Demography and Genealogical Analysis of Massese Sheep, a Native Breed of Tuscany.

This study investigates the genealogical and demographic trends of the Massese sheep breed in Tuscany from 2001 to 2021. The Herd Book kept by the Italian Sheep and Goat Breeders Association (Asso.Na.Pa) provided the data. The descriptive statistics were analyzed using JMP software. The pedigree parameters of a total of 311,056 animals (whole population-WP) were analyzed using CFC, ENDOG, and Pedigree viewer software. A total of 24,586 animals born in the period 2007-2021 represented the Reference Population (RP), and 18,554 animals the Base Population (BP). The demographic results showed an inconsistent trend of offspring registration. This study showed a short period of productivity for both ewes and rams, with means of 1.47 and 19.2 registered newborn ewes and rams, respectively. The genealogical analysis revealed incomplete data, highlighting inaccurate assessments of the relationships among the animals, and inbreeding with large differences among provinces. The average inbreeding coefficient in the WP was 1.16%, and it was 2.26% in the RP. The total number of inbreds was 2790 in the WP, with an average FPED of 13.56%, and 2713 in the RP, with an average FPED of 12.82%. The use of pedigree data is a key and economical approach to calculating inbreeding and relationship coefficients. It is the primary step in genetic management, playing a crucial role in the preservation of a breed. The regular updating of genealogical data is the first step to ensuring the conservation of animal genetic resources, and this study is compromised by the lack of such updates.

Genetic parameters for milk production and type traits in North American and European Alpine and Saanen dairy goat populations.

The development of an across-country genomic evaluation scheme is a promising alternative for enlarging reference populations and successfully implementing genomic selection in small ruminant populations. However, the feasibility of such evaluations depends on the genetic similarity among the populations, and therefore, high connectedness and high genetic correlations between the traits recorded in different countries or populations are needed. In this study, we evaluated the feasibility of performing an across-country genomic evaluation for milk production and type traits in Alpine and Saanen goats from Canada, France, Italy, and Switzerland. Variance components and genetic parameters, including genetic correlations between traits recorded in different countries, were calculated using combined phenotypes, genotypes, and pedigree datasets. The (co)variance component analyses were performed within breed, either based only on pedigree information or also incorporating genomic information. Across-country genetic parameters were calculated for 3 representative traits (i.e., milk yield, fat content, and rear udder attachment). The heritability estimates ranged from 0.10 to 0.50, which are consistent with previous estimates reported in the literature. The genetic correlations for rear udder attachment ranged from 0.75 (between France and Italy, for the Alpine breed without genomic information) to 0.95 (between Canada and France, for the Saanen breed with genomic information), whereas for fat content, between France and Italy, they ranged from 0.75 in the Alpine breed without genomic information to 0.78 in the Alpine breed with genomic information. However, genetic correlations for milk yield were only estimable between France and Italy, with a moderate value of 0.45 for the Alpine breed with or without genomic information, and of 0.22 and 0.26 in the Saanen breed with and without genomic information, respectively. These low genetic correlations for milk yield could be due to several factors, including the trait definition in each country and genotype-by-environment interactions (GxE). The high genetic correlations found for fat content and rear udder attachment indicate that these traits might be more standardized across countries and less affected by GxE effects. Thus, an international genomic evaluation for these traits might be feasible. Further studies should be performed to understand the surprisingly lower genetic correlations between milk yield across countries. Furthermore, additional efforts should be made to increase the genetic connection among the Alpine and Saanen goat populations in the 4 countries included in the analyses.

Genetic Characterization and Population Connectedness of North American and European Dairy Goats.

