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Runs of homozygosity (ROH) are defined as long stretches of DNA homozygous at each polymorphic position. The proportion of genome covered by ROH and their length are indicators of the level and origin of inbreeding. In this study, we analysed SNP chip datasets (obtained using the Axiom OrcunSNP Array) of a total of 702 rabbits from 12 fancy breeds and four meat breeds to identify ROH with different approaches and calculate several genomic inbreeding parameters. The highest average number of ROH per animal was detected in Belgian Hare (~150) and the lowest in Italian Silver (~106). The average length of ROH ranged from 4.001 ± 0.556Mb in Italian White to 6.268 ± 1.355Mb in Ermine. The same two breeds had the lowest (427.9 ± 86.4 Mb, Italian White) and the highest (921.3 ± 179.8 Mb, Ermine) average values of the sum of all ROH segments. More fancy breeds had a higher level of genomic inbreeding (as defined by ROH) than meat breeds. Several ROH islands contain genes involved in body size, body length, pigmentation processes, carcass traits, growth, and reproduction traits (e.g.: AOX1, GPX5, IFRD1, ITGB8, NELL1, NR3C1, OCA2, TRIB1, TRIB2). Genomic inbreeding parameters can be useful to overcome the lack of information in the management of rabbit genetic resources. ROH provided information to understand, to some extent, the genetic history of rabbit breeds and to identify signatures of selection in the rabbit genome.

New climate regimes, variability and extreme events affect the livestock sector in many aspects, ranging from animal welfare, production, reproduction, diseases and their spread, feed quality and availability. Heat stress, especially when combined with excess or low humidity, exacerbates the perceived temperature or the drought conditions, respectively, increasing hazards for animals. Also, cold extremes, extraordinary windy conditions and altered radiation regimes are detrimental to both animals and fodder.In this context, the EU-funded SEBASTIEN project aims to provide stakeholders with a Decision Support System (DSS) for more efficient and sustainable management, and consequent valuation, of the livestock sector in Italy. SEBASTIEN DSS will integrate GIS, environmental and biological variables to generate updated risk maps for livestock diseases and zoonoses and their spread, alerting about the expected occurrence of stressing conditions for animals due to abiotic and biotic factors.The presence of parasites, vectors, and outbreaks will be combined with environmental data, gathered by spatially distributed meteorological and satellite monitoring, to detect conditions that can potentially favor or trigger the spread of related diseases. Sensor-based monitoring data will be integrated with the above information to determine ranges in animal parameters potentially associated with a higher risk of critical pathogen load or density of vectors potential carriers of diseases. Medium to long-term climate forecasts will support predicting possible shifts of favorable conditions that will open up new areas for parasites and pathogens. The vast amounts of data will be integrated and summarized into user-tailored information through a range of techniques, from empirical/statistical indicators to Machine Learning algorithms.

The use of sexed semen to produce purebred replacement heifers allows a large proportion of dairy cows to be mated to beef sires, and quantitative and qualitative improvements to be made to beef production from dairy herds. The major dairy and beef breeds are undergoing rapid genetic improvement as a result of more efficient selection methods, prompting a need to evaluate the meat production of crossbred beef × dairy cattle produced using current genetics. As part of a large project involving 125 commercial dairy farms, we evaluated the combined use of purebreeding with sexed semen and crossbreeding with semen from beef sires, particularly double-muscled breeds. A survey of 1,530 crossbred calves revealed that, whereas purebred dairy calves are destined almost exclusively for veal production, beef × dairy crossbred calves are also destined for beef production after fattening on either the dairy farm of birth or by specialized fatteners. In veal production, compared with Belgian Blue-sired calves (taken as the reference), double-muscled INRA 95-sired calves had a lighter slaughter weight (303 vs. 346 kg), but a greater dressing percent (62.3 vs. 58.4%). Limousin (also known as Limousine)-sired calves had a smaller average daily gain (1.26 vs. 1.34 kg/d), and lighter slaughter (314 vs. 346 kg) and carcass weights (182 vs. 201 kg). Last, Simmental-sired calves had a similar growth rate, but lighter carcass weight (177 vs. 201 kg), smaller dressing percentage (55.3 vs. 58.4%), and smaller muscularity scores (3.25 vs. 3.72). In the case of young bulls and heifers fattened on the dairy farm of birth, Belgian Blue-, Piemontese (also known as Piedmontese)-, and Limousin-sired calves performed similarly; the only exception was that Piemontese-sired calves had a greater dressing percentage. Belgian Blue- and Limousin-sired calves performed similarly when fattened by specialized beef producers. In both veal and beef production, the effects of dam breed were less important than sire breed. Considering the entire project, we can conclude that the combined use of sexed semen for purebreeding and conventional beef semen for terminal crossbreeding improves meat production from dairy herds, especially when the sires are double-muscled beef breeds.

