Horse allergy: Curly Horses can mediate immune tolerance.

American Bashkir Curly Horses are claimed to be hypoallergenic, but this has not been clinically proven. In the present study, the effect of exposure to Curly Horses was investigated in 141 patients allergic to horses by measuring their lung function and nasal patency during Curly Horse contact. Continuous contact with Curly Horses, including riding and brushing, decreased the allergic riders' reactivity as measured by FEV1, PEF, and PNIF. Subsequent visits (up to 40 or more hours of riding) further reduced reactivity to the Curly Horses. Allergic events to horses occurred only in 72 out of 1312 riding hours, mainly in the first ten riding hours.In 41 out of the 141 patients, it was further investigated whether repeated exposure to Curly Horses could induce tolerance to other horses. Patients in the tolerance induction study were tested annually for horse allergy using a nasal provocation test. The tolerance induction study showed that exposure to Curly Horses induced immune tolerance to other horses in 88% of patients who completed the study.To understand the mechanism causing hypoallergenicity, we performed IgE immunoblots to determine whether Curly Horse hairs contain IgE binding proteins. However, no differences in IgE reactivity were found between Curly and non-Curly Horses. Moreover, the immune tolerance induction study patients did not show decreased IgE reactivity to hairs from Curly or non-Curly Horses even though patients had developed tolerance. However, we did find increasing levels of anti-horse IgG antibodies in the study patients.Overall, our data strongly suggests that continuous exposure to Curly Horses can induce immune tolerance, rendering these patients non-reactive to horses. The reason for the reduced clinical allergenicity of Curly Horses remains unclear, but the data suggest that blocking IgG antibodies may be of importance for immune tolerance development.

Unmapped short reads from whole-genome sequencing indicate potential infectious pathogens in german black Pied cattle.

When resequencing animal genomes, some short reads cannot be mapped to the reference genome and are usually discarded. In this study, unmapped reads from 302 German Black Pied cattle were analyzed to identify potential pathogenic DNA. These unmapped reads were assembled and blasted against NCBI's database to identify bacterial and viral sequences. The results provided evidence for the presence of pathogens. We found sequences of Bovine parvovirus 3 and Mycoplasma species. These findings emphasize the information content of unmapped reads for gaining insight into bacterial and viral infections, which is important for veterinarians and epidemiologists.

Effects of DGAT1 on milk performance in Sudanese Butana × Holstein crossbred cattle.

The improvement of milk production of indigenous Sudanese cattle such as Bos indicus Butana and its cross with Holstein is a major goal of the Sudanese government to ensure sufficient healthy nutrition in the country. In this study, we investigated the K232A polymorphism of diacylglycerol acyltransferase (DGAT1), a well-known modulator of milk production in other breeds. We determined allele frequencies and the allele effects on milk production. Therefore, 93 purebred Butana and 203 Butana × Holstein crossbred cattle were genotyped using competitive allele-specific PCR assays. Association analysis was performed using a linear mixed model in R. In purebred Butana cattle, the lysine DGAT1 protein variant K232, which is found to be associated with higher fat and protein contents, as well as higher fat yield was highly frequent at 0.929, while its frequency in Butana × Holstein crossbred cattle was 0.394. Significant effects were found on milk yield (P = 7.6 × 10-20), fat yield (P = 2.2 × 10-17), protein yield (P = 2.0 × 10-19) and lactose yield (P = 4.0 × 10-18) in crossbred cattle. As expected, the protein variant K232 was disadvantageous since it was decreasing milk, protein, and lactose yields by 1.741 kg, 0.063 kg and 0.084 kg, respectively. No significant effects were found for milk fat, protein, and lactose contents. The high frequency of the lysine DGAT1 protein variant K232 in Butana cattle could contribute to their high milk fat content in combination with low milk yield. In Butana × Holstein crossbred cattle, the DGAT1 marker can be used for effective selection and thus genetic improvement of milk production.

Validation of somatic cell score-associated SNPs from Holstein cattle in Sudanese Butana and Butana × Holstein crossbred cattle.

