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The genetic variability and presence of population substructures in 4 native Northern Italian sheep breeds, Alpagota, Brogna, Foza, and Lamon, undergoing in situ conservation, and 1 widespread Italian breed, Bergamasca, were studied by investigating 19 microsatellite markers. The breeds showed considerable genetic variability in terms of number of alleles and heterozygosity, with the exception of Alpagota, which was the least variable (0.607). Nevertheless, a significant deficit of heterozygotes was observed in each breed due to rather increased levels of inbreeding or to the presence of population substructures, probably caused by increased genetic variation in the founder populations. The analyses evidenced clear genetic differentiation (FST = 0.085), reduced levels of admixture, and presence of private alleles among the breeds, confirm- ing their genetic uniqueness. In particular, according to Reynolds genetic distances, Alpagota was the most differentiated, perhaps because it had been bred mostly in a rather isolated area. Loss of any of the investigated breeds would result in a loss of genetic diversity ranging from 0.5 to 1.6% of the total observed gene diversity. Results supported the decision to safeguard these breeds as important reservoirs of genetic diversity and suggested breeding and mating practices to maintain variability and to overcome within-breed sub-structures. [ABSTRACT FROM AUTHOR]

Genetic variation in four indigenous chicken breeds from the Veneto region of Italy was assessed using amplified fragment length polymorphism (AFLP) markers. A total of 99 individuals were analysed using three AFLP primer combinations that produced 70 polymorphisms. Four indigenous Veneto chicken breeds (Ermellinata, Padovana, Pépoi and Robusta) and a reference broiler line were included in the analysis. Breed-specific markers were identified in each breed. The expected heterozygosity did not differ significantly among the indigenous Veneto chicken breeds and the broiler line. The coefficient of gene variation (Gst) value across loci indicated that almost half of the total variability was observed among breeds. Nei's standard genetic distance between pairs of breeds showed that the distance between the broiler line and the Pépoi breed was greater than the distances between the broiler line and the other three chicken breeds. Cluster analysis based on standard genetic distances between breeds indicated that the Padovana and Pépoi breeds were closely related. Factorial analysis based on a binary matrix of the AFLP data showed a clear distinction of all breeds. [ABSTRACT FROM AUTHOR]

The objective of this study was to estimate genetic parameters for conjugated linoleic acid (CLA) and other selected milk fatty acid (FA) content and for unsaturation ratios in the Italian Holstein Friesian population. Furthermore, the relationship of milk FA with milk fat and protein content was considered. One morning milk sample was collected from 990 Italian Holstein Friesian cows randomly sampled from 54 half-sib families, located in 34 commercial herds in the North-eastern part of Italy. Each sample was analyzed for milk percentages of fat and protein, and for single FA percentages (computed as FA weight as a proportion of total fat weight). Heritabilities were moderate for unsaturated FA, ranging from 0.14 for C16:1 to 0.19 for C14:1. Less than 10% of heritability was estimated for each saturated FA content. Heritability for index of desaturation, monounsaturated FA and CLA/trans-11 18:1 ratio were 0.15, 0.14, and 0.15, respectively. Standard errors of the heritability values ranged from 0.02 to 0.06. Genetic correlations were high and negative between C16:0 and C18:0, as well as between C14:0 and C18:0. Genetic correlations of index of desaturation were high and negative with C14:0 and C16:0 (-0.70 and -0.72, respectively), and close to zero (0.03) with C18:0. The genetic correlation of C16:0 with fat percentage was positive (0.74), implying that selection for fat percentage should result in a correlated increase of C16:0, whereas trans-11 C18:1 and cis-9, trans-11 C18:2 contents decreased with increasing fat percentage (-0.69 and -0.55, respectively). Genetic correlations of fat percentage with 14:1/14 and 16:1/16 ratios were positive, whereas genetic correlations of fat percentage with 18:1/18 and CLA/trans-11 18:1 ratios were negative. These results suggest that it is possible to change the milk FA composition by genetic selection, which offers opportunities to meet consumer demands regarding health aspects of milk and dairy products. [ABSTRACT FROM AUTHOR]

Samples of herd milk (506) were analyzed to assess sources of variation for milk coagulation properties (MCP) for 5 different dairy cattle breeds. Data were recorded in 55 single-breed dairy herds in the Trento province, a mountain area in northeast Italy. The 5 cattle breeds were Holstein-Friesian (8 herds), Brown Swiss (16 herds), Simmental (10 herds), Rendena (13 herds), and Alpine Gray (8 herds). Herd milk samples were analyzed for the MCP traits, milk rennet coagulation time (RCT), curd-firming time, and curd firmness (a30), as well as protein and fat percentages, somatic cell count, Soxhlet-Henkel acidity, and bacterial count. An ANOVA was performed to study the effect of breed, herd within breed, DIM, month of lactation, protein and fat percentages, somatic cell score, titratable acidity, and log bacterial count within breed on MCP. Breed was the most important source of variation. In particular, the Rendena breed showed the best MCP traits at 13.5 min and 27.0 mm for RCT and a30, respectively. The Holstein-Friesian breed had the worst coagulation properties at 18.0 min and 17.5 mm for RCT and a30, respectively. The other 3 breeds showed intermediate coagulation properties. The RCT values were better at the beginning of lactation, whereas RCT and a30 values were better in September and October (14.3 min and 25.7 mm, respectively). Among the composition traits, only the titratable acidity affected MCP traits of herd milk positively. [ABSTRACT FROM AUTHOR]