Local breeds represent an underestimated resource in terms not only of their important cultural and economical role in marginal areas, but also because they often own a potential genetic pool well adapted to extreme conditions. This fact is of increasing interest, especially when considering climate global challenges where peculiar and uncommon traits could be advantageous. In this study, we genotyped 24 individuals belonging to the small residual Pagliarola sheep population using the OvineSNP50K array, in order to compare its genomic architecture with other 21 Italian local breeds. Moreover, we performed the fixation index (FST) outlier analysis to identify genes most differentiated between Pagliarola and Merino-derived Italian breeds. All population genetic analyses highlighted that Pagliarola breed represents a distinct genetic unit showing a genetic relationship with Merino-derived breeds underlying the close cultural connection between these breeds related to transhumance. However, Pagliarola breed resulted to be divided into two different sub-populations, named Pagliarola 1 (PAG-1) and Pagliarola 2 (PAG-2). Genetic diversity indices and inbreeding estimated from runs of homozygosity (FROH) indicated that while PAG-1 showed among the highest values, PAG-2 turned out strongly inbred, probably as a consequence of a founder effect. The FST outlier analysis identified the 5 most differentiated single nucleotide polymorphisms, two of which mapping within known genes (MACF1 and GLIS1) reported to be linked to feed efficiency and local adaption. All these information strongly suggest that proper conservation measures should be implemented in order to recover the Pagliarola population and its fundamental local products.HIGHLIGHTS All population genetic analyses highlighted that Pagliarola breed represent a distinct genetic unit, and clusters with the Merino-derived Italian breeds. The breed resulted to be divided into two different sub-populations. For the two Pagliarola sub-populations, the genetic diversity indices suggest a very different genetic makeup. Results from the Bayesian approach identified two know genes (MACF1and GLIS1) related to feed efficiency in livestock species and local adaptation. The information generated in this study strongly suggests that proper conservation measures should be implemented in order to recover the Pagliarola population.

The use of sexed semen to produce purebred replacement heifers allows a large proportion of dairy cows to be mated to double-muscled sires and for quantitative and qualitative improvements to be made to beef production from dairy herds. A survey of 1,285 crossbred calves showed that they are destined not only for veal production (like purebred dairy calves) but also for beef production. Crossbred calves obtained from Belgian Blue sires (sold on average at 34 d of age and 64 kg of weight) had a higher market value (€363/calf) than those obtained from double-muscled INRA 95 sires (€297/calf, used for veal production) and from Limousin sires (€216/calf for veal and €271/calf for beef production). As a sire breed, Simmental did not differ significantly from Belgian Blue, but as a dam breed, the crossbred calves fetched a higher price (€5.11/kg) than when Holstein was the dam breed (€4.50/kg). Compared with heifer calves, crossbred bull calves at sale were younger (34.1 vs. 37.2 d) and heavier (64.0 vs. 62.6 kg of live weight), fetched a higher price (€5.13 vs. €4.99/kg), and had a greater value (€328 vs. €312/calf). As the value of purebred dairy calves was about €80 to €100/calf, we are able to confirm that the combined use of sexed semen for pure-breeding and conventional beef semen for terminal crossbreeding can increase the income from dairy farms, especially when the sires are double-muscled beef bulls.

