Combined Use of Univariate and Multivariate Approaches to Detect Selection Signatures Associated with Milk or Meat Production in Cattle.

Objectives: The aim of this study was to investigate the genomic structure of the cattle breeds selected for meat and milk production and to identify selection signatures between them.

Methods: A total of 391 animals genotyped at 41,258 SNPs and belonging to nine breeds were considered: Angus (N = 62), Charolais (46), Hereford (31), Limousin (44), and Piedmontese (24), clustered in the Meat group, and Brown Swiss (42), Holstein (63), Jersey (49), and Montbéliarde (30), clustered in the Milk group. The population stratification was analyzed by principal component analysis (PCA), whereas selection signatures were identified by univariate (Wright fixation index, F) and multivariate (canonical discriminant analysis, CDA) approaches.

Genomic Analysis of Sarda Sheep Raised at Diverse Temperatures Highlights Several Genes Involved in Adaptations to the Environment and Heat Stress Response.

Livestock expresses complex traits influenced by several factors. The response of animals to variations in climatic factors, such as increases in temperature, may induce heat stress conditions. In this study, animals living at different temperatures were compared using the genome-wide Wright fixation index ().

Analysis of ddRAD-seq data provides new insights into the genomic structure and patterns of diversity in Italian donkey populations.

With more than 150 recognized breeds, donkeys assume relevant economic importance, especially in developing countries. Even if the estimated number of heads worldwide is 53M, this species received less attention than other livestock species. Italy has traditionally been considered one of the cradles of European donkey breeding, and despite a considerable loss of biodiversity, today still counts nine autochthonous populations.

Effect of genotyping density on the detection of runs of homozygosity and heterozygosity in cattle.

Runs of homozygosity (ROHom) are contiguous stretches of homozygous regions of the genome. In contrast, runs of heterozygosity (ROHet) are heterozygosity-rich regions. The detection of these two types of genomic regions (ROHom and ROHet) is influenced by the parameters involved in their identification and the number of available single-nucleotide polymorphisms (SNPs).

Investigation of phenotypic, genetic and genomic background of Milk spectra in Sarda dairy sheep.

Aim 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.

Effects of Age, Fulton's Condition Index (K) and Muscle Fat on Total Mercury Content in Raw, Pre-Canning and Canned Samples of Atlantic Bluefin Tuna ().

A total of 30 samples of Atlantic bluefin tuna were analysed for total mercury concentration. Relationships between total mercury content and age, Fulton's condition index (K) and fat content were statistically evaluated. The effect of muscle status (raw, pre-canning, canned) on mercury content was also investigated.

A transgenerational study on the effect of great-granddam birth month on granddaughter EBV for production traits in Italian Simmental cattle.

Heat tolerance is a key feature of resilient animals. Offspring of animals that suffer environmental stress during pregnancy could show physiological, morphological, and metabolic modifications. This is due to a dynamic reprogramming of the epigenetics of the mammalian genome that occurs in the early life cycle.

Dry Matter Intake Prediction from Milk Spectra in Sarda Dairy Sheep.

Individual dry matter intake (DMI) is a relevant factor for evaluating feed efficiency in livestock. However, the measurement of this trait on a large scale is difficult and expensive. DMI, as well as other phenotypes, can be predicted from milk spectra.

Analysis of runs of homozygosity of cattle living in different climate zones.

Aim of this study was to analyze the distribution and characteristics of runs of homozygosity in Bos taurus taurus and Bos taurus indicus breeds, as well as their crosses, farmed all around the world. With this aim in view, we used single-nucleotide polymorphisms (SNP) genotypes for 3,263 cattle belonging to 204 different breeds. After quality control, 23,311 SNPs were retained for the analysis.

Relationship between inbreeding and milk production traits in two Italian dairy sheep breeds.

