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The Italian Goat Consortium (IGC), joined the effort of many Universities and Research Institutes, in a comprehensive study of the Italian goat population genetic makeup using a medium density (54K) SNPs chip. Currently IGC has geno- typed more than 1,000 animals from more than 30 goat breeds and populations from all Italian geographical and agro- ecological areas of goat rearing. The aim of this work is to obtain a clear picture of the Italian caprine biodiversity, to reconstruct the ancestry, to disentangle the genetic background and to assess the relationships among and within the investigated breeds. To date, the IGC dataset includes about 50 million genotypes. The data were quality checked by excluding markers and individuals on the basis of missing genotypes, minor allele frequency and close individual relatedness. Genetic relationships among and within breeds was investigated by Multi-Dimensional Scaling and Principal Component Analysis. Population structure, ancestry models and admixture were estimated by ADMIXTURE and fastSTRUCTURE software. Finally, phylogenic trees were recon- structed with PHYLIP software suite starting from shared-allele identity by state, and Reynolds distance matrices, while past migration events were modeled with TreeMix software. The results confirmed high levels of genetic polymorphism and confirmed the North-South geographical pattern of diver- sity, previously reported on a smaller sample of Italian goat breeds. The analysis also revealed a pivotal role of Central Italy in connecting the genetic resources of the northern and southern areas of the country, and confirms the genetic isola- tion of insular breeds. Moreover, some breeds show clearly distinctive and homogeneous gene pools, whereas other breeds present complex and, in some cases, dishomogeneous genetic background. Even if "A breed is a group of domestic animals, termed such by common consent of the breeders" (Lush J.L., 1994), genomic tools are useful in understanding the genetic back- ground of populations and in defining their relationships or uniqueness. These tools can complement the traditional ones in providing farmers and their associations a powerful aid for a more conscious management of goat populations and their biodiversity.

La pratica dello stamping-out consiste nell’abbattimento obbligatorio degli animali (malati, infetti, sospetti infetti e, in alcuni casi, sospetti di contaminazione) e nella distruzione delle carcasse. Tale metodo, così come proposto dal Lancisi agli inizi del ‘700, è stato per lungo tempo applicato nel controllo dei focolai di peste bovina, malattia presente in Europa sino alla fine della Grande Guerra e dal devastante impatto economico e sociale. In seguito, lo stamping-out è stato previsto dalla legislazione sanitaria di numerosi Paesi, per il controllo di malattie, alcune esotiche, in grado di causare ingenti perdite economiche e di diffondersi rapidamente da un paese all’altro. Con questo metodo sono state eliminate dal territorio italiano malattie quali l'afta epizootica, la peste suina classica e la peste suina africana. In epoche recenti, a livello internazionale, esso è stato applicato, ad esempio, nel controllo dei focolai di influenza aviare nel Sud-Est asiatico (anche in Italia), di BSE e di peste suina classica in Europa, di afta epizootica nel Regno Unito ed in Sud-America. Il contesto che ha maggiormente contribuito al dibattito sullo stamping-out è quello che si è realizzato nel Regno Unito nel 2001, relativamente al controllo dei focolai di afta epizootica. In quella occasione, sono stati abbattuti oltre 4 milioni di capi, con un costo economico stimato in oltre 3 miliardi di sterline. Questa pratica applicata su così ampia scala ha suscitato un forte impatto psicologico sul pubblico e ha contribuito ad innescare un’ampia discussione nell’opinione pubblica e negli Organismi sanitari internazionali relativamente all’uccisione degli animali, al benessere degli stessi e all’eticità della distruzione delle carcasse. Le evidenze emerse nel corso di tale dibattito si sono parzialmente concretizzate all’interno della normativa europea.

