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Abstract Background Rendena is a dual-purpose cattle breed, which is primarily found in the Italian Alps and the eastern areas of the Po valley, and recognized for its longevity, fertility, disease resistance and adaptability to steep Alpine pastures. It is categorized as 'vulnerable to extinction' with only 6057 registered animals in 2022, yet no comprehensive analyses of its molecular diversity have been performed to date. The aim of this study was to analyse the origin, genetic diversity, and genomic signatures of selection in Rendena cattle using data from samples collected in 2000 and 2018, and shed light on the breed's evolution and conservation needs. Results Genetic analysis revealed that the Rendena breed shares genetic components with various Alpine and Po valley breeds, with a marked genetic proximity to the Original Braunvieh breed, reflecting historical restocking efforts across the region. The breed shows signatures of selection related to both milk and meat production, environmental adaptation and immune response, the latter being possibly the result of multiple rinderpest epidemics that swept across the Alps in the eighteenth century. An analysis of the Rendena cattle population spanning 18 years showed an increase in the mean level of inbreeding over time, which is confirmed by the mean number of runs of homozygosity per individual, which was larger in the 2018 sample. Conclusions The Rendena breed, while sharing a common origin with Brown Swiss, has developed distinct traits that enable it to thrive in the Alpine environment and make it highly valued by local farmers. Preserving these adaptive features is essential, not only for maintaining genetic diversity and enhancing the ability of this traditional animal husbandry to adapt to changing environments, but also for guaranteeing the resilience and sustainability of both this livestock system and the livelihoods within the Rendena valley.

Abstract The African buffalo, Syncerus caffer, is a key species in African ecosystems. Like other large herbivores, it plays a fundamental role in its habitat acting as an ecosystem engineer. Over the last few centuries, African buffalo populations have declined because of range contraction and demographic decline caused by direct or indirect human activities. In Mozambique, historically home to large buffalo herds, the combined effect of colonialism and subsequent civil wars has created a critical situation that urgently needs to be addressed. In this study, we focused on the analysis of genetic diversity of Syncerus caffer caffer populations from six areas of Mozambique. Using genome-wide SNPs obtained from ddRAD sequencing, we examined the population structure across the country, estimated gene flow between areas under conservation management, including national reserves, and assessed the inbreeding coefficients. Our results indicate that all studied populations of Syncerus caffer caffer are genetically depauperate, with a high level of inbreeding. Moreover, buffaloes in Mozambique present a significant population differentiation between southern and central areas. We found an unexpected genotype in the Gorongosa National Park, where buffaloes experienced a dramatic population size reduction, that shares a common ancestry with southern populations of Catuane and Namaacha. This could suggest the past occurrence of a connection between southern and central Mozambique and that the observed population structuring could reflect recent events of anthropogenic origin. All the populations analysed showed high levels of homozygosity, likely due to extensive inbreeding over the last few decades, which could have increased the frequency of recessive deleterious alleles. Improving the resilience of Syncerus caffer caffer in Mozambique is essential for preserving the ecosystem integrity. The most viable approach appears to be facilitating translocations and re-establishing connectivity between isolated herds. However, our results also highlight the importance of assessing intraspecific genetic diversity when considering interventions aimed at enhancing population viability such as selecting suitable source populations.

