Dr Christos Dadousis

Background Genomic prediction faces two main statistical problems: multicollinearity and n ≪ p (many fewer observations than predictor variables). Principal component (PC) analysis is a multivariate statistical method that is often used to address these problems. The objective of this study was to compare the performance of PC regression (PCR) for genomic prediction with that of a commonly used REML model with a genomic relationship matrix (GREML) and to investigate the full potential of PCR for genomic prediction. Methods The PCR model used either a common or a semi-supervised approach, where PC were selected based either on their eigenvalues (i.e. proportion of variance explained by SNP (single nucleotide polymorphism) genotypes) or on their association with phenotypic variance in the reference population (i.e. the regression sum of squares contribution). Cross-validation within the reference population was used to select the optimum PCR model that minimizes mean squared error. Pre-corrected average daily milk, fat and protein yields of 1609 first lactation Holstein heifers, from Ireland, UK, the Netherlands and Sweden, which were genotyped with 50 k SNPs, were analysed. Each testing subset included animals from only one country, or from only one selection line for the UK. Results In general, accuracies of GREML and PCR were similar but GREML slightly outperformed PCR. Inclusion of genotyping information of validation animals into model training (semi-supervised PCR), did not result in more accurate genomic predictions. The highest achievable PCR accuracies were obtained across a wide range of numbers of PC fitted in the regression (from one to more than 1000), across test populations and traits. Using cross-validation within the reference population to derive the number of PC, yielded substantially lower accuracies than the highest achievable accuracies obtained across all possible numbers of PC. Conclusions On average, PCR performed only slightly less well than GREML. When the optimal number of PC was determined based on realized accuracy in the testing population, PCR showed a higher potential in terms of achievable accuracy that was not capitalized when PC selection was based on cross-validation. A standard approach for selecting the optimal set of PC in PCR remains a challenge.

The objective of this study was to evaluate the effect of imputation of single nucleotide polymorphisms (SNP) on the estimation of genomic inbreeding coefficients. Imputed genotypes of 68,127 Italian Holstein dairy cows were analyzed. Cows were initially genotyped with two high density (HD) SNP panels, namely the Illumina Infinium BovineHD BeadChip (678 cows; 777,962 SNP) and the Genomic Profiler HD-150K (641 cows; 139,914 SNP), and four medium density (MD): GeneSeek Genomic Profiler 3 (10,679 cows; 26,151 SNP), GeneSeek Genomic Profiler 4 (33,394 cows; 30,113 SNP), GeneSeek MD (12,030 cows; 47,850 SNP) and the Labogena MD (10,705 cows; 41,911 SNP). After imputation, all cows had genomic information on 84,445 SNP. Seven genomic inbreeding estimators were tested: (i) four PLINK v1.9 estimators (F, F-hat1,F-2,F-3), (ii) two genomic relationship matrix (grm) estimators [VanRaden's 1(st) method, but with observed allele frequencies (F-grm) and VanRaden's 3(rd) method that is allelic free and pedigree dependent (F-grm2)], and (iii) a runs of homozygosity (roh) - based estimator (F-roh). Genomic inbreeding coefficients of each SNP panel were compared with genomic inbreeding coefficients derived from the 84,445 imputation SNP. Coefficients of the HD SNP panels were consistent between genotyped-imputed SNP (Pearson correlations similar to 99%), while variability across SNP panels and estimators was observed in the MD SNP panels, with Labogena MD providing, on average, more consistent estimates. The robustness of Labogena MD, can be partly explained by the fact that 97.85% of the SNP of this panel is included in the 84,445 SNP selected by ANAFIBJ for routine genomic imputations, while this percentage for the other MD SNP panels varied between 55 and 60%. Runs of homozygosity was the most robust estimator. Genomic inbreeding estimates using imputation SNP are influenced by the SNP number of the SNP panel that are included in the imputed SNP, and performance of genomic inbreeding estimators depends on the imputation.

Inbreeding depression has become an urgent issue in cosmopolitan breeds where the massive genetic progress achieved in the latest generations is counterbalanced by a dramatic loss of genetic diversity causing increased health issues. Thus, the aim of this study was to estimate inbreeding depression on productive traits in Holstein dairy cattle. More precisely, we aimed to i) determine the level of inbreeding in 27,735 Italian Holstein dairy cows using pedigree and genotype data, ii) quantify the effect of inbreeding on 305-d in milk yield (MY; kg), fat yield (FY; kg), and protein yield (PY; kg) based on different statistical approaches, iii) determine if recent inbreeding has a more harmful impact than ancestral ones, and iv) quantify chromosomal homozygosity effect on productive traits. Quality control was performed on the autosomal chromosomes resulting in a final dataset of 84,443 single nucleotide polymorphisms. Four statistical models were used to evaluate the presence of inbreeding depression, which included linear regression analysis and division of FPED and FROH into percentile classes. Moreover, FROH was partitioned into i) length classes to assess the role of recent and ancestral inbreeding and ii) chromosome-specific contributions (FROH-CHR). Results evidenced that inbreeding negatively impacted the productive performance of Italian Holstein Friesian cows. However, differences between the estimated FPED and FROH coefficients resulted in different estimates of inbreeding depression. For instance, a 1% increase in FPED and FROH was associated with a decrease in MY of about 44 and 61 kg (P 

