between MUN and the 3 ratios was high (-0.87 ± 0.01) but not unity, suggesting that ratios could provide some further information beyond that provided by MUN with regard to efficiency of nitrogen utilization. Genetic trend of the investigated traits by year of birth of Brown Swiss sires showed how the selection applied in the last 30 yr has led to an increase of both quantity and quality of milk, and a decrease of somatic cell score and MUN. The inclusion of MUN in breeding programs could speed up the process of increasing organic nitrogen such as protein, which is useful for cheese-making, and reducing inorganic nitrogen (MUN) in milk.

Genome-wide association study for cheese yield and curd nutrient recovery in dairy cows.

Cheese production and consumption are increasing in many countries worldwide. As a result, interest has increased in strategies for genetic selection of individuals for technological traits of milk related to cheese yield (CY) in dairy cattle breeding. However, little is known about the genetic background of a cow's ability to produce cheese. Recently, a relatively large panel (1,264 cows) of different measures of individual cow CY and milk nutrient and energy recoveries in the cheese (REC) became available. Genetic analyses showed considerable variation for CY and for aptitude to retain high proportions of fat, protein, and water in the coagulum. For the dairy industry, these characteristics are of major economic importance. Nevertheless, use of this knowledge in dairy breeding is hampered by high costs, intense labor requirement, and lack of appropriate technology. However, in the era of genomics, new possibilities are available for animal breeding and genetic improvement. For example, identification of genomic regions involved in cow CY might provide potential for marker-assisted selection. The objective of this study was to perform genome-wide association studies on different CY and REC measures. Milk and DNA samples from 1,152 Italian Brown Swiss cows were used. Three CY traits expressing the weight (wt) of fresh curd (%CYCURD), curd solids (%CYSOLIDS), and curd moisture (%CYWATER) as a percentage of weight of milk processed, and 4 REC (RECFAT, RECPROTEIN, RECSOLIDS, and RECENERGY, calculated as the % ratio between the nutrient in curd and the corresponding nutrient in processed milk) were analyzed. Animals were genotyped with the Illumina BovineSNP50 Bead Chip v.2. Single marker regressions were fitted using the GenABEL R package (genome-wide association using mixed model and regression-genomic control). In total, 103 significant associations (88 single nucleotide polymorphisms) were identified in 10 chromosomes (2, 6, 9, 11, 12, 14, 18, 19, 27, 28). For RECFAT and RECPROTEIN, high significance peaks were identified in Bos taurus autosome (BTA) 6 and BTA11, respectively. Marker ARS-BFGL-NGS-104610 (∼104.3 Mbp) was highly associated with RECPROTEIN and Hapmap52348-rs29024684 (∼87.4 Mbp), closely located to the casein genes on BTA6, with RECFAT. Genomic regions identified may enhance marker-assisted selection in bovine cheese breeding beyond the use of protein (casein) and fat contents, whereas new knowledge will help to unravel the genomic background of a cow's ability for cheese production.

Genome-wide association of coagulation properties, curd firmness modeling, protein percentage, and acidity in milk from Brown Swiss cows.

