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BackgroundThe detection of regions that affect quantitative traits (QTL), to implement selection assisted by molecular information, remains of particular interest in dairy sheep for which genetic gain is constrained by the high costs of large-scale phenotype and pedigree recording. QTL detection based on the combination of linkage disequilibrium and linkage analysis (LDLA) is the most suitable approach in family-structured populations. The main issue in performing LDLA mapping is the handling of the identity-by-descent (IBD) probability matrix. Here, we propose the use of principal component analysis (PCA) to perform LDLA mapping for milk traits in Sarda dairy sheep.MethodsA resource population of 3731 ewes belonging to 161 sire families and genotyped with the OvineSNP50 Beadchip was used to map genomic regions that affect five milk traits. The paternally and maternally inherited gametes of genotyped individuals were reconstructed and IBD probabilities between them were defined both at each SNP position and at the genome level. A QTL detection model fitting fixed effects of principal components that summarize IBD probabilities was tested at each SNP position. Genome-wide (GW) significance thresholds were determined by within-trait permutations.ResultsPCA resulted in substantial dimensionality reduction, in fact 137 and 32 (on average) principal components were able to capture 99% of the IBD variation at the locus and genome levels, respectively. Overall, 2563 positions exceeded the 0.05 GW significance threshold for at least one trait, which clustered into 75 QTL regions most of which affected more than one trait. The strongest signal was obtained for protein content onOvis aries(OAR) chromosome 6 and overlapped with the region that harbours the casein gene cluster. Additional interesting positions were identified on OAR4 for fat content and on OAR11 for the three yield traits.ConclusionsPCA is a good strategy to summarize IBD probabilities. A large number of regions associated to milk traits were identified. The outputs provided by the proposed method are useful for the selection of candidate genes, which need to be further investigated to identify causative mutations or markers in strong LD with them for application in selection programs assisted by molecular information.

Selective breeding has led to modifications in the genome of many livestock breeds. In this study, we identified the genomic regions that may explain some of the phenotypic differences between two closely related breeds from Sardinia. A total of 44 animals, 20 Sardinian Ancestral Black (SAB) and 24 Sardinian White (SW), were genotyped using the Illumina Ovine 50K array. A total of 68, 38 and 15 significant markers were identified using the case–control genome-wide association study (GWAS), the Bayesian population differentiation analysis (FST) and the Rsb metric, respectively. Comparisons among the approaches revealed a total of 22 overlapping markers between GWAS and FST and one marker between GWAS and Rsb. Three markers detected by Rsb were also located near (

International audience; Domestic species such as cattle (Bos taurus taurus and B. t. indicus) represent attractive biological models to characterize the genetic basis of short term evolutionary response to climate pressure induced by their post-domestication history. Here, using newly generated dense SNP genotyping data, we assessed the structuring of genetic diversity of 21 autochtonous cattle breeds from the whole Mediterranean basin and performed genome-wide association analyses with covariables discriminating the different Mediterranean climate sub-types. This provided insights into both the demographic and adaptive histories of Mediterranean cattle. In particular, a detailed functional annotation of genes surrounding variants associated with climate variations highlighted several biological functions involved in Mediterranean climate adaptation such as thermotolerance, UV protection, pathogen resistance or metabolism with strong candidate genes identified (e.g. NDUFB3, FBN1, METTL3, LEF1, ANTXR2 and TCF7). Accordingly, our results suggest that main selective pressures affecting cattle in Mediterranean area may have been related to variation in heat and UV exposure, in food resources availability and in exposure to pathogens, such as anthrax bacteria (Bacillus anthracis). Furthermore, the observed contribution of the three main bovine ancestries (indicine, European and African taurine) in these different populations suggested that adaptation to local climate conditions may have either relied, on standing genomic variation of taurine origin or adaptive introgression from indicine origin, depending on the local breed origins. Taken together, our results highlight the genetic uniqueness of local Mediterranean cattle breeds and strongly support conservation of these populations

Background In the last 50 years, the diversity of cattle breeds has experienced a severe contraction. However, in spite of the growing diffusion of cosmopolite specialized breeds, several local cattle breeds are still farmed in Italy. Genetic characterization of breeds represents an essential step to guide decisions in the management of farm animal genetic resources. The aim of this work was to provide a high-resolution representation of the genome-wide diversity and population structure of Italian local cattle breeds using a medium-density single nucleotide polymorphism (SNP) array. Results After quality control filtering, the dataset included 31,013 SNPs for 800 samples from 32 breeds. Our results on the genetic diversity of these breeds agree largely with their recorded history. We observed a low level of genetic diversity, which together with the small size of the effective populations, confirmed that several breeds are threatened with extinction. According to the analysis of runs of homozygosity, evidence of recent inbreeding was strong in some local breeds, such as Garfagnina, Mucca Pisana and Pontremolese. Patterns of genetic differentiation, shared ancestry, admixture events, and the phylogenetic tree, all suggest the presence of gene flow, in particular among breeds that originate from the same geographical area, such as the Sicilian breeds. In spite of the complex admixture events that most Italian cattle breeds have experienced, they have preserved distinctive characteristics and can be clearly discriminated, which is probably due to differences in genetic origin, environment, genetic isolation and inbreeding. Conclusions This study is the first exhaustive genome-wide analysis of the diversity of Italian cattle breeds. The results are of significant importance because they will help design and implement conservation strategies. Indeed, efforts to maintain genetic diversity in these breeds are needed. Improvement of systems to record and monitor inbreeding in these breeds may contribute to their in situ conservation and, in view of this, the availability of genomic data is a fundamental resource. Electronic supplementary material The online version of this article (10.1186/s12711-018-0406-x) contains supplementary material, which is available to authorized users.

