Molecular characterization of the Sicilian goat populations

The Sicilian goats are characterized by a strong population admixture structure, caused by geographical location of the farms, influences of natural mating and traditional breeding systems where flock represents an important breeding unit. Nowadays, several local populations are reared in Sicily, some of which do not have a recognized defined genetic structure, having taken origin from several crosses between animals of different breeds/populations sharing the same environment. The aim of this work was to characterize the Sicilian autochthonous goat populations using microsatellite markers and genetic polymorphisms of casein gene

Maedi Visna virus infection and TMEM154 genotypes in Valle del Belìce sheep breed

Maedi Visna (MV) is a viral infection in sheep caused by Lentivirus and characterised by a long incubation period, slow progression, weight loss and eventually death. TMEM154 was reported in the ovine as major candidate gene associated with host susceptibility/resistance. The aim of this study was to verify the prevalence of MV infection within Sicilian herds of Valle del Belìce breed using an ELISA serological test and to estimate the frequencies of the resistant/susceptible genotypes to the TMEM154 gene. Finally, we investigated the association between TMEM154 E/K genotype and MV infectious status. A total of 1,083 animals from different flocks were tested. The ELISA method showed 15.33% (n = 166) of infected individuals. Analyses of the sequences showed the presence of both K and E alleles with frequencies of 0.151 and 0.849, respectively. On the total individuals, only 23 carried KK genotype while 280 were heterozigous EK, and 780 homozygous EE. The locus was in Hardy-Weinberg equilibrium in the breed (p-value <0.05) and observed and expected heterozygosity values were 0.258 and 0.256, respectively. Moreover, a significant association (p-value < 0.001) between TMEM154 genotypes and seroprevalence status (positive vs. negative) was found. This study allowed us to know the prevalence of MV infection in Sicilian flocks of Valle del Belìce breed and could be helpful in establishing selection programs aimed at controlling and eradicating this virus

Assessment of genetic variation for pathogen-specific mastitis resistance in Valle del Belice dairy sheep

Background: Mastitis resistance is a complex and multifactorial trait, and its expression depends on both genetic and environmental factors, including infection pressure. The objective of this research was to determine the genetic basis of mastitis resistance to specific pathogens using a repeatability threshold probit animal model. Results: The most prevalent isolated pathogens were coagulase-negative staphylococci (CNS); 39 % of records and 77 % of the animals infected at least one time in the whole period of study. There was significant genetic variation only for Streptococci (STR). In addition, there was a positive genetic correlation between STR and all pathogens together (ALL) (0.36 ± 0.22), and CNS and ALL (0.92 ± 0.04). Conclusion: The results of our study support the presence of significant genetic variation for mastitis caused by Streptococci and suggest the importance of discriminating between different pathogens causing mastitis due to the fact that they most likely influence different genetic traits. Low heritabilities for pathogen specific-mastitis resistance may be considered when including bacteriological status as a measure of mastitis presence to implement breeding strategies for improving udder health in dairy ewes

Genome-wide scan for Runs of Homozygosity in Valle del Belice sheep

The current availability of very large numbers of single nucleotide polymorphisms (SNPs) throughout the genome makes these markers particularly suitable for the detection of genomic regions where a reduction in heterozygosity occurred and offers new opportunities to improve the accuracy of inbreeding (F) estimates. Runs of homozygosity (ROH) are contiguous lengths of homozygous segments of the genome where the two haplotypes inherited from the parents are identical. Here, we investigated the occurrence and the distribution of ROH in medium-density SNP genotypes (~ 50 000) in order to characterize autozygosity in 512 individuals of Valle del Belice sheep and identify the regions of the genome with high ROH frequencies. A total of 11 629 ROH were identified. All individuals displayed at least one ROH > 1 Mb. The mean value of FROH>1Mb was 0.084\ub10.061. ROH that were shorter than 10 Mb predominated. The highest coverage of chromosome (OAR) by ROH was observed on OAR24, whereas the lowest one was observed on OAR1. A typical pattern was observed for the number of ROH per OAR with higher values in the first three chromosomes. There was a considerable difference among animals for the number of ROH segments and the length of the genome covered by ROH. The genomic regions most commonly associated with ROH were identified by selecting the top 1% of the SNPs most commonly observed in ROH within breed. A total of 239 SNPs were considered as candidate SNPs and we identified 107 potential candidate genes that may be under directional selection. Six genomic regions located on six chromosomes (OAR2, OAR3, OAR4, OAR10, OAR11 and OAR23), corresponding to ROH island, presented hotspot of autozygosity. According to KEGG database, a majority of the genes were involved in multiple signaling and signal transduction pathways in a wide variety of cellular and biochemical processes. The ROH islands spanned several candidate genes which influence traits that are associated with adaptability and with the regulation of immune responses (NPAS2, PDCL3, SERPINF1 and SERPINF2) and we did not identified candidate genes with important influence on milk production traits in sheep. The Valle del Belice breed is subjected to limited breeding selection programs for milk production traits, but shows excellent adaptability to the local environments. Therefore, these results suggest at least a partial role of natural selection in shaping the genome of Valle del Belice sheep breed