The extent to which genomic convergence shapes locally adapted phenotypes in different species remains a fundamental question in evolutionary biology. It would help assessing the relative role of historical contingencies versus determinism in evolution. To bring new insights to this debate we set up a framework which aimed to compare the adaptive trajectories of two domesticated mammal species co-distributed in diversified landscapes. We sequenced the genomes of 160 sheep and 161 goats extensively managed along environmental gradients, including temperature, rainfall, seasonality and altitude, to identify genes and biological processes shaping local adaptation. Allele frequencies at adaptive loci were rarely found to vary gradually along environmental gradients, but rather displayed a discontinuous shift at the extremities of environmental clines. Of the more than 430 adaptive genes identified, only 6 were orthologous between sheep and goats and those responded differently to environmental pressures, suggesting different adaptive mechanisms in these two closely related species. Such diversity of adaptive pathways may result from a high number of biological functions involved in adaptation to multiple eco-climatic gradients, and provides more arguments for the role of contingency and stochasticity in adaptation rather than repeatability and determinism.

Mastitis is one of the most prevalent diseases in dairy cattle and is the cause of considerable economic losses. Alongside somatic cell count (SCC), differential somatic cell count (DSCC) has been recently introduced as a new indicator of intramammary infection. The DSCC is expressed as a count or a proportion (%) of polymorphonuclear neutrophils plus lymphocytes (PMN-LYM) in milk somatic cells. These numbers are complemented to total somatic cell count or to 100 by macrophages (MAC). The aim of this study was to investigate the genetic variation and heritability of DSCC, and its correlation with milk composition, udder health indicators, milk composition, and technological traits in Holstein cattle. Data used in the analysis consisted in single test-day records from 2,488 Holstein cows reared in 36 herds located in northern Italy. Fourier-transform infrared (FTIR) spectroscopy was used to predict missing information for some milk coagulation and cheese-making traits, to increase sample size and improve estimation of the genetic parameters. Bayesian animal models were implemented via Gibbs sampling. Marginal posterior means of the heritability estimates were 0.13 for somatic cell score (SCS); 0.11 for DSCC, MAC proportion, and MAC count; and 0.10 for PMN-LYM count. Posterior means of additive genetic correlations between SCS and milk composition and udder health were low to moderate and unfavorable. All the relevant genetic correlations between the SCC traits considered and the milk traits (composition, coagulation, cheese yield and nutrients recovery) were unfavorable. The SCS showed genetic correlations of -0.30 with the milk protein proportion, -0.56 with the lactose proportion and -0.52 with the casein index. In the case of milk technological traits, SCS showed genetic correlations of 0.38 with curd firming rate (k20), 0.45 with rennet coagulation time estimated using the curd firming over time equation (RCTeq), -0.39 with asymptotic potential curd firmness, -0.26 with maximum curd firmness (CFmax), and of -0.31 with protein recovery in the curd. Differential somatic cell count expressed as proportion was correlated with SCS (0.60) but had only 2 moderate genetic correlations with milk traits: with lactose (-0.32) and CFmax (-0.33). The SCS was highly correlated with the log PMN-LYM count (0.79) and with the log MAC count (0.69). The 2 latter traits were correlated with several milk traits: fat (-0.38 and -0.43 with PMN-LYM and MAC counts, respectively), lactose percentage (-0.40 and -0.46), RCTeq (0.53 and 0.41), tmax (0.38 and 0.48). Log MAC count was correlated with k20 (+0.34), and log PMN-LYM count was correlated with CFmax (-0.26) and weight of water curd as percentage of weight of milk processed (-0.26). The results obtained offer new insights into the relationships between the indicators of udder health and the milk technological traits in Holstein cows.