The objective of this work was to investigate the effects of a single anthelmintic treatment on milk production. In 2008, in a flock of Sarda ewes naturally infected by gastrointestinal nematodes, 162 adult and 72 primiparous ewes were allocated into four groups. For each age class, one group was drenched with albendazole after lamb weaning whilst the other was left untreated as control. The efficacy of single anthelmintic treatment at the beginning of lactation was obtained by a faecal egg count reduction test. The effect of drenching on milk yield and components was studied both using single test date and lactation records. After 1 month geometric mean of eggs per gram of treated ewes decreased up to 1% of the initial value (3.40 eggs/g versus 322.63 eggs/g in primiparous and 2.14 eggs/g versus 312.70 eggs/g in adult ewes). The anthelmintic treatment showed a significant effect only on lactation milk yield of treated adult ewes that produced 19.2 L/year more than control ewes. Production level was investigated as a criterion to apply targeted selective treatment. High producer multiparous ewes produced 32.7 L/year more than control ones. Overall results confirm a beneficial effect of anthelmintic treatment on milk production without any detrimental effect on milk composition only on adult ewes markedly if high producers. Thus, depending on milk price and the required length of the period of discarded milk, the increased milk yield can counterbalance treatment's costs.

The aim of this paper was studying the phenotypic and genetic relationships between udder morphology traits and udder health in dairy sheep. From 2000 to 2008 udder traits, somatic cell count (SCC) and clinical mastitis cases were recorded in an experimental flock consisting each year of around 900 ewes. A logistic regression was performed to evaluate the risk for a ewe of showing either a mastitis or at least 2 daily SCC records greater than 1 × 106 cells/ml in one of its lactations as function of udder traits scored in 1st lactation. 1587 individual udder scores and 39,950 SCC daily records were used for the analysis. Secondly, genetic correlation between lactation mean of somatic cell score and udder traits were estimated by a REML method applied to four bi-trait animal models, using data from 2251 primiparous ewes. Logistic regression results indicated that the risk of mastitis or high SCC values during the productive life increased as the cistern height increased and the degree of udder suspension and udder depth decreased. This suggests that the appraisal of the udder is a useful tool for culling decision aimed at increasing the sanitary status of the flock. The genetic correlation between lactation SCS and udder traits were favourable for udder depth (−0.50 ± 0.12), teat placement (0.39 ± 0.011) and degree of udder suspension (−0.42 ± 0.011) and closed to zero for the degree of separation of the two halves. Thus selection for udder morphology, already implemented in some dairy sheep breeds with the aim of improving machine milkability, will lead to a favourable correlated genetic response on SCC.

Summary The objective of this work was to characterize the complete coding region of the ovine acyl CoA:diacylglycerol acyltransferase 1 (DGAT1) gene of three Italian sheep breeds: Sarda, Altamurana and Gentile di Puglia. Characterization was accomplished by direct sequencing of 8676 bp of the relevant DNA, including introns and partial 5¢ and 3¢ untranslated regions (UTRs). We detected five novel SNPs; one SNP (g.5553C>T) is located in intron 2, has similar frequencies in the three breeds and showed a negative association with milk fat content. More interesting is an SNP in the 5¢ UTR (g.127C>A), the occurrence of which is rare in the higher milk-fat breeds (Altamurana and Gentile di Puglia); it is located in the core sequence of Sp1, a putative binding site of transcription factors. This SNP showed a significant negative association with milk fat content in the Sarda sheep. Because DGAT1 plays a fundamental role in triacylglycerol synthesis, the novel detected SNP in the 5¢ UTR of the DGAT1 gene might explain, at least partially, the variation of fat content in the milk of Sarda sheep.

Articular cartilage regeneration is limited. Embryonic stem (ES) cell lines provide a source of totipotent cells for regenerating cartilage. Anatomical, biomechanical, physiological and immunological similarities between humans and sheep make this animal an optimal experimental model. This study examines the repair process of articular cartilage in sheep after transplantation of ES-like cells isolated from inner cell masses (ICMs) derived from in vitro-produced (IVP) vitrified embryos. Thirty-five ES-like colonies from 40 IVP embryos, positive for stage-specific embryonic antigens (SSEAs), were pooled in groups of two or three, embedded in fibrin glue and transplanted into osteochondral defects in the medial femoral condyles of 14 ewes. Empty defect (ED) and cell-free glue (G) in the controlateral stifle joint served as controls. The Y gene sequence was used to detect ES-like cells in the repair tissue by in situ hybridization (ISH). Two ewes were euthanized at 1 month post-operatively, three each at 2 and 6 months and four at 12 months. Repairing tissue was examined by biomechanical, macroscopic, histological, immunohistochemical (collagen type II) and ISH assays. Scores of all treatments showed no statistical significant differences among treatment groups at a given time period, although ES-like grafts showed a tendency toward a better healing process. ISH was positive in all ES-like specimens. This study demonstrates that ES-like cells transplanted into cartilage defects stimulate the repair process to promote better organization and tissue bulk. However, the small number of cells applied and the short interval between surgery and euthanasia might have negatively affected the results. Copyright © 2009 John Wiley & Sons, Ltd.