The Bos indicus zebu cattle Butana is the most commonly used indigenous dairy cattle breed in Sudan. In the last years, high-yielding Holstein dairy cattle were introgressed into Butana cattle to improve their milk yield and simultaneously keep their good adaption to extreme environmental conditions. With the focus on the improvement of milk production, other problems arose such as an increased susceptibility to mastitis. Thus, genetic selection for mastitis resistance should be considered to maintain healthy and productive cows. In this study, we tested 10 single nucleotide polymorphisms (SNPs) which had been associated with somatic cell score (SCS) in Holstein cattle for association with SCS in 37 purebred Butana and 203 Butana × Holstein crossbred cattle from Sudan. Animals were genotyped by competitive allele-specific PCR assays and association analysis was performed using a linear mixed model. All 10 SNPs were segregating in the crossbred Butana × Holstein populations, but only 8 SNPs in Sudanese purebred Butana cattle. The SNP on chromosome 13 was suggestively associated with SCS in the Butana × Holstein crossbred population (rs109441194, 13:79,365,467, PBF = 0.054) and the SNP on chromosome 19 was significantly associated with SCS in both populations (rs41257403, 19:50,027,458, Butana: PBF = 0.003, Butana × Holstein: PBF = 6.2 × 10-16). The minor allele of both SNPs showed an increase in SCS. Therefore, selection against the disadvantageous minor allele could be used for genetic improvement of mastitis resistance in the studied populations. However, investigations in a bigger population and across the whole genome are needed to identify additional genomic loci.

Design and performance of a bovine 200 k SNP chip developed for endangered German Black Pied cattle (DSN).

BACKGROUND: German Black Pied cattle (DSN) are an endangered dual-purpose breed which was largely replaced by Holstein cattle due to their lower milk yield. DSN cattle are kept as a genetic reserve with a current herd size of around 2500 animals. The ability to track sequence variants specific to DSN could help to support the conservation of DSN's genetic diversity and to provide avenues for genetic improvement. RESULTS: Whole-genome sequencing data of 304 DSN cattle were used to design a customized DSN200k SNP chip harboring 182,154 variants (173,569 SNPs and 8585 indels) based on ten selection categories. We included variants of interest to DSN such as DSN unique variants and variants from previous association studies in DSN, but also variants of general interest such as variants with predicted consequences of high, moderate, or low impact on the transcripts and SNPs from the Illumina BovineSNP50 BeadChip. Further, the selection of variants based on haplotype blocks ensured that the whole-genome was uniformly covered with an average variant distance of 14.4 kb on autosomes. Using 300 DSN and 162 animals from other cattle breeds including Holstein, endangered local cattle populations, and also a Bos indicus breed, performance of the SNP chip was evaluated. Altogether, 171,978 (94.31%) of the variants were successfully called in at least one of the analyzed breeds. In DSN, the number of successfully called variants was 166,563 (91.44%) while 156,684 (86.02%) were segregating at a minor allele frequency > 1%. The concordance rate between technical replicates was 99.83 ± 0.19%. CONCLUSION: The DSN200k SNP chip was proved useful for DSN and other Bos taurus as well as one Bos indicus breed. It is suitable for genetic diversity management and marker-assisted selection of DSN animals. Moreover, variants that were segregating in other breeds can be used for the design of breed-specific customized SNP chips. This will be of great value in the application of conservation programs for endangered local populations in the future.

Whey protein polymorphisms in Sudanese goat breeds.

The aim of the present study was to assess genetic variation that is characteristic for Sudanese goat breeds in the milk whey protein genes (LALBA and BLG). Four Sudanese goat breeds were screened for variability in LALBA and BLG genes at the DNA level by comparative sequencing of five animals per breed. Sixteen SNPs were identified in LALBA: seven in the upstream region, six synonymous, and three in the 3´-UTR. Three novel synonymous SNPs in exon 2 (ss5197800003, ss5197800012, and ss5197800004) were found in Nubian, Desert, and Nilotic, but not in Taggar goats. One SNP in the promoter of LALBA (rs642745519) modifies a predicted transcription factor binding site for Tcfe2a. The SNPs in the 3'-UTR (rs657915405, rs641559728, and rs664225585) affect predicted miRNA target sites. With respect to haplotypes in the exonic region, haplotype LALBA-A is most frequent in Nubian, Desert, and Nilotic goats, while haplotype LALBA-D is prevalent in Taggar goats. In BLG, 30 SNPs were detected: eight in the upstream gene region, two synonymous, 17 intronic, and three in the 3'-UTR. Among the 30 identified SNPs, 15 were novel. Four of these novel SNPs were located in the upstream gene region, one was synonymous, and ten were intronic. The novel synonymous SNP (ss5197800017), located in exon 2, was only found in Nubian and Nilotic goats. The SNPs ss5197800010 and rs635615192 in the promoter are located in predicted binding sites of transcription factors (M6097, Elk3, Elf5, and GABPA). Among seven haplotypes detected in the coding region, haplotype BLG-A is most frequent in Nubian and Nilotic goats while haplotype BLG-B is most frequent in Desert and Taggar goats. The high variability in regulatory gene regions among Sudanese goats could potentially affect the quality and yield of whey proteins in goat milk and provide a wide resource for genetic improvement of milk production and milk technology characteristics.