Thirty-five years of pedigree data has been studied to investigate the role of the Herd Book in maintaining the genetic diversity and control the inbreeding while applying a selection scheme in local cattle breeds. More than 64,000 genealogical records of Maremmana beef cattle born from 1951 to 2019 were used to investigate demographic and genealogical structure of Maremmana breed in a time frame 1980-2015. Along these 35 years, the number of herds in the Herd Book increased 2.5-fold, and the number of pure animals raised from 4,849 to 10,984. The Effective Population Size (Ne) based on inbreeding coefficient (F) rate was 123.5 on average, with large periods under 100 (since 1990 to 2007) or even under 50 (since 2000 to 2005). With the support of the Herd Book, Maremmana recovered from a very critical Ne only in the last timeframe explored attaining a Ne of 380 in 2009, however still critical. The average generation interval for the whole population was 6.31 years, characterized by a larger interval in dams respect to sire (7.16 vs 5.36 years respectively). In 2015, the pedigree completeness index (PCI) over the 6 generation was 94.6% as valuable effect of the raised awareness about data recordings promoted by the Herd Book. In spite of the low population size, the smooth selection pressure (1 out of 10 in sire and 1 out of 2 in dams lines respectively) contributed to keep the inbreeding rate under control, (inbreeding raised from 0% of 1980 to 2.78% in 2015 with an average rate of 0.0725% per year) still improving the genetic make-up of the breed. However, in the last years both the average additive genetic relationships (AGR) and the inbreeding accelerate alarmingly (3.65% in 2017), calling for urgent safeguard measures. Our data support the Herd Book as an effective infrastructure to manage, improve and conserve local genetic resources: contributing to maintain pure animals, stimulate the record of reproductive information, keep inbreeding under observation, increase the effective population size and support the overall economic sustainability of the herds, ultimate in situ conservation sites. A step further into the genomics, likely guided by the Herd Book data, will boost the sustainable conservation of Maremmana genetic diversity, enabling the application of genomic breeding plan and models based on the optimal contribution approach.

Cattle domestication occurred at least twice independently and gave rise to the modern taurine and indicine cattle breeds. European cattle diversity is generally dominated by taurine cattle, although elevated levels of indicine ancestry have been recorded in several breeds from southern Europe. Here we use genome-wide high-density SNP genotyping data to investigate the taurine and indicine ancestry in southern European cattle, based on a dataset comprising 508 individuals from 23 cattle breeds of taurine, indicine and mixed ancestry, including three breeds from Central Italy known to exhibit the highest levels of indicine introgression among southern European breeds. Based on local genomic ancestry analyses, we reconstruct taurine and indicine ancestry genome-wide and along chromosomes. We scrutinise local genomic introgression signals and identify genomic regions that have introgressed from indicine into taurine cattle under positive selection, harbouring genes with functions related to body size and feed efficiency. These findings suggest that indicine-derived traits helped enhance Central Italian cattle through adaptive introgression. The identified genes could provide genomic targets for selection for improved cattle performance. Our findings elucidate the key role of adaptive introgression in shaping the phenotypic features of modern cattle, aided by cultural and livestock exchange among historic human societies.

The buffalo milk industry has economic and social relevance in Italy, as linked to the manufacture of traditional dairy products. To provide an overview of the current status of buffaloes&rsquo, performances on a large scale, almost 1 million milk test-day records from 72,294 buffaloes were available to investigate milk yield, energy corrected milk, fat, protein, and lactose content, and somatic cell score (SCS). Phenotypic correlations between milk traits were calculated and analysis of variance was carried out through a mixed model approach including fixed effect of parity, stage of lactation, sampling time, month of calving, and all their interactions and random effects of buffalo, herd-test-date, and residual. Third-parity buffaloes were the most productive in terms of milk yield, while the lowest solid content was detected in sixth parity buffaloes. A considerable gap between primiparous and multiparous buffaloes was observed for milk yield, especially in early- and mid-lactation. Overall, SCS progressively increased with parity and showed a negative correlation with milk yield in both primiparous (&minus, 0.12) and multiparous (&minus, 0.14) buffaloes. Results suggested that, at the industrial level, milk of primiparous buffaloes may be preferred for transformation purposes, since it was characterized by greater solid content and lower SCS. Results of this study provide a picture of the Italian population of buffaloes under systematic performance records and might be beneficial to both dairy industry and breeding organizations.

In central Asian countries, sheep (Ovis aries) and goats (Capra hircus) represent a key economic resource for millions of people living in rural communities and, at the same time, a critical source of greenhouse gas (GHG) emissions. This study aims to estimate GHG emissions of several economic traits of sheep and goats and investigate sustainable mitigation strategies. It advances beyond previous studies by calculating the GHG emissions of traits of economic importance rather than reporting average animal emission and can thus provide insights for creating better-targeted mitigation strategies. In dairy sheep in Tajikistan, the emission intensity (EI) decreased from 62.4 to 56.7 kg CO2-eq kg−1 of protein as the production of milk increased by 20%. In meat goats raised in Turkmenistan, the EI decreased by 2.6 kg CO2-eq kg−1 of protein when simulating an increase in meat production of + 20%. Improving female fertility by 10% scaled down the EI of meat sheep in Uzbekistan by 36 kg CO2-eq kg−1 of protein. The improvement of meat and milk productions, female fertility, and litter size and the reduction of mortality, and female culling can reduce the emission intensity of sheep and goats globally. Thus, genetic improvement of economic traits is an important global mitigation tool. Furthermore, improvement of national and international sheep and goat strategies can provide policymakers with valuable information to develop regional and global mitigation actions.