Breeders have always been interested in improving the ewes’ milkability, since the milking is the most time-consuming task of dairy sheep farmers. This work was aimed at studying the evolution during the productive life and the individual variability of milk emission traits at machine milking in sheep. Data were recorded in an experimental flock of 889 Sardinian × Lacaune back-cross ewes, by using an automatic device developed by INRA. The analyzed variables (59,615 records) were total milk yield (TMY, ml), machine milk yield (MMY, ml), stripped milk yield (SMY, ml), machine milking time (MMT, s), latency time (LT, s), maximum (MMF) and average (AMF) milk flow (ml/s), collected fortnightly at a.m. and p.m. milking for 4 years. Univariate mixed models were used for estimating the evolution of traits with lactation stage and parity number and the relative weights of sire and individual variances within date and lactation and across lactations. As general trend, MMY and SMY decreased with lactation stage. SMY and its ratio with TMY increased from first to fourth parity. TL increased and MMF and AMF decreased with lactation stage and parity number. Machine milking time decreased with lactation stage and increased in adult ewes less than proportionally to the variation in machine milk yield. Most of milkability traits were highly repeatable within date. Within lactation repeatability was high for MMY, MMF and LT and moderate for TMY, SMY and AMF. Similar within date, within lactation and across lactations repeatability estimates for MMF and LT suggest that these traits are affected by random sources of variation, both environmental and genetic, which are constant in time. The proportion of the sire variance respect to the overall phenotypic variance ranged from 4% for MMT to 27% for MMF. These proportions were particularly high for MMY, LT, AMF and MMF and low for SMY and MMT. All the milk emission traits were favorably correlated between them and with milk yield. Only SMY showed low individual correlation with the other traits. Results suggest that milk emission traits are genetically determined and can be improved through selection. LT and MMF are the most relevant measurements to characterize the ewes’ machine milking speed due to the high repeatability and the favorable correlation with MMT.

Different approaches were applied to investigate prion protein (PrP)-encoding gene effects on udder morphology and milk yield in Sardinian sheep. The PrP genotype of 23,077 animals (10,029 males) was determined. The direct effect of the PrP or a closely linked gene was analyzed at the population-wide level using 2 animal models, based on records from genotyped animals, including only the PrP genotype as a fixed effect. In the female model, the dependent variable was animal performance deviation, calculated as the sum of the individual random effects. The male model was based on daughter yield deviations. Both dependent variables were obtained from the national genetic evaluations of 2005. The significance of pairwise comparisons between genotypes was assessed by using the Tukey-Kramer multiple-comparison procedure. Within-family analyses were performed on sires heterozygous for the PrP gene to detect those genes that affect the traits of interest and are not in linkage disequilibrium with the PrP locus at the population-wide level. The overall results led us to exclude either a direct or a linkage gene effect of the PrP locus on udder morphology or milk yield in Sardinian sheep. A further analysis of males that neglected the relationship matrix was carried out to evaluate the effect on the loss of genetic gain of the different selection pressures applied on resistant and susceptible genotype classes. Significant differences between genotypes were detected for milk yield. These were due to the different selection pressures applied to the PrP genotype classes. Finally, no negative correlated genetic response on the selection traits is expected from the selection for scrapie resistance in the Sardinian breed. However, a loss of genetic gain for milk yield is likely to occur in the future due to the different selection pressures on resistant and susceptible males.

Summary The aim of this work was to develop a strategy for using a genetic analysis for identifying native animals in regions where local breeds have been crossed with improved breeds and then compare that strategy to the overall morphology and breeding histories of the herds for identifying these animals. The experiment included the Sardinian goat population, which is a crossbred of native animals with the Maltese breed. Whole herds were assigned to Maltese (five herds; 49 animals), crossbred (18 herds; 117 animals) or Sardinian (12 herds; 164 animals) groups. For the genetic analysis, genotypes of 22 microsatellites were determined on 330 animals, and basic measurements of genetic diversity were calculated. Genetic variability in the microsatellites was different in the three groups. High positive FIS showed that inbreeding existed in the subpopulations. The index of genetic differentiation, Nei's standard genetic distance and Reynolds’ genetic distance were calculated and found to be significantly different between the three groups. The Sardinian and Maltese groups were the most distant whereas the crossbred group was closer to the Sardinian group. The proportion of the genome derived from two ancestral populations (native Sardinian and Maltese) was assessed using the structure software. Animals were assigned to three clusters on the basis of native Sardinian thresholds. A good correspondence between the empirical (morphology and breeding histories) and the objective genetic analysis was found. Both approaches indicate the presence of three different subpopulations in the Sardinian goat population.

This study is a large-scale survey based on interviews with owners of 151 Sardinian goat farms. The aim was to provide an up to date description of the goat production chain on the island. A multivariate statistical approach was applied to exploit the great number of available variables in the best way. The statistical analysis was carried out in two steps: principal component analysis and successive cluster analysis. In general, Sardinian goat farming showed a remarkable backwardness compared to dairy sheep farming. This is particularly true for farm facilities and productivity. Cluster analysis allowed us to identify five clusters, which corresponded to three principal farming systems. Firstly, a traditional system with little infrastructure and low management and productive levels was identified. Here the most frequent genotype was basically the native Sardinian breed. Secondly, there is a group of farms mainly located in the southwest of Sardinia where the facilities and the management were poor and production was on a low level than dairy sheep farming but generally better developed than the previous cluster. Thirdly, there is a group of farms using a sort of semi-intensive farming system, which was more similar to that of dairy sheep, with relatively high productive and reproductive performance. In conclusion, this study identified different goat farming systems in Sardinia and emphasizes the need to develop strategies, which are able to take this diversity into account.

