1,721,019 research outputs found
Application of genomic tools to breeding and to genetic structure studies in livestock populations
Full text linkThis work is organized into a general introduction, four chapters of experimental contributions and general conclusions. Chapter 1 contains the general introduction, aiming to provide a synopsis about genetic application in animal science. Two main topics were debated in this thesis, modern genomic tools applied in animal breeding and animal biodiversity.
The first two experimental contributions (Chapters 2 and 3) concerned animal breeding programs, particularly the first and the last step: variance components and breeding values estimation, respectively. The contribution about variance components estimation was the result of my abroad period at the University of Georgia (USA). Chapter 3 deals with the estimation of heritability and genomic breeding values for milk fatty acid profile.
Regarding the animal biodiversity, two researches were carried out analyzing both cattle and sheep breeds farmed in Italy. Several statistical approaches were used to identify selection signatures in livestock. Chapter 4 analyzed genetic diversity among five cattle breeds: two purebreds and three crossbreeds raised in Sardinia. In the Chapter 5, in order to highlight genome regions that can differentiate livestock production, selection signatures were investigated among different productive aptitudes in the Italian ovine stock.
Finally, the general conclusions reported in Chapter 6 offered a short overview of the main results obtained during the PhD
Past, present, and future developments in single-step genomic models
No full textSingle-step genomic best linear unbiased predictor (ssGBLUP) is a methodology for estimating breeding values jointly for genotyped and non-genotyped animals. Since its development in the early 2010s, ssGBLUP faced challenges like modelling missing pedigrees, efficiently computing accuracies, ensuring the compatibility between genomic and pedigree information, implementing large-scale genetic evaluations, and using non-genotyped animals for genome-wide association studies, among others. Because of the extensive research and the availability of efficient software packages, those challenges for ssGBLUP were solved. Nowadays, ssGBLUP is the chosen methodology estimating values in almost all livestock populations. This review aims to report the progress of ssGBLUP, outline the current state of the art, and hypothesise about the future of this methodology.Highlights Single-step genomic BLUP is the most popular methodology for genetic evaluations including genotyped and non-genotyped animals. The development of theories and efficient software allows to use single-step for virtually any real dataset. Continuous research in single-step will allow the use of massive amount of data like video recording, omics, among others
Functional Odd- and Branched-Chain Fatty Acid in Sheep and Goat Milk and Cheeses
No full textThe inverse association between the groups of odd-chain (OCFA) and branched-chain (BCFA) and the development of diseases in humans have generated interest in the scientific community. In experiment 1, the extent of the passage of odd- and branched-chain fatty acids (OBCFA) from milk fat to fresh cheese fat was studied in sheep and goats. Milk collected in two milk processing plants in west Sardinia (Italy) was sampled every 2 weeks during spring (March, April and May). In addition, a survey was carried out to evaluate the seasonal variation of the OBCFA concentrations in sheep and goats’ cheeses during all lactation period from January to June. Furthermore, to assess the main differences among the sheep and goat cheese, principal component analysis (PCA) was applied to cheese fatty acids (FA) profile. Concentrations of OBCFA in fresh cheese fat of both species were strongly related to the FA content in the unprocessed raw milk. The average contents of OBCFA were 4.12 and 4.13 mg/100 mg of FA in sheep milk and cheese, respectively, and 3.12 and 3.17 mg/100 mg of FA in goat milk and cheese, respectively. The OBCFA concentration did no differed between milk and cheese in any species. The content of OBCFA was significantly higher in sheep than goats’ dairy products. The OBCFA composition of the cheese was markedly affected by the period of sampling in both species: odd and branched FA concentrations increased from March to June. The seasonal changes of OBCFA in dairy products were likely connected to variations in the quality of the diet. The PCA confirmed the higher nutritional quality of sheep cheese for beneficial FA, including OBCFA compared to the goat one, and the importance of the period of sampling in the definition of the fatty acids profile
Investigation of phenotypic, genetic and genomic background of Milk spectra in Sarda dairy sheep
No full textAim of this study was to analyse the genetic background of milk Fourier transform infrared (FTIR) spectra in dairy sheep. Individual milk FTIR spectra, with 1060 wavenumbers each, were available for 793 adult Sarda breed ewes genotyped at 45,813 SNP. The absorbance values of each wavenumber was analysed using a linear mixed model that included dim class, parity and lambing month as fixed effects and flock-test date and animal as random effects. The model was applied to estimate variance components and heritability and to perform a genome-wide association study for each wavenumber. Average h2 of wavenumbers absorbance was 0.13 +/- 0.08, with the largest values observed in the regions associated with the characteristic bonds of carbonylic and methylenic groups of milk fat (h2 = 0.57 at 1724-1728 cm-1; and h2 = 0.34 at 2811-2834 cm-1, respectively). The absorbance values of wavenumbers were moderately correlated with the estimated heritabilities. After the Bonferroni correction, a total of nine markers were found to be significantly associated with 32 different wavenumbers. Of particular interest was the SNP s63269.1, mapped on chromosome 2, that was found to be associated with 27 wavenumbers. Genes previously found to be related to traits of interest (e.g. disease resistance, milk yield and quality, cheese firmness) are located close to the significant SNP. As expected, the heritability estimated for the absorbance of each wavenumbers seems to be associated with the related milk components