Objective of this study was to estimate genetic parameters of milk coagulation properties (MCPs) and individual laboratory cheese yield (ILCY) in a sample of 1018 Sarda breed ewes farmed in 47 flocks. Rennet coagulation time (RCT), curd-firming time (k 20) and curd firmness (a 30) were measured using Formagraph instrument, whereas ILCY were determined by a micromanufacturing protocol. About 10% of the milk samples did not coagulate within 30 min and 13% had zero value for k 20. The average ILCY was 36%. (Co)variance components of considered traits were estimated by fitting both single- and multiple-trait animal models. Flock-test date explained from 13% to 28% of the phenotypic variance for MCPs and 26% for ILCY, respectively. The largest value of heritability was estimated for RCT (0.23±0.10), whereas it was about 0.15 for the other traits. Negative genetic correlations between RCT and a 30 (−0.80±0.12), a 30 and k 20 (−0.91±0.09), and a 30 and ILCY (−0.67±0.08) were observed. Interesting genetic correlations between MCPs and milk composition (r G>0.40) were estimated for pH, NaCl and casein. Results of the present study suggest to use only one out of three MCPs to measure milk renneting ability, due to high genetic correlations among them. Moreover, negative correlations between ILCY and MCPs suggest that great care should be taken when using these methods to estimate cheese yield from small milk samples.

Using sexed semen to produce purebred replacement heifers makes it possible to mate a large proportion of dairy cows to double-muscled sires and to quantitatively and qualitatively improve beef production and increase the income from dairy herds. Net profit first depends on changes in the farm's overall fertility rate. The objective of this study was to analyze the conception rate in herds using a combination of conventional dairy semen (for pure- and crossbreeding), X-sorted dairy semen (to produce purebred replacement heifers), and conventional beef semen (for terminal crossbreeding). Data were obtained from 50,785 inseminations of 15,580 dairy cows (78% Holstein-Friesian, 15% Brown Swiss, 2% Simmental, and 5% crossbreds) from 106 dairy farms (average milk yield 35.1 ± 9.4 kg/d, with 3.76 ± 0.83% fat and 3.32 ± 0.39% protein contents). To account for the main potential confounders, we used separate generalized linear mixed-effects models for cows and virgin heifers. The results showed that the odds ratio of conception improved (1.00 to 1.34) with an increase in the average milk yield of the herd but worsened (1.12 to 0.70) with an increase in the milk yield of individual cows within herd. The summer months showed a strong reduction in the odds ratio of conception in cows (0.56 in July and August) but not in virgin heifers. Multiparous cows had a lower odds ratio of conception (0.85) than primiparous cows (1.00). The order of insemination did not affect the fertility of the cows or heifers, whereas the odds ratio of conception improved with advancing lactation (1.00 to 2.12). The Simmental cows were more fertile than Holstein-Friesians (1.37 vs. 1.00), whereas the fertility of the heifers was not affected by breed. Taking all these possible confounders into account simultaneously, in pure-breeding the odds ratio of conception using sexed semen did not differ from that using conventional dairy semen in cows (0.90 vs. 1.00) or in virgin heifers (0.95 vs. 1.00). However, crossbreeding using conventional beef and dairy semen improved the odds ratio of conception (1.10 and 1.17, respectively) in cows (1.37 using beef semen) and heifers (1.25 using dairy semen). The proportion of newborn heifer calves was ≥90% using sexed dairy semen. The combined use of sexed semen, especially on heifers, to produce purebred replacement females and beef semen to produce terminal crossbred calves was shown to have the potential to increase overall herd fertility, which could be further improved using sexed dairy semen to produce dairy crossbreds instead of purebred replacement heifers.