Background Articular cartilage has poor intrinsic capacity for regeneration because of its avascularity and very slow cellular turnover. Defects deriving from trauma or joint disease tend to be repaired with fibrocartilage rather than hyaline cartilage. Consequent degenerative processes are related to the width and depth of the defect. Since mesenchymal stem cells (MSCs) deriving from patients affected by osteoarthritis have a lower proliferative and chondrogenic activity, the systemic or local delivery of heterologous cells may enhance regeneration or inhibit the progressive loss of joint tissue. Embryonic stem cells (ESCs) are very promising, since they can self-renew for prolonged periods without differentiation and can differentiate into tissues from all the 3 germ layers. To date only a few experiments have used ESCs for the study of the cartilage regeneration in animal models and most of them used laboratory animals. Sheep, due to their anatomical, physiological and immunological similarity to humans, represent a valid model for translational studies. This experiment aimed to evaluate if the local delivery of male sheep embryonic stem-like (ES-like) cells into osteochondral defects in the femoral condyles of adult sheep can enhance the regeneration of articular cartilage. Twenty-two ewes were divided into 5 groups (1, 2, 6, 12 and 24 months after surgery). Newly formed tissue was evaluated by macroscopic, histological, immunohistochemical (collagen type II) and fluorescent in situ hybridization (FISH) assays. Results Regenerated tissue was ultimately evaluated on 17 sheep. Samples engrafted with ES-like cells had significantly better histologic evidence of regeneration with respect to empty defects, used as controls, at all time periods. Conclusions Histological assessments demonstrated that the local delivery of ES-like cells into osteochondral defects in sheep femoral condyles enhances the regeneration of the articular hyaline cartilage, without signs of immune rejection or teratoma for 24 months after engraftment. Electronic supplementary material The online version of this article (doi:10.1186/s12917-014-0301-9) contains supplementary material, which is available to authorized users.

Background A common dataset was simulated and made available to participants of the XVIth QTL-MAS workshop. Tasks for the participants were to detect QTLs affecting three traits, to assess their possible pleiotropic effects, and to evaluate the breeding values in a candidate population without phenotypes using genomic information. Methods Four generations consisting of 20 males and 1000 females were generated by mating each male with 50 females. The genome consisted of 5 chromosomes, each of 100 Mb size and carrying 2,000 equally distributed SNPs. Three traits were simulated in order to mimic milk yield, fat yield and fat content. Genetic (co)variances were generated from 50 QTLs with pleiotropic effects. Phenotypes for all traits were expressed only in females, and were provided for the first 3 generations. Fourteen methods for detecting single-trait QTL and 3 methods for investigating their pleiotropic nature were proposed. QTL mapping results were compared according to the following criteria: number of true QTL detected; number of false positives; and the proportion of the true genetic variance explained by submitted positions. Eleven methods for estimating direct genomic values of the candidate population were proposed. Accuracies and bias of predictions were assessed by comparing estimated direct genomic values with true breeding values. Results The number of true detections ranged from 0 to 8 across methods and traits, false positives from 0 to 15, and the proportion of genetic variance captured from 0 to 0.82, respectively. The accuracy and bias of genomic predictions varied from 0.74 to 0.85 and from 0.86 to 1.34 across traits and methods, respectively. Conclusions The best results in terms of detection power were obtained by ridge regression that, however, led to a large number of false positives. Good results both in terms of true detections and false positives were obtained by the approaches that fit polygenic effects in the model. The investigation of the pleiotropic nature of the QTL permitted the identification of few additional markers compared to the single-trait analyses. Bayesian and grouped regularized regression methods performed similarly for genomic prediction while GBLUP produced the poorest results.

In quantitative traits loci (QTL) mapping experiments a number of traits are often recorded. Although most QTL-detection methods are based on single trait analysis, several approaches for multi-trait detection have been proposed (Weller et al., 1996; Knott and Haley, 2000). Those methods mainly focus on either increasing power of detecting pleiotropic QTL or discriminating between pleiotropy and linkage, often with the aim of dissecting unfavourable genetic correlation between traits. Nevertheless, when two traits are positively correlated, the detection of genes only affecting one of them could allow the speeding of its genetic improvement.

During the last century, the selection for production traits of the main livestock species has led to a reduction in number of local populations with consequent loss of genetic variability. In Sardinia, the genetic improvement strategy has been based on selection for the local pure breed in sheep, whereas in the other species (cattle, swine and goat), an often unplanned crossbreeding with improved breeds has been applied. In this context, several studies on genetic diversity of these populations have been started with the final aim of recovering the autochthonous genetic types. The global approach involves different steps: - characterization of the farming system and typical products; - morphological and productive evaluation of the animals; - genetic characterization of the populations through molecular DNA analyses (microsatellites, AFLP, mitochondrial DNA, etc.); - creation of nucleus flocks in public farms and germoplasm banks; - organization of herd-books involving farmers interested in the safeguard of local breeds and valorisation of traditional products. A far as the goat population is concerned, Sardinia is the Italian region with the largest goat stock, (209.000 heads, about 23% of the total national stock). Farms are located in mountains, low hills and even plans (Macciotta et al., 2002) resulting in a quite large variability (Brandano and Piras, 1978) in terms of feeding and management techniques; but extensive and semi extensive systems in marginal areas prevail (Carta et al., 2001; Usai et al., 2004). The current population has been constituted by crossbreeding the autochthonous animals with other improved Mediterranean breeds,mainly Maltese goat. The aim of this paper is to study the genetic variability of this population through the analysis of 17 microsatellite markers.

