Genome-wide association study of body morphological traits in Sudanese goats.

Long-term selection of goats for a certain production system and/or different environmental conditions will be reflected in the body morphology of the animals under selection. To investigate the variation contributing to different morphological traits and to identify genomic regions that are associated with body morphological traits in Sudanese goats, we genotyped 96 females belonging to four Sudanese goat breeds with the SNP52 BeadChip. After quality control of the data, the genome-wide association study was performed using 95 goats and 24 027 informative single nucleotide polymorphisms (SNPs). Bicoastal diameter was significantly associated (LOD = 6.32) with snp10185-scaffold1365-620922 on chromosome 2. The minor allele has an additive effect, increasing the bicoastal diameter by 2.6 cm. A second significant association was found between body length and snp56482-scaffold89-467312 on chromosome 3 (LOD = 5.65). The minor allele is associated with increased body length. Additionally, five regions were suggestive for cannon bone, head width, rump length and withers height (LOD > 5). Only one gene (CNTNAP5) is located within the 1-Mb region surrounding the significant SNP for bicoastal diameter on chromosome 2. The body length QTL on chromosome 3 harbors 49 genes. Further research is required to validate the observed associations and to prioritize candidate genes.

Validating genome-wide associated signals for clinical mastitis in German Holstein cattle.

A validation study for six genomic regions previously identified by a genome-wide association study for somatic cell score was conducted with data of clinical mastitis in German Holstein cattle. Out of 10 tested SNPs, five on chromosomes 6, 13 and 19 were significantly associated with clinical mastitis (P < 0.05). Three SNPs on chromosomes 6 and 19 had the same direction of effect as those previously reported in the initial genome-wide association study for somatic cell score. The other two SNPs on chromosome 13 had opposite effects. As well as validating associations within known QTL from previous studies, e.g. chromosomes 6 and 19, novel loci on chromosome 13 were confirmed. Promising candidate genes are, for example: deoxycytidine kinase, immunoglobulin J chain, vitamin D binding protein, forkhead box K2, sodium/hydrogen exchanger 8 and cytoplasmic nuclear factor of activated T-cells 2. Our confirmation study provides additional evidence for the functional role of the linked genomic regions to immune response. This information can be used as a basis for further functional studies for those potential genes.

Genetic diversity of Syrian Arabian horses.

Although Arabian horses have been bred in strains for centuries and pedigrees have been recorded in studbooks, to date, little is known about the genetic diversity within and between these strains. In this study, we tested if the three main strains of Syrian Arabian horses descend from three founders as suggested by the studbook. We examined 48 horses representing Saglawi (n = 18), Kahlawi (n = 16) and Hamdani (n = 14) strains using the Equine SNP70K BeadChip. For comparison, an additional 24 Arabian horses from the USA and three Przewalski's horses as an out group were added. Observed heterozygosis (Ho ) ranged between 0.30 and 0.32, expected heterozygosity (He ) between 0.30 and 0.31 and inbreeding coefficients (Fis ) between -0.02 and -0.05, indicating high genetic diversity within Syrian strains. Likewise, the genetic differentiation between the three Syrian strains was very low (Fst  < 0.05). Hierarchical clustering showed a clear distinction between Arabian and Przewalski's horses. Among Arabian horses, we found three clusters containing either horses from the USA or horses from Syria or horses from Syria and the USA together. Individuals from the same Syrian Arabian horse strain were spread across different sub-clusters. When analyzing Syrian Arabian horses alone, the best population differentiation was found with three distinct clusters. In contrast to expectations from the studbook, these clusters did not coincide with strain affiliation. Although this finding supports the hypothesis of three founders, the genetic information is not consistent with the currently used strain designation system. The information can be used to reconsider the current breeding practice. Beyond that, Syrian Arabian horses are an important reservoir for genetic diversity.

Diversity of mitochondrial DNA in three Arabian horse strains.

