Genetic diversity of Swiss sheep breeds in the focus of conservation research

There is constant pressure to improve evaluation of animal genetic resources in order to prevent their erosion. Maintaining the integrity of livestock species as well as their genetic diversity is of paramount interest for long-term agricultural policies. One major use of DNA techniques in conservation is to reveal genetic diversity within and between populations. Forty-one microsatellites were analysed to assess genetic diversity in nine Swiss sheep breeds and to measure the loss of the overall diversity when one breed would become extinct. The expected heterozygosities varied from 0.65 to 0.74 and 10.8% of the total genetic diversity can be explained by the variation among breeds. Based on the proportion of shared alleles, each of the nine breeds were clearly defined in their own cluster in the neighbour-joining tree describing the relationships among the breeds. Bayesian clustering methods assign individuals to groups based on their genetic similarity and infer the number of populations. In STRUCTURE, this approach pooled the Valais Blacknose and the Valais Red. With BAPS method the two Valais sheep breeds could be separated. Caballero & Toro approach (2002) was used to calculate the loss or gain of genetic diversity when each of the breeds would be removed from the set. The changes in diversity based on between-breed variation ranged from -12.2% (Valais Blacknose) to 0% (Swiss Black Brown Mountain and Mirror Sheep); based on within-breed diversity the removal of a breed could also produce an increase in diversity (-0.6% to + 0.6%). Allelic richness ranged from 4.9 (Valais Red) to 6.7 (Brown Headed Meat sheep and Red Engadine Sheep). Breed conservation decisions cannot be limited to genetic diversity alone. In Switzerland, conservation goals are embedded in the desire to carry the cultural legacy over to future generations.

DNA methylation patterns at the IGF2-H19 locus in sperm of Swiss Landrace and Swiss Large White boars

DNA methylation patterns at the IGF2-H19 locus were investigated in sperm DNA from Swiss Landrace (SL) and Swiss Large White (LW) boars. The putative IGF2 differentially methylated regions (DMR) 0, 1 and 2, a quantitative trait nucleotide (QTN) region in the intron 3 and a CpG island in the intron 4 of the IGF2 gene as well as three regions around porcine CTCF binding sites within the H19 differentially methylated domain (DMD) were selected for the DNA methylation analysis. In both breeds putative IGF2 DMR0, 1, 2 and H19 DMD were hypermethylated. Significant differences in DNA methylation content were found between the two breeds in the two DMD regions proximal to the H19 gene. The IGF2 QTN region and the CpG island in the IGF2 intron 4 were hypomethylated in sperm DNA of both breeds. The methylation analysis revealed significantly more methylated CpG sites in the intron 4 of sperm from the LW breed than in that from SL. No difference was found in global DNA methylation between the two breeds. These results indicate differences in DNA methylation patterns between breeds and it remains to be established whether variation in DNA methylation patterns impacts on phenotypic traits.

Genomewide association for a dominant pigmentation gene in sheep

Most published genomewide association studies (GWAS) in sheep have investigated recessively inherited monogenic traits. The objective here was to assess the feasibility of performing GWAS for a dominant trait for which the genetic basis was already known. A total of 42 Manchega and Rasa Aragonesa sheep that segregate solid black or white coat pigmentation were genotyped using the SNP50 BeadChip. Previous analysis in Manchegas demonstrated a complete association between the pigmentation trait and alleles of the MC1R gene, setting an a priori expectation for GWAS. Multiple methods were used to identify and quantify the strength of population substructure between black and white animals, before allelic association testing was performed for 49 034 SNPs. Following correction for substructure, GWAS identified the most strongly associated SNP (s26449) was also the closest to the MC1R gene. The finding was strongly supported by the permutation tree-based random forest (RF) analysis. Importantly, GWAS identified unlinked SNP with only slightly lower p-values than for s26449. Random forest analysis indicated these were false positives, suggesting interpretation based on both approaches was beneficial. The results indicate that a combined analytical approach can be successful in studies where a modest number of animals are available and substantial population stratification exists.

Inheritance of ectopic ureters in Entlebucher Mountain Dogs

To test the hypothesis of a heritable base of ectopic ureters (EU) in Entlebucher Mountain Dogs (EMD) and to elucidate associated risk factors and mode of inheritance of the disease, 565 EMD were clinically investigated and population genetic analyses performed. Based on the location of the most caudal termination of the ureteral openings, 552 EMD were classified into three phenotype groups trigone, intravesically and extravesically ectopic based on results of abdominal sonography, urethra-cystoscopy and/or contrast-enhanced computed tomography. One-third (32.9%) of the phenotyped animals had normal terminations of both ureters in the bladder trigone, 47.3% had at least one intravesicular ectopic termination and 19.8% had at least one extravesicular ectopic termination. Multivariate mixed logistic regression revealed gender as a risk factor associated with EU as males were more often affected than females. Complex segregation analysis indicated a hereditary basis for EU in EMD and the involvement of a major gene in the occurrence of the extravesicular EU phenotype.

