Genetic profile of scrapie codons 146, 211 and 222 in the PRNP gene locus in three breeds of dairy goats

Polymorphisms at PRNP gene locus have been associated with resistance against classical scrapie in goats. Genetic selection on this gene within appropriate breeding programs may contribute to the control of the disease. The present study characterized the genetic profile of codons 146, 211 and 222 in three dairy goat breeds in Greece. A total of 766 dairy goats from seven farms were used. Animals belonged to two indigenous Greek, Eghoria (n = 264) and Skopelos (n = 287) and a foreign breed, Damascus (n = 215). Genomic DNA was extracted from blood samples from individual animals. Polymorphisms were detected in these codons using Real-Time PCR analysis and four different Custom TaqMan® SNP Genotyping Assays. Genotypic, allelic and haplotypic frequencies were calculated based on individual animal genotypes. Chi-square tests were used to examine Hardy-Weinberg equilibrium state and compare genotypic distribution across breeds. Genetic distances among the three breeds, and between these and 30 breeds reared in other countries were estimated based on haplotypic frequencies using fixation index FST with Arlequin v3.1 software; a Neighbor-Joining tree was created using PHYLIP package v3.695. Level of statistical significance was set at P = 0.01. All scrapie resistance-associated alleles (146S, 146D, 211Q and 222K) were detected in the studied population. Significant frequency differences were observed between the indigenous Greek and Damascus breeds. Alleles 222K and 146S had the highest frequency in the two indigenous and the Damascus breed, respectively (ca. 6.0%). The studied breeds shared similar haplotypic frequencies with most South Italian and Turkish breeds but differed significantly from North-Western European, Far East and some USA goat breeds. Results suggest there is adequate variation in the PRNP gene locus to support breeding programs for enhanced scrapie resistance in goats reared in Greece. Genetic comparisons among goat breeds indicate that separate breeding programs should apply to the two indigenous and the imported Damascus breeds

A genome-wide association study reveals novel SNP markers associated with resilience traits in two Mediterranean dairy sheep breeds

Genetic selection for higher productivity increased dairy sheep susceptibility to diseases and environmental stressors, challenging their health and welfare status and production efficiency. Improving resilience to such stressors can enhance their ability to face these challenges without compromising productivity. Our objective was to estimate genomic heritability and perform genome-wide association studies (GWAS) to detect SNPs and candidate genes associated with three proxy traits for resilience (milk somatic cell count—SCC, lactation persistency—LP, body condition score—BCS) of Chios and Frizarta dairy ewes. We used genome-wide genotypes of 317 Chios and 346 Frizarta ewes. Individual records of milk yield and BCS, and milk samples were collected monthly for two consecutive milking periods; samples were analyzed to determine SCC. The LP was calculated as the regression coefficient of daily milk yield on days from lambing. Within breed, variance components analyses and GWAS were performed using genomic relatedness matrices in single-trait animal linear mixed models. Genomic-based heritability estimates were relatively high (BCS: h2 = 0.54 and 0.55, SCC: h2 = 0.25 and 0.38, LP: h2 = 0.43 and 0.45, for Chios and Frizarta ewes, respectively), compared to previous pedigree-based studies. The GWAS revealed 7 novel SNPs associated with the studied traits; one genome-wide and two suggestive significant SNPs for SCC (Frizarta: rs403061409, rs424064526 and rs428540973, on chromosomes 9, 1 and 12, respectively), one suggestive significant SNP for BCS (Chios: rs424834097 on chromosome 4) and three suggestive significant SNPs for LP (Frizarta: rs193632931 and rs412648955 on chromosomes 1 and 6, Chios: rs428128299 on chromosome 3). Nineteen candidate genes were detected: two for BCS (Chios: POT1, TMEM229A), thirteen for SCC (Frizarta: NTAQ1, ZHX1, ZHX2, LOC101109545, HAS2, DERL1, FAM83A, ATAD2, RBP7, FSTL1, CD80, HCLS1, GSK3B) and four for LP (Frizarta: GRID2, FAIM, CEP70—Chios: GRIP1). Present results show that resilience in the studied dairy sheep breeds is heritable and advance existing knowledge on the genomic background of SCC, LP, and BCS. Future research will quantify effects of different alleles of significant SNPs on the studied traits and search for possible correlations among traits to facilitate their effective incorporation in breeding programs aiming to improve resilience.</p

Genetic profile of scrapie codons 146, 211 and 222 in the PRNP gene locus in three breeds of dairy goats