The effects of inbreeding in livestock species breeds have been well documented and they have a negative impact on profitability. The objective of this study was to evaluate the levels of inbreeding in Sarda (SAR, n = 785) and Valle del Belice (VdB, n = 473) dairy sheep breeds and their impact on milk production traits. Two inbreeding coefficients (F) were estimated: using pedigree (F ), or runs of homozygosity (ROH; F ) at different minimum ROH lengths and different ROH classes.

Study of the Fatty Acid Profile of Milk in Different Sheep Breeds: Evaluation by Multivariate Factorial Analysis.

A multivariate analysis was used to investigate the fatty acid (FA) profile in three different Italian sheep breeds: Comisana, Massese, and Sarda. A sample of 852 animals was considered: 118 Massese, 303 Comisana, 431 Sarda. Sarda sheep were divided into two groups, based on their breeding origin (298 and 133 reared in Sardinia and Tuscany, respectively).

Unravelling the effect of environment on the genome of Sarda breed ewes using Runs of Homozygosity.

Natural adaptation and artificial selection have shaped the genome of modern livestock breeds. Among SNP-based metrics that are used to detect signatures of selection at genome-wide level, runs of homozygosity (ROH) are getting increasing popularity. In this paper, ROH distribution and features of a sample of 823 Sarda breed ewes farmed at different levels of altitude are analysed to investigate the effect of the environment on the patterns of homozygosity.

Investigation of β-hydroxybutyrate in early lactation of Simmental cows: Genetic parameters and genomic predictions.

Genomic information allows for a more accurate calculation of relationships among animals than the pedigree information, leading to an increase in accuracy of breeding values. Here, we used pedigree-based and single-step genomic approaches to estimate variance components and breeding values for β-hydroxybutyrate milk content (BHB). Additionally, we performed a genome-wide association study (GWAS) to depict its genetic architecture.

The Nero Lucano Pig Breed: Recovery and Variability.

The Nero Lucano (NL) pig is a black coat colored breed characterized by a remarkable ability to adapt to the difficult territory and climatic conditions of Basilicata region in Southern Italy. In the second half of the twentieth century, technological innovation, agricultural evolution, new breeding methods and the demand for increasingly lean meat brought the breed almost to extinction. Only in 2001, thanks to local institutions such as: the Basilicata Region, the University of Basilicata, the Regional Breeders Association and the Medio Basento mountain community, the NL pig returned to populate the area with the consequent possibility to appreciate again its specific cured meat products.

The distribution of runs of homozygosity in the genome of river and swamp buffaloes reveals a history of adaptation, migration and crossbred events.

Background: Water buffalo is one of the most important livestock species in the world. Two types of water buffalo exist: river buffalo (Bubalus bubalis bubalis) and swamp buffalo (Bubalus bubalis carabanensis). The buffalo genome has been recently sequenced, and thus a new 90 K single nucleotide polymorphism (SNP) bead chip has been developed.

Genetic Parameters for Tolerance to Heat Stress in Crossbred Swine Carcass Traits.

Data for loin and backfat depth, as well as carcass growth of 126,051 three-way crossbred pigs raised between 2015 and 2019, were combined with climate records of air temperature, relative humidity, and temperature-humidity index. Environmental covariates with the largest impact on the studied traits were incorporated in a random regression model that also included genomic information. Genetic control of tolerance to heat stress and the presence of genotype by environment interaction were detected.

Genomic prediction for latent variables related to milk fatty acid composition in Holstein, Simmental and Brown Swiss dairy cattle breeds.

Genomic selection (GS) reports on milk fatty acid (FA) profiles have been published quite recently and are still few despite this trait represents the most important aspect of milk nutritional and sensory quality. Reasons for this can be found in the high costs of phenotype recording but also in issues related to its nature of complex trait constituted by multiple genetically correlated variables with low heritabilities. One possible strategy to deal with such constraint is represented by the use of dimension reduction methods.

Genome-wide analysis of homozygosity regions in european simmental bulls.