The objective of this study was to investigate the genetic diversity of the Garfagnina (GRF) goat, a breed that currently risks extinction. For this purpose, 48 goats were genotyped with the Illumina CaprineSNP50 BeadChip and analyzed together with 214 goats belonging to 9 other Italian breeds (~25 goats/breed), whose genotypes were available from the AdaptMap project [Argentata (ARG), Bionda dell'Adamello (BIO), Ciociara Grigia (CCG), Di Teramo (DIT), Garganica (GAR), Girgentana (GGT), Orobica (ORO), Valdostana (VAL) and Valpassiria (VSS)]. Comparative analyses were conducted on i) runs of homozygosity (ROH), ii) admixture ancestries and iii) the accuracy of breed traceability via discriminant analysis on principal components (DAPC) based on cross-validation. ROH analyses was used to assess the genetic diversity of GRF, while admixture and DAPC to evaluate its relationship to the other breeds. For GRF, common ROH (more than 45% in GRF samples) was detected on CHR 12 at, roughly 50.25-50.94Mbp (ARS1 assembly), which spans the CENPJ (centromere protein) and IL17D (interleukin 17D) genes. The same area of common ROH was also present in DIT, while a broader region (~49.25-51.94Mbp) was shared among the ARG, CCG, and GGT. Admixture analysis revealed a small region of common ancestry from GRF shared by BIO, VSS, ARG and CCG breeds. The DAPC model yielded 100% assignment success for GRF. Overall, our results support the identification of GRF as a distinct native Italian goat breed. This work can contribute to planning conservation programmes to save GRF from extinction and will improve the understanding of the socio-agro-economic factors related with the farming of GRF.

We studied the genetics of cheese-related latent variables (factors; Fs) for application in dairy cattle breeding. In total, 26 traits, recorded in 1264 Brown Swiss cows, were analyzed through multivariate factor analysis (MFA). Traits analyzed were descriptors of milk quality and yield (including protein fractions) and measures of coagulation, curd firmness (CF), cheese yields (%CY) and nutrient recoveries in the curd (REC). A total of 10 Fs (mutual orthogonal with a varimax rotation) were obtained. To assess the practical use of the Fs into breeding, we inferred their genetic parameters using single and bivariate animal models under a Bayesian framework. Heritability estimates (intra-herd) varied between 0.11 and 0.72 (F3: Yield and F7: --CN, respectively). The Fs underlined basic characteristics of the cheese-making process, milk components and udder health, while retaining 74% of the original variability. The first two Fs were indicators of the CY percentage (F1: %CY) and the CF process (F2: CFt), and presented similar heritability estimates: 0.268 and 0.295, respectively. The third factor was associated with the yield of milk and solids (F3: Yield) characterized by a low heritability (0.108) and the fourth with the cheese nitrogen (N) (F4: Cheese N) that conversely appeared to be characterized by a high heritability (0.618). Three Fs were associated with the proportion of the basic milk caseins on total milk protein (F5: as(1)--CN, F7: --CN, F8: as(2)-CN), also highly heritable (0.565, 0.723 and 0.397, respectively) and 1 factor with the phosphorylated form of the as(1)-CN (F9: as(1)-CN-Ph; 0.318). Moreover, 1 factor was linked to the whey protein -LA (F10: -LA; 0.147). An indicator factor of a cow's udder health (F6: Udder health) was also obtained and showed a moderate heritability (0.204). Although the Fs were phenotypically uncorrelated, considerable additive genetic correlations existed among them, with highest values observed between F10: -LA and F6: Udder health (-0.67) as well as between F9: as(1)-CN-Ph and F3: Yield (-0.60). Our results show the usefulness of MFA in dairy cattle breeding. The ability to replace a large number of variables with a few latent indicators of the same biological meaning marks MFA as a valuable tool for developing breeding strategies to improve cow's cheese-related traits.

It is becoming common to complement genome-wide association studies (GWAS) with gene-set enrichment analysis to deepen the understanding of the biological pathways affecting quantitative traits. Our objective was to conduct a gene ontology and pathway-based analysis to identify possible biological mechanisms involved in the regulation of bovine milk technological traits: coagulation properties, curd firmness modeling, individual cheese yield (CY), and milk nutrient recovery into the curd (REC) or whey loss traits. Results from 2 previous GWAS studies using 1,011 cows genotyped for 50k single nucleotide polymorphisms were used. Overall, the phenotypes analyzed consisted of 3 traditional milk coagulation property measures [RCT: rennet coagulation time defined as the time (min) from addition of enzyme to the beginning of coagulation; k(20): the interval (min) from RCT to the time at which a curd firmness of 20 mm is attained; a(30): a measure of the extent of curd firmness (mm) 30 min after coagulant addition], 6 curd firmness modeling traits [RCTeq: RCT estimated through the CF equation (min); CFp: potential asymptotic curd firmness (mm); k(CF): curd-firming rate constant (% x k(SR): syneresis rate constant (% x min(-1)); CFmax : maximum curd firmness (mm); and t(max) : time to CFmax (min)], 3 individual CY-related traits expressing the weight of fresh curd (%aCY(CURD)), curd solids (%CYSOTIDS), and curd moisture (%CYWATER) as a percentage of weight of milk processed and 4 milk nutrient and energy recoveries in the curd (RECFAT, RECPROTEIN, RECSOLIDS, and RECENERGY calculated as the % ratio between the nutrient in curd and the corresponding nutrient in processed milk), milk pH, and protein percentage. Each trait was analyzed separately. In total, 13,269 annotated genes were used in the analysis. The Gene Ontology and Kyoto Encyclopedia of Genes and Genomes pathway databases were queried for enrichment analyses. Overall, 21 Gene Ontology and 17 Kyoto Encyclopedia of Genes and Genomes categories were significantly associated (false discovery rate at 5%) with 7 traits (RCT, RCTeg, k(CF), RECFAT, RECSOLIDS,%C-Y-SOLIDS and RECENERGY), with some being in common between traits. The significantly enriched categories included calcium signaling pathway, salivary secretion, metabolic pathways, carbohydrate digestion and absorption, the tight junction and the phosphatidylinositol pathways, as well as pathways related to the bovine mammary gland health status, and contained a total of 150 genes spanning all chromosomes but 9, 20, and 27. This study provided new insights into the regulation of bovine milk coagulation and cheese ability that were not captured by the GWAS.