Cheese production is increasing in many countries, and a desire toward genetic selection for milk coagulation properties in dairy cattle breeding exists. However, measurements of individual cheesemaking properties are hampered by high costs and labor, whereas traditional single-point milk coagulation properties (MCP) are sometimes criticized. Nevertheless, new modeling of the entire curd firmness and syneresis process (CFt equation) offers new insight into the cheesemaking process. Moreover, identification of genomic regions regulating milk cheesemaking properties might enhance direct selection of individuals in breeding programs based on cheese ability rather than related milk components. Therefore, the objective of this study was to perform genome-wide association studies to identify genomic regions linked to traditional MCP and new CFt parameters, milk acidity (pH), and milk protein percentage. Milk and DNA samples from 1,043 Italian Brown Swiss cows were used. Milk pH and 3 MCP traits were grouped together to represent the MCP set. Four CFt equation parameters, 2 derived traits, and protein percentage were considered as the second group of traits (CFt set). Animals were genotyped with the Illumina SNP50 BeadChip v.2 (Illumina Inc., San Diego, CA). Multitrait animal models were used to estimate variance components. For genome-wide association studies, the genome-wide association using mixed model and regression-genomic control approach was used. In total, 106 significant marker traits associations and 66 single nucleotide polymorphisms were identified on 12 chromosomes (1, 6, 9, 11, 13, 15, 16, 19, 20, 23, 26, and 28). Sharp peaks were detected at 84 to 88 Mbp on Bos taurus autosome (BTA) 6, with a peak at 87.4 Mbp in the region harboring the casein genes. Evidence of quantitative trait loci at 82.6 and 88.4 Mbp on the same chromosome was found. All chromosomes but BTA6, BTA11, and BTA28 were associated with only one trait. Only BTA6 was in common between MCP and CFt sets. The new CFt traits reinforced the support of MCP signals and provided with additional information on genomic regions that might be involved in regulation of the coagulation process of bovine milk.

Genetic analysis of rennet coagulation time, curd-firming rate, and curd firmness assessed over an extended testing period using mechanical and near-infrared instruments.

The aims of this study were (1) to analyze rennet coagulation time (RCT), curd-firming rate, and curd firmness obtained by extending the standard 30-min testing time to 45 min; (2) to estimate heritabilities of the aforementioned traits determined by mechanical (Formagraph; Foss Electric, Hillerød, Denmark) and near-infrared optical (Optigraph; Ysebaert, Frépillon, France) instruments, and to assess the statistical relevance of their genetic background by using the Bayes factor procedure, the deviance information criterion, and the mean squared error; (3) to estimate phenotypic and genetic relationships between instruments within trait and between traits within instrument; and (4) to obtain correlations for sire rankings based on the used instruments. Individual milk samples were collected from 913 Brown Swiss cows reared in 63 herds located in Trento Province (Italy). Milk coagulation properties (MCP) were measured using 2 different instruments: Formagraph and Optigraph. Both instruments were housed in the same laboratory and operated by the same technician. Each sample was analyzed simultaneously on each instrument. All experimental conditions (milk temperature and the concentration and type of rennet) were identical. For the analysis, univariate and bivariate animal models were implemented using Bayesian methods. Univariate analyses were conducted to test the hypothesis that the traits showed additive genetic determination. Deviance information criterion, Bayes factor, and mean squared error were used as model choice criteria. The main results were that (1) RCT could be measured on all samples by extending the observation time to 45 min, and its genetic parameters (h(2)=0.23) and breeding values could be estimated while avoiding the bias of noncoagulating samples; (2) curd-firming rate could be measured on almost all milk samples, and its genetic parameters could be estimated for the first time on a field data set (h(2)=0.21); (3) for the first time, genetic parameters of curd firmness 45 min after rennet addition (h(2)=0.12) were estimated, and they were compared with curd firmness 30 min after rennet addition (h(2)=0.17); and (4) MCP estimated using the Optigraph appeared to be genetically different from those determined by Formagraph, with the partial exception of RCT (genetic correlation=0.97). Breeding strategies for the improvement of MCP must be planned with caution. Currently, the high throughput, ease of use, and reduced costs of analysis make predictions obtained from mid-infrared spectroscopy (MIRS) on untreated milk samples a promising alternative to produce relevant data at the population level. The use of mechanical lactodynamographs to establish reference data for MIRS calibrations have been already studied, whereas the use of near-infrared optical lactodynamographs as a reference method for MIRS calibrations needs to be investigated.

Prediction of genomic breeding values for dairy traits in Italian Brown and Simmental bulls using a principal component approach.