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 &lt, 1%. The highest rates of mating between half-siblings were observed for CAL and MUP (~9% and 6.5%, respectively), while the highest rate of parent&ndash, offspring mating was ~8% for MUP. Our findings describe the urgent situation of the three Tuscan breeds and support the application of conservation measures and/or the development of breeding programs. Development of breeding strategies is suggested for the Sardinian breeds.

The aim of this work was to develop a new selection index and to estimate the annual genetic response for milk yield (MY), milk components, composite feet and legs (FL) and mammary system (MS) in the Italian Mediterranean Buffalo (IMB) population under different selection indices and breeding objectives. Buffalo milk has excellent nutritional characteristics as a consequence of the high percentage of its constituents. These milk properties are desirable for the dairy industry because mainly used to make Campana buffalo mozzarella PDO cheese. Former breeding objective of the National Association of Buffalo Breeders (ANASB) was based only on the evaluation of kg of mozzarella production (PKM index). Hence, selection by PKM was mainly carried out according to the kg of fat and protein and consequently milk yield. To address the call of mozzarella cheese manufacturers and farmers community, who both asked for a more balanced breeding objective, annual genetic response for the aforementioned traits and correlated response with mozzarella cheese production were estimated using selection index theory. Genetic parameters among traits included in the selection index and traits included in the breeding objectives were estimated using data from 7199 buffalo cows and a pedigree including 19,574 buffalos. A multitrait animal model was fitted using a Bayesian implementation via Gibbs sampling. Three alternative breeding objectives were formulated according to relative weight given to MY, cheese production, FL and MS: 5:45:30:20 (S1), 30:35:15:20 (S2) and 45:45:5:5 (S3). Traits included in the selection index were MY, fat and protein percentage, FL and MS. Cheese production had a negative genetic correlation with MY (-0.54), a null correlation with MS (-0.01), a positive correlation with FL (0.25), fat % (0.15) and protein % (0.28). S1 breeding objective had the largest and positive genetic response in terms of cheese production, fat and protein %. However, MY was strongly penalised, with a negative genetic response. S3 showed the best results with a positive genetic response for all traits included in the breeding objective ranging from 0.02 to 0.05 genetic standard deviation. Relative emphasis of selection criteria in breeding objective S3, namely MY, fat %, protein %, FL and ML were 21%, 15%, 20%, 24% and 20 %, respectively.

Italy is a peninsula extending far into the Mediterranean Sea. The estimated population is 60.4 million people (data 2017). The population is unevenly distributed. The Po Valley, in northern Italy, and the metropolitan areas of Rome and Naples, in central and southern Italy, are densely populated, while the Alps and Apennines highlands, as well as the island of Sardinia are very sparsely populated. The average population density is 201 inhabitants per square kilometre, a value that is higher than that of most western European countries. Italy has a surface area of 301,338 km 2 . The territory is mostly hilly (42%) with plain areas only covering 23%, mainly in the Po Valley, which is the country's largest plain (44,000 km 2 ). The rest of the territory is covered by mountain areas (35%). The Alps, along the northern border, and the Apennines, which form the backbone of the entire peninsula and the island of Sicily, are the largest mountainous systems. Italy lies in the temperate zone but there is a strong climate variation between the northern regions bordering the European continent, and the south, surrounded by the Mediterranean Sea, due to the considerable length of the peninsula (1,200 km). Three main biogeographic regions dominate the country: - the Alpine area, which has a continental mountain climate; - the continental climate area, mainly represented by the Po Valley, characterised by hot summers and severe winters; - the Mediterranean region, covering the central and southern Italian regions and the islands of Sicily and Sardinia. The most important climate trait is the concentration of rainfall during the relatively mild winters and its total absence during the hot summers, associated with a large intra- and inter-annual variability. Italy has a variety of soils as well, originating from several types of parent materials, at different altitudes, under different climate conditions in preceding eras.Dark-brown podzols are very common in the Alps, where rainfall is heavy. In the Apennines, brown podzolic soils predominate, supporting forests, meadows and pastures. Rendzina soils are characteristic of the limestone and magnesium limestone mountain pastures and of many meadows and beech forests of the Apennines. Sparse red-earth soils, rocky soils, clays, dune sands and gravel can be also found.

