Application of genomic tools to breeding and to genetic structure studies in livestock populations

This 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

Genomic investigation of milk production in Italian buffalo

AbstractThe aim of this study was to test the feasibility of genomic selection in the Italian Mediterranean water buffalo, which is farmed mainly in the south Italy for milk, and mozzarella, production. A total of 498 animals were genotyped at 49,164 loci. Test day records (80,417) of milk (MY), fat (FY) and protein (PY) yields from 4127 cows, born between 1975 and 2009, were analysed in a three-trait model. Cows born in 2008 and 2009 with phenotypes and genotypes were selected as validation animals (n = 50). Variance components (VC) were estimated with BLUP and ssGBLUP. Heritabilities for BLUP were 0.25 ? 0.02 (MY), 0.16 ? 0.01 (FY) and 0.25 ? 0.01 (PY). Breeding values were computed using BLUP and ssGBLUP, using VC estimated from BLUP. ssGBLUP was applied in five scenarios, each with a different number of genotypes available: (A) bulls (35); (B) validation cows (50); (C) bulls and validation cows (85); (D) all genotyped cows (463); (E) all genotypes (498). Model validation was performed using the LR method: correlation, accuracy, dispersion, and bias statistics were calculated. Average correlations were 0.71 ? 0.02 and 0.82 ? 0.01 for BLUP and ssGBLUP-E, respectively. Accuracies were also higher in ssGBLUP-E (0.75 ? 0.03) compared to BLUP (0.57 ? 0.03). The best dispersions (i.e. closer to 1) were found for ssGBLUP-C. The use of genotypes only for the 35 bulls did not change the validation values compared to BLUP. Results of the present study, even if based on small number of animals, showed that the inclusion of genotypes of females can improve breeding values accuracy in the Italian Buffalo.HighlightsThe genotypes of males did not improve the predictions.Genotypes of females improve breeding values accuracy.Slight increase in prediction accuracy with weighted ssGBLUP

Farm Animals Are Long Away from Natural Behavior: Open Questions and Operative Consequences on Animal Welfare

The concept of welfare applied to farm animals has undergone a remarkable evolution. The growing awareness of citizens pushes farmers to guarantee the highest possible level of welfare to their animals. New perspectives could be opened for animal welfare reasoning around the concept of domestic, especially farm, animals as partial human artifacts. Therefore, it is important to understand how much a particular behavior of a farm animal is far from the natural one of its ancestors. This paper is a contribution to better understand the role of genetics of the farm animals on their behavior. This means that the naïve approach to animal welfare regarding returning animals to their natural state should be challenged and that welfare assessment should be considered

Farm Animals Are Long Away from Natural Behavior: Open Questions and Operative Consequences on Animal Welfare

The concept of welfare applied to farm animals has undergone a remarkable evolution. The growing awareness of citizens pushes farmers to guarantee the highest possible level of welfare to their animals. New perspectives could be opened for animal welfare reasoning around the concept of domestic, especially farm, animals as partial human artifacts. Therefore, it is important to understand how much a particular behavior of a farm animal is far from the natural one of its ancestors. This paper is a contribution to better understand the role of genetics of the farm animals on their behavior. This means that the naïve approach to animal welfare regarding returning animals to their natural state should be challenged and that welfare assessment should be considered

Genome-wide variability and selection signatures in Italian island cattle breeds

Supplementary data for publication: Cesarani, A., Sorbolini, S., Criscione, A., Bordonaro, S., Pulina, G., Battacone, G., Marletta, D., Gaspa, G., & Macciotta, N. P. P. (2018). Genome-wide variability and selection signatures in Italian island cattle breeds. Animal Genetics, 49(5), 371-383

Past, present, and future developments in single-step genomic models

Single-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

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. The aim of this work was to predict DMI from the milk spectra of 24 lactating Sarda dairy sheep ewes. Three models (Principal Component Regression, Partial Least Squares Regression, and Stepwise Regression) were iteratively applied to three validation schemes: records, ewes, and days. DMI was moderately correlated with the wavenumbers of the milk spectra: the largest correlations (around ±0.30) were observed at ~1100–1330 cm−1 and ~2800–3000 cm−1. The average correlations between real and predicted DMI were 0.33 (validation on records), 0.32 (validation on ewes), and 0.23 (validation on days). The results of this preliminary study, even if based on a small number of animals, demonstrate that DMI can be routinely estimated from the milk spectra

Occurrence of microplastics in the gastrointestinal tract of benthic by-catches from an eastern Mediterranean deep-sea environment

Concern about microplastic pollution little is known about levels in deep-sea species; to fill this knowledge gap, levels of microplastics in the gastrointestinal (GI) tracts of 34 fish from eight different deep-sea by-catches: blackmouth catshark, lesser spotted dogfish, and velvet belly, armless snake eel, hollowsnout grenadier, phaeton dragonet, royal flagfin, and slender snipe eel were measured. All were collected at the same site (east Sardinia, Mediterranean Sea; 40°10'12.49″N, 9°44'12.31″E) using a bottom gillnet at depths between -820/250 and -1148 ft./350 m. Microplastics (MPs) were retrieved in 16 out of 34 fish. At least one microplastic item was found in 48% (33%, E. spinax - 75%, G. melastomus) of the samples. The most frequent was polyethylene (PE), with nine items (filaments, films, fragments) found in five specimens. This preliminary study of by-catches adds new data on MPs ingestion by species inhabiting a deep-sea environment of the Mediterranean.We wish to thank Marcello Ranucci, Giampaolo and Cristian Marongiu, the fishermen working on the Delfino 1, for their professional assistance.Peer reviewe

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

Domestication and evolution of cattle originated different modern breeds in different places worldwide. The interaction between natural and artificial selection and the adaptation to environment shaped the genome, and the three different types of cattle here considered (taurus, indicus, and composite) may harbor different selection signatures. To study the difference among types and region of origin (tropics, temperate, and continental zones), Regions of Homozygosity (ROH) were used. ROH are continuous homozygous chromosomal segments identical by descendent, which characteristics can give information about inbreeding occurrence and natural and artificial selection. Moreover, it had been investigated which genes were mapped in these regions, and if interesting differences pertaining to environmental adaptation or fitness in general, could be observed