Comparing the diversity of the casein genes in the Asian mouflon and domestic sheep- West Asia WGS SNP

Dataset of SNPs identified in the whole genome sequences of 12 domestic sheep individuals originary from West Asia. Sequences were retrieved from NCBI database

Comparing the diversity of the casein genes in the Asian mouflon and domestic sheep - Casein SNPs

A total of 774 SNPs identified mapping to the casein cluster of 40 domestic sheep (Ovis aries) and 17 mouflon (Ovis orientalis

Comparing the diversity of the casein genes in the Asian mouflon and domestic sheep- Mouflon Tehran WGS SNP

Dataset of SNPs identified in the whole genome sequences of 7 mouflon orientalis individuals originary from West Asia. Sequences were retrieved from NCBI database

Comparing the diversity of the casein genes in the Asian mouflon and domestic sheep- South-East Asia WGS SNP

Dataset of SNPs identified in the whole genome sequences of 8 domestic sheep individuals originary from South East Asia. Sequences were retrieved from NCBI database

Comparing the diversity of the casein genes in the Asian mouflon and domestic sheep- Mouflon Tabriz WGS SNP

Dataset of SNPs identified in the whole genome sequences of 17 mouflon orientalis individuals originary from West Asia. Sequences were retrieved from NCBI database

Comparing the diversity of the casein genes in the Asian mouflon and domestic sheep- Europe WGS SNP

Dataset of SNPs identified in the whole genome sequences of 12 domestic sheep individuals originary from West Asia. Sequences were retrieved from NCBI database

Comparing the diversity of the casein genes in the Asian mouflon and domestic sheep- Africa WGS SNP

Dataset of SNPs identified in the whole genome sequences of 10 domestic sheep individuals originary from the north of Africa. Sequences were retrieved from NCBI database

An association analysis between a polymorphism in the <i>SEC24A</i> gene and lipid traits recorded in Duroc pigs

By regulating the expression of low-density lipoprotein receptors (LDLR), the SEC24A protein modulates the clearance of plasma cholesterol in mice. The whole-genome sequencing of five Duroc boars that sired a Duroc purebred experimental population (LIPGEN population, 350 individuals) revealed the segregation of one putative nonsense mutation located at the SEC24A (rs336401826, c.44G>A) gene. Genotyping of this polymorphic site in the LIPGEN population highlighted the existence of a significant departure from the Hardy Weinberg equilibrium (χ2 = 5.05, p-value = 0.024527). Despite the fact that SEC24A inactivation should affect serum lipid concentrations, we did not observe an association between SEC24A genotype and such traits. A thorough revision of the annotation of the SEC24A rs336401826 SNP revealed that this polymorphism is probably located in the 5’UTR of the SEC24A gene, rather than at the beginning of the first exon, hence not introducing the predicted premature stop codon that could truncate the SEC24A protein. Given that the annotation of loss-of-function mutations in pigs is far from perfect, careful manual curation of such mutations is recommended before undertaking the analysis of their effects at the experimental level.HIGHLIGHTSOne mutation (c.44 G>A) predicted to disrupt the SEC24A protein segregates in a Duroc pig population.This polymorphism is not associated with serum lipid levels despite its expected effect on such traits.Manual curation of the annotation of this putative nonsense polymorphism has revealed that it maps to the 5’UTR of the SEC24A gene. One mutation (c.44 G>A) predicted to disrupt the SEC24A protein segregates in a Duroc pig population. This polymorphism is not associated with serum lipid levels despite its expected effect on such traits. Manual curation of the annotation of this putative nonsense polymorphism has revealed that it maps to the 5’UTR of the SEC24A gene.</p

Additional file 7: Figure S1. of Differential expression of mRNA isoforms in the skeletal muscle of pigs with distinct growth and fatness profiles

Validation by RT-qPCR of the differential expression of mRNA isoforms corresponding to the RXRG, SCD, MAFF and ITGA5 genes in HIGH vs LOW pigs. (PPT 132 kb

Porcine genomic regions with eQTL regulating more than four genes (eQTL hotspots).

<p>Porcine genomic regions with eQTL regulating more than four genes (eQTL hotspots).</p