Arabian horse registries classify Arabian horses based on their dam lineages into five main strains. To test the maternal origin of Syrian Arabian horses, 192 horses representing the three major strains Saglawi, Kahlawi, and Hamdani were sequenced for 353 bp of their mitochondrial displacement loop (D-loop) region. Sequencing revealed 28 haplotypes comprising 38 sequence variations. The haplotype diversity values were 0.95, 0.91, and 0.90 in Kahlawi, Hamdani, and Saglawi strains, respectively. The pair-wise population differentiation estimates (Fst) between strains were low, ranging between 0.098 and 0.205. The haplotype diversity and the pair-wise population differentiation estimates (Fst) between strains showed high diversity within individuals of each strain and low variation between the three strains. Mitochondrial haplotypes scattered all over the neighbor-joining tree without clear separation of the three strains. In the median-joining network, the Syrian horses were grouped into seven major haplogroups. These results suggest that more than five ancestors exist that share common maternal haplotypes with other horse breeds.

Milk protein polymorphisms and casein haplotypes in Butana cattle.

Butana is a Bos indicus dairy cattle breed that is well adapted to the local environment of Sudan. The breed has been gradually declining in number due to breed substitution. Therefore, conservation and improvement strategies are required to maintain this breed. The aim of the present study was to assess genetic variation that is characteristic for Butana cattle in the milk protein genes CSN1S1, CSN2, CSN1S2, CSN3, LALBA, and LGB. In a first step, genomic DNA of five unrelated individuals was comparatively sequenced across all exon and flanking sequences. Ninety-three single nucleotide polymorphisms (SNPs) were identified in Butana cattle compared with the Bos taurus reference sequence at Ensembl. We confirmed the recently identified protein variants CSN2*J, CSN2*L, and LALBA*E. Fifty-two SNPs in non-coding regions are novel. Among the novel SNPs, five are located in promoter regions, three of them are in putative transcription factor binding sites (TFBSs) of the CSN1S2 promoter. Fifteen SNPs potentially affect miRNA target sites. In a second step, 50 unrelated Butana cattle were genotyped. This allowed deriving haplotypes for the casein gene cluster on BTA6. The most frequent haplotype was CSN1S1*C-CSN2*A 2 -CSN1S2*A-CSN3*A (C-A 2 -A-A, frequency 0.1546). Considering the newly identified CSN1S2 promoter variants, the most frequent haplotype was C-A 2 -TTC-A-A (0.1046), with TTC as the promoter variant. The information on protein and promoter variants can be used for the development of conservation and breeding strategies for this local breed.

Genomewide study and validation of markers associated with production traits in German Landrace boars.

We present results from a genomewide association study (GWAS) and a single-marker association study. The GWAS was performed with the Illumina PorcineSNP60 BeadChip from which 5 markers were selected for a validation analysis. Genetic effects were estimated for feed intake, weight gain, and traits of fat and muscle tissue in German Landrace boars kept on performance test stations. The GWAS was performed in a population of 288 boars and the validation study for another 432 boars. No statistically significant effect was found in the GWAS after adjusting for multiple testing. Effects of 2 markers, which were significant genomewide before correction for multiple testing (P < 0.00005), could be confirmed in the validation study. The major allele of marker ALGA0056781 on SSC1 was positively associated with both higher weight gain and fat deposition. The effect on live-weight gain was 2.25 g/d in the GWAS (P = 0.0003) and 3.73 g/d in the validation study (P = 0.01) and for back fat thickness was 0.15 mm in the GWAS (P < 0.0001) and 0.20 mm in the validation study (P = 0.02). The marker had similar effects on test-day weight gain (GWAS: 3.85 g/d, P = 0.001; validation study: 6.80 g/d, P = 0.003) and back fat area (GWAS: 0.27 cm(2), P < 0.0001; validation study: 0.35 cm(2), P = 0.03). Marker ASGA0056782 on SSC13 was associated with live-weight gain. The major allele had negative effects in both studies (GWAS: -4.88 g/d, P < 0.0001; validation study: -3.75 g/d, P = 0.02). The effects of these 2 markers would have been excluded based on the GWAS alone but were shown to be significantly trait associated in the validation study indicating a false-negative result. The G protein-coupled receptor 126 (GPR126) gene approximately 200 kb downstream of marker ALGA0001781 was shown to be associated with human height and therefore might explain the association with weight gain in pigs. Several traits were affected in an economically desired direction by the minor allele of the markers, pointing to the possibility of improvement through further selection.