The equine DNAH3 gene: SNP discovery and exclusion of an involvement in recurrent airway obstruction (RAO) in European Warmblood horses

Recurrent airway obstruction is one of the most common airway diseases affecting mature horses. Increased bronchoalveolar mucus, neutrophil accumulation in airways, and airway obstruction are the main features of this disease. Mucociliary clearance is a key component of pulmonary defense mechanisms. Cilia are the motile part of this system and a complex linear array of dynein motors is responsible for their motility by moving along the microtubules in the axonemes of cilia and flagella. We previously detected a QTL for RAO on ECA 13 in a half-sib family of European Warmblood horses. The gene encoding DNAH3 is located in the peak of the detected QTL and encodes a dynein subunit. Therefore, we analysed this gene as a positional and functional candidate gene for RAO. In a mutation analysis of all 62 exons we detected 53 new polymorphisms including 7 non-synonymous variants. We performed an association study using 38 polymorphisms in a cohort of 422 animals. However, after correction for multiple testing we did not detect a significant association of any of these polymorphisms with RAO (P>0.05). Therefore, it seems unlikely that variants at the DNAH3 gene are responsible for the RAO QTL in European Warmblood horses.

Pollen profile from sediment core Höllerer See

(expanded by Eberhard Grüger, Göttingen) The site "Höllerer See" is a lake in the northern foreland of the Alps, about 30 km north of the city of Salzburg/Austria, situated in the south-western part of Oberösterreich/Austria. A 2 m long piston core from this locality, consisting entirely of calcareous gyttja, was studied by pollen analysis. The three lowermost samples (1.98, 1.95 and 1.92 m) were deposited during the Preboreal when Pinus and Betula were still the dominating forest trees. High pollen values of thermophilous woody species (mainly Corylus and Quercus, but also Ulmus, Tilia, Fraxinus) prove the Boreal age of the next younger sample (1.91 m). The following two pollen spectra attest that Alnus (1.89 m) and - later (1.88 m) - Fagus had become important members of the local (Alnus) and the regional (Fagus) vegetation. From this level up to the top of the profile these two tree taxa contribute - together with Betula - always 50 to 80 % to the arboreal pollen sum. The upper 1.89 m of sediment of the Höllerer See core evidently date from the Subboreal and the Subatlantic. As Preboreal sediment was stated at the base of the profile it must be concluded that most of the Boreal and the Atlantic is - for whatever reason - not represented by sediment in this core. As no radiocarbon dates are available age estimates of the distinguished pollen zones can be achieved only by correlating major changes of the former vegetation with historical events which probably influenced the then contemporary vegetation. The pollen grains of the Triticum and Hordeum type found in samples of zone 2.1 might indicate the growing of cereals in the region during the Late Bronze Age. The first pollen grains of Secale date from the boundary Hallstatt/Latène Age (zone 2.2). The cereal curves become continuous in Bavarian times (Bajuwarenzeit, Middle Ages, zone 3.3). The Plantago laceolata curve, continuous since 1.7 m depth (zone 2.1), points to animal breeding since the Early Subatlantic (Hallstattzeit). This curve reaches its absolute maximum in Roman time (zone 3.1). Roman time forest clearance caused a drastic decrease of tree pollen curves (start of zone 3.1). Values of anthropogenic indicators as high as in zone 3.1 are found again - after a distinct decrease in zone 3.2 - not till the Bavarians settled in the region (6th century). Maximal Fagus values and the simultaneous total lack of anthropogenic indicators mark the Migration Period (zone 3.2). The Younger Subatlantic (zone 4) is characterized by a decrease of deciduous forests due to medieval forest clearance. At the same time the conifers Pinus and Picea gained in importance. The lake was probably used for retting hemp in Medieval times. The distinction of the pollen grains of Cannabis and Humulus might not be certain in all cases. It is known that hemp as well as hop was cultivated in the study area. Markers were added to the samples at the beginning of pollen preparation (13500 Lycopodium spores, sample volume 0.5 cm**3) and counted together with the pollen grains. Therefore pollen concentrations can be calculated: Concentration = C * F / V (with C = number of grains of a particular pollen type, V = volume of the untreated pollen sample, F = marker added/marker counted). F ranges from 39 to 1688. Factors that large are not suited to produce reliably interpretable pollen concentrations. Consequently no use was made of the pollen concentrations in this thesis, although a concentration diagram is added.

