Attilio Rossoni

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.

Genetic parameters for functional longevity, type traits, somatic cell scores, milk flow and production in the Italian Brown Swiss

The aim of this study was to estimate genetic parameters for a set of new traits and to update values for production and morphological traits to be used in the selection index of Italian Brown Swiss dairy cattle. Longevity, milking speed and somatic cell scores (SCS) were considered for inclusion in the selection index, and (co)variances with all traits of the selection index were estimated. SCS was considered on a lactation basis while milk flow, the amount of milk (kg) released per time unit (minute), was measured with a flowmeter. Cow functional longevity was the total herd life corrected for the production level. A total of 127,416 first lactation records of cows calving from 1985 to 2003 were considered. In order to maximize the number of records available for each combination of traits, 9 data sets were created. Estimates were obtained from multivariate linear sire models with equal design matrix in subsequent separated analysis. REML algorithms and canonical transformation were used to calculate (co)variance estimates among all traits: functional longevity, milking speed, SCS, 5 production traits (milk, fat and protein yield, fat and protein percent), and 19 type traits. Heritabilities estimated were 0.14±0.02 for SCS, 0.33±0.07 for milk flow, and 0.04±0.01 for functional longevity. Genetic correlation values between SCS and milk yield, fat percent and protein percent were 0.18±0.09, −0.19±0.08, and −0.22±0.08, respectively. Functional longevity had a strong positive genetic correlation with udder depth (0.42±0.10) but a negative correlation with rear leg set (−0.56±0.10). Milk flow was positively correlated with most of the production measures: 0.30±0.18 with milk yield, 0.24±0.17 with fat yields, 0.16±0.20 with protein yield. Additionally, milk flow was genetically correlated with some type traits (0.53±0.14 rear udder width, 0.40±0.16 hock quality, 0.32±0.15 rump angle, −0.25±0.19 udder depth). The correlation between SCS and milk flow showed a value of 0.46±0.26, indicating that faster cows are more susceptible to mastitis.

Genetic parameters for casein and urea content in the Italian Brown Swiss dairy cattle

Abstract A total of 137,753 test day records of 20,745 Italian Brown Swiss dairy cows from 26 provinces of Italy were used to estimate heritability for casein and urea content in milk and their genetic correlations with other production traits and milk somatic cell score. Milk component values were obtained by Fourier Transformed Infrared (IR) Spectroscopy from milk samples collected during national routine recording and were analysed using test day repeatability animal models. Fixed effects included 1,001 levels of herd-test date, 15 classes of days in milk, and 13 classes of age at calving within parity. The variation among cows was large for most of the traits. The heritability value for casein content was 0.31, as for protein content, and genetic and phenotypic correlations between these two traits were large (0.99 and 0.97 respectively). Milk urea content had a heritability of 0.17 and a positive genetic relationship with fat (0.12), null with protein (0.03) and casein (0.002) content and a negative genetic correlation with milk yield (-0.17) suggesting that the genetic improvement for milk urea content would be possible, but genetic gain would be affected by other traits included as selection criteria in the economic index and by their relative economic emphasis.

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.

Predicting haplotype carriers from SNP genotypes in Bos taurus through linear discriminant analysis

BackgroundSNP (single nucleotide polymorphisms) genotype data are increasingly available in cattle populations and, among other things, can be used to predict carriers of specific haplotypes. It is therefore convenient to have a practical statistical method for the accurate classification of individuals into carriers and non-carriers. In this paper, we present a procedure combining variable selection (i.e. the selection of predictive SNPs) and linear discriminant analysis for the identification of carriers of a haplotype on BTA19 (Bos taurus autosome 19) known to be associated with reduced cow fertility. A population of 3645 Brown Swiss cows and bulls genotyped with the 54K SNP-chip was available for the analysis.ResultsThe overall error rate for the prediction of haplotype carriers was on average very low (∼≤1%). The error rate was found to depend on the number of SNPs in the model and their density around the region of the haplotype on BTA19. The minimum set of SNPs to still achieve accurate predictions was 5, with a total test error rate of 1.59.ConclusionsThe paper describes a procedure to accurately identify haplotype carriers from SNP genotypes in cattle populations. Very few misclassifications were observed, which indicates that this is a very reliable approach for potential applications in cattle breeding.

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.