Frate Salimbene de Adam (Parma, 1221 – Montefalcone di Reggio Emilia, 1288) viene considerato il maggior cronista latino del medioevo. La sua fama è legata alla Chronica, scritta in un latino che spesso muta in volgare, ricchissima di racconti e notizie tanto da farne una delle fonti storiche più interessanti per il secolo XIII. In molte parti della Cronaca è avvertibile la coscienza contadina dell’autore, particolarmente attento al clima e agli eventi atmosferici che danneggiano piante e raccolti. In un capitolo dell’opera, relativo all’anno 1286, riferisce di una grande moria di galline e di uomini occorsa in molte città d’Italia, in particolare a Cremona, Piacenza, Parma e Reggio. Descrive sintomi e lesioni comuni a persone ed animali, tra i quali segnala multa apostemata (ascessi purulenti, pustole) a livello cutaneo e vescicula sul cuore. L’Autore riporta le indicazioni di un magister phisicus di non mangiare nè le uova nè la carne delle galline per tutto il mese di maggio. Come conseguenza dell’epidemia parla di un prezzo molto ridotto degli animali. Infine segnala che, in alcuni casi, una terapia a base di marrobio (Marrubium vulgare) aveva evitato la morte delle galline. In base a quanto descritto, è molto probabile che le concomitanti epidemie del pollame e degli uomini siano da attribuirsi al vaiolo, che esordisce con lesioni del tutto analoghe per uomo e volatili. In natura i virus vaiolosi hanno periodi di comparsa sincroni su specie sensibili, benchè si tratti di ceppi diversi e non intertrasmissibili. Da notare che Salimbene parla anche di un mese di febbraio con freddo e gelo intensi e forti nevicate, a conferma di predizioni profetiche nefaste. Le avverse condizioni climatiche e la probabile carenza di cibo potrebbero aver facilitato la comparsa delle epidemie indicate, così come storicamente documentato anche per altre malattie spesso concomitanti quali la peste umana e la peste bovina.

La pratica dello stamping-out consiste nell’abbattimento obbligatorio degli animali (malati, infetti, sospetti infetti e, in alcuni casi, sospetti di contaminazione) e nella distruzione delle carcasse. Tale metodo, così come proposto dal Lancisi agli inizi del ’700, è stato per lungo tempo applicato nel controllo dei focolai di peste bovina, malattia presente in Europa sino alla fine della Grande Guerra e dal devastante impatto economico e sociale. In seguito, lo stamping-out è stato previsto dalla legislazione sanitaria di numerosi Paesi, per il controllo di malattie, alcune esotiche, in grado di causare ingenti perdite economiche e di diffondersi rapidamente da un paese all’altro. Con questo metodo sono state eliminate dal territorio italiano malattie quali l’afta epizootica, la peste suina classica e la peste suina africana. In epoche recenti, a livello internazionale, esso è stato applicato, ad esempio, nel controllo dei focolai di influenza aviare nel Sud-Est asiatico (anche in Italia), di BSE e di peste suina classica in Europa, di afta epizootica nel Regno Unito e in Sud-America. Il contesto che ha maggiormente contribuito al dibattito sullo stamping-out è quello che si è realizzato nel Regno Unito nel 2001, relativamente al controllo dei focolai di afta epizootica.

Bonaventura Corti (1729-1813) was an exemplary erudite of his times, with knowledge in agricultural sciences, botany, meteorology, microscopy and natural sciences. He was collaborator and friend of Lazzaro Spallanzani. In 1772 he was appointed by the Health Authority to give his advice on the mortality manifested in cattle of the area of Reggio Emilia (Po valley, northern Italy). His period was characterised by developments of agriculture to meet the necessities of the growing population, increasingly urbanised, and by the urgency to control the great cattle plague and other animal epidemics causing famine. The Veterinary Schools had not yet been instituted, and practitioners were directed towards the cure of farm, draft and army animals. In order to surrogate the need of specialized experience on animal diseases, and to combat the epidemics affecting continuously the animals, the governments employed the best scientists available, e.g. great physicians as Lancisi, Malpighi, Ramazzini, Vallisnieri and scientists with different experience. Bonaventura Corti was one of the appointed scientists, and gave his opinion with the assistance of a physician, a surgeon, and a farrier. His wide culture and experience permitted him to give useful advises based on climatology, environmental hygiene and the knowledge available at that time on the transmission of communicable diseases. The need emerged was such that Veterinary Schools started to be instituted following the French model, and from 1765 to 1806, seven Veterinary Schools were created in Italy.