Whole genome population genetics analysis of Sudanese goats identifies regions harboring genes associated with major traits.

BACKGROUND: Sudan is endowed with a variety of indigenous goat breeds which are used for meat and milk production and which are well adapted to the local environment. The aim of the present study was to determine the genetic diversity and relationship within and between the four main Sudanese breeds of Nubian, Desert, Taggar and Nilotic goats. Using the 50 K SNP chip, 24 animals of each breed were genotyped. RESULTS: More than 96% of high quality SNPs were polymorphic with an average minor allele frequency of 0.3. In all breeds, no significant difference between observed (0.4) and expected (0.4) heterozygosity was found and the inbreeding coefficients (FIS) did not differ from zero. Fst coefficients for the genetic distance between breeds also did not significantly deviate from zero. In addition, the analysis of molecular variance revealed that 93% of the total variance in the examined population can be explained by differences among individuals, while only 7% result from differences between the breeds. These findings provide evidence for high genetic diversity and little inbreeding within breeds on one hand, and low diversity between breeds on the other hand. Further examinations using Nei's genetic distance and STRUCTURE analysis clustered Taggar goats distinct from the other breeds. In a principal component (PC) analysis, PC1 could separate Taggar, Nilotic and a mix of Nubian and Desert goats into three groups. The SNPs that contributed strongly to PC1 showed high Fst values in Taggar goat versus the other goat breeds. PCA allowed us to identify target genomic regions which contain genes known to influence growth, development, bone formation and the immune system. CONCLUSIONS: The information on the genetic variability and diversity in this study confirmed that Taggar goat is genetically different from the other goat breeds in Sudan. The SNPs identified by the first principal components show high Fst values in Taggar goat and allowed to identify candidate genes which can be used in the development of breed selection programs to improve local breeds and find genetic factors contributing to the adaptation to harsh environments.

Pleiotropic effects of coat colour-associated mutations in humans, mice and other mammals.

The characterisation of the pleiotropic effects of coat colour-associated mutations in mammals illustrates that sensory organs and nerves are particularly affected by disorders because of the shared origin of melanocytes and neurocytes in the neural crest; e.g. the eye-colour is a valuable indicator of disorders in pigment production and eye dysfunctions. Disorders related to coat colour-associated alleles also occur in the skin (melanoma), reproductive tract and immune system. Additionally, the coat colour phenotype of an individual influences its general behaviour and fitness. Mutations in the same genes often produce similar coat colours and pleiotropic effects in different species (e.g., KIT [reproductive disorders, lethality], EDNRB [megacolon] and LYST [CHS]). Whereas similar disorders and similar-looking coat colour phenotypes sometimes have a different genetic background (e.g., deafness [EDN3/EDNRB, MITF, PAX and SNAI2] and visual diseases [OCA2, RAB38, SLC24A5, SLC45A2, TRPM1 and TYR]). The human predilection for fancy phenotypes that ignore disorders and genetic defects is a major driving force for the increase of pleiotropic effects in domestic species and laboratory subjects since domestication has commenced approximately 18,000 years ago.

A comprehensive linkage map and QTL map for carcass traits in a cross between Giant Grey and New Zealand White rabbits.

