Microsatellite imputation using SNP data for parentage verification in four Italian sheep breeds.

Microsatellite markers (MS) have been widely used for parentage verification in most of the livestock species over the past decades mainly due to their high polymorphic information content. In the genomic era, the spread of genotype information as single-nucleotide polymorphism (SNP) has raised the question to effectively use SNPs also for parentage testing. Despite the clear advantages of SNP panels in terms of cost, accuracy, and automation, the transition from MS to SNP markers for parentage verification is still very slow and, so far, only routinely applied in cattle. A major difficulty during this transition period is the need of SNP data for parents and offspring, which in most cases is not yet feasible due to the genotyping cost. To overcome the unavailability of same genotyping platform during the transition period, in this study we aimed to assess the feasibility of a MS imputation pipeline from SNPs in four native sheep dairy breeds: Comisana (N = 331), Massese (N = 210), Delle Langhe (N = 59) and Sarda (N = 1003). Those sheep were genotyped for 11 MS and with the Ovine SNP50 Bead Chip. Prior to imputation, a quality control (QC) was performed, and SNPs located within a window of 2 Mb from each MS were selected. The core of the developed pipeline was made up of three steps: (a) storing of both MS and SNP data in a Variant Call Format file, (b) masking MS information in a random sample of individuals (10%), (c) imputing masked MS based on non-missing individuals (90%) using an imputation program. The feasability of the proposed methodology was assessed also among different training - testing split ratio, population size, number of flanking SNPs as well as within and among breeds. The accuracy of the MS imputation was assessed based on the genotype concordance as well as at parentage verification level in a subset of animals in which assigned parents' MS were available. A total of 8 MS passed the QC, and 505 SNPs were located within the ±2 Mb window from each MS, with an average of 63 SNPs per MS. The results were encouraging since when excluding the worst imputed MS (OARAE129), and regardless on the analyses performed (within and across breeds) for all breeds, we achieved an overall concordance rate over 94%. In addition, on average, the imputed offspring MS resulted in equivalent parentage outcome in 94% of the cases when compared to verification using original MS, highlighting both the feasibility and the eventual practical advantage of using this imputation pipeline.

A comprehensive analysis of the genetic diversity and environmental adaptability in worldwide Merino and Merino-derived sheep breeds.

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.

Using Pedigree and Genomic Data toward Better Management of Inbreeding in Italian Dairy Sheep and Goat Breeds.

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.

Influence of milking units and working vacuum level on the mechanical milking of goats.

The objectives of this study were to evaluate and compare the effect of working vacuum levels (35 and 44 kPa) and liners dimensions (mouthpiece lip diameter and overall length, 20-185 and 22-170 mm) on the main milking characteristics of goats. The results highlight that both the working vacuum level and the liner dimension have influenced the milk flow curve parameters. The maximum variations were found for peak flow rate, which increased significantly with liner dimensions of 20-185 mm at a working vacuum level of 44 kPa as well as average milk flow rate and for plateau phase duration. The incorrect adoption of operative parameters and unsuitable milking machine components, might affect the performance of the mechanical milking and negatively affecting animal productions and welfare.