Background To enhance and extend the knowledge about the global historical and phylogenetic relationships between Merino and Merino-derived breeds, 19 populations were genotyped with the OvineSNP50 BeadChip specifically for this study, while an additional 23 populations from the publicly available genotypes were retrieved. Three complementary statistical tests, Rsb (extended haplotype homozygosity between-populations), XP-EHH (cross-population extended haplotype homozygosity), and runs of homozygosity (ROH) islands were applied to identify genomic variants with potential impact on the adaptability of Merino genetic type in two contrasting climate zones. Results The results indicate that a large part of the Merino’s genetic relatedness and admixture patterns are explained by their genetic background and/or geographic origin, followed by local admixture. Multi-dimensional scaling, Neighbor-Net, Admixture, and TREEMIX analyses consistently provided evidence of the role of Australian, Rambouillet and German strains in the extensive gene introgression into the other Merino and Merino-derived breeds. The close relationship between Iberian Merinos and other South-western European breeds is consistent with the Iberian origin of the Merino genetic type, with traces from previous contributions of other Mediterranean stocks. Using Rsb and XP-EHH approaches, signatures of selection were detected spanning four genomic regions located on Ovis aries chromosomes (OAR) 1, 6 and 16, whereas two genomic regions on OAR6, that partially overlapped with the previous ones, were highlighted by ROH islands. Overall, the three approaches identified 106 candidate genes putatively under selection. Among them, genes related to immune response were identified via the gene interaction network. In addition, several candidate genes were found, such as LEKR1, LCORL, GHR, RBPJ, BMPR1B, PPARGC1A, and PRKAA1, related to morphological, growth and reproductive traits, adaptive thermogenesis, and hypoxia responses. Conclusions To the best of our knowledge, this is the first comprehensive dataset that includes most of the Merino and Merino-derived sheep breeds raised in different regions of the world. The results provide an in-depth picture of the genetic makeup of the current Merino and Merino-derived breeds, highlighting the possible selection pressures associated with the combined effect of anthropic and environmental factors. The study underlines the importance of Merino genetic types as invaluable resources of possible adaptive diversity in the context of the occurring climate changes.

Italy counts a large number of local chicken populations, some without a recognized genetic structure, such as Val Platani (VPL) and Cornuta (COS), which represent noteworthy local genetic resources. In this study, the genotype data of 34 COS and 42 VPL, obtained with the Affymetrix Axiom600KChicken Genotyping Array, were used with the aim to investigate the genetic diversity, the runs of homozygosity (ROH) pattern, as well as the population structure and relationship within the framework of other local Italian and commercial chickens. The genetic diversity indices, estimated using different approaches, displayed moderate levels of genetic diversity in both populations. The identified ROH hotspots harbored genes related to immune response and adaptation to local hot temperatures. The results on genetic relationship and population structure reported a clear clustering of the populations according to their geographic origin. The COS formed a nonoverlapping genomic cluster and clearly separated from the other populations, but showed evident proximity to the Siciliana breed (SIC). The VPL highlighted intermediate relationships between the COS-SIC group and the rest of the sample, but closer to the other Italian local chickens. Moreover, VPL showed a complex genomic structure, highlighting the presence of 2 subpopulations that match with the different source of the samples. The results obtained from the survey on genetic differentiation underline the hypothesis that Cornuta is a population with a defined genetic structure. The substructure that characterizes the Val Platani chicken is probably the consequence of the combined effects of genetic drift, small population size, reproductive isolation, and inbreeding. These findings contribute to the understanding of genetic diversity and population structure, and represent a starting point for designing programs to monitor and safeguard these local genetic resources, in order to define a possible official recognition program as breeds.