Sensor systems (SS) were developed over the last few decades to help dairy farmers manage their herds. Such systems can provide both data and alerts to several productive, behavioral, and physiological indicators on individual cows. Currently, there is still a lack of knowledge on both the proportion of dairy farms that invested in SS and type of SS installed. Additionally, it is still unclear whether the performances of herds equipped with SS differ from those of similar herds managed without any technological aid. Therefore, the aims of this study were (1) to provide an insight into SS spread among Italian dairy farms and (2) to analyze the performances of similar herds equipped or not equipped with SS. To reach the former goal, a large survey was carried out on 964 dairy farms in the northeast of Italy. Farmers were interviewed by the technicians of the regional breeders association to collect information on the type of SS installed on farms and the main parameters recorded. Overall, 42% of the surveyed farms had at least 1 SS, and most of them (72%) reared more than 50 cows. Sensors for measuring individual cow milk yield were the most prevalent type installed (39% of the surveyed farms), whereas only 15% of farms had SS for estrus detection. More sophisticated parameters, such as rumination, were automatically monitored in less than 5% of the farms. To reach the latter goal of the study, a subset of 100 Holstein dairy farms with similar characteristics was selected: half of them were equipped with SS for monitoring at least individual milk yield and estrus, and the other half were managed without any SS. Average herd productive and reproductive data from official test days over 3 yr were analyzed. The outcomes of the comparison showed that farms with SS had higher mature-equivalent milk production. Further clustering analysis of the same 100 farms partitioned them into 3 clusters based on herd productive and reproductive data. Results of the Chi-squared test showed that the proportion of farms equipped with SS was greater in the cluster with the best performance (e.g., higher milk yield and shorter calving interval). However, the presence of a few farms equipped with SS in the least productive cluster for the same parameters pointed out that although the installation of SS may support farmers in time- and labor-saving or in data recording, it is not a guarantee of better herd performance. [ABSTRACT FROM AUTHOR]

The aim of the present study was to investigate sources of variation of milk composition and technological characteristics routinely collected in field conditions in the Italian dairy industry. A total of 40,896 bulk milk records from 620 herds and 10 regions across Italy were analyzed. Composition traits were fat, protein, and casein percentages, urea content, and somatic cell score; and technological characteristics were rennet coagulation time, curd firming time, curd firmness 30 min after rennet addition to milk, and titratable acidity. Data of herd bulk milks were analyzed using a model that included fixed effects of region, herd nested within region, and season of milk analysis. An average good milk quality was reported in the dairy industry (especially concerning fat, protein, and casein percentages), and moderate to high correlations between composition and technological traits were observed. All factors included in the statistical model were significant in explaining the variation of the studied traits except for region effect in the analysis of casein and somatic cell score. Northeast and central-southern Italian regions showed the best performance for composition and technological features, respectively. Traits varied greatly across regions, which could reflect differences in herd management and strategies. Overall, less suitable milk for dairy processing was observed in summer. Results of the present study suggested that a constant monitoring of technological traits in the dairy industry is necessary to improve production quality at herd level and it may be a way to segregate milk according to its processing characteristics. [ABSTRACT FROM AUTHOR]

The aim of this study was to analyze the variation of different genetic diversity measures in 5 Italian local chicken breeds over a 4-yr period of conservation. The local breeds were Ermellinata di Rovigo, Padovana, Pépoi, Robusta Lionata, and Robusta Maculata. A total of 368 samples were chosen for the analysis among the birds hatched in the years 2002 and 2006. Genetic variation over 30 microsatellite loci was analyzed. All 30 microsatellites were polymorphic, with a total number of alleles equal to 251, a mean (±SD) of 8.367 ± 3.378 across populations and 3.233 ± 1.338 within population. After 4 yr of conservation, a loss of alleles occurred for all the microsatellites, with the exception of 4 loci. The total number of alleles and expected heterozygosity estimates significantly decreased during the 4 yr of conservation, whereas no significant differences were detected for the microsatellites polymorphism information content or for the observed heterozygosity estimates. A decrease of the inbreeding coefficient occurred for all the breeds, with the exception of Padovana and Robusta Lionata. All populations showed evidence of a persistent significant deviation from Hardy-Weinberg equilibrium caused by an excess of homozygotes, except Robusta Maculata, which reached the equilibrium in 2006. For Pépoi, Padovana, Ermellinata di Rovigo, and Robusta Maculata, molecular coancestry increased significantly (P < 0.001) after the 4 yr of conservation. No evident genetic structures were detectable within breed, both for 2002 and for 2006 individuals. However, a slight increase in the proportion of membership for each breed had occurred in the year 2006 compared with the data obtained in the year 2002. As consequence, within breed, individuals in 2006 appear more homogeneous, producing clearer, more distinctive and separated groups. Molecular markers analysis helped us monitor the genetic variability of local breeds involved in a conservation scheme, enabling the planning of new strategies for the improvement of in situ conservation schemes. [ABSTRACT FROM AUTHOR]

Abstract: The assessment of a method able to assign individuals to the breed of origin is needed to certify origin and quality of livestock products. A set of 21 microsatellites was tested for breed identification in four native Italian beef breeds: Chianina, Marchigiana, Romagnola, and Piemontese. Two statistical approaches, based on maximum likelihood and on a Bayesian method, were evaluated. Different marker sets, chosen in order of the highest gene diversity and F ST estimates were also tested. The Bayesian method performed better, achieving a correct assignment rate of about 90% even with six microsatellites. The marker sets with the highest gene diversity were shown to perform best. Considering a threshold probability of 90%, only 52.5% of the genotypes were correctly allocated. Such results are mainly due to the low genetic differentiation estimates among breeds (F ST =0.049). These findings suggest that markers with high gene diversity and the presence of private alleles should be investigated and the Bayesian method used. [Copyright &y& Elsevier]

Eggshell and shank color in poultry is an intriguing topic of research due to the roles in selection, breed recognition, and environmental adaptation. This study delves into the genomics foundations of shank and eggshell pigmentation in Italian local chickens through genome-wide association studies analysis to uncover the mechanisms governing these phenotypes. To this purpose, 483 animals from 20 local breeds (n = 466) and 2 commercial lines (n = 17) were considered and evaluated for shank and eggshell color. All animals were genotyped using the Affymetrix Axiom 600 K Chicken Genotyping Array. As regards shank color, the most interesting locus was detected on chromosome Z, close to the TYRP1 gene, known to play a key role in avian pigmentation. Additionally, several novel loci and genes associated with shank pigmentation, skin pigmentation, UV protection, and melanocyte regulation were identified (e.g., MTAP, CDKN2A, CDKN2B). In eggshell, fewer significant loci were identified, including SLC7A11 and MITF on chromosomes 4 and 12, respectively, associated with melanocyte processes and pigment synthesis. This comprehensive study shed light on the genetic architecture underlying shank and eggshell color in Italian native chicken breeds, contributing to a better understanding of this phenomenon which plays a role in breed identification and conservation, and has ecological and economic implications., (Copyright © 2024 The Authors. Published by Elsevier Inc. All rights reserved.)