Genomic prediction of breeding values is routinely performed in several livestock breeding programs around the world, but the size of the training populations and the genetic structure of populations evaluated have, in many instances, limited the increase in the accuracy of genomic estimated breeding values. Combining phenotypic, pedigree, and genomic data from genetically related populations can be a feasible strategy to overcome this limitation. However, the success of across-population genetic evaluations depends on the pedigree connectedness and genetic relationship among individuals from different populations. In this context, this study aimed to evaluate the genetic connectedness and population structure of Alpine and Saanen dairy goats from four countries involved in the European project SMARTER (SMAll RuminanTs Breeding for Efficiency and Resilience), including Canada, France, Italy, and Switzerland. These analyses are paramount for assessing the potential feasibility of an across-country genomic evaluation in dairy goats. Approximately, 9,855 genotyped individuals (with 51% French genotyped animals) and 6,435,189 animals included in the pedigree files were available across all four populations. The pedigree analyses indicated that the exchange of breeding animals was mainly unilateral with flows from France to the other three countries. Italy has also imported breeding animals from Switzerland. Principal component analyses (PCAs), genetic admixture analysis, and consistency of the gametic phase revealed that French and Italian populations are more genetically related than the other dairy goat population pairs. Canadian dairy goats showed the largest within-breed heterogeneity and genetic differences with the European populations. The genetic diversity and population connectedness between the studied populations indicated that an international genomic evaluation may be more feasible, especially for French and Italian goats. Further studies will investigate the accuracy of genomic breeding values when combining the datasets from these four populations.

Genetic parameters of weeping teats in Italian Saanen and Alpine dairy goats and their relationship with milk production and somatic cell score.

This paper reports a quantitative genetics analysis of weeping teats (WT), an abnormality of the mammary gland in goats. Weeping teats are characterized by milk oozing out of the teat or by the presence of multiple cysts near its base. This abnormality has been routinely recorded in Italian Alpine and Saanen goats since 2000 using a score of 0 or 1 (0 = defect not present, 1 = defect present). No information is available on the genetic background of WT or its relationship with production or other udder-related traits. Data obtained by the Italian National Sheep and Goat Breeders Association (Rome, Italy) were used to estimate both heritability of WT and its genetic correlation with milk yield, somatic cell score, and udder traits. The final data set used in the analysis included 2,178 Saanen and 2,309 Alpine primiparous goats kidding from 2009 to 2014. The pedigree data included 7,333 Saanen and 7,421 Alpines, respectively. A threshold-linear multivariate animal model was used to estimate variance and covariance components. A genealogical data analysis was also implemented, including genealogical data completeness, inbreeding, and identification of possible most recent common ancestors. On average, around 4 and 13% of primiparous Saanen and Alpine females kidding from 2009 to 2014 showed mammary gland abnormality, respectively. Weeping teats heritability was 0.27 and 0.26 for Saanen and Alpine, respectively. Genetic correlations between milk production or somatic cell score ranged from -0.16 in Saanen to 0.43 in Alpine, but the standard error of the estimates was very large. Positive genetic correlations were observed among WT and teat characteristics in both Saanen and Alpine. The average inbreeding of abnormality carriers was 2.4 and 5.1 for Saanen and Alpine, respectively. The genealogical data analysis identified 4 common ancestors of affected does in Saanen and 2 in Alpine. These results indicate that WT have a possible genetic background. A genome-wide association study might help in understanding the polygenic or monogenic determination of this abnormality.

Lactation curves of Sarda breed goats estimated with test day models.

Test day records of milk yield (38,765), fat and protein contents (11,357) of Sarda goats (the most numerous Italian goat breed) were analysed with mixed linear models in order to estimate the effects of test date (month and year of kidding for fat and protein contents) parity, number of kids born, altitude of location of flocks (<200 m asl, 200-500 m asl, >500 m asl), flocks within altitude and lactation stage (eight days-in-milk intervals of 30 d each) on milk production. All factors considered in the models affected milk traits significantly. Milk yield was lower in first parity goats than in higher parities whereas fat and protein contents showed an opposite trend. Goats with two kids at parturition had a higher milk yield than goats with one kid and tended to have lower fat and protein percentages. Repeatability between test days within lactation was 0.34, 0.17 and 0.45 for milk yield, fat content and protein content, respectively. Lactation curves of goats farmed at different altitudes were clearly separated, especially for milk yield. Results of the present study highlight differences in milk production traits among the three subpopulations that have been previously identified within the Sarda breed on the basis of the morphological structure of animals and altitude of location of flocks.