BACKGROUND: Genomic resources for the rabbit are still limited compared to many other livestock species. The genomic sequence as well as linkage maps have gaps that hamper their use in rabbit genome research. Therefore, the aims of this study were the improvement of existing linkage maps and the mapping of quantitative trait loci (QTL) for carcass and meat quality traits. The study was performed in a F2 population of an initial cross between Giant Grey (GG) and New Zealand White (NZW) rabbits. The population consisted of 363 F2 animals derived from 9 F1 bucks and 33 F1 does. 186 microsatellite and three SNP markers were informative for mapping. RESULTS: Out of 189 markers, which could be assigned to linkage groups, 110 markers were genetically mapped for the first time. The average marker distance was 7.8 cM. The map across all autosomes reached a total length of 1419 cM. The maternal linkage map was 1.4 times longer than the paternal. All linkage groups could be anchored to chromosomes. On the basis of the generated genetic map, we identified a highly significant QTL (genome-wide significance p < 0.01) for different carcass weights on chromosome 7 with a peak position at 91 cM (157 Mb), a significant QTL (p < 0.05) for bone mass on chromosome 9 at 61 cM (65 Mb), and another one for drip loss on chromosome 12 at 94 cM (128 Mb). Additional suggestive QTL were found on almost all chromosomes. Several genomic loci affecting the fore, intermediate and hind parts of the carcass were identified. The identified QTL explain between 2.5 to 14.6% of the phenotypic variance in the F2 population. CONCLUSIONS: The results present the most comprehensive genetic map and the first genome-wide QTL mapping study for carcass and meat quality traits in rabbits. The identified QTL, in particular the major QTL on chromosome 7, provide starting points for fine mapping and candidate gene search. The data contribute to linking physical and genetic information in the rabbit genome.

A new single nucleotide polymorphism in the rabbit (Oryctolagus cuniculus) myostatin (MSTN) gene is associated with carcass composition traits.

This study aimed at the identification of genetic variations in the myostatin (MSTN) gene and testing their effects on carcass quality traits. We comparatively sequenced Giant Grey (GG) and New Zealand White (NZW) rabbits that were founders of a cross-bred population. Alignment of our sequence data with the GenBank sequence of the rabbit MSTN gene (Ensembl Gene ID ENSOCUG00000012663) identified three single nucleotide polymorphisms (SNPs). The two novel SNPs (c.-125T>C, c.373+234G>A) and one known SNP (c.747+34C>T) were subsequently analysed for linkage with carcass composition traits in 363 F2 animals of the cross GG × NZW. Significant linkage was found between c.373+234G>A and nine carcass composition traits (P < 0.05). No significant effects were found for c.-125T>C and c.747+34C>T. Because the linked SNP is located in intron 1 and no genetic variation was found in the coding region, further investigations are necessary to understand the functional effect of the c.373+234G>A variant on the variability of the traits.

Genotypes of predomestic horses match phenotypes painted in Paleolithic works of cave art.

Archaeologists often argue whether Paleolithic works of art, cave paintings in particular, constitute reflections of the natural environment of humans at the time. They also debate the extent to which these paintings actually contain creative artistic expression, reflect the phenotypic variation of the surrounding environment, or focus on rare phenotypes. The famous paintings "The Dappled Horses of Pech-Merle," depicting spotted horses on the walls of a cave in Pech-Merle, France, date back ~25,000 y, but the coat pattern portrayed in these paintings is remarkably similar to a pattern known as "leopard" in modern horses. We have genotyped nine coat-color loci in 31 predomestic horses from Siberia, Eastern and Western Europe, and the Iberian Peninsula. Eighteen horses had bay coat color, seven were black, and six shared an allele associated with the leopard complex spotting (LP), representing the only spotted phenotype that has been discovered in wild, predomestic horses thus far. LP was detected in four Pleistocene and two Copper Age samples from Western and Eastern Europe, respectively. In contrast, this phenotype was absent from predomestic Siberian horses. Thus, all horse color phenotypes that seem to be distinguishable in cave paintings have now been found to exist in prehistoric horse populations, suggesting that cave paintings of this species represent remarkably realistic depictions of the animals shown. This finding lends support to hypotheses arguing that cave paintings might have contained less of a symbolic or transcendental connotation than often assumed.

Short communication: validation of somatic cell score-associated loci identified in a genome-wide association study in German Holstein cattle.

Recently, we identified 6 genomic loci affecting daughter yield deviations (DYD) for somatic cell score (SCS) in a genome-wide association study (GWAS) performed with German Holstein bulls. In the current study, we tested if these loci were associated with SCS in cows using their own performance data. The study was performed with 1,412 German Holstein cows, of which 483 were daughters of 71 bulls that had been used in the GWAS. We tested 10 single nucleotide polymorphisms (SNP) representing 6 genomic regions that were associated with DYD for SCS in bulls. All tested SNP were significant in cows. Seven of them, located on Bos taurus autosomes (BTA) 6, 13, and 19, had the same direction of effect as those previously reported in the bull population. The most significant associations were detected on BTA6 and BTA19, accounting for 1.8% of the total genetic variance. The major allele of the 2 SNP on BTA6 and the minor allele of the 2 SNP on BTA19 were favorable for lower SCS. The differences between the homozygous genotype classes were up to 15,000 cells/mL. The verification of SNP associated with SCS in this study provides further evidence for the functional role of the linked genomic regions for immune response and contributes to identification of causative mutations. In particular, SNP with minor frequency of the favorable allele possess high potential to reduce SCS in German Holstein cattle by selection.