Abstract Background The presence of goats in the Canary Islands dates back to the late 1st millennium BC, which coincides with the colonization by the Amazigh settlers. However, the exact geographic origin of Canarian goats is uncertain since the Amazigh peoples were distributed over a wide spatial range. Nowadays, three Canarian breeds (Palmera, Majorera and Tinerfeña) are officially recognized, along with two distinct South and North Tinerfeña ecotypes, with the South Tinerfeña and Majorera goats thriving in arid and dry semi-desertic environments and the Palmera and North Tinerfeña goats are adapted to humid and temperate areas that are influenced by trade winds. Genotypes for 224 Canarian goats were generated using the Illumina Goat single nucleotide polymorphism (SNP)50 BeadChip. By merging these data with the genotypes from 1007 individuals of African and Southern European ancestry, our aim was to ascertain the geographic origin of the Canarian goats and identify genes associated with adaptation to diverse environmental conditions. Results The diversity indices of the Canarian breeds align with most of those of the analyzed local breeds from Africa and Europe, except for the Palmera goats that showed lower levels of genetic variation. The Canarian breeds demonstrate a significant genetic differentiation compared to other populations, which indicates a history of prolonged geographic isolation. Moreover, the phylogenetic reconstruction indicated that the ancestry of the Canarian goats is fundamentally North African rather than West African. The ADMIXTURE and the TreeMix analyses showed no evidence of gene flow between Canarian goats and other continental breeds. The analysis of runs of homozygosity (ROH) identified 13 ROH islands while the window-based FST method detected 25 genomic regions under selection. Major signals of selection were found on Capra hircus (CHI) chromosomes 6, 7, and 10 using various comparisons and methods. Conclusions This genome-wide analysis sheds new light on the evolutionary history of the four breeds that inhabit the Canary Islands. Our findings suggest a North African origin of the Canarian goats. In addition, within the genomic regions highlighted by the ROH and FST approaches, several genes related to body size and heat tolerance were identified.

ABSTRACT: 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.

Abstract 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.

Abstract 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 (F ROH) 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 F ST. 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.

Abstract Background During 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. Results Our 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. Conclusions This 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.

Abstract 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.

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.

Abstract Background Assessment of genetic diversity and population structure provides important control metrics to avoid genetic erosion, inbreeding depression and crossbreeding between exotic and locally-adapted cattle breeds since these events can have deleterious consequences and eventually lead to extinction. Historically, the Alpine Arc represents an important pocket of cattle biodiversity with a large number of autochthonous breeds that provide a fundamental source of income for the entire regional economy. By using genotype data from medium-density single nucleotide polymorphism (SNP) arrays, we performed a genome-wide comparative study of 23 cattle populations from the Alpine Arc and three cosmopolitan breeds. Results After filtering, we obtained a final genotyping dataset consisting of 30,176 SNPs for 711 individuals. The local breeds showed high or intermediate values of genetic diversity compared to the highly selected cosmopolitan breeds. Patterns of genetic differentiation, multidimensional scaling, admixture analysis and the constructed phylogenetic tree showed convergence, which indicates the presence of gene flow among the breeds according to both geographic origin and historical background. Among the most differentiated breeds, we identified the modern Brown cattle. In spite of admixture events, several local breeds have preserved distinctive characteristics, which is probably due to differences in genetic origin and geographic location. Conclusions This study represents one of the most comprehensive genome-wide analysis of the Alpine cattle breeds to date. Using such a large dataset that includes the majority of the local breeds found in this region, allowed us to expand knowledge on the evaluation and status of Alpine cattle biodiversity. Our results indicate that although many of the analyzed local breeds are listed as endangered, they still harbor a large amount of genetic diversity, even when compared to some cosmopolitan breeds. This finding, together with the reconstruction of the phylogeny and the relationships between these Alpine Arc cattle breeds, provide crucial insights not only into the improvement of genetic stocks but also into the implementation of future conservation strategies.

Livestock European diffusion followed different human migration waves from the Fertile Crescent. In sheep, at least two diffusion waves have shaped the current breeds' biodiversity generating a complex genetic pattern composed by either primitive or fine-wool selected breeds. Among primitive breeds, aside from sharing common ancestral genomic components, they also show several traits such as the policeraty, large horns in the ram, short tail, and a moulting fleece, considered as ancestral. Although most of the primitive breeds characterized by these traits are confined on the very edge of Northern Europe, several residual populations are also scattered in the Mediterranean region. In fact, although in Italy a large number of local breeds are already extinct, others are listed as critically endangered, and among these there is the Quadricorna breed which is a four-horned sheep characterized by several ancestral traits. In this context we genotyped 47 individuals belonging to the Quadricorna sheep breed, a relict and endangered breed, from Central and Southern Italy. In doing so we used the Illumina OvineSNP50K array in order to explore its genetic diversity and to compare it with other 33 primitive traits-related, Mediterranean and Middle-East breeds, with the specific aim to reconstruct its origin. After retaining 35,680 SNPs following data filtering, the overall genomic architecture has been explored by using genetic diversity indices, Principal Component Analysis (PCA) and admixture analysis, while the genetic relationships and migration events have been inferred using a neighbor-joining tree based on Reynolds' distances and by the maximum likelihood tree as implemented in treemix. Multiple convergent evidence from all our population genetics analyses, indicated that the two Quadricorna populations differ from all the other Italian breeds, while they resulted to be very close to the Middle Eastern and primitive European breeds. In addition, the genetic diversity indices highlighted values comparable with those of most of the other analyzed breeds, despite the two populations exhibit slightly different genetic indices suggesting different levels of genomic inbreeding and drift (FIS and FROH). The admixture analysis does not suggest any signal of recent gene exchange with other Italian local breeds, highlighting a rather ancestral purity of the two populations, while on the other hand the treemix analysis seems to suggest an ancient admixture with other primitive European breeds. Finally, all these evidences seem to trace back the residual Quadricorna sheep to an early Neolithic spread, probably following a Mediterranean route and that urgent conservation actions are needed in order to keep the breed and all related cultural products alive.

