Robertsonian translocation 1;29 (rob(1;29)), a widespread chromosomal anomaly affecting cattle fertility, appears to have originated from a common ancestor. This study utilizes routine SNP data to ...investigate the chromosomal region associated with rob(1;29) and confirm the presence of a shared haplotype among carriers in diverse Italian breeds. Three datasets were employed: Dataset 1 included 151 subjects from 5 beef cattle breeds genotyped with the GGP Bovine 33 k SNP chip; Dataset 2 encompassed 800 subjects from 32 Italian breeds genotyped with the Illumina 50 k SNP chip, sourced from the BOVITA dataset; Dataset 3 combined Dataset 2 with 21 karyologically tested subjects from breeds with a high carrier frequency, genotyped using the Affymetrix 65 K SNP chip. FST analysis pinpointed a distinctive genomic region on the first six Mb of BTA29, the centromeric region involved in the translocation. Haplotype comparisons within this non-recombining region revealed a common haplotype shared among all carriers, supporting the theory of a common ancestor. Principal component and haplotype analysis allowed clear differentiation of rob(1;29) homozygous and heterozygous carriers. Expanding to Dataset 2 revealed rob(1;29) carriers in unexpected breeds, all sharing the same ancestral haplotype. Notably, previously untested breeds, including Cinisara, exhibited a high carrier prevalence (nearly 50%), confirmed by karyological analysis. This study validates the presence of a shared haplotype among all identified rob(1;29) carriers, reinforcing the common ancestor theory as the origin of this translocation's spread throughout the cattle population. Furthermore, it underscores the potential of SNP data analysis as a rapid, accurate, and cost-effective tool for broad rob(1;29) screening, given the translocation's consistent nature across all analyzed breeds.
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 and heat stress pose significant challenges to livestock. Local breeds, particularly small ruminants, are gaining importance due to their adaptability to harsh climates. However, the ...extensive system they are commonly reared in leaves them exposed to the effects of climate change. This study aims to describe the distribution and climate-related challenges faced by registered Italian sheep and goat breeds over the past seven decades. Geolocalized data from all registered small ruminant farms were combined with climatic information retrieved from the “ERA-5-Land hourly data from 1950 to present” dataset. These data were used to calculate average daily temperature, temperature humidity index (THI), and total precipitation during summer. Additionally, THI-based heat waves (HWs) were examined, including the yearly number of HW days and mean THI during HW days. These data were analysed through linear regression models including region or breed, year, and their interaction as fixed factors. The climate data indicate a concerning trend of rising summer temperatures, THI, and HW frequency and intensity, particularly over the past three decades. Central-northern Italy, including the Po Valley and the Alpine Arch, is the most affected region, impacting breeds like Rosset and Brogne sheep, and Lariana and Frisa Valtellinese goats. This is of particular concern because these populations have not been selected for hot climates, and their already small population size exacerbates the problem. Conversely, southern Italy, characterized by hotter and drier temperatures, remained relatively stable. Breeds from this region, such as Girgentana and Nicastrese goats and Nera di Arbus sheep, might represent excellent case studies for climatic adaptation and potential resources for selection for resilience in the face of ongoing climate changes. The findings presented here are essential for the development of monitoring and intervention strategies for breeds facing future vulnerabilities, as well as for designing experiments to explore environmental adaptability in small ruminants.
Shepherd and hunting dogs have undergone divergent selection for specific tasks, resulting in distinct phenotypic and behavioural differences. Italy is home to numerous recognized and unrecognized ...breeds of both types, providing an opportunity to compare them genomically. In this study, we analysed SNP data obtained from the CanineHD BeadChip, encompassing 116 hunting dogs (representing 6 breeds) and 158 shepherd dogs (representing 9 breeds). We explored the population structure, genomic background, and phylogenetic relationships among the breeds. To compare the two groups, we employed three complementary methods for selection signature detection: F
, XP-EHH, and ROH. Our results reveal a clear differentiation between shepherd and hunting dogs as well as between gun dogs vs. hounds and guardian vs. herding shepherd dogs. The genomic regions distinguishing these groups harbour several genes associated with domestication and behavioural traits, including gregariousness (WBSRC17) and aggressiveness (CDH12 and HTT). Additionally, genes related to morphology, such as size and coat colour (ASIP and TYRP1) and texture (RSPO2), were identified. This comparative genomic analysis sheds light on the genetic underpinnings of the phenotypic and behavioural variations observed in Italian hunting and shepherd dogs.
