Fabiola Canavesi

Relationship between somatic cell count and functional longevity assessed using survival analysis in Italian Holstein–Friesian cows

The relationship between somatic cell scores (SCS) and longevity was assessed for Italian Holstein–Friesian dairy cows using survival analysis. The data of somatic cell count (SCC) test day information of 512 979 cows were provided by nine provinces from Northern Italy. Pedigree information was extracted from the national herd book. Two survival models were run: a model similar to the one used for genetic evaluation on length of productive life, and a second one adding the phenotypic level of ten classes of test-day SCS of the cow. A cow with a test-day in the highest class of phenotypic level for SCS had more than three times greater risk of being culled when compared to risk for the class with the lowest SCS level. The genetic correlation between the risk of being culled and SCS was estimated to be 0.31, based on the correlation between sire EBV. The rank of bulls resulting from the genetic evaluation on survival did not change significantly with the inclusion of SCS in the model (rank correlation of 0.98). It is concluded that the phenotypic level of SCS plays an important role in culling decision of farmers of Italian Holstein–Friesian dairy cows and SCS is genetically associated to the functional longevity of cows.

Genetic Correlation Patterns Between Somatic Cell Score and Protein Yield in the Italian Holstein-Friesian Population

Genetic parameters for somatic cell score (SCS) in the Italian Holstein-Friesian population were estimated addressing the pattern of genetic correlation with protein yield in different parities (first, second, and third) and on different days in milk within each parity. Three approaches for parameter estimation were applied using random samples of herds from the national database of the Italian Holstein Association. Genetic correlations for lactation measures (305-d protein yield and lactation SCS) were positive in the first parity (0.31) and close to zero in the second (0.01) and third (0.09) parities. These results indicated that larger values of SCS were genetically associated with increased production. The second and third sets of estimates were based on random regression test-day models, modeling the shape of lactation curve with the Wilmink function and fourth-order Legendre polynomials, respectively. Genetic correlations from both random regression models showed a specific pattern associated with days in milk within and across parities. Estimates varied from positive to negative in the first and second parity, and from null to negative in the third parity. Patterns were similar for both random regression models. The average overall correlation between SCS and protein yield was zero or slightly positive in the first lactation and ranged from zero to negative in later lactations. Correlation estimates differed by parity and stage of lactation. They also demonstrated the dubiousness of applying a single genetic correlation measure between SCS and protein in setting selection strategies. Differences in magnitude and the sign of genetic correlations between SCS and yields across and within parities should be accounted for in selection schemes.

A genome scan for quantitative trait loci affecting milk somatic cell score in Israeli and Italian Holstein cows by means of selective DNA pooling with single- and multiple-marker mapping.

Mastitis is an important and common dairy cattle disease affecting milk yield, quality, and consumer safety as well as cheese yields and quality. Animal welfare and residues of the antibiotics used to treat mastitis cause public concern. Considerable genetic variation may allow selection for increased resistance to mastitis. Because of high genetic correlation to milk somatic cell score (SCS), SCS can serve as a surrogate trait for mastitis resistance. The present study intended to identify quantitative trait loci (QTL) affecting SCS in Israeli and Italian Holstein dairy cattle (IsH and ItH, respectively), using selective DNA pooling with single and multiple marker mapping. Milk samples of 4,788 daughters of 6 IsH and 7 ItH sires were used to construct sire-family high- and low-tail pools, which were genotyped at 123 (IsH) and 133 (ItH) microsatellite markers. Shadow correction was used to obtain pool allele frequency estimates. Frequency difference between the tails and empirical standard error of D, SE(D), were used to obtain P-values. All markers significant by single marker mapping were also significant by multiple marker mapping, but not vice versa. Combining both populations, 22 QTL on 21 chromosomes were identified; all corresponded to previous reports in the literature. Confidence intervals were set by chi-squared drop method. Heterozygosity of QTL was estimated at 44.2%. Allele substitution effects ranged from 1,782 to 4,930 cells/mL in estimated breeding value somatic cell count units. Most (80%) of the observed variation in estimated breeding value somatic cell score could be explained by the QTL identified under the stringent criteria. The results found here can be used as a basis for further genome-wide association studies for the same trait.