Understanding the relationships among geography, climate, and genetics is increasingly important for animal farming and breeding. In this study, we examine these inter-relationships in the context of local cattle and sheep breeds distributed along the Italian territory. To this aim, we used redundancy analysis on genomic data from previous projects combined with geographical coordinates and corresponding climatic data. The effect of geographic factors (latitude and longitude) was more important in sheep (26.4%) than that in cattle (13.8%). Once geography had been partialled out of analysis, 10.1% of cattle genomic diversity and 13.3% of that of sheep could be ascribed to climatic effects. Stronger geographic effects in sheep can be related to a combination of higher pre-domestication genetic variability together with biological and productive specificities. Climate alone seems to have had less impact on current genetic diversity in both species, even if climate and geography are greatly confounded. Results confirm that both species are the result of complex evolutionary histories triggered by interactions between human needs and environmental conditions.

The Maremmana cattle is an ancient Podolian-derived Italian breed raised in semi-wild conditions with distinctive morphological and adaptive traits. The aim of this study was to detect potential selection signatures in Maremmana using medium-density single nucleotide polymorphism array. Putative selection signatures were investigated combining three statistical approaches designed to quantify the excess of haplotype homozygosity either within (integrated haplotype score, iHS) or among pairs of populations (Rsb and XP-EHH), and contrasting the Maremmana with a single reference population composed of a pool of seven Podolian-derived Italian breeds. Overall, the three haplotype-based analyses revealed selection signatures distributed over 19 genomic regions. Of these, six relevant candidate regions were identified by at least two approaches. We found genomic signatures of selective sweeps spanning genes related to mitochondrial function, muscle development, growth, and meat traits (SCIN, THSD7A, ETV1, UCHL1, and MYOD1), which reflects the different breeding schemes between Maremmana (semi-wild conditions) and the other Podolian-derived Italian breeds (semi-extensive). We also identified several genes linked to Maremmana adaptation to the environment of the western-central part of Italy, known to be hyperendemic for malaria and other tick-borne diseases. These include several chemokine (C-C motif) ligand genes crucially involved in both innate and adaptive immune responses to intracellular parasite infections and other genes playing key roles in pulmonary disease (HEATR9, MMP28, and ASIC2) or strongly associated with malaria resistance/susceptibility (AP2B1). Our results provide a glimpse into diverse selection signatures in Maremmana cattle and can be used to enhance our understanding of the genomic basis of environmental adaptation in cattle.

Abstract Background In the last 50 years, the diversity of cattle breeds has experienced a severe contraction. However, in spite of the growing diffusion of cosmopolite specialized breeds, several local cattle breeds are still farmed in Italy. Genetic characterization of breeds represents an essential step to guide decisions in the management of farm animal genetic resources. The aim of this work was to provide a high-resolution representation of the genome-wide diversity and population structure of Italian local cattle breeds using a medium-density single nucleotide polymorphism (SNP) array. Results After quality control filtering, the dataset included 31,013 SNPs for 800 samples from 32 breeds. Our results on the genetic diversity of these breeds agree largely with their recorded history. We observed a low level of genetic diversity, which together with the small size of the effective populations, confirmed that several breeds are threatened with extinction. According to the analysis of runs of homozygosity, evidence of recent inbreeding was strong in some local breeds, such as Garfagnina, Mucca Pisana and Pontremolese. Patterns of genetic differentiation, shared ancestry, admixture events, and the phylogenetic tree, all suggest the presence of gene flow, in particular among breeds that originate from the same geographical area, such as the Sicilian breeds. In spite of the complex admixture events that most Italian cattle breeds have experienced, they have preserved distinctive characteristics and can be clearly discriminated, which is probably due to differences in genetic origin, environment, genetic isolation and inbreeding. Conclusions This study is the first exhaustive genome-wide analysis of the diversity of Italian cattle breeds. The results are of significant importance because they will help design and implement conservation strategies. Indeed, efforts to maintain genetic diversity in these breeds are needed. Improvement of systems to record and monitor inbreeding in these breeds may contribute to their in situ conservation and, in view of this, the availability of genomic data is a fundamental resource.