Age at first calving (AFC) represents the nonproductive period of ∼2 yr in Holstein cows, and thus, it has a relevant effect on the cost of rearing replacements in the dairy herd. In the present study, we aimed to evaluate genetic and genomic aspects of AFC in the Italian Holstein population. Data of 4,206,218 heifers with first calving between 1996 and 2020 were used. Age at first calving averaged 26.09 ± 3.07 mo and decreased across years. Heritability was estimated using a linear animal model which included the fixed effects of herd-year-season of birth and classes of gestation length, and the random animal additive genetic effect fitted to a pedigree-based relationship matrix. The EBV and genomically EBV (GEBV) were obtained, and they were standardized to mean 100 and standard deviation 5, where animals above the mean are those contributing to reduce AFC. Heritability estimates of AFC ranged from 0.031 to 0.045. The trend of sires' GEBV was favorable and indicated a reduced AFC across years. Approximate genetic correlations between GEBV of AFC and GEBV of other economically important traits were calculated on a subset of genotyped females born after 2015. Moderate favorable associations of AFC with production traits (0.39-0.51), udder depth (0.40), interval from first to last insemination in heifer (-0.43), and longevity (0.34) were assessed. Overall, the greatest lifetime productive performances and most favorable days open in first lactation were observed when heifers calved at 22 to 23 mo. In contrast, progeny of sires with GEBV of AFC above the mean yielded more milk, fat, and protein in first lactation, and had shorter days open than progeny of sires with GEBV of AFC below the mean. Results suggested that breeding strategies to improve AFC should be pursued, also considering genetic correlations between AFC and traits which are already part of the Italian Holstein breeding objective. The inclusion of AFC in an aggregate index is expected to contribute to enhance farm income., (The Authors. Published by Elsevier Inc. on behalf of the American Dairy Science Association®. This is an open access article under the CC BY license (http://creativecommons.org/licenses/by/4.0/).)

Gestation length (GL) can potentially affect health and performance of both the dam and the newborn calf, and it is controlled by two genetic components, direct and maternal. This means that both the calf (direct effect) and the cow (maternal effect) genotypes contribute to determine GL and its variability. The aims of the present study were to estimate direct and maternal variance components of GL, develop a routine genetic evaluation of GL in Italian Holstein and evaluate potential (un)favourable associations with traits for which selection is undertaken in this population. A multiple-trait repeatability linear animal model was employed for the estimation of variance components considering GL in first and later parities as different traits. The posterior mean (PM) of heritability of the direct effect was 0.43 for first parity and 0.35 for later parities. The PM of heritability of the maternal effect was lower, being 0.08 for primiparae and 0.06 for pluriparae. The posterior standard deviation (PSD) of the heritability estimates was small, ranging from 0.001 to 0.005. The relationship of direct and maternal effects with important traits such as milk yield and fertility indicated that selecting for extreme GL, longer or shorter, may have negative consequences on several traits, suggesting that GL has an intermediate optimum in dairy cattle. In conclusion, this study reveals that selecting an intermediate GL in the Italian Holstein population is advisable. Although scarcely variable compared to other conventional traits for which Italian Holstein is selected, GL is heritable and a deeper knowledge can be useful for decision-making at the farm level., (© 2023 The Authors. Journal of Animal Breeding and Genetics published by John Wiley & Sons Ltd.)

Among Italian dairy cattle, the Holstein is the most reared breed for the production of Parmigiano Reggiano protected designation of origin cheese, which represents one of the most renowned products in the entire Italian dairy industry. In this work, we used a medium-density genome-wide data set consisting of 79,464 imputed SNPs to study the genetic structure of Italian Holstein breed, including the population reared in the area of Parmigiano Reggiano cheese production, and assessing its distinctiveness from the North American population. Multidimensional scaling and ADMIXTURE approaches were used to explore the genetic structure among populations. We also investigated putative genomic regions under selection among these 3 populations by combining 4 different statistical methods based either on allele frequencies (single marker and window-based) or extended haplotype homozygosity (EHH; standardized log-ratio of integrated EHH and cross-population EHH). The genetic structure results allowed us to clearly distinguish the 3 Holstein populations; however, the most remarkable difference was observed between Italian and North American stock. Selection signature analyses identified several significant SNPs falling within or closer to genes with known roles in several traits such as milk quality, resistance to disease, and fertility. In particular, a total of 22 genes related to milk production have been identified using the 2 allele frequency approaches. Among these, a convergent signal has been found in the VPS8 gene which resulted to be involved in milk traits, whereas other genes (CYP7B1, KSR2, C4A, LIPE, DCDC1, GPR20, and ST3GAL1) resulted to be associated with quantitative trait loci related to milk yield and composition in terms of fat and protein percentage. In contrast, a total of 7 genomic regions were identified combining the results of standardized log-ratio of integrated EHH and cross-population EHH. In these regions candidate genes for milk traits were also identified. Moreover, this was also confirmed by the enrichment analyses in which we found that the majority of the significantly enriched quantitative trait loci were linked to milk traits, whereas the gene ontology and pathway enrichment analysis pointed to molecular functions and biological processes involved in AA transmembrane transport and methane metabolism pathway. This study provides information on the genetic structure of the examined populations, showing that they are distinguishable from each other. Furthermore, the selection signature analyses can be considered as a starting point for future studies in the identification of causal mutations and consequent implementation of more practical application., (© 2023, The Authors. Published by Elsevier Inc. and Fass Inc. on behalf of the American Dairy Science Association®. This is an open access article under the CC BY license (http://creativecommons.org/licenses/by/4.0/).)