Worldwide frequency distribution of the 'Gait keeper' mutation in the DMRT3 gene.

For centuries, domestic horses have represented an important means of transport and served as working and companion animals. Although their role in transportation is less important today, many horse breeds are still subject to intense selection based on their pattern of locomotion. A striking example of such a selected trait is the ability of a horse to perform additional gaits other than the common walk, trot and gallop. Those could be four-beat ambling gaits, which are particularly smooth and comfortable for the rider, or pace, used mainly in racing. Gaited horse breeds occur around the globe, suggesting that gaitedness is an old trait, selected for in many breeds. A recent study discovered that a nonsense mutation in DMRT3 has a major impact on gaitedness in horses and is present at a high frequency in gaited breeds and in horses bred for harness racing. Here, we report a study of the worldwide distribution of this mutation. We genotyped 4396 horses representing 141 horse breeds for the DMRT3 stop mutation. More than half (2749) of these horses also were genotyped for a SNP situated 32 kb upstream of the DMRT3 nonsense mutation because these two SNPs are in very strong linkage disequilibrium. We show that the DMRT3 mutation is present in 68 of the 141 genotyped horse breeds at a frequency ranging from 1% to 100%. We also show that the mutation is not limited to a geographical area, but is found worldwide. The breeds with a high frequency of the stop mutation (>50%) are either classified as gaited or bred for harness racing.

Development of an in vitro index to characterize fertilizing capacity of boar ejaculates.

The aim of this research was the selection of spermatozoa parameters related to boar fertility performance and their combination into an in vitro index. A first set (data set 1) of 36 Pietrain boars with 138 ejaculates from two seasons with 5083 single-sire inseminations from 34 farms was used to determine correlations between in vitro sperm quality parameters and fertility performance. 2970 ejaculates representing a second set (data set 2) served calculation of seasonal and age effects on semen quality. Morphological spermatozoa parameters were estimated manually with a phase contrast microscope on the day of semen collection, whereas mitochondrial activity and viability were analyzed by double-staining with rhodamine123/propidium iodide on day 2 of semen storage using flow cytometry. Sperm motility was tested on day 7 by thermoresistance (TRT) after 30min (TRT1) and 300min (TRT2) incubation at 38̊C using computer-assisted semen analysis (CASA). Correlations revealed four independent sperm quality parameters qualifying as relevant predictors of boar fertility: (i) percentage of spermatozoa with proximal cytoplasmic droplets, (ii) percentage of spermatozoa with active mitochondria, (iii) beat cross frequency of progressively motile spermatozoa in TRT1, and (iv) oscillation measure of the actual path of progressively motile spermatozoa in TRT2. There were no significant effects of sperm concentration, ejaculate volume, and total number of sperm cells per ejaculate on litter size (LS) and on pregnancy rate (PR). Our findings suggest the usefulness of sperm quality parameters based on adjusted range of methods and enable the construction of an in vitro index as a means to predicting boar fertility.

Two SNPs in the SILV gene are associated with silver coat colour in ponies.

In horses, a pigment dilution acting only on black eumelanin is the so-called silver coat colour, which is characterized by a chocolate-to-reddish body with a white mane and tail. Using information from other species, we focused our study on SILV as a possible candidate gene for the equine silver phenotype. A 1559-bp genomic fragment was sequenced in 24 horses, and five SNPs were detected. Two of the five SNPs (DQ665301:g.697A>T and DQ665301:g.1457C>T) were genotyped in 112 horses representing eight colour phenotypes. Both mutations were completely associated with the silver phenotype: all eumelanin-producing horses (blacks and bays) with atypical white mane and tail were carriers of the [g.697T; g.1457T] haplotype. We identified this haplotype as well as the silver phenotype only in Shetland ponies and Icelandic horses. Horses without eumelanin (chestnuts) were carriers of the [g.697T; g.1457T] haplotype, but they showed no phenotypic effect. The white or flaxen mane often detected in chestnuts is presumably based on another SILV mutation or on polymorphisms in other genes.