Identification of Differentially Expressed Genes after Endurance Runs in Karbadian Horses to Determine Candidates for Stress Indicators and Performance Capability.

RNA sequencing makes it possible to uncover genetic mechanisms that underlie certain performance traits. In order to gain a deeper insight into the genetic background and biological processes involved in endurance performance in horses, the changes in the gene expression profiles induced by endurance runs over long (70 km) and short (15 km) distances in the blood of Kabardian horses (Equus caballus) were analyzed. For the long-distance runs, we identified 1484 up- and 691 downregulated genes, while after short-distance runs, only 13 up- and 8 downregulated genes (FC > |1.5|; p < 0.05) were found. These differentially expressed genes (DEGs) are involved in processes and pathways that are primarily related to stress response (interleukin production, activation of inflammatory system) but also to metabolism (carbohydrate catabolic process, lipid biosynthesis, NADP metabolic process). The most important genes involved in these processes therefore represent good candidates for the monitoring and evaluation of the performance of horses in order to avoid excessive demands when endurance performance is required, like ACOD1, CCL5, CD40LG, FOS, IL1R2, IL20RA, and IL22RA2, on the one hand, and, on the other hand, for assessing the suitability of a horse for endurance races, like GATA2, GYG1, HIF1A, MOGAT1, PFKFB3, PLIN5, SIK1, and STBD1.

Whole-Genome Sequencing Data Reveal New Loci Affecting Milk Production in German Black Pied Cattle (DSN).

German Black Pied (DSN) is considered an ancestral population of the Holstein breed. The goal of the current study was to fine-map genomic loci for milk production traits and to provide sequence variants for selection. We studied genome-wide associations for milk-production traits in 2160 DSN cows. Using 11.7 million variants from whole-genome sequencing of 304 representative DSN cattle, we identified 1980 associated variants (-log10(p) ≥ 7.1) in 13 genomic loci on 9 chromosomes. The highest significance was found for the MGST1 region affecting milk fat content (-log10(p) = 11.93, MAF = 0.23, substitution effect of the minor allele (ßMA) = -0.151%). Different from Holstein, DGAT1 was fixed (0.97) for the alanine protein variant for high milk and protein yield. A key gene affecting protein content was CSN1S1 (-log10(p) = 8.47, MAF = 049, ßMA = -0.055%) and the GNG2 region (-log10(p) = 10.48, MAF = 0.34, ßMA = 0.054%). Additionally, we suggest the importance of FGF12 for protein and fat yield, HTR3C for milk yield, TLE4 for milk and protein yield, and TNKS for milk and fat yield. Selection for favored alleles can improve milk yield and composition. With respect to maintaining the dual-purpose type of DSN, unfavored linkage to genes affecting muscularity has to be investigated carefully, before the milk-associated variants can be applied for selection in the small population.

Refining the evolutionary tree of the horse Y chromosome.

The Y chromosome carries information about the demography of paternal lineages, and thus, can prove invaluable for retracing both the evolutionary trajectory of wild animals and the breeding history of domesticates. In horses, the Y chromosome shows a limited, but highly informative, sequence diversity, supporting the increasing breeding influence of Oriental lineages during the last 1500 years. Here, we augment the primary horse Y-phylogeny, which is currently mainly based on modern horse breeds of economic interest, with haplotypes (HT) segregating in remote horse populations around the world. We analyze target enriched sequencing data of 5 Mb of the Y chromosome from 76 domestic males, together with 89 whole genome sequenced domestic males and five Przewalski's horses from previous studies. The resulting phylogeny comprises 153 HTs defined by 2966 variants and offers unprecedented resolution into the history of horse paternal lineages. It reveals the presence of a remarkable number of previously unknown haplogroups in Mongolian horses and insular populations. Phylogenetic placement of HTs retrieved from 163 archaeological specimens further indicates that most of the present-day Y-chromosomal variation evolved after the domestication process that started around 4200 years ago in the Western Eurasian steppes. Our comprehensive phylogeny significantly reduces ascertainment bias and constitutes a robust evolutionary framework for analyzing horse population dynamics and diversity.