Background: Availability of single nucleotide polymorphism (SNP) genotyping arrays and progress in statistical analyses have allowed the identification of genomic regions and genes under selection in chicken. In this study, SNP data from the 600 K Affymetrix chicken array were used to detect signatures of selection in 23 local Italian chicken populations. The populations were categorized into four groups for comparative analysis based on live weight (heavy vs light) and geographical area (Northern vs Southern Italy). Putative signatures of selection were investigated by combining three extended haplotype homozygosity (EHH) statistical approaches to quantify excess of haplotype homozygosity within (iHS) and between (Rsb and XP-EHH) groups. Presence of runs of homozygosity (ROH) islands was also analysed for each group., Results: After editing, 541 animals and 313,508 SNPs were available for statistical analyses. In total, 15 candidate genomic regions that are potentially under selection were detected among the four groups: eight within a group by iHS and seven by combining the results of Rsb and XP-EHH, which revealed divergent selection between the groups. The largest overlap between genomic regions identified to be under selection by the three approaches was on chicken chromosome 8. Twenty-one genomic regions were identified with the ROH approach but none of these overlapped with regions identified with the three EHH-derived statistics. Some of the identified regions under selection contained candidate genes with biological functions related to environmental stress, immune responses, and disease resistance, which indicate local adaptation of these chicken populations., Conclusions: Compared to commercial lines, local populations are predominantly reared as backyard chickens, and thus, may have developed stronger resistance to environmental challenges. Our results indicate that selection can play an important role in shaping signatures of selection in local chicken populations and can be a starting point to identify gene mutations that could have a useful role with respect to climate change., (© 2023. The Author(s).)

The identification of the dwarf phenotype in chicken is based on body weight, height, and shank length, leaving the differentiation between dwarf and small breeds ambiguous. The aims of the present study were to characterize the sequence variations associated with the dwarf phenotype in three Italian chicken breeds and to investigate the genes associated with their phenotype. Five hundred and forty-one chickens from 23 local breeds (from 20 to 24 animals per breed) were sampled. All animals were genotyped with the 600 K chicken SNP array. Three breeds were described as "dwarf", namely, Mericanel della Brianza (MERI), Mugellese (MUG), and Pepoi (PPP). We compared MERI, MUG, and PPP with the four heaviest breeds in the dataset by performing genome-wide association studies. Results showed significant SNPs associated with dwarfism in the MERI and MUG breeds, which shared a candidate genomic region on chromosome 1. Due to this similarity, MERI and MUG were analyzed together as a meta-population, observing significant SNPs in the LEMD3 and HMGA2 genes, which were previously reported as being responsible for dwarfism in different species. In conclusion, MERI and MUG breeds seem to share a genetic basis of dwarfism, which differentiates them from the small PPP breed.

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 < 0.01). Further, when considering the extreme inbreeding percentile classes moving from the 5th lowest to the 95th highest, there was a reduction of -263 kg and -561 kg per lactation for FPED and FROH. Increased inbreeding, estimated by FPED and FROH, had also a negative effect on PY and FY, either fit as a regressor or percentile classes. When evaluating the impact of inbreeding based on runs of homozygosity (ROH) length classes, longer ROH (over 8 Mb) had a negative effect in all traits, indicating that recent inbreeding might be more harmful than the ancestral one. Finally, results within chromosome homozygosity highlighted specific chromosomes with a more deleterious effect on productive traits., (© The Author(s) 2023. Published by Oxford University Press on behalf of the American Society of Animal Science.)

The recovery, safeguarding, and valorization of autochthonous poultry breeds may contribute toward the preservation of animal biodiversity and utilization of marginal lands that otherwise offer little agricultural or industrial value. A key strategy in promoting local breeds involves the characterization of morphological traits and productive performances, which are influenced by the breed's genetic make-up as well as its environment. The Mugellese breed is an Italian local poultry breed originating in the Mugello area of north-east Tuscany. It is characterized by frugality, resilience and resistance to disease, cold, and heat stress. Moreover, these birds are particularly suitable for free-range farming. The Mugellese chicken is described as a dwarf breed with a medium neck, broad shoulders, fairly long and horizontal wings, wide, and well-developed breast (especially in the hen). Over the course of a 1-yr observation and data collection period, involving 23 breeders and 405 adult chickens, the Mugellese breed showed the following performances: 1) a hen-day egg production characterized by 2 major peaks: the first in the spring time (March-April, 65.75%), and the second in the late summer period (August-September, 51.86%); 2) high true fertility values (94.35%) throughout the entire breeding season; 3) a weight gain of 732.44 ± 117.06 g and a feed conversion ratio of 3.94 ± 2.42 at an age of 140 d; 4) a slaughter yield of 77.80% (± 3.91); v) a respective protein, fat, and mineral content in the yolk and albumen were: 27.21 ± 4.21 g, 57.77 ± 1.03 g and 3.47 ± 0.40 g per 100 g of yolk; and 82.50 ± 0.57 g, 0.12 ± 0.01 g and 5.43 ± 0.34 g per 100 g of albumen. More data are needed to validate the data obtained in this trial., Competing Interests: DISCLOSURES The authors declare that they have no competing interests., (Copyright © 2022 The Authors. Published by Elsevier Inc. All rights reserved.)

