Species fraud and product mislabelling in processed food, albeit not being a direct health issue, often results in consumer distrust. Therefore methods for quantification of undeclared species are needed. Targeting mitochondrial DNA, e.g. CYTB gene, for species quantification is unsuitable, due to a fivefold inter-tissue variation in mtDNA content per cell resulting in either an under- (-70%) or overestimation (+160%) of species DNA contents. Here, we describe a reliable two-step droplet digital PCR (ddPCR) assay targeting the nuclear F2 gene for precise quantification of cattle, horse, and pig in processed meat products. The ddPCR assay is advantageous over qPCR showing a limit of quantification (LOQ) and detection (LOD) in different meat products of 0.01% and 0.001%, respectively. The specificity was verified in 14 different species. Hence, determining F2 in food by ddPCR can be recommended for quality assurance and control in production systems.

White Galloway cattle exhibit three different white coat colour phenotypes, that is, well marked, strongly marked and mismarked. However, mating of individuals with the preferred well or strongly marked phenotype also results in offspring with the undesired mismarked and/or even fully black coat colour. To elucidate the genetic background of the coat colour variations in White Galloway cattle, we analysed four coat colour relevant genes: mast/stem cell growth factor receptor (KIT), KIT ligand (KITLG), melanocortin 1 receptor (MC1R) and tyrosinase (TYR). Here, we show that the coat colour variations in White Galloway cattle and White Park cattle are caused by a KIT gene (chromosome 6) duplication and aberrant insertion on chromosome 29 (Cs29 ) as recently described for colour-sided Belgian Blue. Homozygous (Cs29 /Cs29 ) White Galloway cattle and White Park cattle exhibit the mismarked phenotype, whereas heterozygous (Cs29 /wt29 ) individuals are either well or strongly marked. In contrast, fully black individuals are characterised by the wild-type chromosome 29. As known for other cattle breeds, mutations in the MC1R gene determine the red colouring. Our data suggest that the white coat colour variations in White Galloway cattle and White Park cattle are caused by a dose-dependent effect based on the ploidy of aberrant insertions and inheritance of the KIT gene on chromosome 29.

BackgroundIn Nile tilapia sex determination is governed by a male heterogametic system XX/XY either on LG1 or LG23. The latter carries a Y-specific duplicate of the amh gene, which is a testis-determining factor. Allelic variants in the amh gene demonstrated to be major triggers for autosomal and temperature-dependent sex reversal. Further, QTL on LG23 and LG20 show a temperature-responsiveness with influence on the phenotypic sex relative to the sex chromosomes. Here we present a ddRADseq based approach to identify genomic regions that show unusual large differentiation in terms of fixation index (FST) between temperature-treated pseudomales and non-masculinized females using a comparative genome-scan. Genome-wide associations were identified for the temperature-dependent sex using a genetically all-female population devoid of amh-ΔY.ResultsTwenty-two thousand three hundred ninety-two SNPs were interrogated for the comparison of temperature-treated pseudomales and females, which revealed the largest differentiation on LG23. Outlier FST-values (0.35–0.44) were determined for six SNPs in the genomic interval (9,190,077–11,065,693) harbouring the amh gene (9,602,693–9,605,808), exceeding the genome-wide low FST of 0.013. Association analysis with a set of 9104 selected SNPs confirmed that the same genomic region on LG23 exerts a significant effect on the temperature-dependent sex.ConclusionsThis study highlights the role of LG23 in sex determination, harbouring major determinants for temperature-dependent sex reversal in Nile tilapia. Furthermore FST outlier detection proves a powerful tool for detection of sex-determining regions in fish genomes.Electronic supplementary materialThe online version of this article (doi:10.1186/s12864-017-3930-0) contains supplementary material, which is available to authorized users.

Feet and leg problems have a major effect on the well-being and lifespan of the dairy cow and thus are economically important to the dairy farmer. Apart from approaches using genetic selection for classical traits from conformation scoring, attempts for genetic improvement can be based either on records of individual disease cases or on records of disorder status at time of hoof trimming. In this study, 1,962 first-lactation cows were subjected to hoof trimming with an assessment of disorder status for sole hemorrhage as a binary trait. Cows were from 7 large commercial herds in Mecklenburg-Western Pomerania (northeastern Germany) that had similar housing with cubicles, slatted flooring, little use of straw for bedding, and total mixed ration feeding. Cows were trimmed and assessed once, focusing on cows in the first half of the lactation. Herds were visited at intervals to enable recording of cohorts at a similar stage of lactation. Each cohort or herd-visit included between 31 and 165 cows. Additional measurements included body weight, back fat thickness, and body condition at time of trimming. Further data on dairy production, conformation scores, and reproductive performance were merged after collection of records had finished. The DNA extracted from blood of 1,183 cows was used for analysis with a custom-made array of 384 single nucleotide polymorphisms (SNP). The SNP were selected according to results from the literature for effects in classical conformation traits, from biochemical pathway analysis, and from comparative analysis of putative candidate genes in cattle, pigs, and sheep. Selection of cohorts of cows for SNP chip analysis was such that cohorts with extreme frequencies of disorders and cohorts with slightly deviating housing systems were excluded in this first step. The results from a mixed threshold model analysis with genotype included as a fixed effect and accounting for relationships among animals revealed that the intronic SNP rs29017173 (A/G) within the IQ motif-containing GTPase-activating protein 1 (IQGAP1, Bos taurus autosome 21) was significantly associated with disorder status. Back-transformed means of disorder status for the 3 genotypes were 0.37 (AA), 0.52 (AG), and 0.56 (GG). Using the full data set of 1,962 cows, including the less-suitable cohorts, gave back-transformed means of 0.51 (AA), 0.58 (AG), and 0.62 (GG). As SNP rs29017173 is included on the Illumina BovineSNP50 DNA Analysis BeadChip (Illumina Inc., San Diego, CA), a sample of 2,394 artificial insemination sires from the German calibration sample for genomic selection from birth years 1998 to 2003 was studied for possible correlated effects. The A/G polymorphism of SNP rs29017173 studied here was also associated with substantial effects for feet and leg traits from the classical conformation score system. Selection using this polymorphism will be facilitated by the fact that the same allele is favored for all traits with substantial effects.

Brenig (2014):A study based on records taken at time of hoof trimming reveals a strong association between the IQ motif-containing GTPase-activiating protein 1 (IQGAP1) gene and sole hemorrhage in Holstein cattle.