Epigenetic dysregulation of GATA1 is involved in myelodysplastic syndromes dyserythropoiesis.

Myelodysplastic syndromes (MDS) are characterized by dyserythropoiesis resulting in anemia. This pathological hallmark is incompletely understood. Notch signaling has been linked to impaired erythropoietic and megakaryopoietic development of CD34+ progenitor cells, but its role in MDS is unclear. We have analyzed the transcriptional activity of Notch pathway elements and its association with the key erythroid factor globin transcription factor 1 (GATA1) and the apoptosis regulatory gene B-cell lymphoma-xl (BCLxl) in MDS. The methylation of GATA1 erythroid promoter CpG dinucleotides flanking cis-regulatory elements, including an N-box suppressor binding site for HES1 and a GATA-box binding site, was examined in normal and MDS erythropoiesis. We have generated a kinetic in vitro model of MDS erythropoiesis using CD34+ bone marrow cells from healthy donors (n = 7) and patients with MDS (low risk: RA/n = 6, RARS/n = 3; high risk: RAEB/n = 4, RAEB-T/n = 2). RNA expression of GATA1, BCLxl, DLK1, Notch1, HES1, and HERP2 was measured by real-time RT-PCR (qPCR). DNA methylation at seven CpG dinucleotides of the GATA1 gene promoter was quantitatively analyzed by pyrosequencing of bisulfite-treated genomic DNA at any specific time point. For the Notch pathway elements, no conclusive expression differences were found between MDS and normal erythropoiesis. But we found steadily up-regulated RNA expression of GATA1 and of BCLxl during late normal erythropoietic differentiation. In contrast, during MDS, erythropoiesis a loss of typical up-regulation of GATA1 and BCLxl was observed. Hypermethylation of CpG dinucleotides flanking the repressor HES1 binding site within the 5' region of GATA1 was detected particularly during late MDS erythropoiesis. Interestingly, decremental GATA1 promotor methylation values were seen during normal erythropoiesis matching GATA1 RNA up-regulation. Our data show that the critical erythropoietic transcription factor GATA1 as well as the antiapoptotic molecule BCLxl fails to be normally up-regulated during MDS erythropoiesis. The higher residual 5'-GATA1 methylation values in MDS erythropoiesis but decremental loss thereof in normal erythropoiesis suggest a gene dose effect for GATA1 during erythropoiesis being finely tuned by CpG methylation. Its dysregulation may contribute to the ineffective erythropoiesis observed in MDS.

Y-Chromosomal Insights into Breeding History and Sire Line Genealogies of Arabian Horses.

The Y chromosome is a valuable genetic marker for studying the origin and influence of paternal lineages in populations. In this study, we conducted Y-chromosomal lineage-tracing in Arabian horses. First, we resolved a Y haplotype phylogeny based on the next generation sequencing data of 157 males from several breeds. Y-chromosomal haplotypes specific for Arabian horses were inferred by genotyping a collection of 145 males representing most Arabian sire lines that are active around the globe. These lines formed three discrete haplogroups, and the same haplogroups were detected in Arabian populations native to the Middle East. The Arabian haplotypes were clearly distinct from the ones detected in Akhal Tekes, Turkoman horses, and the progeny of two Thoroughbred foundation sires. However, a haplotype introduced into the English Thoroughbred by the stallion Byerley Turk (1680), was shared among Arabians, Turkomans, and Akhal Tekes, which opens a discussion about the historic connections between Oriental horse types. Furthermore, we genetically traced Arabian sire line breeding in the Western World over the past 200 years. This confirmed a strong selection for relatively few male lineages and uncovered incongruences to written pedigree records. Overall, we demonstrate how fine-scaled Y-analysis contributes to a better understanding of the historical development of horse breeds.

Whole mitochondrial genome sequencing of domestic horses reveals incorporation of extensive wild horse diversity during domestication.