We examined the latent structure of 26 cheese related phenotypes in dairy cattle. Traits related to milk yield and quality (8 traits), milk protein fractions (8 traits), coagulation and curd firmness indicators (CF, 5 traits) and cheese-making phenotypes (cheese yields (%CY) and nutrient recoveries in the curd (REC), 5 traits) were analysed through multivariate factor analysis (MFA) using a varimax rotation. All phenotypes were measured in 1264 Brown Swiss cows. Ten mutual orthogonal, latent variables (factors; Fs) were obtained explaining 74% of the original variability. These Fs captured basic concepts of the cheese-making process. More precisely, the first 4 Fs, sorted by variance explained, were able to capture the underlying structure of the CY percentage (F1: %CY), the CF process with time (F2: CFt), the milk and solids yield (F3: Yield) and the presence of nitrogen (N) in the cheese (F4: Cheese N). Moreover, 4 Fs (F5: as(1)-beta-CN, F7: kappa-beta-CN, F8: as(2)-CN and F9: as(1)-CN-Ph) were related to the basic milk caseins and 1 factor was associated with the -LA whey protein (F10: alpha-LA). A factor describing udder health status (F6: Udder health), mainly loaded on lactose, other nitrogen compounds in the milk and SCS, was also obtained. Further, we inferred the effects of some potential sources of variation (e.g. stage of lactation and parity) including feeding and management systems. Stage of lactation had a significant effect for 7 of the 10 Fs, followed by parity of the cow (3 Fs), dairy system and feeding (3 Fs). Our work demonstrates the usefulness of MFA in reducing a large number of variables to a few latent factors with biological meaning and representing groups of traits that describe a complex process like cheese-making. Such an approach would be a valuable tool for studying the influence of different production environments and individual animal factors on protein composition and cheese-making related traits.

The aim of this study was to perform genome-wide associations (GWAS) and gene-set enrichment analyses with protein composition and cheesemaking-related latent variables (factors; F) in a cohort of 1,011 Italian Brown Swiss cows. Factor analysis was applied to identify latent structures of 26 phenotypes related to bovine milk quantity and quality, protein fractions [αS1-, αS2-, β-, and κ-casein (CN), β-lactoglobulin, and α-lactalbumin (α-LA)], coagulation and curd firming at time t (CFt) measures, and cheese properties [cheese yield (%CY) and nutrients recovery in the curd] of individual cows. Ten orthogonal F were extracted, explaining 74% of the original variability. Factor 1%CY underlined the %CY characteristics, F2CFt was related to the CFt process parameters, F3Yield was considered as descriptor of milk and solids yield, whereas F4Cheese N underscored the presence of nitrogenous compounds (N) into the cheese. Four more F were related to the milk caseins (F5αS1-β-CN, F7β-κ-CN, F8αS2-CN, and F9αS1-CN-Ph) and 1 F was linked to the whey protein (F10α-LA); 1 F underlined the udder health status (F6Udder health). All cows were genotyped with the Illumina BovineSNP50 Bead Chip v.2 (Illumina Inc., San Diego, CA). Single marker regression GWAS were fitted. Gene-set enrichment analysis was run on GWAS results, using the Gene Ontology and Kyoto Encyclopedia of Genes and Genomes pathway databases, to reveal ontologies or pathways associated with the F. All F but F3Yield showed significance in GWAS. Signals in 10 Bos taurus autosomes (BTA) were detected. High peaks on BTA6 (∼87 Mbp) were found for F6β-κ-CN, F5αS1-β-CN, and at the tail of BTA11 (∼104 Mbp) for F4Cheese N. Gene-set enrichment analyses showed significant results (false discovery rate at 5%) for F8αS2-CN, F1%CY, F4Cheese N, and F10α-LA. For F8αS2-CN, 33 Gene Ontology terms and 3 Kyoto Encyclopedia of Genes and Genomes categories were enriched, including terms related to ion transport and homeostasis, neuron function or part, and GnRH signaling pathway. Our results support the feasibility of factor analysis as a dimension reduction technique in genomic studies and evidenced a potential key role of αS2-CN in milk quality and composition.

The fatty acid (FA) profile has a considerable impact on the nutritional and technological quality of milk and dairy products. The molecular mechanism underlying the regulation of fat metabolism in bovine mammary gland have been not completely elucidated. We conducted genome-wide association studies (GWAS) across 65 milk FAs and fat percentage in 1,152 Brown Swiss cows. In total, we identified 175 significant single nucleotide polymorphism (SNPs) spanning all chromosomes. Pathway analyses revealed that 12: 0 was associated with the greatest number of overrepresented categories/pathways (e.g. mitogen-activated protein kinase (MAPK) activity and protein phosphorylation), suggesting that it might play an important biological role in controlling milk fat composition. An Associated Weight Matrix approach based on SNP co-associations predicted a network of 791 genes related to the milk FA profile, which were involved in several connected molecular pathways (e. g., MAPK, lipid metabolism and hormone signalling) and undetectable through standard GWAS. Analysis of transcription factors and their putative target genes within the network identified BACH2, E2F3 and KDM5A as key regulators of milk FA metabolism. These findings contribute to increasing knowledge of FA metabolism and mammary gland functionality in dairy cows and may be useful in developing targeted breeding practices to improve milk quality.