Ruminant production has been an essential part of human activities worldwide since ancient times. The expected increase in world population and per capita income, with an increase in the amount and prevalence of animal products in human diet, urbanisation, with a concentration of population in urban areas and an increase in losses in the supply chain, and the growing concern over the environmental impact of animal farming require a long-term global strategy for a more intensive and sustainable ruminant production. Therefore, solutions to increase the supply of high-quality products of ruminant origin, without harming human health, animal welfare, and environment, should consider the following interconnected issues discussed in this review: (a) effects of meat, milk and dairy products consumption on human health, focussing on the imbalance caused by their insufficient consumption, and the alleged increased incidence of certain diseases due to their consumption; (b) importance of the sustainable intensification of ruminant production systems (e.g. better feed conversion and higher production output per unit of input introduced into the farming system); (c) environmental impact of ruminant production; (d) improvement of animal performance by improving animal welfare; (e) adaptation of ruminants to climate change; (f) sustainable ruminant feeding (e.g. precision feeding techniques, optimisation of grazing systems, and use of unconventional feeds); (g) challenges posed by production intensification to animal breeding and conservation of animal biodiversity; and (h) strategies to increase ruminant production in developing countries, thus achieving food security in vast areas of the planet affected by fast growth of human population.

Genomic regions subjected to selection frequently show signatures such as within-population reduced nucleotide diversity and outlier values of differentiation among differentially selected populations. In this study, we analyzed 50K SNP genotype data of 373 animals belonging to 23 sheep breeds of different geographic origins using the Rsb (extended haplotype homozygosity) and FST statistical approaches, to identify loci associated with the fat-tail phenotype. We also checked if these putative selection signatures overlapped with regions of high-homozygosity (ROH). The analyses identified novel signals and confirmed the presence of selection signature in genomic regions that harbor candidate genes known to affect fat deposition. Several genomic regions that frequently appeared in ROH were also identified within each breed, but only two ROH islands overlapped with the putative selection signatures. The results reported herein provide the most complete genome-wide study of selection signatures for fat-tail in African and Eurasian sheep breeds; they also contribute insights into the genetic basis for the fat tail phenotype in sheep, and confirm the great complexity of the mechanisms that underlie quantitative traits, such as the fat-tail.

Variations in body weight and in the distribution of body fat are associated with feed availability, thermoregulation, and energy reserve. Ethiopia is characterized by distinct agro-ecological and human ethnic farmer diversity of ancient origin, which have impacted on the variation of its indigenous livestock. Here, we investigate autosomal genome-wide profiles of 11 Ethiopian indigenous sheep populations using the Illumina Ovine 50 K SNP BeadChip assay. Sheep from the Caribbean, Europe, Middle East, China, and western, northern and southern Africa were included to address globally, the genetic variation and history of Ethiopian populations. Population relationship and structure analysis separated Ethiopian indigenous fat-tail sheep from their North African and Middle Eastern counterparts. It indicates two main genetic backgrounds and supports two distinct genetic histories for African fat-tail sheep. Within Ethiopian sheep, our results show that the short fat-tail sheep do not represent a monophyletic group. Four genetic backgrounds are present in Ethiopian indigenous sheep but at different proportions among the fat-rump and the long fat-tail sheep from western and southern Ethiopia. The Ethiopian fat-rump sheep share a genetic background with Sudanese thin-tail sheep. Genome-wide selection signature analysis identified eight putative candidate regions spanning genes influencing growth traits and fat deposition (NPR2, HINT2, SPAG8, INSR), development of limbs and skeleton, and tail formation (ALX4, HOXB13, BMP4), embryonic development of tendons, bones and cartilages (EYA2, SULF2), regulation of body temperature (TRPM8), body weight and height variation (DIS3L2), control of lipogenesis and intracellular transport of long-chain fatty acids (FABP3), the occurrence and morphology of horns (RXFP2), and response to heat stress (DNAJC18). Our findings suggest that Ethiopian fat-tail sheep represent a uniquely admixed but distinct genepool that presents an important resource for understanding the genetic control of skeletal growth, fat metabolism and associated physiological processes.