The aim of this study was to conduct a genome-wide comparative analysis of 8 local Italian chicken breeds (Ermellinata di Rovigo, Millefiori di Lonigo [PML], Polverara Bianca, Polverara Nera, Padovana, Pepoi [PPP], Robusta Lionata, and Robusta Maculata), all under a conservation plan, to understand their genetic diversity and population structure. A total of 152 animals were analyzed using the Affymetrix Axiom 600 K Chicken Genotyping Array. The levels of genetic diversity were highest and lowest in PML and PPP, respectively. The results of genomic inbreeding based on runs of homozygosity (ROH; F ROH ) showed marked differences among breeds and ranged from 0.161 (PML) to 0.478 (PPP). Furthermore, in all breeds, short ROH (<4 Mb in length) were more frequent than long segments. Patterns of genetic differentiation, model-based clustering, and neighbor networks showed that most breeds formed nonoverlapping clusters and were clearly separate populations. The 2 Polverara breeds shared a similar genetic background and showed the lowest genetic differentiation in comparison with purebred lines; the local populations showed separated groups. PPP and PML were closer to the group of the purebred broiler lines (BRSA, BRSB, BRDA, and BRDB). Six genomic regions are presented as hotspots of autozygosity among the Italian chicken breeds, with candidate genes involved in multiple morphological phenotypes as breast muscle, muscle dry matter content, and body weight. This study is the first exhaustive genome-wide analysis of the diversity of these Italian local chickens from Veneto region. We conclude that breeds have conserved authentic genetic patterns. The results are of significant importance because they will help design and implement conservation strategies. In fact, the conservation of these breeds may also have positive impacts on the local economy, niche traditional markets, and offering a source of high-quality products to consumers. In this context, genomic information may play a crucial role in the management of local breeds., (Copyright © 2020. Published by Elsevier Inc.)

It is known that heat stress affects dairy cow performance in multiple ways: physiological, behavioral, reproductive, and productive. The aim of the present study was to determine if a threshold of temperature-humidity index (THI) exists for multiple milk production traits (milk yield, fat-corrected milk, protein and fat yield and percentage, energy-corrected milk, cheese production, and cheese yield) in Italian Brown Swiss dairy cows from the period 15 d before the day of the Italian Breeders Association test-day sampling. A 10-yr data set (2009-2018) containing 202,776 test-day records of 23,296 Brown Swiss cows was matched with the maximum THI. In all parities considered, no THI thresholds were observed for milk yield in Brown Swiss. In contrast, a THI threshold of 75 was identified for fat-corrected milk. No THI threshold was found for fat percentage, but fat yield showed the highest THI thresholds in cows of first and second parity. Protein yield and cheese production were affected by heat stress with average THI threshold of 74. The THI thresholds identified indicate that the Brown Swiss breed has higher thermal tolerance versus literature values reported for Holstein cows. As THI rises, Brown Swiss cows tend to produce the same volume of milk, but with a decreasing quality with regard to components. Further study is necessary to estimate the genetic component of heat tolerance, in Brown Swiss cattle, considering that the correct estimation of THI thresholds represents the first step to identify components that could be included in selection procedures., (The Authors. Published by Elsevier Inc. and Fass Inc. on behalf of the American Dairy Science Association®. This is an open access article under the CC BY-NC-ND license (http://creativecommons.org/licenses/by-nc-nd/4.0/).)

The aim of the present study was to assess genetic variation and heritability of a novel indicator of udder health, milk differential somatic cell count (DSCC), which represents the percentage of neutrophils plus lymphocytes in the total somatic cell count (SCC). Furthermore, we estimated genetic and phenotypic correlations of DSCC with other milk traits routinely measured in Italian Holstein cows. Besides DSCC, test-day data included milk yield, composition traits (i.e., fat, protein, casein, and lactose percentages), pH, milk urea nitrogen, and SCC. After editing, the final data set included 10,709 test-day records of 5,142 cows in 299 herds. Mean of DSCC was 62.07%, which means that macrophages were approximately 38% of total SCC. Comparing our results with the literature offered compelling evidence of the importance of acquiring information about the proportion of the different cell types in milk to better define the udder health status. In addition, our analysis revealed, for the first time, that DSCC is a heritable trait, and heritability (0.08 ± 0.02) was higher than that of traditional somatic cell score (0.04 ± 0.02). Nevertheless, heritability of DSCC is still low compared with milk yield and quality traits. Single-trait analysis within parity showed that DSCC was less heritable in primiparous than in multiparous cows, whereas bivariate analysis confirmed that DSCC and somatic cell score were 2 different traits, as their genetic and phenotypic correlations differed from unity. From a genetic point of view, the DSCC was positively weakly associated with milk yield, lactose percentage, and milk urea nitrogen, and negatively associated with pH. Our findings contributed to the understanding of the genetic background of DSCC and are a precursor to the potential use of DSCC in breeding programs to enhance cow resistance to mastitis. However, further research is needed to determine the weight this novel trait should receive in a selection program aimed to reduce udder health problems., (Copyright © 2019 American Dairy Science Association. Published by Elsevier Inc. All rights reserved.)

The aim of the present study was to characterize alternative somatic cell count (SCC) traits that could be exploited in genetic selection for mastitis resistance. Data were from 66,407 first-parity Holsteins in 404 herds. Novel SCC traits included average somatic cell score (SCS, log-transformation of SCC) in early lactation (SCS&#95;150), standard deviation of SCS of the entire lactation (SCS&#95;SD), the presence of at least one test-day (TD) SCC >400,000 cells/mL in the lactation, and the ratio of number of TD SCC >400,000 cells/mL to total number of TD in the lactation. Novel traits and lactation-mean SCS (SCS&#95;LM) were analyzed using linear mixed or logistic regression models, including month of calving, year of calving, number of TD, and milk yield as fixed effects, and herd and residual as random terms. A multitrait linear animal model was applied to a random subset of 152 herds (n = 22,695 cows) to assess heritability of and genetic correlations between SCC traits. Alternative SCC traits were affected by the environmental factors included in the model; in particular, results suggested a seasonal effect and a tendency toward an improvement of the udder health status in the last years. Association was also found between novel SCC traits and milk production. Alternative SCC traits exhibited coefficients of additive genetic variation that were similar to or larger than that of traditional SCS&#95;LM. Heritability of novel SCC traits was smaller than heritability of SCS&#95;LM (0.126 ± 0.014), ranging from 0.044 ± 0.008 (SCS&#95;SD) to 0.087 ± 0.010 (SCS&#95;150). Genetic correlations between SCC traits ranged from 0.217 ± 0.096 (SCS&#95;150 and SCS&#95;SD) to 0.969 ± 0.010 (SCS&#95;LM and SCS&#95;150). Alternative SCC traits exhibited additive genetic variation that is potentially exploitable in breeding programs of Italian Holstein population to improve resistance to mastitis., (Copyright © 2018 American Dairy Science Association. Published by Elsevier Inc. All rights reserved.)