Small ruminant lentiviruses (SRLVs) are a heterogeneous group of viruses of sheep, goat, and wild ruminants responsible of lifelong persistent infection leading to a multisystem chronic disease. Increased evidences indicate that host genetic factors could influence the individual SRLV resistance. The present study was conducted on the Garfagnina goat breed, an Italian goat population registered on the Tuscan regional repertory of genetic resources at risk of extinction. Forty-eight adult goats belonging to a single flock were studied. SRLV diagnosis was achieved by serological tests and 21 serologically positive animals were identified. All animals were genotyped with the Illumina GoatSNP60 BeadChip and a genome-wide scan was then performed on the individual marker genotypes, in an attempt to identify genomic regions associated with the infection. One SNP was found significant (P 

Simple Summary Recently, high-throughput instruments have been used to analyze milk differential somatic cell count, represented by the combined proportion of polymorphonuclear leukocytes and lymphocytes, providing indirect information on the udder inflammation status of dairy cows. No information is available about the relationship between differential somatic cell count and milk quality, so the aim of this study was to investigate the effect of differential somatic cell count on the composition of a large number of individual milk samples. Results showed that milk quality worsened when differential somatic cell count was high. In particular, it was evidenced lower milk fat, protein, casein contents and casein index, and augmented milk fatty acids could be found with an increasing differential somatic cell count level. These findings confirmed that differential somatic cell count could be a new informative tool for dairy farmers to monitor the quality of milk. Abstract Recent available instruments allow to record the number of differential somatic cell count (DSCC), representing the combined proportion of polymorphonuclear leukocytes and lymphocytes, on a large number of milk samples. Milk DSCC provides indirect information on the udder health status of dairy cows. However, literature is limited regarding the effect of DSCC on milk composition at the individual cow level, as well as its relation to the somatic cell score (SCS). Hence, the aims of this study were to (i) investigate the effect of different levels of DSCC on milk composition (fat, protein, casein, casein index, and lactose) and (ii) explore the combined effect of DSCC and SCS on these traits. Statistical models included the fixed effects of days in milk, parity, SCS, DSCC and the interaction between SCS x DSCC, and the random effects of herd, animal within parity, and repeated measurements within cow. Results evidenced a decrease of milk fat and an increase in milk fatty acids at increasing DSCC levels, while protein, casein and their proportion showed their lowest values at the highest DSCC. A positive association was found between DSCC and lactose. The interaction between SCS and DSCC was important for lactose and casein index, as they varied differently upon high and low SCS and according to DSCC levels.

Simple Summary The Bardigiano horse is a native Italian breed bred for living in rural areas, traditionally used in agriculture. The breed counts about 3000 horses, and it is nowadays mainly used for recreational purposes. The relatively small size and the closed status of the breed raise the issue of monitoring genetic diversity. We therefore characterized the breed's genetic diversity based on molecular data. We showed a critical reduction of genetic variability mainly driven by past bottlenecks. We also highlighted homozygous genomic regions that might be the outcome of directional selection in recent years, in line with the conversion of Bardigiano horses from agricultural to riding purposes. Horses are nowadays mainly used for sport and leisure activities, and several local breeds, traditionally used in agriculture, have been exposed to a dramatic loss in population size and genetic diversity. The loss of genetic diversity negatively impacts individual fitness and reduces the potential long-term survivability of a breed. Recent advances in molecular biology and bioinformatics have allowed researchers to explore biodiversity one step further. This study aimed to evaluate the loss of genetic variability and identify genomic regions under selection pressure in the Bardigiano breed based on GGP Equine70k SNP data. The effective population size based on Linkage Disequilibrium (N-e) was equal to 39 horses, and it showed a decline over time. The average inbreeding based on runs of homozygosity (ROH) was equal to 0.17 (SD = 0.03). The majority of the ROH were relatively short (91% were

The prediction of traditional goat milk coagulation properties (MCP) and curd firmness over time (CFt) parameters via Fourier-transform infrared (FTIR) spectroscopy can be of significant economic interest to the dairy industry and can contribute to the breeding objectives for the genetic improvement of dairy goat breeds. Therefore, the aims of this study were to (1) explore the variability of milk FTIR spectra from 4 goat breeds (Camosciata delle Alpi, Murciano-Granadina, Maltese, and Sarda), and to assess the possible discriminant power of milk FTIR spectra among breeds, (2) assess the viability to predict coagulation traits by using milk FTIR spectra, and (3) quantify the effect of the breed on the prediction accuracy of MCP and CFt parameters. In total, 611 individual goat milk samples were used. Analysis of variance of measured MCP and CFt parameters was carried out using a mixed model including the farm and pendulum as random factors, and breed, parity, and days in milk as fixed factors. Milk spectra for each goat were collected over the spectral range from wavenumber 5,011 to 925 × cm−1. Discriminant analysis of principal components was used to assess the ability of FTIR spectra to identify breed of origin. A Bayesian model was used to calibrate equations for each coagulation trait. The accuracy of the model and the prediction equation was assessed by cross-validation (CRV; 80% training and 20% testing set) and stratified CRV (SCV; 3 breeds in the training set, one breed in the testing set) procedures. Prediction accuracy was assessed by using coefficient of determination of validation (R2VAL), the root mean square error of validation (RMSEVAL), and the ratio performance deviation. Moreover, measured and FTIR predicted traits were compared in the SCV procedure by assessing their least squares means for the breed effect, Pearson correlations, and variance heteroscedasticity. Results showed the feasibility of using FTIR spectra and multivariate analyses to correctly assign milk samples to their breeds of origin. The R2VAL values obtained with the CRV procedure were moderate to high for the majority of coagulation traits, with RMSEVAL and ratio performance deviation values increasing as the coagulation process progresses from rennet addition. Prediction accuracy obtained with the SCV were strongly influenced by the breed, presenting general low values restricting a practical application. In addition, the low Pearson correlation coefficients of Sarda breed for all the traits analyzed, and the heteroscedastic variances of Camosciata delle Alpi, Murciano-Granadina, and Maltese breeds, further indicated that it is fundamental to consider the differences existing among breeds for the prediction of milk coagulation traits.