The large number of markers available compared with phenotypes represents one of the main issues in genomic selection. In this work, principal component analysis was used to reduce the number of predictors for calculating genomic breeding values (GEBV). Bulls of 2 cattle breeds farmed in Italy (634 Brown and 469 Simmental) were genotyped with the 54K Illumina beadchip (Illumina Inc., San Diego, CA). After data editing, 37,254 and 40,179 single nucleotide polymorphisms (SNP) were retained for Brown and Simmental, respectively. Principal component analysis carried out on the SNP genotype matrix extracted 2,257 and 3,596 new variables in the 2 breeds, respectively. Bulls were sorted by birth year to create reference and prediction populations. The effect of principal components on deregressed proofs in reference animals was estimated with a BLUP model. Results were compared with those obtained by using SNP genotypes as predictors with either the BLUP or Bayes_A method. Traits considered were milk, fat, and protein yields, fat and protein percentages, and somatic cell score. The GEBV were obtained for prediction population by blending direct genomic prediction and pedigree indexes. No substantial differences were observed in squared correlations between GEBV and EBV in prediction animals between the 3 methods in the 2 breeds. The principal component analysis method allowed for a reduction of about 90% in the number of independent variables when predicting direct genomic values, with a substantial decrease in calculation time and without loss of accuracy.

Genetic evaluations for measures of the milk-flow curve in the Italian Brown Swiss population.

The objective of this study was to estimate heritabilities and genetic correlations between milk-release parameters, somatic cell score, milk yield, and udder functional traits in the Italian Brown Swiss population. Data were available from 37,511 cows over a span of 12 yr (1997-2008) from 1,592 herds. Milking flows were recorded for each individual once during lactation. Three different analyses were performed to estimate variance components for all the traits of interest. The first analysis included single control data milk yield, somatic cell score, maximum milk flow, average milk flow, time of plateau, decreasing time, and total milking time, whereas the second analysis included milk-release parameters as well as total udder score, udder depth, and 305-d milk yield and somatic cell score as dependent variables. The third analysis included total milking time, 305-d milk yield and somatic cell score, total udder score, udder depth, and ratios of maximum milk flow over total milking time (R1), time of plateau (R2), and decreasing time (R3) to estimate the relationship between the shape of the milk-release curves and important milking traits. Results from the first and second analysis found similar heritabilities for milkability traits ranging from 0.05 to 0.41 with genetic correlations between production traits and flow traits ranging from low to moderate values. Positive genetic correlations were found among production, somatic cell score, and milkability traits. The third analysis showed that R1 had the greatest heritability of the ratio traits (0.37) with large genetic correlations with R2 and R3, a low correlation with 305-d somatic cell score, and no correlation with 305-d milk yield. Estimated responses to selection over 5 generations were also calculated using different indexes, which included either flow or ratio traits. The results of this study show that it is possible to use information collected through portable flowmeters to improve milkability traits. Using a set of variables or traits to describe the overall release of milk can be an advantageous selection strategy to decrease management costs while maintaining milk production.

Short communication: characterization of a monoclonal antibody for kappa-casein B of cow's milk.

A monoclonal antibody (antik-B) against an oligopeptide of 23 AA corresponding to the region 131-153 of bovine kappa-casein (kappa-CN) B was generated using the Human Combinatorial Antibody Library (HuCAL) technology. Both AA substitutions distinguishing kappa-CN A and B are located in that region (positions 136 and 148). In this study, the reactivity of antik-B to milk samples collected from cows previously genotyped as CSN3*AA, CSN3*AB, and CSN3*BB was tested. According to Western blot results, antik-B recognized kappa-CN B and it showed no cross-reactivity toward kappa-CN A and other milk proteins. Furthermore, a modified Western blot method, urea-PAGE Western blot, was set up to assess the reactivity of antik-B toward all isoforms of kappa-CN B. In conclusion, antik-B was specific to kappa-CN B in milk and it seemed to be reactive toward all its isoforms.

Quantitative trait loci affecting milk yield and protein percentage in a three-country Brown Swiss population.