Genome-wide association study for somatic cell score in Valdostana Red Pied cattle breed using pooled DNA

BackgroundMastitis is a major disease of dairy cattle occurring in response to environmental exposure to infective agents with a great economic impact on dairy industry. Somatic cell count (SCC) and its log transformation in somatic cell score (SCS) are traits that have been used as indirect measures of resistance to mastitis for decades in selective breeding. A selective DNA pooling (SDP) approach was applied to identify Quantitative Trait Loci (QTL) for SCS in Valdostana Red Pied cattle using the Illumina Bovine HD BeadChip.ResultsA total of 171 SNPs reached the genome-wide significance for association with SCS. Fifty-two SNPs were annotated within genes, some of those involved in the immune response to mastitis. On BTAs 1, 2, 3, 4, 9, 13, 15, 17, 21 and 22 the largest number of markers in association to the trait was found. These regions identified novel genomic regions related to mastitis (1-Mb SNP windows) and confirmed those already mapped. The largest number of significant SNPs exceeding the threshold for genome-wide significant signal was found on BTA 15, located at 50.43-51.63 Mb.ConclusionsThe genomic regions identified in this study contribute to a better understanding of the genetic control of the mastitis immune response in cattle and may allow the inclusion of more detailed QTL information in selection programs.

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.

A whole genome scan for QTL affecting milk protein percentage in Italian Holstein cattle, applying selective milk DNA pooling and multiple marker mapping in a daughter design

We report on a complete genome scan for quantitative trait loci (QTL) affecting milk protein percentage (PP) in the Italian Holstein-Friesian cattle population, applying a selective DNA pooling strategy in a daughter design. Ten Holstein-Friesian sires were chosen, and for each sire, about 200 daughters, each from the high and low tails of estimated breeding value for PP, were used to construct milk DNA pools. Sires and pools were genotyped for 181 dinucleotide microsatellites covering all cattle autosomes. Sire marker allele frequencies in the pools were obtained by shadow correction of peak height in the electropherograms. After quality control, pool data from eight sires were used for all subsequent analyses. The QTL heterozygosity estimate was lower than that of similar studies in other cattle populations. Multiple marker mapping identified 19 QTL located on 14 chromosomes (BTA1, 2, 3, 4, 5, 6, 8, 9, 12, 14, 17, 20, 23 and 27). The sires were also genotyped for seven polymorphic sites in six candidate genes (ABCG2, SPP1, casein kappa, DGAT1, GHR and PRLR) located within QTL regions of BTA6, 14 and 20 found in this study. The results confirmed or excluded the involvement of some of the analysed markers as the causative polymorphic sites of the identified QTL. The QTL identified, combined with genotype data of these candidate genes, will help to identify other quantitative trait genes and clarify the complex QTL patterns observed for a few chromosomes. Overall, the results are consistent with the Italian Holstein population having been under long-term selection for high PP.

Quantitative trait loci mapping for conjugated linoleic acid, vaccenic acid and ∆9-desaturase in Italian Brown Swiss dairy cattle using selective DNA pooling

A selective DNA pooling approach was applied to identify QTL for conjugated linoleic acid (CLA), vaccenic acid (VA) and Δ(9) -desaturase (D9D) milk content in Italian Brown Swiss dairy cattle. Milk samples from 60 animals with higher values (after correction for environmental factors) and 60 animals with lower values for each of these traits from each of five half-sib families were pooled separately. The pools were genotyped using the Illumina BovineSNP50 BeadChip. Sire allele frequencies were compared between high and low tails at the sire and marker level for SNPs for which the sires were heterozygous. An r procedure was implemented to perform data analysis in a selective DNA pooling design. A correction for multiple tests was applied using the proportion of false positives among all test results. BTA 19 showed the largest number of markers in association with CLA. Associations between SNPs and the VA and Δ(9) -desaturase traits were found on several chromosomes. A bioinformatics survey identified genes with an important role in pathways for milk fat and fatty acids metabolism within 1 Mb of SNP markers associated with fatty acids contents.

Detection of QTL for milk protein percentage in Italian Friesian cattle by AFLP markers and selective genotyping

