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Additional file 4. Alignment of the repetitive elements at the beginning and end of the 6-kb candidate segment. Pairwise alignment of the reference sequences (BosTaurus8) of LINE BovB at the beginning of the 6-kb candidate segment and LINE BovB at the end of the segment. This file shows the huge level of similarity between the start and end of the candidate segment as is also obvious in Fig. 2d.

The domestication of wild Aurochs (Bos primigenius) is among the greatest achievements of mankind that had immense impact on the development of human society. Our understanding of the transformation from Aurochs to modern breeds is still not resolved as neither of the two hypotheses, single v. multiple origin domestication, have not been decisively rejected. To improve our understanding of cattle domestication we have sequenced the complete mitogenome of 196 individuals using NGS. Our sample encompassed 50 ‘new’ breeds and covered a large number of Central and South East European cattle breeds thus fulfilling the missing gap on the route from the Fertile Crescent to the Western Europe. We have performed the comprehensive complete mitogenome phylogenetic analyses, comprising 498 bovine samples (300 from the GenBank) from more than 100 cattle breeds. With the exception of very rare haplogroups (C, E, R, I and T7), mitogenomes sequenced here were classified within all known haplogroups (T1’2’3, T1, ..., T5 and T6), including even haplotypes assigned to the haplogroup P and Q. Up to now, haplogroup P was found only in the ancient West European Aurochs samples and the one sample from the modern Korean cattle. The existence of the haplogroup P (‘Aurochs’) was confirmed on the original sample and its four female relatives, sampled additionally. This is a direct evidence of the continuity and presence of Aurochs genes in modern breeds that further increases the possibility of multiple origin of cattle domestication, while we were not able to exclude post-domestication admixture. The haplogroup Q, here found in three individuals with two unique haplotypes, has diverged from the ‘macro-haplogroup T’ more than 35 thousand years ago and also indicates the presence of Aurochs genes in modern breeds. We have observed a large, newly arisen, divergence within ‘macro-haplogroup T’, with the new, rather deeply, rooted branches (non-classified haplogrups) prompting for the urgent reclassification of the cattle mitogenomic systematics.

Additional file 1: Fig. S1. Pedigree of the albino calves. As the red highlighted paths show, both albinos and all carriers of the SNPs g.39829806G>A and g.39864148C>T can be traced back to a single natural service sire (B1). Symbols are as follows: squares = males, circles = females, filled symbols = albinos (homozygous for both SNPs), symbols with dot inside = heterozygous individuals, symbols with question mark inside = genotype unknown, crossed out symbols = no material available. For bull S2, 50K genotype data was available from previous studies; however, no material for targeted genotyping was available.

Background Bovine progressive degenerative myeloencephalopathy (Weaver syndrome) is a neurodegenerative disorder in Brown Swiss cattle that is characterized by progressive hind leg weakness and ataxia, while sensorium and spinal reflexes remain unaffected. Although the causal mutation has not been identified yet, an indirect genetic test based on six microsatellite markers and consequent exclusion of Weaver carriers from breeding have led to the complete absence of new cases for over two decades. Evaluation of disease status by imputation of 41 diagnostic single nucleotide polymorphisms (SNPs) and a common haplotype published in 2013 identified several suspected carriers in the current breeding population, which suggests a higher frequency of the Weaver allele than anticipated. In order to prevent the reemergence of the disease, this study aimed at mapping the gene that underlies Weaver syndrome and thus at providing the basis for direct genetic testing and monitoring of today’s Braunvieh/Brown Swiss herds. Results Combined linkage/linkage disequilibrium mapping on Bos taurus chromosome (BTA) 4 based on Illumina Bovine SNP50 genotypes of 43 Weaver-affected, 31 Weaver carrier and 86 Weaver-free animals resulted in a maximum likelihood ratio test statistic value at position 49,812,384 bp. The confidence interval (0.853 Mb) determined by the 2-LOD drop-off method was contained within a 1.72-Mb segment of extended homozygosity. Exploitation of whole-genome sequence data from two official Weaver carriers and 1145 other bulls that were sequenced in Run4 of the 1000 bull genomes project showed that only a non-synonymous SNP (rs800397662) within the PNPLA8 gene at position 49,878,773 bp was concordant with the Weaver carrier status. Targeted SNP genotyping confirmed this SNP as a candidate causal mutation for Weaver syndrome. Genotyping for the candidate causal mutation in a random sample of 2334 current Braunvieh animals suggested a frequency of the Weaver allele of 0.26 %. Conclusions Through combined use of exhaustive sequencing data and SNP genotyping results, we were able to provide evidence that supports the non-synonymous mutation at position 49,878,773 bp as the most likely causal mutation for Weaver syndrome. Further studies are needed to uncover the exact mechanisms that underlie this syndrome., Genetics Selection Evolution, 48, ISSN:0999-193X, ISSN:1297-9686