SummaryGlobally, rural cattle keeping communities actively select and breed indigenous cattle to satisfy their interests and enhance adaptation to local landscapes. This study investigated how traditional systems in Uganda have shaped the morphometric population structure of indigenous cattle breeds. Ten linear morphometric traits were interrogated amongst 801 female cattle, comprising 46 Nganda (Bos indicus), 368 Ankole (B. taurus indicus) and 387 East African shorthorn zebu (EASZ,B. indicus). The study cattle were obtained evenly at random from 209 herds in their agro-ecological zones (AEZs) where they have been nurtured by traditional cattle keeping communities throughout Uganda. Age, AEZs and breed significantly influenced the variation of linear morphometric traits exhibiting a gradient of low, intermediate and high dimensions among the EASZ, Nganda and Ankole cattle, respectively. Likewise, the linear morphometric trait (Mahalanobis squared distance) diversity was significantly different exhibiting a gradient of low, intermediate and high variation between Nganda and EASZ, Ankole and Nganda, and Ankole and EASZ cattle, respectively. These findings demonstrate the role of agro-ecological fitness in the evolution of indigenous cattle morphometric population structure in Uganda. The study outcomes further provide a motivation to search for genes associated with the diverse morphometric features.

Made available in DSpace on 2018-12-11T16:49:56Z (GMT). No. of bitstreams: 0 Previous issue date: 2017-10-01 Ministero dell’Istruzione, dell’Università e della Ricerca Background: The availability of the bovine genome sequence and SNP panels has improved various genomic analyses, from exploring genetic diversity to aiding genetic selection. However, few of the SNP on the bovine chips are polymorphic in buffalo, therefore a panel of single nucleotide DNA markers exclusive for buffalo was necessary for molecular genetic analyses and to develop genomic selection approaches for water buffalo. The creation of a 90K SNP panel for river buffalo and testing in a genome wide association study for milk production is described here. Methods: The genomes of 73 buffaloes of 4 different breeds were sequenced and aligned against the bovine genome, which facilitated the identification of 22 million of sequence variants among the buffalo genomes. Based on frequencies of variants within and among buffalo breeds, and their distribution across the genome, inferred from the bovine genome sequence, 90,000 putative single nucleotide polymorphisms were selected to create an Axiom® Buffalo Genotyping Array 90K. Results: This 90K “SNP-Chip” was tested in several river buffalo populations and found to have *70% high quality and polymorphic SNPs. Of the 90K SNPs about 24K were also found to be polymorphic in swamp buffalo. The SNP chip was used to investigate the structure of buffalo populations, and could distinguish buffalo from different farms. A Genome Wide Association Study identified genomic regions on 5 chromosomes putatively involved in milk production. Conclusion: The 90K buffalo SNP chip described here is suitable for the analysis of the genomes of river buffalo breeds, and could be used for genetic diversity studies and potentially as a starting point for genome-assisted selection programmes. This SNP Chip could also be used to analyse swamp buffalo, but many loci are not informative and creation of a revised SNP set specific for swamp buffalo would be advised. AIA-LGS Associazione Italiana Allevatori–Laboratorio Genetica e Servizi Fondazione Parco Tecnologico Padano Bioinformatics core Parco Tecnologico Padano Animal Genomics and Improvement Laboratory BARC USDA-ARS Department of Animal Science Iowa State University Institute of Zootechnics Università Cattolica del S. Cuore ANASB-Associazione Nazionale Allevatori Specie Bufalina Universidade Estadual Paulista (UNESP) Câmpus de Araçatuba COMSATS Institute of Information Technology Dipartimento di Scienze Zootecniche ed Ispezione degli Alimenti Facoltà di Agraria Università degli Studi di Napoli Federico II Universidade Federal De Minas Gerais (UFMG) Affymetrix UK Ltd Davies Research Centre School of Animal and Veterinary Sciences University of Adelaide Department of Animal Science University of Arkansas Recombinetics Inc. Council on Dairy Cattle Breeding, 4201 Northview Dr. One Town Centre Universidade Estadual Paulista (UNESP) Câmpus de Araçatuba

We genotyped 58 single nucleotide polymorphisms (SNPs) in 25 candidate genes in about 800 Italian Holstein sires. Fifty-six (minor allele frequency >0.02) were used to evaluate their association with single traits: milk yield (MY), milk fat yield (FY), milk protein yield (PY), milk fat percentage (FP), milk protein percentage (PP), milk somatic cell count (MSCC); and complex indexes: longevity, fertility and productivity-functionality type (PFT), using deregressed proofs, after adjustment for familial relatedness. Thirty-two SNPs were significantly associated (proportion of false positives