The aim of the present study was to determine the allele frequencies of the diacylglycerol acyltransferase (DGAT1) K232A mutation in Italian Holstein bulls and to estimate the effect of the mutation on milk yield, composition, somatic cell score, and coagulation traits (rennet coagulation time and curd firmness). For this purpose, 349 Italian Holstein bulls were genotyped for the DGAT1 mutation on chromosome 14. Association analysis was performed by regressing the number of copies for the K allele on the deregressed estimated breeding value of the individual. Breeding values were calculated using field data routinely collected in Northeast Italy. The frequencies of the AA, KA, and KK genotypes were 59.6, 32.1, and 8.3%, respectively, and the minor allele frequency (K variant) was 24.7%. The K allele was significantly associated with greater fat yield and fat, protein, and casein percentages and with reduced protein:fat ratio. The association between the DGAT1 mutation and somatic cell score was not significant, whereas a favorable association between presence of the K allele and milk coagulation properties was found. Results from the present study confirmed the effect of the diallelic DGAT1 polymorphism K232A on milk production traits and, for the first time, provided evidence that this mutation also affects milk coagulation properties in the Italian Holstein breed., (Copyright © 2018 American Dairy Science Association. Published by Elsevier Inc. All rights reserved.)

The aim of this study was to compare the intra and inter genetic variability and population structure of 7 indigenous chicken breeds of the Veneto region, through a novel panel of 64 SNP, each located in an exonic region and mostly on different chromosomes. A total of 753 blood samples from 7 local chicken breeds (Ermellinata di Rovigo, Millefiori di Lonigo, Polverara, Pepòi, Robusta Lionata, Robusta Maculata, and Padovana) was collected and analyzed. Two strains of Polverara (Nera and Bianca) and Padovana (Dorata and Camosciata) were included in the study. The observed heterozygosity ranged from 0.124 (Pèpoi) to 0.244 (Ermellinata di Rovigo), and the expected heterozygosity varied from 0.132 (Millefiori di Lonigo) to 0.300 (Ermellinata di Rovigo). Global FIS results (0.114) indicated a low-medium inbreeding effect, with values ranging from 0.008 (Millefiori di Lonigo) to 0.223 (Ermellinata di Rovigo). Pairwise FST values (0.167) for all populations ranged from 0.020 (Polverara Nera and Polverara Bianca) to 0.193 (Robusta Lionata and Polverara Nera), indicating that the studied breeds were genetically highly differentiated. The software STRUCTURE was used to detect the presence of population substructures, and the most probable number of clusters (K) of the 10 chicken populations was at K = 8. The affiliation was successful in all Veneto chicken breeds. The present SNP marker results, compared with previous data obtained using microsatellites, provided a reliable estimate of genetic diversity within and between the studied breeds, and demonstrated the utility of the proposed panel as a rapid, efficient, and cost-effective tool for periodical monitoring of the genetic variability among poultry populations. In addition, the present SNP panel could represent a resource for a systematic approach with relevant impact on breeding program decisions and could turn out to be a reliable tool for genetic traceability of indigenous chicken meat. Adoption of a periodical monitoring system of genetic diversity is a fundamental tool in conservation actions and should increase the value of typical and niche products., (© 2017 Poultry Science Association Inc.)

Advances in DNA-based marker technology have enabled the identification of genomic regions underlying complex phenotypic traits in livestock species. The incorporation of detected quantitative trait loci into genetic evaluation provides great potential to enhance selection accuracies, hence expediting the genetic improvement of economically important traits. The objective of the present study was to investigate 96 single nucleotide polymorphisms (SNP) located in 53 candidate genes previously reported to have effects on milk production and quality traits in a population of highly selected Holstein-Friesian bulls. A total of 423 semen samples were used to genotype the bulls through a custom oligo pool assay. Forty-five SNP in 32 genes were found to be associated with at least 1 of the tested traits. Most significant and favorable SNP trait associations were observed for polymorphisms located in CCL3 and AGPAT6 genes for fat yield (0.037 and 0.033 kg/d, respectively), DGKG gene for milk yield (0.698 kg/d), PPARGC1A, CSN1S1, and AGPAT6 genes for fat percentage (0.127, 0.113, and 0.093%, respectively), GHR gene for protein (0.064%) and casein percentage (0.053%), and TLR4 gene for fat (0.090%), protein (0.066%), and casein percentage (0.050%). Somatic cell score was favorably affected by GHR (-0.095) and POU1F1 (-0.137), and interesting SNP-trait associations were observed for polymorphisms located in CSN2, POU1F1, and AGPAT6 genes for rennet coagulation time (-0.592, -0.558, and -0.462 min, respectively), and GHR and CSN2 genes for curd firmness 30 min after rennet addition (1.264 and 1.183 mm, respectively). In addition to the influence of individual SNP, the effects of composite genotypes constructed by grouping SNP according to their individual effects on traits considered in the analysis were also examined. Favorable and significant effects on milk traits were observed for 2 composite genotypes, one including 10 SNP and the other 4 SNP. The former was associated with an increase of milk (0.075 kg/d), fat (0.097 kg/d), protein (0.083 kg/d), and casein yields (0.065 kg/d), and the latter was associated with an increase of fat (0.244%), protein (0.071%), and casein percentage (0.047%). Although further research is required to validate the identified SNP loci in other populations and breeds, our results can be considered as a preliminary foundation for further replication studies on gene-assisted selection programs., (Copyright © 2017 American Dairy Science Association. Published by Elsevier Inc. All rights reserved.)