The objective of this paper was identifying QTL that affect fat and protein yields in dairy sheep independently of milk yield. Data were collected in an experimental flock of 887 ewes organized in a daughter design. QTL detection focused on OAR7 where 13 microsatellites were available. The genetic abilities to produce fat and protein independently from the ability to produce milk were estimated as the residuals of the regression of EBV for fat and protein yields on EBV for milk yield. One QTL affecting fat yield (CWP=0.00009) and one QTL affecting protein yield (CWP=0.006) were detected. The most probable QTL location was 115.3 cM in the Sheep Best Position Linkage Map Version 4.7 for both traits. No QTL affecting milk yield was detected. The analysis of fat and protein yields independently of milk yield is an effective strategy to identify chromosomal regions affecting milk composition with no detrimental effect on milk yield.

The effect of different flushing techniques on reproductive performance in Sarda ewes mated while grazing a mature pasture of Italian ryegrass (herbage allowance, 2700 g DM per head per day) was assessed. Sixty adult ewes were allotted to four groups (n = 15). Estrus of ewes in the control group (C) was synchronised, using the ram effect and progesterone administration, but they received no dietary supplement before the introduction of intact rams. Ewes in the other groups were offered a supplement of soybean-meal (SBM), from Day 7 before, through day of ram introduction (short-term flushing, SF); from Day 14 before, through Day 2 after entire ram introduction (medium-term flushing, MF); or from Day 14 before, through Day 21 after ram introduction (long-term flushing, LF). Estrus was not synchronised in the LF group. The amount of SBM offered was 270 g day−1, but actual average intake was 180–210 g day−1. Synchronisation did not affect date of first observed estrus. Flushing resulted in greater ovulation rate (OR) than C: 1.70, compared with 1.29 CL per ewe ovulating, (P LF > SF > C, and tended to differ between MF and C (1.60 vs. 1.14, P < 0.13). Flushing did not result in higher intake of energy or crude protein, because intake of pasture was decreased in flushed ewes, but was related to greater (P < 0.03) intake of digestible protein in the pre-mating period. Under current market conditions, medium-term flushing can be profitable for Sardinian sheep farmers.

Different grazing backgrounds and type of flushing were compared; treatments were three availability levels of herbage (Italian ryegrass grazed continuously by lactating ewes and kept close to 30, 60 and 90 mm sward height) and three flushing diets: control, unsupplemented, 250 g day−1 whole corn grain and 270 g day−1 soybean meal. Both concentrates were offered from 2 weeks before to 3 weeks after ram introduction. Herbage allowance during flushing was 1804 g dry matter (DM) day−. Ovulation rate (OR) was higher in ewes coming from the 90 mm grazing than from 30 mm (1.60 vs. 1.18 ova per ewe ovulating, P < 0.08) and 60 mm (1.27 ova per ewe ovulating, not significant); soybean meal-fed ewes ovulated more than whole corn grain counterparts (1.67 vs. 1.11 ova per ewe ovulating, P < 0.02) and control ewes (1.25 ova per ewe ovulating, P < 0.08). The OR increase from soybean meal compared with whole corn was associated with higher intake of herbage, energy and crude protein as well as higher plasma insulin level before ram introduction.

In the last few decades, farm animal genetic diversity has rapidly declined, mainly due to changing market demands and intensification of agriculture. But, since the removal of single species can affect the functioning of global ecosystems, it is in the interest of international community to conserve the livestock genetics and to maintain biodiversity. Increasing awareness on the reduction of breed diversity has prompted global efforts for conservation of farm animal breeds. The goals of conservation are to keep genetic variation as gene combinations in a reversible form and to keep specific genes of interest. For this purpose two types of strategies are usually proposed: in situ and ex situ conservation. In situ conservation is the breed maintaining within the livestock production system, in its environment through the enhancement of its production characteristics. Ex situ in vivo conservation is the safeguard of live animals in zoos, wildlife parks, experimental farms or other specialized centres. Ex situ in vitro conservation is the preservation of genetic material in haploid form (semen and oocytes), diploid (embryos) or DNA sequences. In the last few years, ex situ in vitro conservation programs of livestock genetic resources have focused interest on cryopreservation of gametes, embryos and somatic cells as well as testis and ovarian tissues, effectively lengthening the genetic lifespan of individuals in a breeding program even after the death. However, although significant progress has been made in semen, oocytes and embryo cryopreservation of several domestic species, a standardized procedure has not been established yet. The aim of the present review is to describe the cryobanking purposes, the collection goals, the type of genetic material to store and the reproductive biotechnologies utilized for the cryopreservation of farm animal gametes and embryos.