The study of Runs of Homozygosity (ROH) is a useful approach for the characterization of the genome of livestock populations. Due to their high relationship with autozygosity, ROH allow to make inference about population genetic history, to estimate the level of inbreeding, to assess within breed heterogeneity and to detect the footprints of selection on livestock genomes. Aim of this study was to investigate the distribution of runs of homozygosity in bulls belonging to five European Simmental populations and to assess the relationship between three production traits (milk yield, fat and protein contents) and autozygosity.

Genetics of Arthrogryposis and Macroglossia in Piemontese Cattle Breed.

Arthrogryposis and macroglossia are congenital pathologies known in several cattle breeds, including Piemontese. As variations in single genes were identified as responsible for arthrogryposis in some breeds, we decided: (i) to test the hypothesis of a similar genetic determinism for arthrogryposis in the Piemontese breed by genotyping affected and healthy animals with a high-density chip and applying genome-wide association study (GWAS), and canonical discriminant analysis (CDA) procedures, and (ii) to investigate with the same approach the genetic background of macroglossia, for which no genetic studies exist so far. The study included 125 animals (63 healthy, 30 with arthrogryposis, and 32 with macroglossia).

Use of the Multivariate Discriminant Analysis for Genome-Wide Association Studies in Cattle.

Genome-wide association studies (GWAS) are traditionally carried out by using the single marker regression model that, if a small number of individuals is involved, often lead to very few associations. The Bayesian methods, such as BayesR, have obtained encouraging results when they are applied to the GWAS. However, these approaches, require that an a priori posterior inclusion probability threshold be fixed, thus arbitrarily affecting the obtained associations.

Use of multivariate factor analysis of detailed milk fatty acid profile to perform a genome-wide association study in Italian Simmental and Italian Holstein.

Milk fatty acid (FA) profile is a clear example of complex and multiple correlated traits whose genetic basis is difficult to assess. Although genome-wide association (GWA) studies have been successful in the identification of significant genetic variants for complex traits, when correlated phenotypes are analysed separately, the outcomes are difficult to compare and interpret in a metabolic context. Here, we performed a multivariate factor analysis (MFA) on Italian Simmental and Italian Holstein milk fat profiles to extract latent unobserved factors able to explain correlation structure and common metabolic function among different FAs.

Variance components using genomic information for 2 functional traits in Italian Simmental cattle: Calving interval and lactation persistency.

Functional traits, such as fertility and lactation persistency, are becoming relevant breeding goals for dairy cattle. Fertility is a key element for herd profitability and animal welfare; in particular, calving interval (CIN) is an indicator of female fertility that can be easily recorded. Lactation persistency (LPE; i.

Prediction of Milk Coagulation Properties and Individual Cheese Yield in Sheep Using Partial Least Squares Regression.

The objectives of this study were (i) the prediction of sheep milk coagulation properties (MCP) and individual laboratory cheese yield (ILCY) from mid-infrared (MIR) spectra by using partial least squares (PLS) regression, and (ii) the comparison of different data pre-treatments on prediction accuracy. Individual milk samples of 970 Sarda breed ewes were analyzed for rennet coagulation time (RCT), curd-firming time (k20), and curd firmness (a30) using the Formagraph instrument; ILCY was measured by micro-manufacturing assays. An Furier-transform Infrared (FTIR) milk-analyzer was used for the estimation of the milk gross composition and the recording of MIR spectrum.

Bias in heritability estimates from genomic restricted maximum likelihood methods under different genotyping strategies.

We investigated the effects of different strategies for genotyping populations on variance components and heritabilities estimated with an animal model under restricted maximum likelihood (REML), genomic REML (GREML), and single-step GREML (ssGREML). A population with 10 generations was simulated. Animals from the last one, two or three generations were genotyped with 45,116 SNP evenly distributed on 27 chromosomes.

Conservation status and historical relatedness of Italian cattle breeds.

Background: In the last 50 years, the diversity of cattle breeds has experienced a severe contraction. However, in spite of the growing diffusion of cosmopolite specialized breeds, several local cattle breeds are still farmed in Italy. Genetic characterization of breeds represents an essential step to guide decisions in the management of farm animal genetic resources.