Genetic parameters and selection for casein content in Italian Holstein and Brown Swiss.

A total of more than 2,000,000 records on casein contents were collected in Lombardia (Italy) during routine milk recording of Italian Holstein and Brown Swiss dairy cows. Variance components for casein were estimated as well as all the genetic correlations of casein with production and type traits considered in selection. According to the heritabilities estimated (12.4% for Brown and 9.36% for Holstein), breeding values were calculated for bulls and compared to the breeding values for total protein. The results of two different selection scenarios were compared for each breed when including protein or casein as selection criterion. Genetic progress expected for all traits selected were compared after 10 years of selection. The genetic variability of casein allows the use of this trait as selection criterion with the estimation of breeding values and its inclusion in selection indexes. Ranking of breeding values for casein and protein are very similar in both breeds. But some differences in genetic values for casein exist for the same level of breeding value for protein. Nevertheless results in genetic gain differ between breeds depending mainly on genetic correlations with the other traits selected. The positive results in selection response estimated for several traits suggest to the Brown Swiss Association the replacement of protein selection with casein. In contrast the smaller effects estimated for the Italian Holstein suggest to wait for more casein data collected before any change in selection program

Evaluation of stallions based on linear description of their daughters

The purpose of our work was an objective evaluation of mares of the Czech warmblood horse based on the linear description, as well as the evaluation of the benefits of stallion breeding based on the linear description of their daughters and - for specific stallions - the evaluation of certain individual exterior traits which are passed on by stallions to their offspring. Stallion horses with at least 7 descendants were used for the evaluation and determination of the values, mares which underwent a linear description of traits at the age of 3 years. For this evaluation we used available data from the year 1996 to 2012, a total including 251 stallions and 4709 mares and more than 500 000 records related to the linear description. The data were gathered from the database of the Central Register of Horse Breeding at Slatiñany in the Czech Republic. These data were manually compiled using Excel 2007 and then processed and evaluated according to the objectives of the present study using the linear model GLM as well as the statistical programme Scheffe. The results of the study showed a convincing statistical influence of the stallions on all the monitored exterior traits analyzed on the mares for the father-factor, and after evaluating all the general exterior traits the statistical difference among the stallions was seen as convincing. We found out that in most cases the breed had no convincing statistical influence on the analyzed traits of the linear description. On the contrary, in terms of the other effects (father and year of measurement) we found a convincing statistical influence on all traits of the linear description. For some stallions we evaluated particular traits of linear description, which they pass on to their female offspring using charts and graphics. Afterwards we compared reciprocally certain stallions according to the traits of the linear description.O

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

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

Analysis of BTA6 in Bruna Italiana and Pezzata Rossa cattle assayed with 2,535 SNPs

A high density SNP marker panel (54,000 SNPs) was used to investigate the genome of 775 Bruna Italiana and 493 Pezzata Rossa bulls. Observed and expected heterozygosities were calculated overall and per chromosome. In both breeds, values were not significantly different. Bos taurus Chromosome 6 (BTA6), carrying the casein loci, was analysed in higher detail. Overall, 2,535 markers were assayed on this chromosome. After discarding monomorphic markers, those having more than 10 missing values, and those having minor allele frequency below 2%, 1,814 and 2,061 SNPs were retained in Bruna Italiana and Pezzata Rossa, respectively. To detect signatures of ancient and recent selection, we calculated FIS inbreeding coefficient values of all BTA6 polymorphic markers, within sliding windows of groups of 5 adjacent SNPs and within 122 adjacent regions spanning 1 Mb intervals. These preliminary analyses indicated that genotyping of several thousand SNPs potentially allows the detection of the footprint of selection dodging the confounding effects of the population demographic history (i.e., effective population size, genetic structure, and mating pattern). A wider understanding of how and where selection shaped patterns of genetic variation along the genome may provide important insights into the dynamics of evolutionary change, facilitating both the identification of functionally significant genomic regions and genotype-phenotype correlations. Outlining such regions could allow focusing the fine mapping strategy to identify candidate genes and causative mutations affecting important economic or adaptive traits