Several studies have investigated the differentiation of mitochondrial DNA in Eurasian, African and American cattle as well as archaeological bovine material. A global survey of these studies shows that haplogroup distributions are more stable in time than in space. All major migrations of cattle have shifted the haplogroup distributions considerably with a reduction of the number of haplogroups and/or an expansion of haplotypes that are rare or absent in the ancestral populations. The most extreme case is the almost exclusive colonization of Africa by the T1 haplogroup, which is rare in Southwest Asian cattle. In contrast, ancient samples invariably show continuity with present-day cattle from the same location. These findings indicate strong maternal founder effects followed by limited maternal gene flow when new territories are colonized. However, effects of adaptation to new environments may also play a role., Facultad de Ciencias Veterinarias, Instituto de Genética Veterinaria

Iranian livestock diversity is still largely unexplored, in spite of the interest in the populations historically reared in this country located near the Fertile Crescent, a major livestock domestication centre. In this investigation, the genetic diversity and differentiation of 10 Iranian indigenous fat-tailed sheep breeds were investigated using 18 microsatellite markers. Iranian breeds were found to host a high level of diversity. This conclusion is substantiated by the large number of alleles observed across loci (average 13.83, range 7-22) and by the high within-breed expected heterozygosity (average 0.75, range 0.72-0.76). Iranian sheep have a low level of genetic differentiation, as indicated by the analysis of molecular variance, which allocated a very small proportion (1.67%) of total variation to the between-population component, and by the small fixation index (FST = 0.02). Both Bayesian clustering and principal coordinates analysis revealed the absence of a detectable genetic structure. Also, no isolation by distance was observed through comparison of genetic and geographical distances. In spite of high within-breed variation, signatures of inbreeding were detected by the FIS indices, which were positive in all and statistically significant in three breeds. Possible factors explaining the patterns observed, such as considerable gene flow and inbreeding probably due to anthropogenic activities in the light of population management and conservation programmes, are discussed.

Since its domestication, about 5000 years ago, the donkey (Equus asinus) has been extensively used as a work or draft animal in agricultural activities and for the transportation of people and goods. In the last century, technology improvement and growing mechanization strongly affected agriculture and the management and use of this livestock species in the industrialized countries. Nowadays, the use of donkeys for work or transport has almost disappeared, together with the need for mules or hinny breeding. During the last five decades, Italian autochthonous donkey populations suffered from a severe reduction in population size, which led to the extinction of several breeds. At present, eight breeds remain, all classified by FAO as critically endangered or endangered: Asinara, Pantesco, Grigio Siciliano, Romagnolo, Amiatino, Sardo Grigio, Martina Franca, and Ragusano. To evaluate the extant genetic variability of Italian donkeys, we typed 16 microsatellite loci in 258 individuals from these breeds. The results highlighted moderate levels of inbreeding ( F (IS) = 0.127) and a significant partition of genetic variation into breeds, as suggested by fixation index ( F (ST) = 0.109) and analysis of molecular variance (10.86% of total variation assigned to the between-breeds level) analyses. This was confirmed by a Bayesian clustering procedure that also highlighted a further partitioning at lower hierarchical levels corresponding to the farms of origin. This evidence suggests that an effective management strategy for Italian donkey populations should focus on breeds as conservation units. However, this requires a synergic management strategy at the farm level to maintain diversity and avoid inbreeding.

We employed mtDNA and nuclear SNPs to investigate the genetic diversity of sheep breeds of three countries of the Mediterranean basin: Albania, Greece, and Italy. In total, 154 unique mtDNA haplotypes were detected by means of D-loop sequence analysis. The major nucleotide diversity was observed in Albania. We identified haplogroups, A, B, and C in Albanian and Greek samples, while Italian individuals clustered in groups A and B. In general, the data show a pattern reflecting old migrations that occurred in postneolithic and historical times. PCA analysis on SNP data differentiated breeds with good correspondence to geographical locations. This could reflect geographical isolation, selection operated by local sheep farmers, and different flock management and breed admixture that occurred in the last centuries.