Genetics of casein content in Brown Swiss and Italian Holstein dairy cattle breeds

Over 2,000,000 records of casein contents were collected from herds of Brown Swiss (BS) and Italian Holstein Friesian (HF) dairy cows in northern Italy during routine milk recording. Variance components for casein and genetic correlations of casein with production and type traits considered in selection were estimated from a sample of 200,484 test day records for 26,279 BS cows and 376,652 for 41,543 HF cows. A multivariate multi-model REML estimation of variance components was made. Models for production included the fixed effects for herd-test day, year of evaluation, days in milk, month of calving and age at calving within parity. Models for type traits were defined accordingly to the model officially used for each breed for breeding value estimation. Breeding values for casein yield and content were calculated from estimated heritabilities (Brown 0.12; Holstein 0.09). Estimates were similar for protein and casein yield and content while genetic correlations with traits in the actual selection indexes differed between breeds. These differences, together with the greater emphasis now given to protein in the selection index of the Brown Swiss than in the Italian Holstein Friesian, suggest that a direct selection for casein could be more advantageous in Brown than in Holstein cows. The Brown breeders association could soon include casein yield and content directly in their selection criteria while that of Holstein cows would wait for a longer term casein data collection.

Identification and validation of copy number variants in Italian Brown Swiss dairy cattle using Illumina Bovine SNP50 Beadchip

The determination of copy number variation (CNV) is very important for the evaluation of genomic traits in several species because they are a major source for the genetic variation, influencing gene expression, phenotypic variation, adaptation and the development of diseases. The aim of this study was to obtain a CNV genome map using the Illumina Bovine SNP50 BeadChip data of 651 bulls of the Italian Brown Swiss breed. PennCNV and SVS7 (Golden Helix) software were used for the detection of the CNVs and Copy Number Variation Regions (CNVRs). A total of 5,099 and 1,289 CNVs were identified with PennCNV and SVS7 software, respectively. These were grouped at the population level into 1101 (220 losses, 774 gains, 107 complex) and 277 (185 losses, 56 gains and 36 complex) CNVR. Ten of the selected CNVR were experimentally validated with a qPCR experiment. The GO and pathway analyses were conducted and they identified genes (false discovery rate corrected) in the CNVR related to biological processes cellular component, molecular function and metabolic pathways. Among those, we found the FCGR2B , PPARα , KATNAL1 , DNAJC15 , PTK2 , TG , STAT family , NPM1 , GATA2 , LMF1 , ECHS1 genes, already known in literature because of their association with various traits in cattle. Although there is variability in the CNVRs detection across methods and platforms, this study allowed the identification of CNVRs in Italian Brown Swiss, overlapping those already detected in other breeds and finding additional ones, thus producing new knowledge for association studies with traits of interest in cattle.

Genetic parameters estimation and genetic evaluation for longevity in Italian Brown Swiss bulls

Abstract Direct longevity EBV of Italian Brown Swiss sires were predicted using a Weibull proportional hazards model. This trait was defined as the risk of culling from first calving. Records from 511,596 Brown Swiss cows with first calving from 1985 to 2005 were used. The model include fixed (age at first calving) and random (sire’s additive genetic) time independent effects, fixed (herd, parity, quantile of mature equivalent deviation from the yearly herd mature equivalent average, and regression on the dynamic herd size) and random (herd-year with log-gamma distribution) time dependent effects. Predicted breeding values for functional longevity, expressed as relative risk ratios, ranged from 0.58 to 1.69. The EBV were standardized with mean 100 and standard deviation 12. EBV were positively submitted to Interbull trend validation procedure in order to assess EBV variation over time and the possibility of including them in the international exchange of bull indexes.

Assessment of 29 candidate genes for milk traits in Italian dairy cattle

The Italian Bracco is one of the oldest pointing dog breed, used for hunting ever since the Renaissance time; paintings of the 14th century show hunting sceneries with dogs similar to the present day Bracco. The breed has been officially registered by ENCI (the Italian cynological club) in 1949, when the definitive standard was established. In this work, we report the first results of a study aimed at measuring morphological traits in this breed, as a part of a more comprehensive study whose objective is to identify the characters that have the potential of being genetically improved. R. Ciampolini1, F. Cecchi1, A. Bramante1, F. Casetti2, S. Presciuttini1