Additional file 2: Figure S2. Identification of a common haplotype on BTA4. Description: Genotypes of a subset of 32 Weaver carriers and 13 Weaver-affected offspring were scanned for regions of homozygosity surrounding the main and secondary peaks. The segment of interest consisted of 197 SNPs between positions 44,387,787 and 47,598,264Â bp. Carets (^) indicate the position of the secondary peak (47,598,264Â bp), asterisks (*) indicate the position of the main peak (49,812,384Â bp). Red bars indicate shared haplotype segments, green bars indicate the common haplotype shared by both Weaver-affected and carrier animals.

Additional file 1: Table S1. Primers used for Sanger sequencing and genotyping the insertion in the 3’-UTR of RXFP2.

The inheritance mode of the horns status in sheep is more complicated than it may appear at first glance. It is influenced by sex, but also differs between breeds. Previous studies postulated that a 1.8-kb insertion within the 3‘-UTR of the relaxin/insulin-like family peptide receptor 2 gene (RXFP2) on sheep chromosome 10 is causing polledness in sheep. We re-sequenced a region of about 250, 000 bp covering the RFXP2 gene locus and the flanking upstream region in a total of 24 sheep from 6 completely horned and 6 completely polled breeds. We identified the same indel polymorphism published before segregating perfectly with horns status in these breeds. After establishment of a multiplex PCR for efficient genotyping, we tested for the indel polymorphism in a total of 435 sheep with breed-specific or individually known horns status from 1) 17 completely polled breeds (208 sheep), 2) 8 completely horned breeds (84 sheep), 3) single or multiple crossings of completely polled with completely horned breeds (18 sheep), and 4) 9 breeds with sex-limited and/or variable horns status (125 sheep). The RXFP23’-UTR indel polymorphism segregated perfectly in completely polled and completely horned breeds. A sex-dependent horns status of sheep heterozygous for the indel polymorphism was observed for completely polled breeds and for their crossings with completely horned breeds: Male sheep carrying the genotype del/ins were horned, whereas female sheep with this genotype were polled. However, one heterozygous multiple crossed ewe with horn rudiments disputes complete association. Unexpectedly, this segregation pattern was not or at least not completely reproducible in breeds with sex-limited and/or variable horns status. For the breeds Alpine Steinschaf and Bavarian Forest, it can be summarized that the occurrence of the del/ins genotype on the one hand, and a scurs/small horns phenotype on the other hand showed no regular pattern. Moreover, our samples originating from even more southern European regions (Bovec sheep, Cres sheep, Travnička Pramenka and Walachenschaf) as well as from Africa (Dorper and Kamerun sheep) clearly disclaim causal relationship or segregation of the RXFP23’-UTR indel polymorphism with horns status. In this group of sheep, we observed almost all combinations of indel genotypes, sex and phenotypes of horns status. Therefore we conclude that the 3’-UTR RXFP2 indel polymorphism is not a useful marker for horns status in sheep breeds with sex-limited and/or variable horns status.