Quantitative trait loci (QTL) mapping projects have been implemented mainly in the Holstein dairy cattle breed for several traits. The aim of this study is to map QTL for milk yield (MY) and milk protein percent (PP) in the Brown Swiss cattle populations of Austria, Germany, and Italy, considered in this study as a single population. A selective DNA pooling approach using milk samples was applied to map QTL in 10 paternal half-sib daughter families with offspring spanning from 1,000 to 3,600 individuals per family. Three families were sampled in Germany, 3 in Italy, 1 in Austria and 3 jointly in Austria and Italy. The pools comprised the 200 highest and 200 lowest performing daughters, ranked by dam-corrected estimated breeding value for each sire-trait combination. For each tail, 2 independent pools, each of 100 randomly chosen daughters, were constructed. Sire marker allele frequencies were obtained by densitometry and shadow correction analyses of 172 genome-wide allocated autosomal markers. Particular emphasis was placed on Bos taurus chromosomes 3, 6, 14, and 20. Marker association for MY and PP with a 10% false discovery rate resulted in nominal P-values of 0.071 and 0.073 for MY and PP, respectively. Sire marker association tested at a 20% false discovery rate (within significant markers) yielded nominal P-values of 0.031 and 0.036 for MY and PP, respectively. There were a total of 36 significant markers for MY, 33 for PP, and 24 for both traits; 75 markers were not significant for any of the traits. Of the 43 QTL regions found in the present study, 10 affected PP only, 8 affected MY only, and 25 affected MY and PP. Remarkably, all 8 QTL regions that affected only MY in the Brown Swiss, also affected MY in research reported in 3 Web-based QTL maps used for comparison with the findings of this study (http://www.vetsci.usyd.edu.au/reprogen/QTL_Map/; http://www.animalgenome.org/QTLdb/cattle.html; http://bovineqtl.tamu.edu/). Similarly, all 10 QTL regions in the Brown Swiss that affected PP only, affected only PP in the databases. Thus, many QTL appear to be common to Brown Swiss and other breeds in the databases (mainly Holstein), and an appreciable fraction of QTL appears to affect MY or PP primarily or exclusively, with little or no effect on the other trait. Although QTL information available today in the Brown Swiss population can be utilized only in a within family marker-assisted selection approach, knowledge of QTL segregating in the whole population should boost gene identification and ultimately the implementation and efficiency of an individual genomic program.

Estimation of genetic parameters for perinatal sucking behavior of Italian Brown Swiss calves.

Brown Swiss breeders sometimes experience difficulties in feeding calves because of the weak sucking ability of the calves in the early days of life. For the welfare of the calves, they should be suckled by their dams or should aggressively ingest colostrum immediately after birth. The composition of colostrum changes rapidly during the first few days of lactation, and the ability of calves to absorb the Ig decreases quickly as well. The aim of this study was to increase our knowledge of environmental and genetic components affecting the sucking response, to evaluate the possibility of selecting for this trait. Sucking ability was recorded in 3 categories (drank from the milk bucket nipple or bottle without help, drank with help, did not drink) at 5 post-natal meals (6, 12, 24, 48, and 72 h from birth). Records were analyzed with 2 different models: a single-trait threshold sire model, in which all observations were analyzed as a single trait with 5 levels, and a multiple-trait threshold liability sire model, in which meal-by-meal observations were analyzed as 5 different binary traits. Management procedures, the interval between birth and meals, parity, and season of birth were environmental factors affecting the variability in sucking ability. The heritability estimate for the single-trait analysis was 0.14, whereas heritabilities for the multiple-trait analysis were 0.26, 0.22, 0.21 0.12, and 0.13 for the first, second, third, fourth, and fifth meal, respectively. Estimated genetic correlations among traits were high (0.82 to 0.99). This study suggests the possibility of selection based on sucking ability. Future collection of larger data sets on the sucking response of calves in the first 2 meals after birth would increase the accuracy of genetic parameter estimates.