Fogera cattle are among indigenous breeds of cattle in the northern part of Ethiopia. However, their response to heat stress (HS) under different seasonal variations has not been well investigated. This study was aimed to determine physiological, hematological, biochemical, and growth parameters of Fogera cattle calves to HS during dry season, short rainy, and long rainy. A total of 72 calves (24 for each season) that were 6 months of age with an equal number of males and females were evaluated for physiological, hematological, biochemical, and growth parameters. Daily ambient temperature (AT) and relative humidity (RH) were recorded two times per day during the study periods from which the daily average temperature–humidity index (THI) was calculated. The study revealed higher AT and THI during dry and short seasons while higher RH was observed during the long rainy season. Physiological parameters except rectal temperature were affected by the seasons. Hematological parameters were also affected by season except for packed cell volume. Biochemical and growth parameters were also significantly affected by the seasons. THI was positively related with physiological but negatively with growth parameters. Thus, the THI value of 66 can be considered as optimum for high weight gain and normal physiological response to HS in Fogera cattle calves under their current production system.

The Pentro horse population is an autochthonous breed from a breeding area characterized by climatic and geographicpeculiarities. The horse population is interesting because of its rusticity, however, has run the risk of loosing its identitybecause of the introduction of exotic genetic material. This study presents data of the genetic characterization by meansof microsatellite markers. A total of 12 microsatellite loci were used to score 147 individuals among those with the Pentrophenotype, as well as 16 individuals representing the variable part of the population. Allele frequencies were calculatedfor each locus, with the mean number of alleles (Nall = 6.7) and the expected heterozygosity (He = 0.724). The meanobserved heterozygosity was 0.695. The obtained data were used to compare the genetic structure of the Pentro horseto six other Italian breeds. The N-J tree computed on individual genetic distances showed that 93% of Pentro horses clusteredtogether.

Casertana is an Italian autochthonous pig breed. In the past, the breed was common in Campania and the surrounding area in South Italy because it was valued for its productive performance, particularly regarding the fattening tendency, but in recent decades, autochthonous swine have been replaced by cosmopolitan lean-type pigs and the Casertana breed also experienced a dramatic reduction in numbers. Concern over the preservation of genetic resources and the increased demand for regional food suggest a new way of maintaining the breed. Unfortunately, few recent data on the morpho- logical as well as on the productive traits are available. To ascertain the characteristics of the Casertana breed a pro- ductive trial was performed by comparing Casertana and Large White pure breed and their cross. Sixteen females and 6 males of pure breed Casertana and 18 females and 2 males of pure breed Italian Large White were mated twice to pro- duce Casertana, Large White and Casertana x Large White piglets. The average number of piglets born was significant- ly lower in Casertana gilts, but no difference in the number of weaned piglets among genetic types was observed. Sixty- eight animals of the three genetic types were reared outdoors and received two distinct diets differing in energy content. Pigs were weighted individually every month to calculate average daily gain. Morphological traits of Casertana pigs were also recorded. A total of 54 animals (21 Casertana at 151 kg live weight, 15 crossbreed at 157 kg live weight and 18 Large White at 179 kg live weight) were slaughtered and data on carcasses were collected. Average daily weight gain differed markedly (P< 0.05) among genetic types (450; 552; 695 g/d, respectively for Casertana; Casertana x Large White; Large White) and consequently the slaughter weight also differed. Casertana showed higher dressing percentages that the Italian Large White (P< 0.05). Backfat thickness was also clearly affected by genetic type (P< 0.05): Casertana pigs had the highest value (44.91 mm). The diet had no influence on the average daily weight gain and backfat thick- ness. However, pigs fed with higher energy component had higher (P< 0.05) dressing percentage.