The aim of this study was to investigate the effect of pregnancy stage on milk yield, composition traits, and milk coagulation properties in Italian Holstein cattle. The data set included 25,729 records from 3,995 first-parity cows calving between August 2010 and August 2013 in 167 herds. The traits analyzed were milk yield (kg/d), fat (%), protein (%), casein (%), and lactose (%) contents, pH, somatic cell score, rennet coagulation time (min), and curd firmness (mm). To better understand the effect of gestation on the aforementioned traits, each record was assigned to one of the following classes of pregnancy stage: (1) nonpregnant, (2) pregnant from 1 to 120d, (3) pregnant from 121 to 210d, and (4) pregnant from 211 to 310d. Gestation stage significantly influenced all studied traits with the exception of somatic cell score. Milk production decreased and milk quality improved from the fourth month of pregnancy onward. For all traits, nonpregnant cows performed very similarly to cows in the first period of gestation. Rennet coagulation time and curd firmness were influenced by pregnancy stage, especially in the last weeks of gestation when milk had better coagulation characteristics; this information should be accounted for to adjust test-day records in genetic evaluation of milk coagulation properties., (Copyright © 2016 American Dairy Science Association. Published by Elsevier Inc. All rights reserved.)

Background: Recently, selection for milk technological traits was initiated in the Italian dairy cattle industry based on direct measures of milk coagulation properties (MCP) such as rennet coagulation time (RCT) and curd firmness 30 min after rennet addition (a30) and on some traditional milk quality traits that are used as predictors, such as somatic cell score (SCS) and casein percentage (CAS). The aim of this study was to shed light on the causal relationships between traditional milk quality traits and MCP. Different structural equation models that included causal effects of SCS and CAS on RCT and a30 and of RCT on a30 were implemented in a Bayesian framework., Results: Our results indicate a non-zero magnitude of the causal relationships between the traits studied. Causal effects of SCS and CAS on RCT and a30 were observed, which suggests that the relationship between milk coagulation ability and traditional milk quality traits depends more on phenotypic causal pathways than directly on common genetic influence. While RCT does not seem to be largely controlled by SCS and CAS, some of the variation in a30 depends on the phenotypes of these traits. However, a30 depends heavily on coagulation time. Our results also indicate that, when direct effects of SCS, CAS and RCT are considered simultaneously, most of the overall genetic variability of a30 is mediated by other traits., Conclusions: This study suggests that selection for RCT and a30 should not be performed on correlated traits such as SCS or CAS but on direct measures because the ability of milk to coagulate is improved through the causal effect that the former play on the latter, rather than from a common source of genetic variation. Breaking the causal link (e.g. standardizing SCS or CAS before the milk is processed into cheese) would reduce the impact of the improvement due to selective breeding. Since a30 depends heavily on RCT, the relative emphasis that is put on this trait should be reconsidered and weighted for the fact that the pure measure of a30 almost double-counts RCT.

The study aimed to characterize muscle fiber type of the pectoralis major muscle of slow-growing chickens belonging to the Padovana local breed, the commercial strain Berlanda gaina, and their cross. Forty-five chickens (both males and females) from the different genotypes were grown up to 180 d. Histochemical and morphometrical analyses were performed to characterize muscle fiber types, myofiber density, and myofiber size of the different genotypes. The effects of genotype, sex, and their interaction were estimated. Muscle samples appeared almost entirely made up of IIB fiber type, whereas a low percentage of area (5 to 6%) was composed of hypercontracted fiber. Myofiber density was significantly higher (P < 0.05) in Padovana strains and cross-sectional area was significantly lower (P < 0.01) than in Berlanda strain. Muscle fiber characteristics appeared not to be affected by the interaction of genotype × sex.

Predictions of growth are important factors that contribute to the profitability of an operation in poultry production. Modern commercial hybrids have a higher body growth in comparison with the local purebreds. However a niche market for meat and egg poultry production needs to be established using local purebreds to promote biodiversity. The aim of this study was to model the growth response of male and female chickens belonging to 5 local Italian populations: a commercial slow-growing hybrid (Berlanda, B), the Padovana pure breed [2 plumage varieties: silver, argentata (PA) and chamois, camosciata (PC)], and their crosses PC×B and PC×PA. A total of 398 one-day-old birds were reared until 180 d of age under indoor conditions. The linear and 3 nonlinear models (logistic, Gompertz, and Richards) were compared to study the growth patterns of these chicken populations. Significant (P < 0.01) differences were observed among the genotypes for several curve parameters. In males, PC×B showed the lowest age at inflection point, B showed the highest age and BW, whereas PA showed the highest age and the lowest weight. In females, the age at the inflection point did not differ among the groups; B showed the highest weight. All the nonlinear models gave a good fit of male and female data with R(2) ranging from 0.992 and 0.999, but the logistic equation had higher value of root mean square error than the Gompertz and the Richards values. Based on residual sum of squares for both sexes, the Richards model was better (P < 0.05) than the logistic but not superior to the Gompertz. The logistic equation showed an overestimation of initial BW for all the groups and sex. For Italian local chicken populations, the Richards model requires a measure of BW recorded at 90 d or after to obtain a good fit of the asymptotic weight. However, the Gompertz model has the advantage that it requires one less parameter than the Richards model.

The objectives of this research were to estimate genetic parameters for body condition score (BCS) and locomotion (LOC), and to assess their relationships with angularity (ANG), milk yield, fat and protein content, and fat to protein content ratio (F:P) in the Italian Holstein Friesian breed. The Italian Holstein Friesian Cattle Breeders Association collects type trait data once on all registered first lactation cows. Body condition score and LOC were introduced in the conformation scoring system in 2007 and 2009, respectively. Variance (and covariance) components among traits were estimated with a Bayesian approach via a Gibbs sampling algorithm and an animal model. Heritability estimates were 0.114 and 0.049 for BCS and LOC, respectively. The genetic correlation between BCS and LOC was weak (-0.084) and not different from zero; therefore, the traits seem to be genetically independent, but further investigation on possible departures from linearity of this relationship is needed. Angularity was strongly negatively correlated with BCS (-0.612), and strongly positively correlated with LOC (0.650). The genetic relationship of milk yield with BCS was moderately negative (-0.386), and was moderately positive (0.238) with LOC. These results indicate that high-producing cows tend to be thinner and tend to have better locomotion than low-producing cows. The genetic correlation of BCS with fat content (0.094) and F:P (-0.014) was very weak and not different from zero, and with protein content (0.173) was weak but different from zero. Locomotion was weakly correlated with fat content (0.071), protein content (0.028), and F:P (0.074), and correlations were not different from zero. Phenotypic correlations were generally weaker than their genetic counterparts, ranging from -0.241 (BCS with ANG) to 0.245 (LOC with ANG). Before including BCS and LOC in the selection index of the Italian Holstein breed, the correlations with other traits currently used to improve type and functionality of animals need to be investigated., (Copyright © 2013 Elsevier Masson SAS. All rights reserved.)