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; FROH) showed marked differences among breeds and ranged from 0.161 (PML) to 0.478 (PPP). Furthermore, in all breeds, short ROH (

BackgroundDuring the Neolithic expansion, cattle accompanied humans and spread from their domestication centres to colonize the ancient world. In addition, European cattle occasionally intermingled with both indicine cattle and local aurochs resulting in an exclusive pattern of genetic diversity. Among the most ancient European cattle are breeds that belong to the so-called Podolian trunk, the history of which is still not well established. Here, we used genome-wide single nucleotide polymorphism (SNP) data on 806 individuals belonging to 36 breeds to reconstruct the origin and diversification of Podolian cattle and to provide a reliable scenario of the European colonization, through an approximate Bayesian computation random forest (ABC-RF) approach.ResultsOur results indicate that European Podolian cattle display higher values of genetic diversity indices than both African taurine and Asian indicine breeds. Clustering analyses show that Podolian breeds share close genomic relationships, which suggests a likely common genetic ancestry. Among the simulated and tested scenarios of the colonization of Europe from taurine cattle, the greatest support was obtained for the model assuming at least two waves of diffusion. Time estimates are in line with an early migration from the domestication centre of non-Podolian taurine breeds followed by a secondary migration of Podolian breeds. The best fitting model also suggests that the Italian Podolian breeds are the result of admixture between different genomic pools.ConclusionsThis comprehensive dataset that includes most of the autochthonous cattle breeds belonging to the so-called Podolian trunk allowed us not only to shed light onto the origin and diversification of this group of cattle, but also to gain new insights into the diffusion of European cattle. The most well-supported scenario of colonization points to two main waves of migrations: with one that occurred alongside with the Neolithic human expansion and gave rise to the non-Podolian taurine breeds, and a more recent one that favoured the diffusion of European Podolian. In this process, we highlight the importance of both the Mediterranean and Danube routes in promoting European cattle colonization. Moreover, we identified admixture as a driver of diversification in Italy, which could represent a melting pot for Podolian cattle.

Background Climate and farming systems, several of which are considered as low-input agricultural systems, vary between goat populations from Northern and Southern Italy and have led to different management practices. These processes have impacted genome shaping in terms of inbreeding and regions under selection and resulted in differences between the northern and southern populations. Both inbreeding and signatures of selection can be pinpointed by the analysis of runs of homozygosity (ROH), which provides useful information to assist the management of this species in different rural areas. Results We analyzed the ROH distribution and inbreeding (FROH) in 902 goats from the Italian Goat Consortium2 dataset. We evaluated the differences in individual ROH number and length between goat breeds from Northern (NRD) and Central-southern (CSD) Italy. Then, we identified the signatures of selection that differentiate these two groups using three methods: ROH, ΔROH, and averaged FST. ROH analyses showed that some Italian goat breeds have a lower inbreeding coefficient, which is attributable to their management and history. ROH are longer in breeds that are undergoing non-optimal management or with small population size. In several small breeds, the ROH length classes are balanced, reflecting more accurate mating planning. The differences in climate and management between the NRD and CSD groups have resulted in different ROH lengths and numbers: the NRD populations bred in isolated valleys present more and shorter ROH segments, while the CSD populations have fewer and longer ROH, which is likely due to the fact that they have undergone more admixture events during the horizontal transhumance practice followed by a more recent standardization. We identified four genes within signatures of selection on chromosome 11 related to fertility in the NRD group, and 23 genes on chromosomes 5 and 6 related to growth in the CSD group. Finally, we identified 17 genes on chromosome 12 related to environmental adaptation and body size with high homozygosity in both groups. Conclusions These results show how different management practices have impacted the level of genomic inbreeding in two Italian goat groups and could be useful to assist management in a low-input system while safeguarding the diversity of small populations.

Local adaptation of animals to the environment can abruptly become a burden when faced with rapid climatic changes such as those foreseen for the Italian peninsula over the next 70 years. Our study investigates the genetic structure of the Italian goat populations and links it with the environment and how genetics might evolve over the next 50 years. We used one of the largest national datasets including > 1000 goats from 33 populations across the Italian peninsula collected by the Italian Goat Consortium and genotyped with over 50 k markers. Our results showed that Italian goats can be discriminated in three groups reflective of the Italian geography and its geo-political situation preceding the country unification around two centuries ago. We leveraged the remarkable genetic and geographical diversity of the Italian goat populations and performed landscape genomics analysis to disentangle the relationship between genotype and environment, finding 64 SNPs intercepting genomic regions linked to growth, circadian rhythm, fertility, and inflammatory response. Lastly, we calculated the hypothetical future genotypic frequencies of the most relevant SNPs identified through landscape genomics to evaluate their long-term effect on the genetic structure of the Italian goat populations. Our results provide an insight into the past and the future of the Italian local goat populations, helping the institutions in defining new conservation strategy plans that could preserve their diversity and their link to local realities challenged by climate change.