K-casein (K-CN) represents one of the most important proteins determining the manufacturing properties of milk,because of its essential role in micelle formation and stabilisation.Several genetic variants of K-CN have been described in goats. To investigate the occurrence of seven alleles and theirdistribution among breeds, a total of 170 animals, from six different breeds reared in Italy (Cilentana Nera, Derivata diSiria, Maltese, Jonica, Garganica and Cashmere), have been analysed in this paper by the primer extension method.Alleles A and B were found to be the most represented in all the analysed breeds; allele D is present only in Maltese andCashmere animals with a very low frequency; while allele G has been found in all but two (Garganica and Cashmere)breeds. Alleles C, E and F were not present in the material used for this study.

The aim of the research was to compare gene transcription profiles of Musculus longissimus dorsi (MLD) between pigs fed diets with high (HED) or low (LED) energy contents. Two groups of 4 Casertana pigs were reared from 3 to 12 months of age in the same environmental conditions and fed HED or LED. In the HED, the ave rage daily gain and back fat thickness were significantly (P

An individual variability in β-lactoglobulin content has been previously observed in Girgentana goat milk by HPLC analysis. To identify eventual mutations affecting the transcription level of the gene, the prooter region was characterized in goats showing an anomalous phenotype, consisting in a reduced content of β-lactoglobulin respect to α-lactoalbumine. A single nucleotide substitution not previously reported has been detected. A PCR-RFLP procedure was developed for fast detection of the mutation in different goat breeds: Girgentana, Garganica, Sarda, Alpine, Montefalcone and Saanen. The Montefalcone goat showed the highest frequency of the mutation, confirming one more the peculiarity of this breed.

An individual variability in β-lactoglobulin content has been previously observed in Girgentana goat milk by HPLC analysis. To identify eventual mutations affecting the transcription level of the gene, the prooter region was characterized in goats showing an anomalous phenotype, consisting in a reduced content of β-lactoglobulin respect to α-lactoalbumine. A single nucleotide substitution not previously reported has been detected. A PCR-RFLP procedure was developed for fast detection of the mutation in different goat breeds: Girgentana, Garganica, Sarda, Alpine, Montefalcone and Saanen. The Montefalcone goat showed the highest frequency of the mutation, confirming one more the peculiarity of this breed.

In order to determine candidate genes involved in production traits, the mRNA levels of muscle tissue of extremely different pig breeds (genotypes) were studied using microarray tool. Casertana, an autochthonous breed characterized by slow growth and a massive accumulation of backfat, was compared to Large White and to crossbred Duroc x Landrace x Large White)pigs. The differential expression of muscle genes was evaluated on 3 pigs for each genetic type using a microarray consisting of 10,665 oligos. Animals were of the same age and raised in the same environmental conditions. Muscle tissues were collected at 3, 6, 9, and 11 months and a total of 219 (157 genes in the two main clusters) genes showed differential expression between genetic types. Time series cluster analysis indicated that Casertana breed had a different pattern of gene expressions compared to the Large White and the crossbreed. For Casertana pigs, a first cluster showed 105 genes under expressed at 3 months of age and a second cluster indicated 52 genes over expressed at 3 months of age, in comparison to the other genetic types. As expected, some of the differentially expressed genes were in the category of “contractile fiber” and transcriptional factors involved in muscle development and differentiation.

Tyrosinase-related protein 1 (TYRP1) has been shown to play a fundamental role in pigmentation both in human and mouse. In this work, we aimed to characterize the variability of the caprine TYRP1 gene and investigate its segregation in a wide array of goat breeds. By partially sequencing the coding region of the TYRP1 gene in 18 individuals from eight different breeds, we were able to identify a synonymous nucleotide substitution at exon 3 (c.483C>T). An extensive survey of Iberian and Balearic (N=175), Italian (N=99), Swiss (N=54), Asian (N=14), Canarian (N=92) and North African (N=117) goats with different coat colours was carried out. We found that the C-allele has a different distribution in European vs African breeds, being almost fixed in the latter. Moreover, the C-allele showed an increased frequency in white coated breeds (Girgentana, Grigia Molisana, Blanca de Rasquera and Saanen) when compared with those displaying a dark pigmentation (Cilentana Nera, Azpi Gorri and Murciano- Granadina). This could be due to genetic drift, migration and other factors associated with the demographic history of breeds under analysis or to a genetic hitchhiking event (c.483C>T frequencies would be shaped by a neighbouring causal mutation differentially selected in white and black goats). More refined studies will be needed to distinguish between these two alternative explanations.