Polymorphisms at PRNP gene locus have been associated with resistance against classical scrapie in goats. Genetic selection on this gene within appropriate breeding programs may contribute to the control of the disease. The present study characterized the genetic profile of codons 146, 211 and 222 in three dairy goat breeds in Greece. A total of 766 dairy goats from seven farms were used. Animals belonged to two indigenous Greek, Eghoria (n = 264) and Skopelos (n = 287) and a foreign breed, Damascus (n = 215). Genomic DNA was extracted from blood samples from individual animals. Polymorphisms were detected in these codons using Real-Time PCR analysis and four different Custom TaqMan® SNP Genotyping Assays. Genotypic, allelic and haplotypic frequencies were calculated based on individual animal genotypes. Chi-square tests were used to examine Hardy-Weinberg equilibrium state and compare genotypic distribution across breeds. Genetic distances among the three breeds, and between these and 30 breeds reared in other countries were estimated based on haplotypic frequencies using fixation index FST with Arlequin v3.1 software; a Neighbor-Joining tree was created using PHYLIP package v3.695. Level of statistical significance was set at P = 0.01. All scrapie resistance-associated alleles (146S, 146D, 211Q and 222K) were detected in the studied population. Significant frequency differences were observed between the indigenous Greek and Damascus breeds. Alleles 222K and 146S had the highest frequency in the two indigenous and the Damascus breed, respectively (ca. 6.0%). The studied breeds shared similar haplotypic frequencies with most South Italian and Turkish breeds but differed significantly from North-Western European, Far East and some USA goat breeds. Results suggest there is adequate variation in the PRNP gene locus to support breeding programs for enhanced scrapie resistance in goats reared in Greece. Genetic comparisons among goat breeds indicate that separate breeding programs should apply to the two indigenous and the imported Damascus breeds

A genome-wide association study reveals novel SNP markers associated with resilience traits in two Mediterranean dairy sheep breeds

Genetic selection for higher productivity increased dairy sheep susceptibility to diseases and environmental stressors, challenging their health and welfare status and production efficiency. Improving resilience to such stressors can enhance their ability to face these challenges without compromising productivity. Our objective was to estimate genomic heritability and perform genome-wide association studies (GWAS) to detect SNPs and candidate genes associated with three proxy traits for resilience (milk somatic cell count—SCC, lactation persistency—LP, body condition score—BCS) of Chios and Frizarta dairy ewes. We used genome-wide genotypes of 317 Chios and 346 Frizarta ewes. Individual records of milk yield and BCS, and milk samples were collected monthly for two consecutive milking periods; samples were analyzed to determine SCC. The LP was calculated as the regression coefficient of daily milk yield on days from lambing. Within breed, variance components analyses and GWAS were performed using genomic relatedness matrices in single-trait animal linear mixed models. Genomic-based heritability estimates were relatively high (BCS: h2 = 0.54 and 0.55, SCC: h2 = 0.25 and 0.38, LP: h2 = 0.43 and 0.45, for Chios and Frizarta ewes, respectively), compared to previous pedigree-based studies. The GWAS revealed 7 novel SNPs associated with the studied traits; one genome-wide and two suggestive significant SNPs for SCC (Frizarta: rs403061409, rs424064526 and rs428540973, on chromosomes 9, 1 and 12, respectively), one suggestive significant SNP for BCS (Chios: rs424834097 on chromosome 4) and three suggestive significant SNPs for LP (Frizarta: rs193632931 and rs412648955 on chromosomes 1 and 6, Chios: rs428128299 on chromosome 3). Nineteen candidate genes were detected: two for BCS (Chios: POT1, TMEM229A), thirteen for SCC (Frizarta: NTAQ1, ZHX1, ZHX2, LOC101109545, HAS2, DERL1, FAM83A, ATAD2, RBP7, FSTL1, CD80, HCLS1, GSK3B) and four for LP (Frizarta: GRID2, FAIM, CEP70—Chios: GRIP1). Present results show that resilience in the studied dairy sheep breeds is heritable and advance existing knowledge on the genomic background of SCC, LP, and BCS. Future research will quantify effects of different alleles of significant SNPs on the studied traits and search for possible correlations among traits to facilitate their effective incorporation in breeding programs aiming to improve resilience