Recently, a general deterioration of milk coagulation properties (MCP) has been observed in Italy; thus, the prediction of noncoagulating (NC) milk, defined as milk not forming a curd within 30min from rennet addition, is of immediate interest in the Italian cheese industry. The present study investigated the ability of mid-infrared (MIR) spectroscopy to predict NC milk using individual and bulk samples from Holstein cows. Samples were selected according to MIR analysis to cover the range of coagulation time between 5 and 60min. Milks were then analyzed for MCP through the reference instrument (Formagraph) over an extended testing period of 60min to identify coagulating and NC samples. Measured traits were rennet coagulation time, curd-firming time, and curd firmness 30 and 60min after rennet addition. Results showed no specific spectral information distinguishing NC from coagulating samples. The most accurate prediction model was developed for rennet coagulation time followed by curd-firming time and curd firmness 30min after rennet addition, whereas curd firmness 60min after enzyme addition could not be accurately predicted. Based on these findings, MIR spectroscopy might be proposed in payment systems to reward or penalize milk according to MCP. Moreover, the ability of MIR spectroscopy to predict the MCP of samples that form a curd beyond 30min from enzyme addition may be of interest for genetic improvement of coagulation traits in dairy breeds, because until now most studies have excluded NC information from genetic analysis, leading to possible biases in the estimation of genetic parameters and in the prediction of sire's merit for MCP., (Copyright © 2013 American Dairy Science Association. Published by Elsevier Inc. All rights reserved.)

The objectives of this study were to determine genetic variation and to analyze population structure of 6 Italian local chicken breeds involved in a conservation program. Twenty microsatellite markers were investigated in 337 birds belonging to 6 breeds: Ermellinata di Rovigo, Robusta Maculata, Robusta Lionata, Pépoi, Padovana, and Polverara; a commercial layer cross was used as reference. One hundred twelve alleles were detected in the overall population, with a mean number of 5.6 +/- 2.1 alleles per locus. For the local breeds, the observed and expected heterozygosity ranged from a minimum of 0.240 to a maximum of 0.413 and from 0.243 to 0.463 for the Pépoi and Polverara breeds, respectively. Deviation from Hardy-Weinberg equilibrium was observed in 5 breeds and in the commercial cross. The overall population heterozygote deficiency was 0.427, the average inbreeding coefficient was 0.097, and the heterozygote deficiency due to breed subdivisions was 0.437. Reynolds' distances were used to draw an unrooted neighbor-joining tree, which topology gave information on the genetic origin of these breeds and confirmed their known history. The estimated molecular kinship within a breed ranged from 0.559 to 0.769, evidencing high coancestry. Structure analysis was performed to detect the presence of population substructures. Inferred clusters corresponded to the different breeds, without presence of admixture. The exception was the Polverara breed, for which a more complex genetic structure was found. The results supported the decision of safeguarding these breeds as an important reservoir of genetic diversity and confirmed the usefulness of microsatellite markers to characterize and to monitor genetic variability in local chicken breeds.

The present study was a contribution on the genetic characterization of the Burlina local cattle breed, and an approach to understanding the relationships between Burlina, Holstein Friesian and Brown Swiss which represent the majority of the dairy cattle reared nowadays in North-East Italy. The obtained results helped to clarify the genetic diversity and distinctiveness of Burlina population. In particular, the low genetic distance between Burlina and Holstein Friesian and the assignment of a moderate percentage of Burlina animals to Holstein Friesian suggested that crosses between them took place in the past, while crosses with Brown Swiss seemed to be less frequent. However, analyses of marker genotypes, showed a cluster with only Burlina individuals, which demonstrates the genetic distinctness of this breed. The Burlina breed showed the highest variability among the analysed breeds and its inbreeding coefficient was low. The data contribute to the feasibility of a conservation and selection programme for this breed and the results are useful for the implementation of a conservation strategy that should aim to conserve animals where the contribution from foreign breeds is as small as possible.

Milk coagulation properties (MCP) are an important aspect in assessing cheese-making ability. Several studies showed that favorable conditions of milk reactivity with rennet, curd formation rate, and curd strength, as well as curd syneresis, have a positive effect on the entire cheese-making process and subsequently on the ripening of cheese. Moreover, MCP were found to be heritable, but little scientific literature is available about their genetic aspects. The aims of this study were to estimate heritability of MCP and genetic correlations among MCP and milk production and quality traits. A total of 1,071 Italian Holstein cows (progeny of 54 sires) reared in 34 herds in Northern Italy were sampled from January to July 2004. Individual milk samples were collected during the morning milking and analyzed for coagulation time (RCT), curd firmness (a30), pH, titratable acidity, fat, protein, and casein contents, and somatic cell count. About 10% of individual milk samples did not coagulate in 31 min, so they were removed from the analyses. Estimates of heritability for RCT and a30 were 0.25 +/- 0.04 and 0.15 +/- 0.03, respectively. Estimates of genetic correlations between MCP traits and milk production traits were negligible except for a30 with protein and casein contents (0.44 +/- 0.10 and 0.53 +/- 0.09, respectively). Estimates of genetic correlations between MCP traits and somatic cell score were strong and favorable, as well as those between MCP and pH and titratable acidity. Selecting for high casein content, milk acidity, and low somatic cell count might be an indirect way to improve MCP without reducing milk yield and quality traits.