Multiple ovulation and embryo transfer (MOET) is a very important tool for the genetic improvement and preservation of endangered livestock. However, the success of a MOET programme highly depends on the number of transferable embryos in response to a superovulation treatment. Thus, the aim of this study was to compare the number and quality of embryos produced during natural oestrus under porcine FSH treatment without the use of progesterone devices to more traditional protocols. Forty Sarda sheep were divided into 2 groups: without sponges (WS) (n = 20) and with sponges (S) containing 40mg FGA for 12 d (n = 20) (control group); 350 I.U. of porcine FSH per sheep was administered in eight decreasing doses twice daily starting four days after estrus was detected (Day 0) in group WS and 48 h before sponge removal in group S. A single i.m. dose of 125 μg of cloprostenol was administered on Day 6 after estrus in group WS to induce luteolysis. Sheep were naturally mated 24 h after cloprostenol injection or sponge removal. Seven days after mating, an inguinal laparotomy was performed and the number of corpora lutea (CL) recorded. Embryos were recovered surgically by flushing each uterine horn. A total of 38 fresh and 22 vitrified embryos were transferred in pairs into 3 groups of recipients seven days after estrus detection: fresh embryos from group S (S-F) (n = 9), fresh embryos from group WS (WS-F) (n = 10) and vitrified embryos from group WS (WS-V) (n = 11). Data on the number of corpora lutea (CL), recovered ova and embryos (OER), and quality 1-2 and 3 embryos (EQ(1-2), EQ(3)) per ewe were analyzed by ANOVA. Recovery (RR), fertility (FR) and quality 1-2 embryo (Q(1-2)R) rates per treatment were analyzed by a Chi Square analysis. A Chi Square analysis was also applied to pregnancy rate (PR), lambing rate (LR) and twinning rate (TR) of fresh and vitrified embryos in order to analyze embryo transfer results. Among all superovulation variables analysed, results show statistically significant differences in mean number of CL/ ewe (9.3 ± 3.9 vs 7 ± 3.2), RR (67% vs 80 %) and FR (100% vs 80%) (P < 0.05) between WS and S groups respectively. There were no significant differences in PR (78%, 70% and 82%), LR (67%, 60% and 59%) and TR (71%, 71% and 44.4%) among S-F, WS-F and WS-V groups respectively. In conclusion, it is possible to produce a good number of transferable embryos during natural oestrus avoiding the use of sponges.

Dairy sheep have been farmed traditionally in the Mediterranean basin in southern Europe, central Europe, eastern Europe, and in Near East countries. Currently, dairy sheep farming systems vary from extensive to intensive according to the economic relevance of the production chain and the specific environment and breed. Modern breeding programs were conceived in the 1960s. The most efficient selection scheme for local dairy sheep breeds is based on pyramidal management of the population with the breeders of nucleus flocks at the top, where pedigree and official milk recording, artificial insemination, controlled natural mating, and breeding value estimation are carried out to generate genetic progress. The genetic progress is then transferred to the commercial flocks through artificial insemination or natural-mating rams. Increasing milk yield is still the most profitable breeding objective for several breeds. Almost all milk is used for cheese production and, consequently, milk content traits are very important. Moreover, other traits are gaining interest for selection: machine milking ability and udder morphology, resistance to diseases (mastitis, internal parasites, scrapie), and traits related to the nutritional value of milk (fatty acid composition). Current breeding programs based on the traditional quantitative approach have achieved appreciable genetic gains for milk yield. In many cases, further selection goals such as milk composition, udder morphology, somatic cell count, and scrapie resistance have been implemented. However, the possibility of including other traits of selective interest is limited by high recording costs. Also, the organizational effort needed to apply the traditional quantitative approach limits the diffusion of current selection programs outside the European Mediterranean area. In this context, the application of selection schemes assisted by molecular information, to improve either traditional dairy traits or traits costly to record, seems to be attractive in dairy sheep. At the moment, the most effective strategy seems to be the strengthening of research projects aimed at finding causal mutations along the genes affecting traits of economic importance. However, genome-wide selection seems to be unfeasible in most dairy sheep breeds.

Connectedness across flocks of the registered population of the Sardinian dairy sheep breed was evaluated. Used criteria were: number of sires used in the same contemporary group; number of direct links and the average within and between contemporary group relationship coefficients. Dataset including yearlings’ first lactation records of 1990 and 2008 were compared to evaluate the effect of coupling artificial insemination with controlled natural mating on connectedness. An increase of number of sires and direct links were registered between 1990 and 2008. These results confirm that the across years prolonged use of well planned moderate rates of artificial insemination had a strong effect on the overall statistical connectedness across flocks so permitting more accurate estimations of the management and genetic effects. As a whole, the decreasing of the average relationship within flock coupled to a marked enhance of the average relationship between contemporary groups, indicates that the genetic connectedness of the Sardinian registered population presents a clearly increasing trend. This fact assures that current genetic evaluations are reliable across flocks.

The fatty acid (FA) profile of milk fat may affect the nutritional and market value of sheep dairy products. In this study we present repeatability estimates and results of quantitative trait loci (QTL) detection analyses for FA profile of sheep milk obtained by a genome scan approach applied to an experimental Sardinian × Lacaune back-cross population. The experimental flock was constituted by 967 daughters of 10 F1 sires corresponding to a classical daughter design for QTL detection. Fatty acid contents were determined twice in the middle of 2nd (847 records) and 3rd lactation (795 records) by gas chromatography. Means, standard deviations as well as raw correlations were calculated for the 17 most abundant fatty acids, their sums and ratios, based on 1454 records from 727 ewes with two samplings. A repeated measurement model including, as a fixed effect, the year of production by management group interaction and the random effects of sire and animal within sire was applied to all the analysed variables. For each trait R2 statistics associated with the fixed part of the model, the sire and the animal within sire components of the total variation were estimated. The genotypes at 146 microsatellite markers spanning the 26 ovine autosomes were available. The individual solutions for the 727 ewes with two records were used as phenotypes for QTL analyses. An across-family single trait QTL analysis was carried out by within-family linear regression. Chromosome locations significant at least at the 5% chromosome-wise level were retained. The overall pattern of raw correlations showed that FA profile is a very complex system resulting from numerous inter-relationships between basic FA. The portion of variation absorbed by the fixed part of the model differed markedly across variables, as showed by R2 statistics which ranged from 11.3% to 78.3%. FA showed large variability in terms of repeatability estimates, which ranged between 14.1% for C18:3 and 57.3% for C4. The most repeatable FA were C4, C14:1 and C17. For almost all the analysed variables, significant genome locations were found. Only for C4 was no genome region affecting the trait variability identified. The highest number of significant locations was found for C14_1 and its ratio with C14. The most significant QTL were detected for C14 and C16 on OAR 11 and for monounsaturated FA (MUFA) on OAR 6. A total of 82 locations significant at least at the 5% chromosome-wise threshold were detected. The present study suggests that for fatty acid profile of sheep milk both classical quantitative genetic approach and genomic information based selection approaches will be realistic options in the future.