Inheritance of proportionate dwarfism in Angus cattle

Objective To determine the mode of inheritance of congenital proportionate dwarfism in Angus and Angus crossbred cattle, initially detected in two commercial beef herds in northern New South Wales. Design Matings of normal carrier sires to unrelated cows of diverse breeds, and of one carrier sire to his unaffected daughters. An unrelated Piedmontese bull was also mated to unaffected daughters of the carrier sires. Procedure Two carrier Angus bulls and nine unaffected daughters, all of whom were completely indistinguishable from normal animals, were purchased for controlled breeding studies under known nutritional and disease conditions. Affected and carrier individuals were examined for the presence of obvious chromosomal abnormalities. Results Angus dwarfism has been successfully reproduced under controlled experimental conditions over successive years using unrelated dams and is undoubtedly heritable. The high frequency of occurrence of affected individuals (23/61 = 0.38 +/- .06) among the progeny of matings of the Angus sires to unrelated females of diverse breeding is not compatible with recessive inheritance, because of the negligible frequency of proportionate dwarfism in the breeds of the dams. Both paternal and maternal transmission of the defect was demonstrated, so that imprinting in the strict sense of a gene that is only expressed when received from the male parent appears not to be involved. Tested individuals showed no evidence of gross chromosomal abnormality. Dominant autosomal inheritance with incomplete penetrance was indicated by the lack of expression of the defective gene in the two Angus sires and in three unaffected daughters who produced dwarf calves from matings to the Piedmontese bull. Conclusions The mode of inheritance is that of a single autosomal dominant gene with a penetrance coefficient of 0.75 +/- 0.12, estimated from the observed incidence of 23/61 affected offspring of the two carrier Angus bulls mated to unrelated dams. Simple genetic models involving either (i) an unstable mutant which changes at high frequency to the expressed dominant dwarfing allele during gametogenesis, or (ii) a dominant allele with penetrance determined by an unlinked modifying locus, are shown to be compatible with the experimental data. Both models indicate that penetrance of the dwarfing gene may possibly be higher in matings involving carrier daughters of the two Angus bulls.

Genetic parameters and predicted response to selection for lean growth in an Australian commercial nucleus pig herd

Genetic parameters for performance traits in a pig population were estimated using a multi-trait derivative-free REML algorithm. The 2590 total data included 922 restrictively fed male and 1668 ad libitum fed female records. Estimates of heritability (standard error in parentheses) were 0.25 (0.03), 0.15 (0.03), and 0.30 (0.05) for lifetime daily gain, test daily gain, and P2-fat depth in males, respectively; and 0.27 (0.04) and 0.38 (0.05) for average daily gain and P2-fat depth in females, respectively. The genetic correlation between P2-fat depth and test daily gain in males was -0.17 (0.06) and between P2-fat and lifetime average daily gain in females 0.44 (0.09). Genetic correlations between sexes were 0.71 (0.11) for average daily gain and -0.30 (0.10) for P2-fat depth. Genetic response per standard deviation of selection on an index combining all traits was predicted at $AU120 per sow per year. Responses in daily gain and backfat were expected to be higher when using only male selection than when using only female selection. Selection for growth rate in males will improve growth rate and carcass leanness simultaneously.

Successful artificial insemination (AI) in the koala using neat and extended semen collected by electroejaculation (EE)

Presently AI in the koala has been based on the insemination of fresh undiluted semen collected with an artificial vagina (1). While this approach has been extremely successful, further refinement and implementation of AI for use with cryopreserved semen will require protocols that incorporate diluted semen collected by EE. Recent studies have shown that koala semen is likely to have an "ovulation factor" such that over-dilution may result in ovulation failure (2). The current study determined whether AI of EEed neat and/or diluted semen was capable of inducing a luteal phase and/or resulted in the production of pouch young. All koalas were inseminated in the breeding season between day 2 and 5 of oestrus and subsequently monitored for evidence of parturition (day 35) and return of oestrus. Successful induction of a luteal phase was based on evidence of an elevated progesterone concentration 28 days after insemination (2). All semen samples were collected by EE and seminal characteristics recorded (3). The diluent used for semen extension was Tris-citrate glucose (TCG) which contained antibiotics but no egg yolk (4). AI was conducted on conscious koalas using a "Cook koala insemination catheter" and a glass rod used to mimic penile thrusting (1). Three insemination treatments were used; (A) 1mL of undiluted semen (n = 9); (B) 2mL of 1:1 diluted semen (n = 9); and (C) 1 mL of 1:1 diluted semen (n = 9). The results of the AI trial are shown in Table 1. This study has shown that it is possible to use both neat and diluted semen (1:1; 1 or 2 mL) to successfully produce koala offspring at conception rates similar to those achieved following natural mating. Interestingly, dilution of semen had no apparent detrimental effect on induction of a luteal phase following AI.