The objective was to investigate the pattern of linkage disequilibrium (LD) in three local beef breeds, namely, Calvana (n = 174), Mucca Pisana (n = 270), and Pontremolese (n = 44). As a control group, samples of the Italian Limousin breed (n = 100) were used. All cattle were genotyped with the GeneSeek GGP-LDv4 33k SNP chip containing 30,111 SNPs. The genotype quality control for each breed was conducted separately, and SNPs with call rate < 0.95 and minor allele frequency (MAF) > 1% were used for the analysis. LD extent was estimated in PLINK v1.9 using the squared correlation between pairs of loci (r(2)) across autosomes. Moreover, r(2) values were used to calculate historical and contemporary effective population size (N-e) in each breed. Average r(2) was similar in Calvana and Mucca Pisana (similar to 0.14) and higher in Pontremolese (0.17); Limousin presented the lowest LD extent (0.07). LD up to 0.11-0.15 was persistent in the local breeds up to 0.75 Mbp, while in Limousin, it showed a more rapid decay. Variation of different LD levels across autosomes was observed in all the breeds. The results demonstrated a rapid decrease in Ne across generations for local breeds, and the contemporary population size observed in the local breeds, ranging from 41.7 in Calvana to 17 in Pontremolese, underlined the demographic alarming situation.

Cheese production is increasing in many countries, and a desire toward genetic selection for milk coagulation properties in dairy cattle breeding exists. However, measurements of individual cheesemaking properties are hampered by high costs and labor, whereas traditional single-point milk coagulation properties (MCP) are sometimes criticized. Nevertheless, new modeling of the entire curd firmness and syneresis process (CFt equation) offers new insight into the cheesemaking process. Moreover, identification of genomic regions regulating milk cheesemaking properties might enhance direct selection of individuals in breeding programs based on cheese ability rather than related milk components. Therefore, the objective of this study was to perform genome-wide association studies to identify genomic regions linked to traditional MCP and new CFt parameters, milk acidity (pH), and milk protein percentage. Milk and DNA samples from 1,043 Italian Brown Swiss cows were used. Milk pH and 3 MCP traits were grouped together to represent the MCP set. Four CFt equation parameters, 2 derived traits, and protein percentage were considered as the second group of traits (CFt set). Animals were genotyped with the Illumina SNP50 BeadChip v.2 (Illumina Inc., San Diego, CA). Multitrait animal models were used to estimate variance components. For genome-wide association studies, the genome-wide association using mixed model and regression-genomic control approach was used. In total, 106 significant marker traits associations and 66 single nucleotide polymorphisms were identified on 12 chromosomes (1, 6, 9, 11, 13, 15, 16, 19, 20, 23, 26, and 28). Sharp peaks were detected at 84 to 88 Mbp on Bos taurus autosome (BTA) 6, with a peak at 87.4 Mbp in the region harboring the casein genes. Evidence of quantitative trait loci at 82.6 and 88.4 Mbp on the same chromosome was found. All chromosomes but BTA6, BTA11, and BTA28 were associated with only one trait. Only BTA6 was in common between MCP and CFt sets. The new CFt traits reinforced the support of MCP signals and provided with additional information on genomic regions that might be involved in regulation of the coagulation process of bovine milk.

Simple Summary: The recent alarming reports on global climate change and the challenges facing the agricultural sector to meet the increase in meat consumption, impose research in biodiversity. An important genetic pool of local breeds might play a crucial role in the near future to address these challenges. Although Italy is considered as one of the richest countries in biodiversity, there are autochthonous cattle breeds under extinction. To safeguard biodiversity and increase genetic diversity within breeds, appropriate management tools must be developed. To achieve this, precise knowledge of the population structure and genetic diversity per breed are required. This study analyzed pedigree data of six local beef breeds: Calvana, Mucca Pisana, and Pontremolese (from the region of Tuscany), all under extinction, and Sarda, Sardo Bruna, and Sardo Modicana, from the island of Sardinia, that are larger in number but of lower productivity. In addition, the study investigated the population structure of the cosmopolitan beef breeds, Charolais and Limousine, reared in the same regions and undergoing selection. The high mating percentage between relatives for Mucca Pisana and Calvana is an alarming situation for these breeds. The population structure of the Sardinian breeds suggests the application of breeding programs. Abstract: The aim was to investigate the population structure of eight beef breeds: three local Tuscan breeds under extinction, Calvana (CAL), Mucca Pisana (MUP), and Pontremolese (PON); three local unselected breeds reared in Sardinia, Sarda (SAR), Sardo Bruna (SAB), and Sardo Modicana (SAM); and two cosmopolitan breeds, Charolais (CHA) and Limousine (LIM), reared in the same regions. An effective population size ranges between 14.62 (PON) to 39.79 (SAM) in local breeds, 90.29 for CHA, and 135.65 for LIM. The average inbreeding coefficients were higher in Tuscan breeds (7.25%, 5.10%, and 3.64% for MUP, CAL, and PON, respectively) compared to the Sardinian breeds (1.23%, 1.66%, and 1.90% in SAB, SAM, and SAR, respectively), while for CHA and LIM they were