Eight dairy flocks, comprising a total of 323 indigenous Passirian goats from northern Italy, were examined to determine the seroprevalence and clinical incidence of small ruminant lentivirus (SRLV) infections and to identify the SRLV subtypes. The seroprevalence was 81.5% (55–95%). The clinical incidence was 2.5% (0–8.3%) and was apparently low due to the practice of culling clinically affected animals. Phylogenetic analysis of eight PCR fragments (one sample from each flock) revealed that all proviruses belonged to the SRLV subtype B1, which suggests a common source of infection. Subtype B1 being the only circulating SRLV, coupled with the fact that mixed herd systems are very rare in South Tyrol, gives hope that an eradication programme in goats can be successful even without including sheep as long as sheep are kept strictly and permanently isolated.

The aim of this work was to develop a strategy for using a genetic analysis for identifying native animals in regions where local breeds have been crossed with improved breeds and then compare that strategy to the overall morphology and breeding histories of the herds for identifying these animals. The experiment included the Sardinian goat population, which is a crossbred of native animals with the Maltese breed. Whole herds were assigned to Maltese (five herds; 49 animals), crossbred (18 herds; 117 animals) or Sardinian (12 herds; 164 animals) groups. For the genetic analysis, genotypes of 22 microsatellites were determined on 330 animals, and basic measurements of genetic diversity were calculated. Genetic variability in the microsatellites was different in the three groups. High positive F(IS) showed that inbreeding existed in the subpopulations. The index of genetic differentiation, Nei's standard genetic distance and Reynolds' genetic distance were calculated and found to be significantly different between the three groups. The Sardinian and Maltese groups were the most distant whereas the crossbred group was closer to the Sardinian group. The proportion of the genome derived from two ancestral populations (native Sardinian and Maltese) was assessed using the structure software. Animals were assigned to three clusters on the basis of native Sardinian thresholds. A good correspondence between the empirical (morphology and breeding histories) and the objective genetic analysis was found. Both approaches indicate the presence of three different subpopulations in the Sardinian goat population.

Breeders are increasingly interested in improving the machine milkability of Sardinian dairy sheep by selection for udder morphology. Nine-point linear scales were developed to appraise teat placement, degree of suspension of the udder, udder depth, and degree of separation of the 2 halves. Repeatabilities within and across lactation were estimated on an experimental flock. Ewes were scored at least 3 times a year from 1999 to 2003. Within-lactation repeatabilities were greater than 0.70 for all linear traits, whereas across-lactation repeatabilities ranged from 0.59 to 0.66. The first linear combination of basic traits, obtained by principal component analysis, was highly correlated with teat placement, degree of suspension of the udder, and udder depth and showed an across-lactation repeatability of 0.76. These results indicate that an accurate evaluation of animals is possible by a single, early lifetime score. Genetic parameters of linear udder traits were estimated using a REML method applied to a sire model. Data were selected from 76,984 scores of Sardinian yearling ewes collected by 31 classifiers from 1999 to 2004. Two models were compared, one fitting the contemporary group effect as fixed and the other as random. Heritabilities of udder traits ranged from 0.19 to 0.31. The model with the random contemporary group effect produced slightly higher heritabilities and higher correlations between the sires' estimated breeding values and the daughters' average scores. As a whole, the genetic correlations between udder traits were favorable, indicating that selection for one trait will produce a positive evolution of the overall udder conformation. In particular, the degree of suspension of the udder was highly correlated with udder depth (0.82). Genetic correlations with milk yield were unfavorable but generally low, with the exception of udder depth (-0.48). Genetic trends were estimated using an animal model. Only udder depth showed a negative constant genetic trend. Overall results indicated that genetic improvement of the udder morphology of Sardinian ewes is feasible, with major emphasis on teat placement and degree of udder suspension, traits showing the highest heritabilities and low unfavorable genetic correlations with milk yield.

El estudio de la diversidad genetica de la poblacion ovina de Cerdena ha permitido la identificacion de una poblacion ovina no muy numerosa denominada Pecora Nera di Arbus. Dicha poblacion esta compuesta por unas 1000 ovejas, localizadas en el suroeste de Cerdena (region Medio-Campidano), fundamentalmente en la zona existente alrededor del pueblo de Arbus. Las principales caracteristicas de esta raza son su vellon de color negro, su pequeno tamano, sus pequenos pabellones auriculares, o la ausencia de los mismas, asi como la alta presencia de cuernos en ambos sexos. Estos rasgos ancestrales hacen ver que la poblacion no ha sido sometida a ningun tipo de seleccion, y que su cria ha estado enfocada principalmente hacia la produccion de leche y el color blanco del vellon, al que se ha establecido la linea blanca predominante en el ovino de Cerdena. Actualmente, esta en marcha un programa para promocionar esta nueva raza. Se basa principalmente en la produccion de lana negra para ser utilizada naturalmente para ropa sin tintes quimicos.