We targeted quantitative trait loci (QTL) for milk protein percentage (P%) in two Italian Holstein granddaughter design families using selective genotyping in combination with high throughput amplified fragment length polymorphism (AFLP) markers. A total of 64 extreme high and low sires in respect to estimated breeding value (EBV) for P% (EBVP%) were genotyped with 25 AFLP primer combinations that revealed 305 and 291 polymorphisms in the two families. Association between markers and EBVP% was investigated by a linear model only on bands having paternal origin (105 and 96 AFLP bands in family D and S, respectively). Although no marker was significantly associated with the target trait after correction for multiple comparisons, 17 AFLP markers, significant without correction for multiple tests, were considered suggestive of the presence of a QTL. Eleven of these were successfully located on six Bos taurus (BTA) chromosomes by radiation hybrid or in-silico mapping. Ten of these mapped in the immediate neighbourhood (less than 10 cM) of already described QTL for P%. Suggestive association was verified in four regions by microsatellites analysis: one on BTA 10; one on BTA 28; and two on BTA 18. Microsatellites identified significant effects by single marker and interval mapping analyses on BTA 10 and BTA 28, while they were only suggestive of the presence of QTL on BTA 18. In summary, our results firstly indicate that AFLP markers may be used to seek QTL exploiting a selective genotyping approach in GDD, a wide used experimental design in cattle; secondly, propose two approaches for AFLP mapping, namely in-silico mapping exploiting most updated release from the bovine whole genome sequencing project, and physical mapping exploiting a panel of Bovine/Hamster Radiation Hybrids; and thirdly, provide new information on QTLs for an economic important trait in a never investigated Holstein cattle population. AFLP in combination with selective genotyping can be a useful strategy for QTL searching in minor livestock species, sometimes having large economic impact in marginal areas, where more informative markers are still poorly developed.

Bimodality and the genetics of milk flow traits in the Italian Holstein-Friesian breed

The overall goal of this study was to investigate milk flow traits in Italian Holstein-Friesian cows and, in particular, the bimodality of milk flow, defined as delayed milk ejection at the start of milking. Using a milkometer, 2,886 records were collected from 133 herds in northern Italy from 2001 to 2007. All records included 5 time-period measurements for milk flow, somatic cell score (SCS), milk yield, 8 udder type traits, and the presence or absence of bimodality in milk flow. Genetic parameters were estimated using linear animal models for continuous traits such as milk flow, udder type, SCS, and milk production, whereas bimodality was analyzed as a categorical trait. With the exception of decreasing time (which had a very small heritability value of 0.06), heritability values for milk flow traits were moderate, ranging from 0.10 (ascending time) to 0.41 (maximum milk flow). In addition, moderate to high genetic correlations were estimated between total milking time and other time measures (from 0.78 to 0.87), and among time flow traits (from 0.62 to 0.91). The decreasing time was the trait most genetically correlated with udder type traits, with correlation values of 0.92 with rear udder height, 0.85 with rear udder width, and 0.73 with teat placement. Large udders with strong attachments were also associated with greater milk production. Heritability estimated for bimodality was 0.43, and its genetic correlation with milk flow traits and SCS indicated a sizable genetic component underlying this trait. Bimodality was negatively associated with milk production; shorter milking times and greater peak milk levels were genetically correlated with more frequent bimodal flows, indicating that faster milk release would result in an increase in bimodal patterns. The negative genetic correlation of bimodality with SCS (-0.30) and the genetic correlation between milk flow traits and SCS suggest that the relationship between milkability and SCS is probably nonlinear and that intermediate flow rates are optimal with respect to mastitis susceptibility. Quicker milk flow over a shorter period would increase the frequency of bimodal curves in milking, whereas the correlation between bimodality and both ascending and descending time was less clear.

Genetic parameters of fatty acids in Italian Brown Swiss and Holstein cows

The aim of this study was to estimate the genetic parameters and to predict experimental breeding values (EBVs) for saturated (SFA), unsaturated (UFA), monounsaturated (MUFA) and polyunsaturated (PUFA) fatty acids, the ratio of fatty acids, and the productive traits in Italian Brown Swiss (BSW) and Holstein Friesian (HOL) cattle. Test-day yields from 235,658 HOL and 21,723 BSW cows were extracted from the Italian HOL and BSW Associations databases from November 2009 to October 2012 out of 3310 herds. The milk samples collected within the routine milk recording scheme were processed with the Milkoscan™ FT 6500 Plus (Foss, Hillerød, Denmark) for the identification of SFA, UFA, MUFA and PUFA composition in milk. Genetic parameters for fatty acids and productive traits were estimated on 1,765,552 records in HOL and 255,592 records in BSW. Heritability values estimated for SFA, UFA, MUFA and PUFA ranged from 0.06 to 0.18 for the BSW breed and from 0.10 to 0.29 for HOL. The genetic trends for the fatty acids were consistent between traits and breeds. Pearson’s and Spearman’s correlations among EBVs for SFA, UFA, MUFA and PUFA and official EBVs for fat percentage were in the range 0.32 to 0.54 for BSW and 0.44 to 0.64 for HOL. The prediction of specific EBVs for milk fatty acids and for the ratio among them may be useful to identify the best bulls to be selected with the aim to improve milk quality in terms of fat content and fatty acid ratios, achieving healthier dairy productions for consumers.