Driven by the large amount of goat milk destined for cheese production, and to pioneer the goat cheese industry, the objective of this study was to assess the effect of farm in predicting goat milk-coagulation and curd-firmness traits via Fourier-transform infrared spectroscopy. Spectra from 452 Sarda goats belonging to 14 farms in central and southeast Sardinia (Italy) were collected. A Bayesian linear regression model was used, estimating all spectral wavelengths' effects simultaneously. Three traditional milk-coagulation properties [rennet coagulation time (min), time to curd firmness of 20 mm (min), and curd firmness 30 min after rennet addition (mm)] and 3 curd-firmness measures modeled over time [rennet coagulation time estimated according to curd firmness change over time (RCTeq), instant curd-firming rate constant, and asymptotical curd firmness] were considered. A stratified cross validation (SCV) was assigned, evaluating each farm separately (validation set; VAL) and keeping the remaining farms to train (calibration set) the statistical model. Moreover, a SCV, where 20% of the goats randomly taken (10 replicates per farm) from the VAL farm entered the calibration set, was also considered (SCV80). To assess model performance, coefficient of determination (R2VAL) and the root mean squared error of validation were recorded. The R2VAL varied between 0.14 and 0.45 (instant curd-firming rate constant and RCTeq, respectively), albeit the standard deviation was approximating half of the mean for all the traits. Although average results of the 2 SCV procedures were similar, in SCV80, the maximum R2VAL increased at about 15% across traits, with the highest observed for time to curd firmness of 20 mm (20%) and the lowest for RCTeq (6%). Further investigation evidenced important variability among farms, with R2VAL for some of them being close to 0. Our work outlined the importance of considering the effect of farm when developing Fourier-transform infrared spectroscopy prediction equations for coagulation and curd-firmness traits in goats.

Background: Body weight (BW) is an economically important trait in the broiler (meat-type chickens) industry. Under the assumption of polygenicity, a “large” number of genes with “small” efects is expected to control BW. To detect such efects, a large sample size is required in genome-wide association studies (GWAS). Our objective was to conduct a GWAS for BW measured at 35 days of age with a large sample size. Methods: The GWAS included 137,343 broilers spanning 15 pedigree generations and 392,295 imputed single nucleotide polymorphisms (SNPs). A false discovery rate of 1% was adopted to account for multiple testing when declaring signifcant SNPs. A Bayesian ridge regression model was implemented, using AlphaBayes, to estimate the contribution to the total genetic variance of each region harbouring signifcant SNPs (1 Mb up/downstream) and the combined regions harbouring non-signifcant SNPs. Results: GWAS revealed 25 genomic regions harbouring 96 signifcant SNPs on 13 Gallus gallus autosomes (GGA1 to 4, 8, 10 to 15, 19 and 27), with the strongest associations on GGA4 at 65.67–66.31 Mb (Galgal4 assembly). The association of these regions points to several strong candidate genes including: (i) growth factors (GGA1, 4, 8, 13 and 14); (ii) leptin receptor overlapping transcript (LEPROT)/leptin receptor (LEPR) locus (GGA8), and the STAT3/STAT5B locus (GGA27), in connection with the JAK/STAT signalling pathway; (iii) T-box gene (TBX3/TBX5) on GGA15 and CHST11 (GGA1), which are both related to heart/skeleton development); and (iv) PLAG1 (GGA2). Combined together, these 25 genomic regions explained ~30% of the total genetic variance. The region harbouring signifcant SNPs that explained the largest portion of the total genetic variance (4.37%) was on GGA4 (~65.67–66.31 Mb). Conclusions: To the best of our knowledge, this is the largest GWAS that has been conducted for BW in chicken to date. In spite of the identifed regions, which showed a strong association with BW, the high proportion of genetic variance attributed to regions harbouring non-signifcant SNPs supports the hypothesis that the genetic architecture of BW35 is polygenic and complex. Our results also suggest that a large sample size will be required for future GWAS of BW35.