Genome-wide analysis reveals the patterns of genetic diversity and population structure of 8 Italian local chicken 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 (<4 Mb in length) were more frequent than long segments. Patterns of genetic differentiation, model-based clustering, and neighbor networks showed that most breeds formed nonoverlapping clusters and were clearly separate populations. The 2 Polverara breeds shared a similar genetic background and showed the lowest genetic differentiation in comparison with purebred lines; the local populations showed separated groups. PPP and PML were closer to the group of the purebred broiler lines (BRSA, BRSB, BRDA, and BRDB). Six genomic regions are presented as hotspots of autozygosity among the Italian chicken breeds, with candidate genes involved in multiple morphological phenotypes as breast muscle, muscle dry matter content, and body weight. This study is the first exhaustive genome-wide analysis of the diversity of these Italian local chickens from Veneto region. We conclude that breeds have conserved authentic genetic patterns. The results are of significant importance because they will help design and implement conservation strategies. In fact, the conservation of these breeds may also have positive impacts on the local economy, niche traditional markets, and offering a source of high-quality products to consumers. In this context, genomic information may play a crucial role in the management of local breeds

Genome wide Copy Number Variation (CNV) detection in Cinisara cattle breed

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

Distribution of functional variants within Runs of Homozygosity in four Italian cattle breeds

Several methods have been used to identify genomic regions subjected to selective sweeps. An alternative method can make use of runs of homozygosity (ROH), defined as stretches of homozygous regions in a genome. The aim of the present study was to detect selective sweeps using ROH in four cattle breeds. Individuals of Cinisara (71), Modicana (72),Reggiana (168) and Italian Holstein (96) were genotyped with the Illumina Bovine50SNP v2 BeadChip. To identify genomic regions that were most commonly associated with ROH within each breed, the percentage of occurrences of a single nucleotide polymorphism (SNP) in ROH was calculated across animals. The genomic regions most commonly associated with ROH were identified by selecting the top 1% of the SNPs most commonly observed in ROH in each breed. This approach resulted in the identification of 11 genomic regions in the Cinisara and Italian Holstein, and 8 in Modicana and Reggiana showing increased frequency of ROH. Generally, ROH patterns differed between breeds. There were two commons genomic regions between breed pairs, and in particular one in BTA6 between Modicana and Reggiana and one in BTA10 between Cinisara and Italian Holstein. A highly homozygous region (> 45% of individuals with ROH) was found only in Modicana breed in BTA6 (6:37,019,972- 39,069,719) within a QTL affecting milk fat and protein concentration. In these genomic regions we identified from 126 to 347 genes for each breed. According to Panther and KEGG database, a majority of the genes was involved in multiple signaling and signal transduction pathways in a wide variety of cellular and biochemical processes. Several of these genes were also comprised in a list of genes related to phenotypes for which cattle breeds have been subjected to strong positive selection. For most genes associated with ROH islands, a biological link to traits such as milk yield and composition, reproduction, immune response, coat colour, genetic disorders and resistance/susceptibility to infectious and diseases, which are known to be under selection, can be hypothesized. These results showed that selective sweeps detected with ROH approach are shared among breeds and that scanning the genome for ROH might be an alternative or complementary strategy to detect selective sweep related with important economically traits

Genome-wide scan for runs of homozygosity identifies potential candidate genes associated with local adaptation in Valle del Belice sheep

Background: Because very large numbers of single nucleotide polymorphisms (SNPs) are now available throughout the genome, they are particularly suitable for the detection of genomic regions where a reduction in heterozygosity has occurred and they offer new opportunities to improve the accuracy of inbreeding (F F) estimates. Runs of homozygosity (ROH) are contiguous lengths of homozygous segments of the genome where the two haplotypes inherited from the parents are identical. Here, we investigated the occurrence and distribution of ROH using a medium-dense SNP panel to characterize autozygosity in 516 Valle del Belice sheep and to identify the genomic regions with high ROH frequencies. Results: We identified 11,629 ROH and all individuals displayed at least one ROH longer than 1 Mb. The mean value of F F estimated from ROH longer than1 Mb was 0.084 \uc2\ub1 0.061. ROH that were shorter than 10 Mb predominated. The highest and lowest coverages of Ovis aries chromosomes (OAR) by ROH were on OAR24 and OAR1, respectively. The number of ROH per chromosome length displayed a specific pattern, with higher values for the first three chromosomes. Both number of ROH and length of the genome covered by ROH varied considerably between animals. Two hundred and thirty-nine SNPs were considered as candidate markers that may be under directional selection and we identified 107 potential candidate genes. Six genomic regions located on six chromosomes, corresponding to ROH islands, are presented as hotspots of autozygosity, which frequently coincided with regions of medium recombination rate. According to the KEGG database, most of these genes were involved in multiple signaling and signal transduction pathways in a wide variety of cellular and biochemical processes. A genome scan revealed the presence of ROH islands in genomic regions that harbor candidate genes for selection in response to environmental stress and which underlie local adaptation. Conclusions: These results suggest that natural selection has, at least partially, a role in shaping the genome of Valle del Belice sheep and that ROH in the ovine genome may help to detect genomic regions involved in the determinism of traits under selection