BACKGROUND: DNA target enrichment by micro-array capture combined with high throughput sequencing technologies provides the possibility to obtain large amounts of sequence data (e.g. whole mitochondrial DNA genomes) from multiple individuals at relatively low costs. Previously, whole mitochondrial genome data for domestic horses (Equus caballus) were limited to only a few specimens and only short parts of the mtDNA genome (especially the hypervariable region) were investigated for larger sample sets. RESULTS: In this study we investigated whole mitochondrial genomes of 59 domestic horses from 44 breeds and a single Przewalski horse (Equus przewalski) using a recently described multiplex micro-array capture approach. We found 473 variable positions within the domestic horses, 292 of which are parsimony-informative, providing a well resolved phylogenetic tree. Our divergence time estimate suggests that the mitochondrial genomes of modern horse breeds shared a common ancestor around 93,000 years ago and no later than 38,000 years ago. A Bayesian skyline plot (BSP) reveals a significant population expansion beginning 6,000-8,000 years ago with an ongoing exponential growth until the present, similar to other domestic animal species. Our data further suggest that a large sample of wild horse diversity was incorporated into the domestic population; specifically, at least 46 of the mtDNA lineages observed in domestic horses (73%) already existed before the beginning of domestication about 5,000 years ago. CONCLUSIONS: Our study provides a window into the maternal origins of extant domestic horses and confirms that modern domestic breeds present a wide sample of the mtDNA diversity found in ancestral, now extinct, wild horse populations. The data obtained allow us to detect a population expansion event coinciding with the beginning of domestication and to estimate both the minimum number of female horses incorporated into the domestic gene pool and the time depth of the domestic horse mtDNA gene pool.

Capture Sequencing to Explore and Map Rare Casein Variants in Goats.

Genetic variations in the four casein genes CSN1S1, CSN2, CSN1S2, and CSN3 have obtained substantial attention since they affect the milk protein yield, milk composition, cheese processing properties, and digestibility as well as tolerance in human nutrition. Furthermore, milk protein variants are used for breed characterization, biodiversity, and phylogenetic studies. The current study aimed at the identification of casein protein variants in five domestic goat breeds from Sudan (Nubian, Desert, Nilotic, Taggar, and Saanen) and three wild goat species [Capra aegagrus aegagrus (Bezoar ibex), Capra nubiana (Nubian ibex), and Capra ibex (Alpine ibex)]. High-density capture sequencing of 33 goats identified in total 22 non-synonymous and 13 synonymous single nucleotide polymorphisms (SNPs), of which nine non-synonymous and seven synonymous SNPs are new. In the CSN1S1 gene, the new non-synonymous SNP ss7213522403 segregated in Alpine ibex. In the CSN2 gene, the new non-synonymous SNPs ss7213522526, ss7213522558, and ss7213522487 were found exclusively in Nubian and Alpine ibex. In the CSN1S2 gene, the new non-synonymous SNPs ss7213522477, ss7213522549, and ss7213522575 were found in Nubian ibex only. In the CSN3 gene, the non-synonymous SNPs ss7213522604 and ss7213522610 were found in Alpine ibex. The identified DNA sequence variants led to the detection of nine new casein protein variants. New variants were detected for alpha S1 casein in Saanen goats (CSN1S1 ∗C1), Bezoar ibex (CSN1S1 ∗J), and Alpine ibex (CSN1S1 ∗K), for beta and kappa caseins in Alpine ibex (CSN2 ∗F and CSN3 ∗X), and for alpha S2 casein in all domesticated and wild goats (CSN1S2 ∗H), in Nubian and Desert goats (CSN1S2 ∗I), or in Nubian ibex only (CSN1S2 ∗J and CSN1S2 ∗K). The results show that most novel SNPs and protein variants occur in the critically endangered Nubian ibex. This highlights the importance of the preservation of this endangered breed. Furthermore, we suggest validating and further characterizing the new casein protein variants.

An Agouti-Signaling-Protein Mutation is Strongly Associated with Melanism in European Roe Deer (Capreolus capreolus).

Although the European roe deer (Capreolus capreolus) population of North-West Germany has a remarkable number of melanistic specimens between 10% and 25%, the underlying genetic mutation-causing melanism is still unknown. We used a gene targeting approach focusing on MC1R and ASIP as important genes of coat coloration. Overall, 1384 bp of MC1R and 2039 bp of ASIP were sequenced in 24 specimens and several SNPs were detected. But only the ASIP-SNP c.33G>T completely segregated both phenotypes leading to the amino acid substitution p.Leu11Phe. The SNP was further evaluated in additional 471 samples. Generally, all black specimens (n = 33) were homozygous TT, whereas chestnut individuals were either homozygote GG (n = 436) or heterozygote GT (n = 26). Considering the fact that all melanistic animals shared two mutated alleles of the strongly associated SNP, we concluded that melanism is inherited in a recessive mode in European roe deer.