Assessment of the production traits of goats resistant to classical scrapie

The objectives were to determine the genetic profile of dairy goats in Greece regarding their resistance to classical scrapie and to assess the possible impact of selection for scrapie resistance on other economically important animal traits. A total of 766 dairy goats from seven farms were used. Goats belonged to two indigenous Greek, Eghoria (n = 264) and Skopelos (n = 287), and a foreign breed Damascus (n = 215). Nuclear DNA was extracted from individual blood samples. Polymorphisms of interest at codons 146 (N/S/D), 211 (R/Q) and 222 (Q/K) were detected using Real-Time PCR analysis and four different Custom TaqMan® SNP Genotyping Assays. Genotypic, allelic and haplotypic frequencies were calculated. Chi-square tests were used to compare genotypic distribution across breeds. Moreover, genetic distances among the three breeds, and between these and 27 breeds reared in other countries were estimated based on haplotypic frequencies using fixation index FST. All scrapie resistance-associated alleles (146S, 146D, 211Q and 222K) were detected in the studied goats. Significant genetic profile differences (P0.0003). Results suggest there is adequate variation in the PRNP gene locus to support breeding programmes for enhanced scrapie resistance in goats reared in Greece. Genetic differences among all goat breeds indicate that selective breeding programmes towards scrapie resistance should be developed independently for each breed of interest. In this regard, our results suggest that separate breeding programmes should apply to the indigenous Greek and Damascus breeds with alleles 222K and 146S being the best candidates, respectively. Selection for the latter is not expected to compromise animal productivity and udder health. Nevertheless, continuous monitoring of selective breeding programmes is advised to safeguard against possible emerging side effects on animal performance and genetic diversity.Η παρούσα διατριβή είχε ως στόχους τον προσδιορισμό της γονοτυπικής σύνθεσης του ελληνικού πληθυσμού αιγών ως προς την ανθεκτικότητά τους στην κλασική μορφή της τρομώδους νόσου και τη διερεύνηση τυχόν επιπτώσεων στις αποδόσεις και την υγεία των ζώων που θα μπορούσαν να αναμένονται από την εφαρμογή ενός προγράμματος γενετικής επιλογής, ανθεκτικών για την τρομώδη νόσο, αιγών. Χρησιμοποιήθηκαν 766 γαλακτοπαραγωγές αίγες, από 7 εκτροφές, των φυλών Εγχώρια (n=264), Σκοπέλου (n=287) και Δαμασκού (n=215). Πυρηνικό DNA απομονώθηκε από ατομικά δείγματα αίματος και αναλύθηκε με την τεχνική της αλυσιδωτής αντίδρασης της πολυμεράσης σε πραγματικό χρόνο (Real-Time PCR), χρησιμοποιώντας τέσσερα μίγματα TaqMan, για την ανίχνευση των πολυμορφισμών στα κωδικόνια 146 (N/S/D), 211 (R/Q) και 222 (Q/K) του γονιδίου PRNP. Υπολογίστηκαν οι γονοτυπικές, αλληλικές και απλοτυπικές συχνότητες. Πραγματοποιήθηκε σύγκριση της γονοτυπικής κατανομής μεταξύ των φυλών με τη δοκιμή χ2. Επιπρόσθετα, εκτιμήθηκαν οι γενετικές αποστάσεις μεταξύ των τριών φυλών και μεταξύ αυτών και 27 φυλών αιγών που εκτρέφονται σε άλλες χώρες με τη χρήση του δείκτη FST. Στο σύνολο των αιγών, παρατηρήθηκαν όλα τα προστατευτικά αλληλόμορφα (146S, 146D, 211Q, 222K). Η γενετική σύγκριση έδειξε σημαντικές διαφορές (P0,0003). Ωστόσο, παρατηρήθηκαν κάποιες αρχικά στατιστικά σημαντικές συσχετίσεις (P<0,05). Τα αποτελέσματα κατέδειξαν πολυμορφικότητα ως προς το γονίδιο PRNP η οποία ευνοεί την εφαρμογή προγραμμάτων γενετικής επιλογής ανθεκτικών για την κλασική τρομώδη νόσο αιγών. Οι γενετικές συγκρίσεις μεταξύ των φυλών υποστηρίζουν την σημασία εφαρμογής ειδικά σχεδιασμένων προγραμμάτων ανάλογα με τη γονοτυπική σύνθεση της κάθε φυλής ενδιαφέροντος. Ειδικότερα, καταδεικνύεται η ανάγκη εφαρμογής ξεχωριστών προγραμμάτων για τις εγχώριες φυλές (Εγχώρια και Σκοπέλου) και τη φυλή Δαμασκού με ιδανικότερους υποψήφιους τα αλληλόμορφα 222K και 146S, αντίστοιχα. Η εφαρμογή των προγραμμάτων αυτών δεν αναμένεται να έχει αρνητική επίδραση στην παραγωγικότητα και την υγεία του μαστού των υπό μελέτη φυλών. Ωστόσο, συστήνεται ο έλεγχος και η επίβλεψη της εφαρμογής τους ώστε να εξασφαλισθεί η έγκαιρη αντιμετώπιση τυχόν ανεπιθύμητων επιπτώσεων σε άλλα σημαντικά χαρακτηριστικά και τη γενετική ποικιλότητα