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

Several investigations have recently searched for significant association between gene polymorphisms and milk traits in livestock and model species. In several cases, it remains rather difficult to assess if the observed effects are caused by the mutation tested, by a nearby mutation in the same gene or by a mutation in a different gene or DNA region in linkage disequilibrium with the former. As a consequence, only in a few cases (e.g., κ-casein, SCD, DGAT1) the causative mutation seems to have been identified and, even when evidence is rather clear, genetic heterogeneity and genetic background may influence the size of allele substitution effects. Therefore, the significance of gene-trait associations and the estimate of their effect have to be verified in any new population in which this information is planned to be used, to estimate its actual utility in gene assisted breeding. In the SelMol project, we selected 29 candidate genes on the basis of known relationships between physiological or biochemical processes and evidence of significant association with milk traits in cattle, in related (e.g., sheep and goats) and model (e.g., mouse) species. A total of 106 SNPs were selected, using either information available in literature, or in silico, searching the NCBI dbSNP database. SNPs found significantly associated in other investigations were preferentially targeted. Otherwise non-synonymous SNPs and those in putative control regions (e.g., in promoter binding sites) were selected from dbSNP. If within a gene no SNP having one of these characteristics was available in dbSNP, synonymous SNPs, occurring in introns and untranslated non-control regions were chosen. DNA was extracted from semen of elite sires. SNPs polymorphism was confirmed by screening a panel of 32 individuals each of Pezzata Rossa (PR), Bruna Italiana (BI), and Frisona Italiana (FI) dairy cattle breeds. A total of 73 SNPs were confirmed as polymorphic in at least one breed: 63 in PR, 61 in BI, and 68 in FI. Polymorphic SNPs were genotyped on 400 individuals of PR and 600 of BI. Statistical tests were applied to detect selection sweeps, significant association to EBVs and phenotypic traits related to milk production and quality (milk yield, protein and fat yield and percentage), together with a number of functional traits (fertility, SCS as indicator of mastitis resistance, conformational traits, and milkability)

Estimated breeding values and association mapping for persistency and total milk yield using natural cubic smoothing splines

BackgroundFor dairy producers, a reliable description of lactation curves is a valuable tool for management and selection. From a breeding and production viewpoint, milk yield persistency and total milk yield are important traits. Understanding the genetic drivers for the phenotypic variation of both these traits could provide a means for improving these traits in commercial production.MethodsIt has been shown that Natural Cubic Smoothing Splines (NCSS) can model the features of lactation curves with greater flexibility than the traditional parametric methods. NCSS were used to model the sire effect on the lactation curves of cows. The sire solutions for persistency and total milk yield were derived using NCSS and a whole-genome approach based on a hierarchical model was developed for a large association study using single nucleotide polymorphisms (SNP).ResultsEstimated sire breeding values (EBV) for persistency and milk yield were calculated using NCSS. Persistency EBV were correlated with peak yield but not with total milk yield. Several SNP were found to be associated with both traits and these were used to identify candidate genes for further investigation.ConclusionNCSS can be used to estimate EBV for lactation persistency and total milk yield, which in turn can be used in whole-genome association studies.Klara L. Verbyla and Arunas P. Verbyl

Genetic selection for reduced somatic cell counts in sheep milk: A review

Mastitis is an in\ufb02ammation of the udder, mainly caused by bacteria, and leads to economic loss, due to discarded milk, reduced milk production, reduced milk quality and increased health costs in both dairy sheep and cattle. Selecting for increased genetic resistance to mastitis can be done directly or indirectly, with the indirect selection corresponding to a prediction of the bacteriological status of the udder based on traits related to the infection. The most frequently used indirect method is currently milk somatic cell count (SCC) or somatic cell score (SCS). This review reports the state of the art relating to the genetic basis of mastitis resistance in sheep and explores the opportunities to use SCC as selection criterion in a breeding programme to improve resistance to mastitis in sheep, discussing the actual situation and prospects for improvement. It has been stressed, in particular, that although it is unlikely that selection for mastitis resistance by the farmers on their own will be successful, there is good prospect for genetic improvement if reliable pedigree and performance recording is implemented across \ufb02ocks, combined with breeding value estimation. To achieve this, a strong and well-structured organization to implement and support the programme is essential

Modeling and simulation of a synthetic genetic circuit that implements a multicelled behavior in a growing microcolony of E. coli