Cheese production and consumption are increasing in many countries worldwide. As a result, interest has increased in strategies for genetic selection of individuals for technological traits of milk related to cheese yield (CY) in dairy cattle breeding. However, little is known about the genetic background of a cow's ability to produce cheese. Recently, a relatively large panel (1,264 cows) of different measures of individual cow CY and milk nutrient and energy recoveries in the cheese (REC) became available. Genetic analyses showed considerable variation for CY and for aptitude to retain high proportions of fat, protein, and water in the coagulum. For the dairy industry, these characteristics are of major economic importance. Nevertheless, use of this knowledge in dairy breeding is hampered by high costs, intense labor requirement, and lack of appropriate technology. However, in the era of genomics, new possibilities are available for animal breeding and genetic improvement. For example, identification of genomic regions involved in cow CY might provide potential for marker-assisted selection. The objective of this study was to perform genome-wide association studies on different CY and REC measures. Milk and DNA samples from 1,152 Italian Brown Swiss cows were used. Three CY traits expressing the weight (wt) of fresh curd (%CYCURD), curd solids (%CYSOLIDS), and curd moisture (%CYWATER) as a percentage of weight of milk processed, and 4 REC (RECFAT, RECPROTEIN, RECSOLIDS, and RECENERGY, calculated as the % ratio between the nutrient in curd and the corresponding nutrient in processed milk) were analyzed. Animals were genotyped with the Illumina BovineSNP50 Bead Chip v.2. Single marker regressions were fitted using the GenABEL R package (genome-wide association using mixed model and regression–genomic control). In total, 103 significant associations (88 single nucleotide polymorphisms) were identified in 10 chromosomes (2, 6, 9, 11, 12, 14, 18, 19, 27, 28). For RECFAT and RECPROTEIN, high significance peaks were identified in Bos taurus autosome (BTA) 6 and BTA11, respectively. Marker ARS-BFGL-NGS-104610 (∼104.3 Mbp) was highly associated with RECPROTEIN and Hapmap52348-rs29024684 (∼87.4 Mbp), closely located to the casein genes on BTA6, with RECFAT. Genomic regions identified may enhance marker-assisted selection in bovine cheese breeding beyond the use of protein (casein) and fat contents, whereas new knowledge will help to unravel the genomic background of a cow's ability for cheese production.

The objectives of this study were to explore the use of Fourier-transform infrared (FITR) spectroscopy on 458 goat milk samples for predicting cheese-making traits, and to test the effect of the farm variability on their prediction accuracy. Calibration equations were developed using a Bayesian approach with three different scenarios: i) a random cross-validation (CV) [80% calibration (CAL); 20% validation (VAL) set], ii) a stratified CV [(SCV), 13 farms used as CAL, and the remaining one as VAL set], and iii) a SCV where 20% of the goats randomly selected from the VAL farm were included in the CAL set (SCV80). The best prediction performance was obtained for cheese yield solids, justifying for its practical application at population level. Overall results were similar to or outperformed those reported for bovine milk. Our results suggest considering specific procedures for calibration development to propose reliable tools applicable along the dairy goat chain.

Preserving diversity of indigenous pig (Sus scrofa) breeds is a key factor to (i) sustain the pork chain (both at local and global scales) including the production of high-quality branded products, (ii) enrich the animal biobanking and (iii) progress conservation policies. Single nucleotide polymorphism (SNP) chips offer the opportunity for whole-genome comparisons among individuals and breeds. Animals from twenty European local pigs breeds, reared in nine countries (Croatia: Black Slavonian, Turopolje; France: Basque, Gascon; Germany: Schwabisch-Hällisches Schwein; Italy: Apulo Calabrese, Casertana, Cinta Senese, Mora Romagnola, Nero Siciliano, Sarda; Lithuania: Indigenous Wattle, White Old Type; Portugal: Alentejana, Bísara; Serbia: Moravka, Swallow-Bellied Mangalitsa; Slovenia: Krškopolje pig; Spain: Iberian, Majorcan Black), and three commercial breeds (Duroc, Landrace and Large White) were sampled and genotyped with the GeneSeek Genomic Profiler (GGP) 70 K HD porcine genotyping chip. A dataset of 51 Wild Boars from nine countries was also added, summing up to 1186 pigs (~ 49 pigs/breed). The aim was to: (i) investigate individual admixture ancestries and (ii) assess breed traceability via discriminant analysis on principal components (DAPC). Albeit the mosaic of shared ancestries found for Nero Siciliano, Sarda and Moravka, admixture analysis indicated independent evolvement for the rest of the breeds. High prediction accuracy of DAPC mark SNP data as a reliable solution for the traceability of breed-specific pig products.

The objective of this study was to develop formulas based on milk composition of individual goat samples for predicting cheese yield (%CY) traits (fresh curd, milk solids, and water retained in the curd). The specific aims were to assess and quantify (1) the contribution of major milk components (fat, protein, and casein) and udder health indicators (lactose, somatic cell count, pH, and bacterial count) on %CY traits (fresh curd, milk solids, and water retained in the curd); (2) the cheese-making method; and (3) goat breed effects on prediction accuracy of the %CY formulas. The %CY traits were analyzed in duplicate from 600 goats, using an individual laboratory cheese-making procedure (9-MilCA method; 9 mL of milk per observation) for a total of 1,200 observations. Goats were reared in 36 herds and belonged to 6 breeds (Saanen, Murciano-Granadina, Camosciata delle Alpi, Maltese, Sarda, and Sarda Primitiva). Fresh %CY (%CYCURD), total solids (%CYSOLIDS), and water retained (%CYWATER) in the curd were used as response variables. Single and multiple linear regression models were tested via different combinations of standard milk components (fat, protein, casein) and indirect udder health indicators (UHI; lactose, somatic cell count, pH, and bacterial count). The 2 %CY observations within animal were averaged, and a cross-validation (CrV) scheme was adopted, in which 80% of observations were randomly assigned to the calibration (CAL) set and 20% to the validation (VAL) set. The procedure was repeated 10 times to account for sampling variability. Further, the model presenting the best prediction accuracy in CrV (i.e., comprehensive formula) was used in a secondary analysis to assess the accuracy of the %CY predictive formulas as part of the laboratory cheese-making procedure (within-animal validation, WAV), in which the first %CY observation within animal was assigned to CAL, and the second to the VAL set. Finally, a stratified CrV (SCrV) was adopted to assess the %CY traits prediction accuracy across goat breeds, again using the best model, in which 5 breeds were included in CAL and the remaining one in the VAL set. Fitting statistics of the formulas were assessed by coefficient of determination of validation (R2VAL) and the root mean square error of validation (RMSEVAL). In CrV, the formula with the best prediction accuracy for all %CY traits included fat, casein, and UHI (R2VAL = 0.65, 0.96, and 0.23 for %CYCURD, %CYSOLIDS, and %CYWATER, respectively). The WAV procedure showed R2VAL higher than those obtained in CrV, evidencing a low effect of the 9-MilCA method and, indirectly, its high repeatability. In the SCrV, large differences for %CYCURD and %CYWATER among breeds evidenced that the breed is a fundamental factor to consider in %CY predictive formulas. These results may be useful to monitor milk composition and quantify the influence of milk traits in the composite selection indices of specific breeds, and for the direct genetic improvement of cheese production.