Tyrosinase-related protein 1 (TYRP1) has been shown to play a fundamental role in pigmentation both in human and mouse. In this work, we aimed to characterize the variability of the caprine TYRP1 gene and investigate its segregation in a wide array of goat breeds. By partially sequencing the coding region of the TYRP1 gene in 18 individuals from eight different breeds, we were able to identify a synonymous nucleotide substitution at exon 3 (c.483C>T). An extensive survey of Iberian and Balearic (N=175), Italian (N=99), Swiss (N=54), Asian (N=14), Canarian (N=92) and North African (N=117) goats with different coat colours was carried out. We found that the C-allele has a different distribution in European vs African breeds, being almost fixed in the latter. Moreover, the C-allele showed an increased frequency in white coated breeds (Girgentana, Grigia Molisana, Blanca de Rasquera and Saanen) when compared with those displaying a dark pigmentation (Cilentana Nera, Azpi Gorri and Murciano- Granadina). This could be due to genetic drift, migration and other factors associated with the demographic history of breeds under analysis or to a genetic hitchhiking event (c.483C>T frequencies would be shaped by a neighbouring causal mutation differentially selected in white and black goats). More refined studies will be needed to distinguish between these two alternative explanations.

Leptin is an adipocyte-derived hormone acting as a major regulator for food intake and energy homeostatis. Previous studies have focused on association between polymorphisms in the coding region of the leptin pig gene and economically important traits. This work was aimed to study the leptin (LEP) gene at the promoter region to search for polymorphisms that could led to a different gene expression regulation. In a 1213 bp 5’ UTR region we identified 15 new single nucleotide polymorphisms (SNP) and 2 deletion (del) in two pig breeds characterized by different fat content namely Casertana (CT) and Large White (LW). In order to investigate whether the polymorphism affects the transcriptional activity of the leptin promoter we evaluated the in vitro reporter-gene activity driven by two constructs harbouring different haplotype and we found a two fold difference in transcription efficiency (Pin vitro results and backfat thikness (BF) and average daily weight gain (ADG) phenotypes, in the considered breeds and we found a weak association of the different allele with backfat thickness. The polymorphisms identified in the 5’-flanking region of the LEP gene may serve as a basis for future studies even in different breeds and might provide molecular data that can be used in the selection schemes.

The Italian Podolian is an autochthonous breed belonging to the grey steppe cattle group. In the past, the Podolian was present throughout all of the Adriatic and the southern part of Italy, but now it is restricted to four regions and displays morphological differences according to the region. It is thought that the Podolian contributed heavily to the genetic make-up of the Chianina and Romagnola breeds, while contrasting opinions exist regarding the relationship between the Podolian and the Piemontese. This paper aimed at characterizing genetic variability and structure by means of microsatellite loci to assess the relationship between the Podolian and the most relevant European breeds, and to detect evidence of selection in the considered breeds by investigating the existence of outlier loci. The DNA of 134 Italian Podolian individuals from 14 different herds in 4 breeding areas were collected, genotyped at 30 microsatellite loci and compared to 13 Italian and European breeds, including the grey type ones and using N’dama as the outgroup. The Podolian showed the highest values of observed heterozygosity and polymorphism content. Moreover in a subset of 50 samples (chosen according to geographic origin), polymorphism data analysis evidenced the absence of a geographically determined genetic structure. The hierarchical population clustering evidenced a Podolian cluster at K=5 and phylogenetic tree based on Reynold’s distances confirmed the genetic links between the Podolian breeds. Two loci presented significantly low FST values, suggesting that they could be under the effect of balanced selection. It can be concluded that Italian Podolian has no genetic subdivision, contains a notable amount of genetic variability and is closely related to the other Podolian type breeds.