Climate change has the potential to adversely affect the health of livestock, with consequences to animal welfare, greenhouse gas emissions, productivity, human health and livelihoods. Phenotypic plasticity is the ability of a genotype to produce different phenotypes, depending on environmental, biotic or abiotic conditions; it is a factor influencing and modifying the genes of animal and plant organisms, to adaptation to climate change. Among the various climate variables, heat stress has been reported to be the most detrimental factor to the economy of the livestock industry. There are a number of candidate genes that are associated with adaptation of ruminants, monogastric and poultry to heat stress. For instance, the genes encoding leptin, thyroid hormone receptor, insulin growth factor-1, growth hormone receptor, are associated with the impacts of heat stress on the physiological pathways of domestic animals such as dairy cows, beef cattle, buffaloes, poultry, pigs and horses. This review aims to highlight genes and traits that are involved with thermo-tolerance of domestic animals to sustain production and to cope with climate change. Selection and experimental evolution approaches have shown that plasticity is a trait that can evolve when under direct selection and has a correlated response to some specific traits. Therefore, new breeding goals should be defined for the potential of livestock species to acquire plasticity for adaptation to the current climate changing conditions.Highlights Heat stress compromises feed intake, growth, milk and meat quality and quantity, resulting in a significant financial burden to global livestock. Genetic selection and nutritional intervention are key strategies to consider in Animal Genetic Resources in hot environments. Information from gene expression or genome-wide association studies can be used to further improve the accuracy of selection.

Copy Number Variations (CNVs) are classes of polymorphic genomic regions including deletions, duplications and insertions of DNA fragments from at least 0.5 kb up to several Mb. CNV represents an important source of genetic variability that provides genomics structural information complementary to the single nucleotide polymorphism (SNP) data. Some CNVs have been shown to be important in both normal phenotypic variability and disease susceptibility in livestock. Several approaches to identify CNVs including FISH, aCGH, SNP array or NGS, were proposed and among these SNP genotyping is relatively low cost, high-throughput and high coverage method. The aim of this study was to identify the CNVs in 71 animals of Cinisara breed using Illumina BovineSNP50 BeadChip v2. PennCNV software, which incorporates Log R ratio and B allele frequency at each SNP marker, was used to identify CNVs. Seven animals showed not shared CNVs, as well as autosomes 19, 21, 22. Chromosome 25 presented no CNVs at all. A final number of 322 CNVs were detected. The average number of CNVs was 4.5 per individual, with an average length and median size of 143.04 kb and 122.14 kb, respectively. All CNVs were grouped in CNV regions (CNVRs) and a total of 107 CNVRs, ranged from 50 to ~500 kb, were detected, which covered 4.90 Mb of polymorphic sequence and corresponded to 0.18% of the total genome length. In particular, we found 81 CNVRs with only gain (duplication), 22 with only loss (deletion), and four CNVRs with both. Furthermore, 8 CNVRs with >1%, 77 with >2.5%, and 22 with >5% frequency, were found. CNVRs having the highest frequency were located on Chr3:120501439-120647330 and Chr23:34673581-35007295, whereas the greatest number of genes was mapped in only one CNVR located on Chr 17:74123863-74393620. A total of 241 genes were included in the identified CNVRs. According to KEGG and DAVID database, most of the genes were involved in multiple signaling and signal transduction pathways in a wide variety of cellular and biochemical processes, such as immune response, adaptability, and olfactory receptors pathway. Further studies, using different algorithms and validating the CNVs discovered, will be conducted to corroborate these preliminary results on the CNVRs detected. These results will be used for the investigation of genomic changes and features of interest in the Cinisara breed, such as for association with functional or production traits and for biodiversity studies.