Analysis of selection effect based on kappa casein gene on milk yield production of Iranian Sarabi cattle breed using stochastic simulation.

PCR-RFLP was used to genotype 87 Sarabi native cattle of north-western Iran for A and B alleles of kappa casein gene. A 350 bp length of exon 4 and intron 4 was amplified and digested with HinfI endonuclease. Samples were loaded on agarose gel (2%) and genotyped under UV light. Allele frequency of desirable B allele was 0.57. Stochastic simulation was used to generate milk yield trait for a population of 4950 females and 50 males for 15 overlapping generations. Population parameters included 1100 and 436 kg for average milk yield and phenotypic deviation, respectively; with heritability of 0.27. Additive and dominance effects of Kappa Casein gene were considered as 187.63 and 50.37 kg, respectively. Two methods were considered for selection of males based on the first phenotypic record of their dams (PAS) or molecular information of each male, individually (GAS). Females were always selected on their first phenotypic record. Although, there was a significant difference between polygenic and major gene genetic response between two methods after the 5th generations, but there was no significant difference for the sum of polygenic and major gene response. After 15 generations of selection there was no significant difference between inbreeding coefficient under two methods. Selection plan for males based on one single major gene had no advantage over the conventional selection based on dam record in native Sarabi breed.

Polymorphism of the bovine POU1F1 gene: allele frequencies and effects on milk production in three Iranian native breeds and Holstein cattle of Iran.

The aim of this study was to estimate the allele frequencies in polymorphic site of exon six of POU1F1 gene in three Iranian native and Holstein cattle. Genomic DNA was extracted from 3 Iranian native cattle breeds, including 97 Mazandarani, 87 Sarabi, 112 Golpaygani and also 110 Holstein cattle. A 451 bp fragment of intron 5 and exon 6 were amplified and digested with HinfI restriction enzyme. Frequencies of allele A were 0.37, 0.27, 0.34 and 0.21 for Mazandarani, Sarabi, Golpaygani and Holstein cattle, respectively. Significant differences in genotype frequencies were found between Mazandarani or Golpaygani and Holstein cattle. No significant differences in genotype frequencies were found between Sarabi and Holstein cattle. Transition A to G in nucleotide 1256 is responsible for HinfI(-) allele. No significant association was observed between POU1F1 polymorphism and milk production. Differences in allelic frequency between native Bos indicus breeds (Mazandarani, Golpaygani) and Holstein at the present study might be due to differences in origin breeds, low number of samples and/or as the effect of natural selection in native breeds.

Detection of novel single-nucleotide polymorphisms (SNPs) in the CYP21 gene and association analysis of two SNPs for CYP21 and ESR2 with litter size in a commercial sow population.

Altogether 129 F1 sows from a commercial sow farm with at least four litters were genotyped for the oestrogen receptor 2 gene (ESR2) and cytochrome P450 hydroxylase 21 gene (CYP21) and investigated for associations on the litter-size parameters: total number born and number born alive. Five novel polymorphisms were found in the 3'-untranslated region for the CYP21 gene. Genotype and allele frequencies for the CYP21 (position 3462G > A) single-nucleotide polymorphism (SNP) were 0.434 (GG), 0.504 (AG), 0.062 (AA) and 0.69 (G):0.31 (A), respectively. No association was found between this polymorphism and litter-size parameters. For the ESR2 gene, the SNP in exon 5 associated with an amino acid substitution MET (allele A) > VAL (allele G) was investigated. Only two genotypes were found leading to allele frequencies of 0.34 (A):0.66 (G). Only number born alive piglets were significantly increased for the AG genotype (p = 0.034) with 11.64 piglets per sow and litter in comparison with the GG genotype, leading to only 10.96 piglets per sow and litter. From these data, it can be concluded that the investigated SNP of the ESR2 gene is associated with the number of liveborn piglets in the commercial population considered, and hence could be useful in selection for litter size. Therefore, this gene should be investigated in additional populations.