Trente-huit brebis laitieres de race Sarde ont ete reparties dans deux lots equilibres sur des criteres zootechniques. Elles ont ete soumises a une photoperiode artificielle controlee : jours longs (JL : 15 h 30 L, 8 h 30 D) ou jours courts (JC : 8 h 30 L, 15 h 30 D) depuis 25 j avant la mise bas jusqu'au 150 e jour de la lactation. Les brebis des deux lots ont ensuite ete soumises brutalement au meme traitement photoperiodique (12h L, 12h D). Pendant toute l'experience, les brebis ont recu ad libitum une ration a base de foin de luzerne et d'un aliment concentre du commerce dont la proportion a ete maintenue constante dans la ration. Par rapport aux brebis en JC, celles qui etaient en JL ont eu une production laitiere accrue en moyenne de 25,3 %. Apres 150 j de lactation, l'allongement de la duree d'eclairement pour les brebis en JC (+3 h 30) a permis de maintenir la production laitiere brute a son niveau initial (-8,0 %), alors que pour les brebis en JL, la diminution de la duree d'eclairement (-3 h 30) a entraine une forte baisse de la production laitiere (-37,7 % entre J145 et J187). En JL les taux butyreux (TB) et proteique (TP) du lait ont eu tendance a baisser par rapport a ceux des brebis en JC : les ecarts maximaux, qui apparaissent apres 30 a 40j, ont ete de 14,2 g/litre pour le TB et de 11,0 g/litre pour le TP. L'augmentation brutale de la duree d'eclairement (exJC) a ete defavorable par rapport a sa diminution (exJL), aussi bien pour le TB (-7,8 g/litre) que pour le TP (-6,5 g/litre). Les quantites volontairement ingerees, qui etaient identiques en fin de gestation, se sont differenciees a partir du 25 e jour de lactation. Ainsi, entre J28 et J150 les consommations totales moyennes des brebis en JL ont ete de 16,3 % superieures a celles des brebis en JC. Apres le changement de photoperiode, la difference d'ingestion a fortement diminue pour s'etablir en moyenne a + 6,2 % dans le lot JL par rapport au lot JC. En fin d'essai, lorsque les photoperiodes etaient identiques depuis plus de 30 j, les consommations totales de MS ont ete tres proches pour les deux lots de brebis. Au total, la duree d'eclairement agit a differentes echelles de temps : d'abord sur le volume de lait, ensuite sur sa composition et enfin sur les quantites volontairement ingerees. Apres 100 j de traitement photoperiodique constant il semble s'installer un etat refractaire aux effets de la photoperiode.

Nematode parasites and mastitis are the major animal health constraints in sheep. The aim of this study was estimating the genetic (co)variances of nematode parasites resistance and somatic cell count in dairy sheep. From 2000 to 2008, Somatic Cell Score (SCS) and Faecal Egg Count (FEC) records were available on an eperimental population consisting of �� 4�� backcross ewes and 80�� their daughters. Data were processed independently for each subpopulation in order to adjust for specific environmental ef - fects and to obtain lactation records for both traits to be used in the genetic analysis. Variance components Variance components estimation was performed by using the REML method applied to a bi-trait repeatability animal model. Heritabilities of lactation SCS (LSCS) and FEC were 0.1�� and 0.1�� . Genetic correlation was 0.21, whereas phenotypic correlation was 0.01. The estimated heritabilities confirm that both traits could be selected by the classical quantitative approach. The genetic correlation estimate between LSCS and FEC suggests The genetic correlation estimate between LSCS and FEC suggests that selection for one of the two traits would not have any detrimental effect on the other one.

Background The least absolute shrinkage and selection operator (LASSO) can be used to predict SNP effects. This operator has the desirable feature of including in the model only a subset of explanatory SNPs, which can be useful both in QTL detection and GWS studies. LASSO solutions can be obtained by the least angle regression (LARS) algorithm. The big issue with this procedure is to define the best constraint (t), i.e. the upper bound of the sum of absolute value of the SNP effects which roughly corresponds to the number of SNPs to be selected. Usai et al. (2009) dealt with this problem by a cross-validation approach and defined t as the average number of selected SNPs overall replications. Nevertheless, in small size populations, such estimator could give underestimated values of t. Here we propose two alternative ways to define t and compared them with the "classical" one. Methods The first (strategy 1), was based on 1,000 cross-validations carried out by randomly splitting the reference population (2,000 individuals with performance) into two halves. The value of t was the number of SNPs which occurred in more than 5% of replications. The second (strategy 2), which did not use cross-validations, was based on the minimization of the Cp-type selection criterion which depends on the number of selected SNPs and the expected residual variance. Results The size of the subset of selected SNPs was 46, 189 and 64 for the classical approach, strategy 1 and 2 respectively. Classical and strategy 2 gave similar results and indicated quite clearly the regions were QTL with additive effects were located. Strategy 1 confirmed such regions and added further positions which gave a less clear scenario. Correlation between GEBVs estimated with the three strategies and TBVs in progenies without phenotypes were 0.9237, 0.9000 and 0.9240 for classical, strategy 1 and 2 respectively. Conclusions This suggests that the Cp-type selection criterion is a valid alternative to the cross-validations to define the best constraint for selecting subsets of predicting SNPs by LASSO-LARS procedure.