Genetic diversity has become an urgent matter not only in small local breeds but also in more specialized ones. While the use of genomic data in livestock breeding programs increased genetic gain, there is increasing evidence that this benefit may be counterbalanced by the potential loss of genetic variability. Thus, in this study, we aimed to investigate the genetic diversity in the Italian Holstein dairy cattle using pedigree and genomic data from cows born between 2002 and 2020. We estimated variation in inbreeding, effective population size, and generation interval and compared those aspects prior to and after the introduction of genomic selection in the breed. The dataset contained 84,443 single-nucleotide polymorphisms (SNPs), and 74,485 cows were analyzed. Pedigree depth based on complete generation equivalent was equal to 10.67. A run of homozygosity (ROH) analysis was adopted to estimate SNP-based inbreeding (F ROH ). The average pedigree inbreeding was 0.07, while the average F ROH was more than double, being equal to 0.17. The pattern of the effective population size based on pedigree and SNP data was similar although different in scale, with a constant decrease within the last five generations. The overall inbreeding rate (ΔF) per year was equal to +0.27% and +0.44% for F ped and F ROH throughout the studied period, which corresponded to about +1.35% and +2.2% per generation, respectively. A significant increase in the ΔF was found since the introduction of genomic selection in the breed. This study in the Italian Holstein dairy cattle showed the importance of controlling the loss of genetic diversity to ensure the long-term sustainability of this breed, as well as to guarantee future market demands.

The objective of this study was to estimate inbreeding coefficients in Holstein dairy cattle using imputed SNPs data. A data set of 95,540 Italian Holstein dairy cows from the routine genomic evaluations of the Italian National Association of Holstein, Brown, and Jersey Breeders were analyzed, with 84,445 imputed SNP. Ten widely used genomic inbreeding estimators were tested, including 4 PLINK v1.9 estimators (F, FHAT1, FHAT2, FHAT3), 3 genomic relationship matrix (GRM)-based methods [VanRaden's first method with observed allele frequencies (FGRM) or with fixed frequencies at 0.5 (FGRM05), VanRaden's third method, allelic frequency free and pedigree regressed (FGRM2)], runs of homozygosity (ROH)-based estimators in a complete (FROH) and simplified version (FROH2), and proportion of homozygous SNP (FPH). Pairwise comparisons among them were made, including the comparison with traditional pedigree-based inbreeding coefficients (FPED). Our results showed variability among the genomic inbreeding estimators. Coefficients of FGRM and FHAT3 were >1, meaning that more variability has been lost than the variability that existed in the base population. Regarding the remaining ones, FGRM05, FROH, FROH2, and FPH provided coefficients within the [0,1] space and are considered comparable to FPED. Not comparable to FPED, yet with an interpretable value, can be considered the coefficients of F, FHAT2, and FGRM2. Estimators based on ROH had the highest correlation with pedigree-based coefficients (0.59–0.66), among all estimators tested. In this study, Spearman correlations were shown to possibly provide a clearer estimation of the strength of the relationship between estimators. We hypothesize that imputation might cause extreme genomic inbreeding values that deserves further investigation.

In the present study, GeneSeek GGP-LDv4 33k single nucleotide polymorphism chip was used to detect runs of homozygosity (ROH) in eight Italian beef cattle breeds, six breeds with distribution limited to Tuscany (Calvana, Mucca Pisana, Pontremolese) or Sardinia (Sarda, Sardo Bruna and Sardo Modicana) and two cosmopolitan breeds (Charolais and Limousine). ROH detection analyses were used to estimate autozygosity and inbreeding and to identify genomic regions with high frequency of ROH, which might reflect selection signatures. Comparative analysis among breeds revealed differences in length and distribution of ROH and inbreeding levels. The Charolais, Limousine, Sarda, and Sardo Bruna breeds were found to have a high frequency of short ROH (similar to 15.000); Calvana and Mucca Pisana presented also runs longer than 16 Mbp. The highest level of average genomic inbreeding was observed in Tuscan breeds, around 0.3, while Sardinian and cosmopolitan breeds showed values around 0.2. The population structure and genetic distances were analyzed through principal component and multidimensional scaling analyses, and resulted in a clear separation among the breeds, with clusters related to productive purposes. The frequency of ROH occurrence revealed eight breed-specific genomic regions where genes of potential selective and conservative interest are located (e.g. MYOG, CHI3L1, CHIT1 (BTA16), TIMELESS, APOF, OR10P1, OR6C4, OR2AP1, OR6C2, OR6C68, CACNG2 (BTA5), COL5A2 and COL3A1 (BTA2)). In all breeds, we found the largest proportion of homozygous by descent segments to be those that represent inbreeding events that occurred around 32 generations ago, with Tuscan breeds also having a significant proportion of segments relating to more recent inbreeding.