This dataset contains Fastq files of sequencing data used in the study "Microbiota differences induced by divergent selection for birth weight environmental variability in mice". The data includes the 16S rRNA sequencing reads generated from the fecal microbiota of pregnant mice. Metadata associated with each sample are also provided. The data were analyzed to characterize the digestive microbial differentiation that may have been caused by the selection breeding process between two divergent mouse lines for environmental birth weight variance (https://www.ucm.es/otri/complutransfer-lineas-de-raton-de-laboratorio-divergentes-para-homogeneidad-y-robustez).

This dataset contains Fastq files of sequencing data used in the study "Microbiota differences induced by divergent selection for birth weight environmental variability in mice". The data includes the 16S rRNA sequencing reads generated from the fecal microbiota of pregnant mice. Metadata associated with each sample are also provided. The data were analyzed to characterize the digestive microbial differentiation that may have been caused by the selection breeding process between two divergent mouse lines for environmental birth weight variance (https://www.ucm.es/otri/complutransfer-lineas-de-raton-de-laboratorio-divergentes-para-homogeneidad-y-robustez).

This dataset contains Fastq files of sequencing data used in the study "Microbiota differences induced by divergent selection for birth weight environmental variability in mice". The data includes the 16S rRNA sequencing reads generated from the fecal microbiota of pregnant mice. Metadata associated with each sample are also provided. The data were analyzed to characterize the digestive microbial differentiation that may have been caused by the selection breeding process between two divergent mouse lines for environmental birth weight variance (https://www.ucm.es/otri/complutransfer-lineas-de-raton-de-laboratorio-divergentes-para-homogeneidad-y-robustez).

In this study, the availability of the Ovine HD SNP BeadChip (HD-chip) and the development of an imputation strategy provided an opportunity to further investigate the extent of linkage disequilibrium (LD) at short distances in the genome of the Spanish Churra dairy sheep breed. A population of 1686 animals, including 16 rams and their half-sib daughters, previously genotyped for the 50K-chip, was imputed to the HD-chip density based on a reference population of 335 individuals. After assessing the imputation accuracy for beagle v4.0 (0.922) and fimpute v2.2 (0.921) using a cross-validation approach, the imputed HD-chip genotypes obtained with beagle were used to update the estimates of LD and effective population size for the studied population. The imputed genotypes were also used to assess the degree of homozygosity by calculating runs of homozygosity and to obtain genomic-based inbreeding coefficients. The updated LD estimations provided evidence that the extent of LD in Churra sheep is even shorter than that reported based on the 50K-chip and is one of the shortest extents compared with other sheep breeds. Through different comparisons we have also assessed the impact of imputation on LD and effective population size estimates. The inbreeding coefficient, considering the total length of the run of homozygosity, showed an average estimate (0.0404) lower than the critical level. Overall, the improved accuracy of the updated LD estimates suggests that the HD-chip, combined with an imputation strategy, offers a powerful tool that will increase the opportunities to identify genuine marker-phenotype associations and to successfully implement genomic selection in Churra sheep.

In this study, we demonstrate the use of a genome-wide association mapping together with RNA-seq in a reduced number of samples, as an efficient approach to detect the causal mutation for a Mendelian disease. Junctional epidermolysis bullosa is a recessive genodermatosis that manifests with neonatal mechanical fragility of the skin, blistering confined to the lamina lucida of the basement membrane and severe alteration of the hemidesmosomal junctions. In Spanish Churra sheep, junctional epidermolysis bullosa (JEB) has been detected in two commercial flocks. The JEB locus was mapped to Ovis aries chromosome 11 by GWAS and subsequently fine-mapped to an 868-kb homozygous segment using the identical-by-descent method. The ITGB4, which is located within this region, was identified as the best positional and functional candidate gene. The RNA-seq variant analysis enabled us to discover a 4-bp deletion within exon 33 of the ITGB4 gene (c.4412_4415del). The c.4412_4415del mutation causes a frameshift resulting in a premature stop codon at position 1472 of the integrin β4 protein. A functional analysis of this deletion revealed decreased levels of mRNA in JEB skin samples and the absence of integrin β4 labeling in immunohistochemical assays. Genotyping of c.4412_4415del showed perfect concordance with the recessive mode of the disease phenotype. Selection against this causal mutation will now be used to solve the problem of JEB in flocks of Churra sheep. Furthermore, the identification of the ITGB4 mutation means that affected sheep can be used as a large mammal animal model for the human form of epidermolysis bullosa with aplasia cutis. Our approach evidences that RNA-seq offers cost-effective alternative to identify variants in the species in which high resolution exome-sequencing is not straightforward.