Mannara dogs have long been bred in Sicily (Italy) to work alongside shepherds as flock guardians. This study provides a morphologic, genealogic, and genomic characterisation of the Mannara dog, ...useful in light of its recognition process and to improve the breed standard. Morphologic measurements of body, head, and chest were taken on 111 adult Mannara dogs. The whole population pedigree was used to calculate the inbreeding coefficient (F) and five effective population size (N
e
) parameters. Twelve Mannara dogs were genotyped using the Canine 230 K SNP BeadChips and compared with Maremma sheepdog, Caucasian shepherd dog, Cane Corso Italiano, and Neapolitan mastiff for population structure, heterozygosity, and runs of homozygosity. The morphometric evaluation showed that Mannara dogs generally accords with the provisional standard and can be classified as a large/giant, meso-dolicomorphic, and mesocephalic breed. The population consists of 375 individuals, one third of which are founders and the remaining belong to 58 litters; presenting low inbreeding (F = 0.7%) and balanced sires and dams. The N
e
estimates range widely: two (N
eN
=159 and N
eFi
=50) exceed the FCI limit for breed recognition and one (N
eCi
=25) did not. Genetically, all the included populations are well distinct, with the Maremma sheepdog being the nearest to the Mannara dog. Five Mannara have a single ancestral component, while the others show higher admixed proportions. The genomic inbreeding and heterozygosity confirm the good management of the breed. Our analyses suggest that the Mannara breed should continue the recognition process, pivotal to preserving an invaluable canine resource for the Sicilian agriculture.
Highlights
The morphometric measurements of Mannara dogs generally accords with the provisional standard.
The pedigree analysis reveals that the population is well managed and meets the criteria for FCI recognition.
The Mannara dog presents a unique genomic 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.
We analyzed the ROH distribution and inbreeding (F
) 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
. 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.
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.
The Fonni's dog is an ancient Sardinian breed for livestock and property guarding. In recent years, the number of new registrations to the breeding book has slumped and, thus, this breed risks being ...lost forever. This work refocuses attention to the Fonni's dog, analysing its genomic makeup and comparing different phenotypical and genetic evaluation scores. Thirty Fonni's dogs were ranked by their general accordance to the breed typicality (typicality score) and to the provisional standard by official judges (judges' score). They were genotyped with a 230K SNP BeadChip and compared with 379 dogs of 24 breeds. Genomically, the Fonni's dogs placed themselves near shepherd dogs and showed a unique genetic signature, which was used to create the genomic score. This score better correlated with typicality (ρ = 0.69,
< 0.0001) than the judges' score (ρ = 0.63,
= 0.0004), which showed little variability among the included dogs. Hair texture or colour were significantly associated in the three scores. The Fonni's dog is confirmed as a well-distinguished breed, despite being selected mainly for its work abilities. The evaluation criteria used during dog expositions can be improved to increase their variability and include elements typical of the breed. The recovery of the Fonni's dog would be possible only with a shared vision between the Italian kennel club and breeders, and the support of regional programs.
The inbreeding coefficient is an important parameter for livestock management. Small ruminant breeders and associations mainly rely on pedigree information, but genomic tools are gaining relevance, ...overcoming possible pedigree inconsistencies. This study investigates the relationship between pedigree-based and genomic inbreeding in two goat and four sheep dairy breeds. Pedigree and genomic data (medium-density SNPchip) were obtained for 3107 goats and 2511 sheep. We estimated pedigree depth (number of fully traced generations, FullGen) and inbreeding (FPED), as well as two genomic inbreeding indexes, using runs of the homozygosity (FROH) and genomic relationship matrix (FGRM). The correlation between the inbreeding coefficients was assessed. A linear regression model (LRM) was fitted for estimating FPED from FROH. After quality control on genomic data, we retained 5085 animals. Mean inbreeding values were low, with higher FROH than FPED and FGRM. Breed differences can partially depend on different managements. The correlation between FPED and FROH was the highest and directly related to pedigree depth. The best LRM was chosen for FullGen ≥4 and ≥6 for goats and sheep, respectively; after excluding animals with extreme residuals, a new refined regression equation was calculated. Since massive genotyping is not affordable to small ruminant breeders, it is important to understand the distinction and relationship between differently calculated inbreeding coefficients, also in view of the introduction of genomic enhanced breeding values. Our study highlights the importance of accurate pedigree information and, especially if not obtainable, of calculating genomic-based inbreeding coefficients. A better estimation of animals’ relatedness contributes to improve animal breeding and conservation.
The Comune di Sicilia, a local goat breed from Sicily (Italy), is currently undergoing recognition as a distinct breed. This study aims to characterize the population both phenotypically and ...genomically to advance its recognition process. A total of 78 subjects from two locations were enrolled, and their phenotypic data, including qualitative traits and morphometric measurements of adult animals, were recorded and statistically analyzed. The goats were genotyped using the Illumina 50 k Goat SNPchip, comparing them with 473 goats from 15 Italian breeds. Population structure, phylogenetic relationships, admixture, and genomic inbreeding were analyzed. Additionally, subjects with different morphological traits were compared using FST and runs of homozygosity, leading to the identification of potential candidate genes associated with anotia and wattle presence in goats. The Comune di Sicilia breed exhibited distinctive genomic and phenotypic features, setting it apart from other breeds in the same region. However, moderate variability, possibly influenced by selection practices, was also observed. To ensure the breed’s preservation and prevent excessive inbreeding, a comprehensive approach considering both morphology and genomic background is recommended. This study contributes valuable insights into the genetic peculiarities of the Comune di Sicilia goat, supporting its recognition as a unique and valuable breed.
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