Efficiency Analysis and Identification of Best Practices and Innovations in Dairy Sheep Farming

The adoption of the best practices is crucial for the survival of the dairy sheep farms that operate under extensive and/or semi-extensive systems. In this study, an efficiency analysis was implemented to reveal the best observed practices applied by the more efficient dairy sheep farms. Data Envelopment Analysis was used on data from 60 dairy sheep farms that rear Manech or Basco-bearnaise, and Lacaune breeds under semi-extensive systems in France. The main characteristics of the most efficient farms are presented and a comparative economic analysis is applied between the fully efficient and less efficient farms, highlighting the optimal farm structure and determining the major cost drivers in sheep farming. The most efficient farmers provided information within the iSAGE Horizon 2020 project regarding the management practices that enhance their sustainability. The results show that there is room for improvement in semi-extensive dairy sheep farming. The most efficient farms rear smaller flocks than the less efficient farms and achieve higher milk yields. Fixed capital, labor, and feeding constitute the main cost drivers. Results show that farms should exploit economies of scale in the use of labor and infrastructure to reduce their cost per product, as well as their uptake practices and innovations, related mainly to modern breeding and reproduction methods, efficient feeding practices and digital technologies

Economic Performance of Dairy Sheep Farms in Less-Favoured Areas of Greece: A Comparative Analysis Based on Flock Size and Farming System

Dairy sheep farming is a significant agricultural sector in Mediterranean countries, providing income and employment opportunities in less-favoured areas (LFAs). The economic performance of dairy sheep farms is of significant interest to LFAs. However, relevant literature is scarce. The objectives here were to evaluate the economic performance of dairy sheep farms in LFAs of Greece and perform a comparative analysis based on flock size and farming system. In total, 19 and 26 dairy sheep farms for two production periods were used. Farm technical (flock size, production, grazing and nutritional management) and economic (income and variable costs) data were collected. The economic performance of farms was estimated using Happy Goats, a decision support tool for small ruminant farming. Estimated economic parameters were analysed by flock size (≤150 ewes vs. >150 ewes) and farming system (intensive/semi-intensive vs. semi-extensive). Results showed that 37% and 31% of farms were operating with losses in each production period, respectively. Based on nutritional management, ewes produced about 50 kg less milk per milking period. Smaller and semi-extensive farms had significantly (p p < 0.05) lower average gross margin was reported for smaller compared to larger farms. Results suggest a better economic perspective for larger flock sizes

Association of Hard Ticks (Ixodidae) Infestation with Milk Production and Udder Health of Extensively Reared Dairy Goats

Extensively reared ruminants are seasonally exposed to ticks. Tick-related production losses and health issues have been well documented in cows and sheep but not in goats where relevant literature is scarce. The objective here was to investigate the association of hard tick infestation with milk production and udder health of dairy goats reared extensively. A cross-sectional study was carried out during May and June, in two dairy goat farms. The farms were located in Central and Northern Greece and were representative of typical extensive production systems. A total of 304 goats (n = 152 from each farm) were randomly selected. Each goat was examined for presence of hard ticks. Daily milk yield and quality characteristics were recorded. Udder health status was determined by milk somatic cell count (SCC) and total viable count (TVC). Tick infestation prevalence was 28.6%; it was associated with a significant (p &lt; 0.001) increase in SCC and TVC (84.0% and 78.6%, respectively). The latter meant that infested goats were 3.7 times more prone to udder health problems (p &lt; 0.001). There were not any significant effects (p &gt; 0.05) on milk production. Overall, results suggest that control of tick infestation in extensively reared dairy goat herds is important for enhancing health and welfare status

Efficiency Analysis as a Tool for Revealing Best Practices and Innovations: The Case of the Sheep Meat Sector in Europe

The slow adoption of innovations is a key challenge that the European sheep sector faces for its sustainability. The future of the sector lies on the adoption of best practices, modern technologies and innovations that can improve its resilience and mitigate its dependence on public support. In this study, the concept of technical efficiency was used to reveal the most efficient sheep meat farms and to identify the best practices and farm innovations that could potentially be adopted by other farms of similar production systems. Data Envelopment Analysis was applied to farm accounting data from 458 sheep meat farms of intensive, semi-intensive and extensive systems from France, Spain and the UK, and the structural and economic characteristics of the most efficient farms were analyzed. These best farmers were indicated through a survey, which was conducted within the Innovation for Sustainable Sheep and Goat Production in the Europe (iSAGE) Horizon 2020 project, the management and production practices and innovations that improve their economic performance and make them better than their peers