MOESM1 of A missense variant in the coil1A domain of the keratin 25 gene is associated with the dominant curly hair coat trait (Crd) in horse

Additional file 1: Table S1. List of animals included in the study. This table provides detailed information about identification, pedigree, phenotypes and genotypes of animals included in the study. The full pedigree is also provided. Table S2a. Details on markers and haplotypes in the mapped region. This table provides markers and their position, including the KRT25 variant along ECA11. Colors are used to depict haplotypes, assuming 18 founder haplotypes (12 “non-curly” haplotypes carried by crossbreed animals as well as the six most frequent other haplotypes, including one “curly” haplotype). Haplotypes are given for each animal, according to pedigree data. Table S2b. Delineation of the critical mapping region by haplotype analysis. Haplotypes were sorted out according to their sequence and the associated coat phenotype. Critical recombination events are easily detected by color changes and help identify the upper and lower bounds of the mapping interval. Table S3. PCR primers used to genotype candidate genes. This table provides detailed information about chromosome positions, alleles, gene names, ID, primer sequences, fragment lengths and Tm. Table S4. Statistics on genome-wide detection of functional variants. Table S4 provides statistics on variant detection based on NGS sequencing, with numbers of new and known variants (whole genome and genes) according to their consequence as predicted by VEP. Positional candidate variants are also reported. Table S5. List of gene variants predicted to impact protein functionality. Table S5 includes chromosome positions, alleles, gene ID and functional annotations. The last column (Existing variation) indicates variants; which were already known in dbSNP. Table S6. Concordant variants identified in the critical mapping interval. Table S6 includes chromosome positions, alleles, functional annotations and gene ID for concordant variants. Table S7. Horses genotyped by PCR and Sanger sequencing. Horse names, phenotype and genotype for the KRT24:g.21932167G>T, Top2A:g.22186465C>T and Top2A: g.22191762G>T variants are presented. Table S8. Pedigree information for the progeny of Walker’s Prince T and Dravkvallons Ite O Maguzu. Table S8 provides pedigree and phenotype data obtained from breeders and the Curly horse pedigree database ( http://www.curlyhorses.info/mainsearch.asp ). Table S9. Comparison of NCBI and Ensembl annotations within the keratin cluster on ECA11. Annotation features are listed along ECA11, from position 2,136,900 to 2,197,100 pb; some discrepancy is observed upstream of the critical mapping interval

Mapping of the rex coat trait in the rabbit families.

<p>A whole genome scan performed on 187 rabbits for 47 microsatellites localized the rex phenotype (INRAR) on rabbit chromosome 14 within an interval of 40 cM. Fine mapping refined the localization within a 0.5 cM (⊖ = 0 ; LOD = 78) region flanked by microsatellites INRA051and INRA086.</p

The rex hair trait in rabbit.

<p>(A) A normal rabbit coat (A1), a rex rabbit with a castor coat (A2) and an <i>orylag</i>® with a castor coat (A3). (B) Cross section of a fibre bundle of a normal rabbit coat (B1), a rex rabbit (B2) and an <i>orylag</i>® (B3). (C) Skin cross section of a hair follicle group of a normal rabbit coat (C1), a rex rabbit (C2) and an <i>orylag</i>® (C3). Arrows indicate the differences in shape and diameters of primary central hair follicles and their hair.</p

The 1362delA mutation in exon 9 of LIPH in rex rabbits.

<p>(A) Electropherograms of the LIPH exon 9 sequence from a normal common type rabbit (WT), a rex and a heterozygous are shown. The red line indicates the location of the mutation. In heterozygous rabbits there is an overlap of both allele sequences (purple box). (B) Deduced alignment of LIPH proteins between rex and normal common type rabbits. (C) C-terminal conservation in mammalians.</p

Primers used for RT–PCR.

<p>Primers used for RT–PCR.</p

Mean length (± standard deviation) of outer coat, inner coat, fibre diameter and coarse fibre content (defined as the content of fibres having a fibre diameter larger than 30 µm) in rex and normal G2 rabbit coats.

<p>Mean length (± standard deviation) of outer coat, inner coat, fibre diameter and coarse fibre content (defined as the content of fibres having a fibre diameter larger than 30 µm) in rex and normal G2 rabbit coats.</p

LIPH expression in rabbit skin.

<p>LIPH was detected by RT-PCR (ex 7–10) in rabbit skin of 5 common and 5 rex rabbits. The expected product size is 753 pb.</p

Primers used for genomic amplification.

<p>Primers used for genomic amplification.</p

Lipase activity of wild-type <i>LIPH</i> and 1362delA <i>LIPH</i> mutant constructs.

<p>Values obtained are shown as a percentage of that observed in cells transfected with the empty vector (pcDNA3.1+, control).</p

<i>LIPH</i> expression at three different fetal stages (days 19, 25 and 29) corresponding respectively to the formation of the central primary, lateral primary and secondary hair follicles.

<p>(Bars = 20 µm). (A) Q-PCR expression of <i>LIPH</i> mRNA in the <i>orylag®</i> rabbit skin (light blue bars) and in the normal rabbit skin (dark blue bars). The Y axis represents the relative expression level of <i>LIPH</i>. (B) Histology (ROAN staining) of <i>orylag®</i> (B1) and normal rabbit skins (B2). (C) Immunohistochemistry of <i>orylag®</i> (C1) and normal rabbit skins (C2).</p