Background: The absence of horns, called polled phenotype, is the favored trait in modern cattle husbandry. To date, polled cattle are obtained primarily by dehorning calves. Dehorning is a practice that raises animal welfare issues, which can be addressed by selecting for genetically hornless cattle. In the past 20 years, there have been many studies worldwide to identify unique genetic markers in complete association with the polled trait in cattle and recently, two different alleles at the POLLED locus, both resulting in the absence of horns, were reported: (1) the Celtic allele, which is responsible for the polled phenotype in most breeds and for which a single candidate mutation was detected and (2) the Friesian allele, which is responsible for the polled phenotype predominantly in the Holstein-Friesian breed and in a few other breeds, but for which five candidate mutations were identified in a 260-kb haplotype. Further studies based on genome-wide sequencing and high-density SNP (single nucleotide polymorphism) genotyping confirmed the existence of the Celtic and Friesian variants and narrowed down the causal Friesian haplotype to an interval of 145 kb. [br/]Results: Almost 6000 animals were genetically tested for the polled trait and we detected a recombinant animal which enabled us to reduce the Friesian POLLED haplotype to a single causal mutation, namely a 80 kb duplication. Moreover, our results clearly disagree with the recently reported perfect co-segregation of the POLLED mutation and a SNP at position 1 390 292 bp on bovine chromosome 1 in the Holstein-Friesian population. [br/]Conclusion: We conclude that the 80-kb duplication, as the only remaining variant within the shortened Friesian haplotype, represents the most likely causal mutation for the polled phenotype of Friesian origin.

[Background] Since the pig is one of the most important livestock animals worldwide, mapping loci that are associated with economically important traits and/or traits that influence animal welfare is extremely relevant for efficient future pig breeding. Therefore, the purpose of this study was a genome-wide mapping of quantitative trait loci (QTL) associated with nine body composition and bone mineral traits: absolute (Fat, Lean) and percentage (FatPC, LeanPC) fat and lean mass, live weight (Weight), soft tissue X-ray attenuation coefficient (R), absolute (BMC) and percentage (BMCPC) bone mineral content and bone mineral density (BMD)., [Methods] Data on the nine traits investigated were obtained by Dual-energy X-ray absorptiometry for 551 pigs that were between 160 and 200 days old. In addition, all pigs were genotyped using Illumina’s PorcineSNP60 Genotyping BeadChip. Based on these data, a genome-wide combined linkage and linkage disequilibrium analysis was conducted. Thus, we used 44 611 sliding windows that each consisted of 20 adjacent single nucleotide polymorphisms (SNPs). For the middle of each sliding window a variance component analysis was carried out using ASReml. The underlying mixed linear model included random QTL and polygenic effects, with fixed effects of sex, housing, season and age., [Results] Using a Bonferroni-corrected genome-wide significance threshold of P, [Conclusions] Our QTL mapping approach identified 72 QTL, some of which confirmed results of previous studies in pigs. However, we also detected significant associations that have not been published before and were able to identify a number of new and promising candidate genes, such as ZNF608.

Background The mode of inheritance of horn status in sheep is far more complex than a superficial analysis might suggest. Observations, which were mostly based on crossbreeding experiments, indicated that the allele that results in horns is dominant in males and recessive in females, and some authors even speculated about the involvement of more than two alleles. However, all recent genome-wide association analyses point towards a very strong effect of a single autosomal locus on ovine chromosome 10, which was narrowed down to a putatively causal insertion polymorphism in the 3′-untranslated region of the relaxin/insulin-like family peptide receptor 2 gene (RXFP2). The main objective of this study was to test this insertion polymorphism as the causal mutation in diverse sheep breeds, including breeds with a variable and/or sex-dependent horn status. Results After re-sequencing a region of about 246 kb that covered the RFXP2 gene and its flanking regions for 24 sheep from six completely horned and six completely polled breeds, we identified the same insertion polymorphism that was previously published as segregating with horn status in these breeds. Multiplex PCR genotyping of 489 sheep from 34 breeds and some crosses between sheep breeds showed a nearly perfect segregation of the insertion polymorphism with horn status in sheep breeds of Central and Western European origin. In these breeds and their crossings, heterozygous males were horned and heterozygous females were polled. However, this segregation pattern was not, or at least not completely, reproducible in breeds with sex-dependent and/or variable horn status, especially in sheep that originated from even more southern European regions and from Africa. In such breeds, we observed almost all possible combinations of genotype, sex and horn status phenotype. Conclusions The 1.78-kb insertion polymorphism in the 3′-untranslated region of RXFP2 and SNPs in the 3′-UTR, exon 14 and intron 11 of this gene that we analyzed in this study cannot be considered as the only cause of polledness in sheep and are not useful as a universal marker to define the genetic horn status in sheep. Electronic supplementary material The online version of this article (doi:10.1186/s12711-016-0256-3) contains supplementary material, which is available to authorized users.