[Analysis of the genetic structure of the breeding nucleus of the Russian population of purebred Thoroughbred horses at the Extension locus using molecular DNA typing]. / Analiz geneticheskoi struktury plemennogo iadra Rossiiskoi populiatsii chistokrovnykh verkhovykh loshadei po lokusu Extension s ispol'zovaniem molekuliarnoi DNK diagnostiki.

Results of the first in Russia survey of the gene pool of the breeding nucleus of the Russian population of thoroughbred horses by means of PCR analysis of the E (Extension) locus MC1R gene mutations are presented. The data on the structure of breeding populations from the leading stud farms Voskhod and Oros with regard to color phenotypes as well as genotype and allele frequencies are presented. The population structure parameters are discussed with respect to possible specific features of microevolution processes.

[Pregnancy with an intra-uterine device in place (author's transl)]. / Gravidität bei Intrauterinpessar in situ--Kasuistik.

Report on a 33 year old gravida 3 para 2 which was referred at 24 weeks gestation by ultra-sound with an intra-uterine device in place. The patient was referred for therapeutic abortion ab 10 weeks gestation by dates. Since the pregnancy was in fact 24 weeks the risks were explained to the mother and continuation of the pregnancy recommended. At approximately 36 weeks gestation a healthy make infant 2600 grams was delivered by double footling breech spontaneous delivery. A cavernous hemangioma of the right knee was probably not due to the intra-uterine device but an incidental occurance. The Copper-T intra-uterine device was removed under general anesthesia fourteen weeks following delivery.

PIP: A 33 year old woman, 3 gravida, 2 para, was examined after receiving approval for abortion under the medical indication, due to X-ray exposure and use of anti-depressant drugs. She had become pregnant in spite of an in situ Copper T device, and underwent an ultrasonic examination to determine its position. As the pregnancy was already in the 24th week, it was decided to carry the pregnancy to term. In the 36th week of pregnancy a healthy male baby with a cavernous hemangioma of the right knee was delivered by breech birth. The hemangioma was probably not due to the IUD. The IUD was removed 14 weeks post partum under general anesthesia.

[Antistreptolysin-titre under the use of traditional methods and after saturation with dextran sulfate]. / Der Antistreptolysintiter unter Anwendung der herkömmlichen Methodik und nach Absättigung mit Dextransulfat

1,700 blood samples of healthy test persons without clinically and paraclinically provable streptococcal diseases were examined for their content of antistreptolysin. Beside the usual method parallel determinations were carried out after addition of dextran sulfate. Thus increases of unspecific antistreptolysin titres shall be in most cases excluded, above all by the influence of the lipoproteins. The absorption of dextran sulfate led to the decrease of the antistreptolysin titre by 12.33%. Furthermore could be proved that the average antistreptolysin titre of female test persons is ca. 20 antistreptolysin units below the titre of male test persons, that seasonal variations of the antistreptolysin titre with the highest titres appear in the first and third quarter which may be explained by a bad unspecific defensive condition, that, furthermore, the antistreptolysin titres increase to the 14th year and then continuously decrease and that in new-born children the arithmetic mean value of the antistreptolysin units is significantly higher than in their mothers. Hereby an active influence of the placenta on the transmission of antibodies seems to be possible. Though a slightly increased financial expenditure is necessary for dextran sulfate, temporarily and concerning working technique, however, no larger loads appear, it is justifiable to perform the determination of antistreptolysin titres only by means of dextran sulfate-absorbed sera, since in this way a considerable number of unspecific and misleading reactions can be excluded.