Synthetic Biology is a relatively new discipline, born at the beginning of the New Millennium, that brings the typical engineering approach (abstraction, modularity and standardization) to biotechnology. These principles aim to tame the extreme complexity of the various components and aid the construction of artificial biological systems with specific functions, usually by means of synthetic genetic circuits implemented in bacteria or simple eukaryotes like yeast. The cell becomes a programmable machine and its low-level programming language is made of strings of DNA. This work was performed in collaboration with researchers of the Department of Electrical Engineering of the University of Washington in Seattle and also with a student of the Corso di Laurea Magistrale in Ingegneria Biomedica at the University of Bologna: Marilisa Cortesi. During the collaboration I contributed to a Synthetic Biology project already started in the Klavins Laboratory. In particular, I modeled and subsequently simulated a synthetic genetic circuit that was ideated for the implementation of a multicelled behavior in a growing bacterial microcolony. In the first chapter the foundations of molecular biology are introduced: structure of the nucleic acids, transcription, translation and methods to regulate gene expression. An introduction to Synthetic Biology completes the section. In the second chapter is described the synthetic genetic circuit that was conceived to make spontaneously emerge, from an isogenic microcolony of bacteria, two different groups of cells, termed leaders and followers. The circuit exploits the intrinsic stochasticity of gene expression and intercellular communication via small molecules to break the symmetry in the phenotype of the microcolony. The four modules of the circuit (coin flipper, sender, receiver and follower) and their interactions are then illustrated. In the third chapter is derived the mathematical representation of the various components of the circuit and the several simplifying assumptions are made explicit. Transcription and translation are modeled as a single step and gene expression is function of the intracellular concentration of the various transcription factors that act on the different promoters of the circuit. A list of the various parameters and a justification for their value closes the chapter. In the fourth chapter are described the main characteristics of the gro simulation environment, developed by the Self Organizing Systems Laboratory of the University of Washington. Then, a sensitivity analysis performed to pinpoint the desirable characteristics of the various genetic components is detailed. The sensitivity analysis makes use of a cost function that is based on the fraction of cells in each one of the different possible states at the end of the simulation and the wanted outcome. Thanks to a particular kind of scatter plot, the parameters are ranked. Starting from an initial condition in which all the parameters assume their nominal value, the ranking suggest which parameter to tune in order to reach the goal. Obtaining a microcolony in which almost all the cells are in the follower state and only a few in the leader state seems to be the most difficult task. A small number of leader cells struggle to produce enough signal to turn the rest of the microcolony in the follower state. It is possible to obtain a microcolony in which the majority of cells are followers by increasing as much as possible the production of signal. Reaching the goal of a microcolony that is split in half between leaders and followers is comparatively easy. The best strategy seems to be increasing slightly the production of the enzyme. To end up with a majority of leaders, instead, it is advisable to increase the basal expression of the coin flipper module. At the end of the chapter, a possible future application of the leader election circuit, the spontaneous formation of spatial patterns in a microcolony, is modeled with the finite state machine formalism. The gro simulations provide insights into the genetic components that are needed to implement the behavior. In particular, since both the examples of pattern formation rely on a local version of Leader Election, a short-range communication system is essential. Moreover, new synthetic components that allow to reliably downregulate the growth rate in specific cells without side effects need to be developed. In the appendix are listed the gro code utilized to simulate the model of the circuit, a script in the Python programming language that was used to split the simulations on a Linux cluster and the Matlab code developed to analyze the data

Proposal of an udder health genetic index for the Italian Holstein Friesian based on first lactation data

Genetic correlations between udder conformation traits and SCS were estimated in Italian Holstein Friesian data. A total of 1,268,762 first parity Italian Holstein cows had information both on conformation traits and SCC. Test day SCC were transformed to SCS and they were geometrically averaged from 5 to 305 days to obtain a lactation measure (LSCS). Two data sets were analysed. The first data set included 11.203 records and was used in 8 two-trait analyses, considering information on LSCS, and one conformation trait at a time. Models used included the fixed effect of herd-year-season for LSCS, and for conformation traits the fixed effect of herd-year-date of scoring and the interaction of age at calving in months by season of calving. Heritabilities ranged from 0.05 (udder balance) to 0.24 (udder depth) for conformation traits and 0.14 for LSCS. Genetic correlations with LSCS were -0.31 for udder depth and 0.28 for rear udder width. Other genet- ic correlations for conformation traits and LSCS varied from -0.16 to -0.03. A second data set, including 4398 records was extracted to estimate genetic correlations between 5 traits that are being considered for inclu- sion in an udder health index. Using these estimates, and literature estimates for direct mastitis resistance, an udder health index (UHI) for the Italian Holstein was proposed : UHI = -15 EBV SCS + 1.5 EBVFUA + 0.15 EBV UDD, where EBV are the estimated breeding values for SCS, fore udder attachment (FUA), and udder depth (UDD). Selection for lower value of SCS, shallow udder with stronger fore attachment should result in increased mastitis resistance. The inclusion of milking speed in the udder health index was not proposed because of its non-linear relationship with SCS and the low reliability of data collection in Italy for this trait