Effect of genotyping density on the detection of runs of homozygosity and heterozygosity in cattle
No full textAligning phenotypic and genetic trends: comparing trends from threshold and linear models in pigs
No full textThis study aimed to compare phenotypic and genetic trends when genomic breeding values (GEBV) were computed using linear and threshold models or when GEBV were transformed to the probability scale for wean-to-finish mortality (WFM) and front leg structure (FLS). A total of 270,064 and 998,289 observations were available for WFM measured on crossbred and FLS measured on purebred, respectively. The total number of animals in the analyses was 577,947 for WFM and 1,079,080 for FLS. The number of purebred genotyped animals was 274,365 and 239,075 for WFM and FLS, respectively. Incidences were 9.71% for WFM and 13.31% for FLS. Heritabilities on the observed scale were 0.04 for WFM and 0.23 for FLS, whereas on the liability scale they were 0.08 and 0.38. When using linear models, we applied two approaches to convert GEBV to probabilities: (1) we standardized the GEBV deviated from the mean GEBV based on the additive genetic variance and then transformed them into probabilities; (2) we used an approximation to the liability scale and then transformed the approximated liabilities to the probability scale. Genetic and phenotypic trends were obtained by averaging GEBV and phenotypes based on the birth year for animals with phenotypes. Spearman correlations among raw and transformed GEBV within trait were all ≥0.98, suggesting minimal changes when selecting candidates based on GEBV from linear or threshold models and their transformation to probabilities. The slopes of genetic trends based on raw GEBV from linear models were significantly different from zero. The sign of the slopes suggests that selections have been directed toward desirable phenotypes. After the transformation into the probability scale, genetic trends computed based on GEBV from linear and threshold models aligned the phenotypic trend for FLS. For WFM, the genetic and phenotypic trends showed less alignment, possibly due to the lower trait incidence, low heritability, and susceptibility to environmental influences. The close association between genetic and phenotypic trends for FLS was also confirmed by the slopes of the regressions of GEBV on the probability scale or phenotypes on the year of birth. Results of the present study demonstrated that GEBV from the linear scale can be transformed into the probability scale with a strong alignment with GEBV transformed from the liability scale. Aligning genetic and phenotypic trends, however, depends on the model, heritability, and trait incidence
Use of discriminant statistical procedures for an early detection of persistent lactations in dairy cows
No full textEffect of heat stress on milk production traits and milk coagulation properties in dairy sheep
No full textHeat stress in farmed animals is becoming a problem of great importance even in temperate climates, especially due to the increase in average global temperatures. Previous studies conducted on sheep have reported negative effects of heat stress on milk yield and composition and on the cheesemaking properties. The study of the effect of heat stress in sheep is complicated by the seasonality of calving and the overlap of the effects of the lactation stage with those of the climate. The aim of this work was to study the effects of heat stress in dairy sheep through a repeated measures model, separating the lactation stage and climate effects. The dataset included 2,695 repeated measurements of 555 Sardinian sheep, raised in 34 farms in Sardinia. The analyzed phenotypes were milk yield, fat, protein, lactose and somatic cell contents, milk coagulation properties (rennet clotting time, curd firming time, curd firmness), and individual laboratory cheese yield (ILCY). Temperature and humidity values of the day of the survey and of the 3 previous days were provided by the regional agency for the protection of the environment (Agenzia Regionale per la Protezione dell'Ambiente of the Sardinia Region). Climate data were then used to calculate the respective temperature and humidity indices. The effect of the temperature-humidity index (THI) was evaluated using a linear mixed model that considered stage of lactation (DIM), parity, maximum value of hourly THI calculated over 24 h (THImax) class (divided into quartiles), DIM × THI interaction, and sampling date; the farm and the animal were considered random effects. The DIM × THI interaction was significant for all parameters except somatic cells and curd firmness. Milk yield showed an increase from the first to the third THImax class and a reduction in the fourth class (THI > 73); this trend was the same in the 3 lactation stages (early, mid, and late). Fat content showed an opposite trend, independent of the lactation stage. Proteins decreased linearly at the beginning and mid lactation whereas they showed no significant changes at the end of lactation. Lactose was reduced in the fourth class of THImax, both in mid and late lactation. Rennet clotting time showed different patterns depending on DIM, whereas ILCY showed worse values as THImax increased, especially in early and mid lactation. The study of THI in the different phases of lactation made it possible to separate the 2 effects on the parameters studied and highlighted how in dairy sheep, heat stress leads to a reduction in production and a general worsening of the quality of the milk
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