Chronic pastern dermatitis (CPD), also known as chronic progressive lymphedema (CPL), is a skin disease that affects draft horses. This disease causes painful lower-leg swelling, nodule formation, and skin ulceration, interfering with movement. The aim of this whole-genome scan was to identify quantitative trait loci (QTL) for CPD in German draft horses. We recorded clinical data for CPD in 917 German draft horses and collected blood samples from these horses. Of these 917 horses, 31 paternal half-sib families comprising 378 horses from the breeds Rhenish German, Schleswig, Saxon-Thuringian, and South German were chosen for genotyping. Each half-sib family was constituted by only one draft horse breed. Genotyping was done for 318 polymorphic microsatellites evenly distributed on all equine autosomes and the X chromosome with a mean distance of 7.5 Mb. An across-breed multipoint linkage analysis revealed chromosome-wide significant QTL on horse chromosomes (ECA) 1, 9, 16, and 17. Analyses by breed confirmed the QTL on ECA1 in South German and the QTL on ECA9, 16, and 17 in Saxon-Thuringian draft horses. For the Rhenish German and Schleswig draft horses, additional QTL on ECA4 and 10 and for the South German draft horses an additional QTL on ECA7 were found. This is the first whole-genome scan for CPD in draft horses and it is an important step toward the identification of candidate genes.

Source/description: We identified a total of 21 781 equine microsatellites on the second horse genome assembly Equ-Cab2.0 (Table S1), which can be accessed at http://www. tiho-hannover.de/einricht/zucht/index.htm. These microsatellites cover the horse genome with a mean distance of 112 kb and a median distance of 75 kb (Table S2). Most of the repeat motifs (72%) were dinucleotide repeats of AC, GT and AT with frequencies of 26.4%, 26.0% and 19.4%. Trinucleotide repeats represented 3.8%, tetranucleotide repeats 17.6% and pentanucleotide repeats 1.6% of all simple sequence repeats (SSR). We identified adjacent SINE and LINE elements and the corresponding gene ID for 5549 (25.5%) intragenic microsatellites. Primer pairs were designed for 12 246 microsatellites after masking repetitive elements.Identification of microsatellites and their assignment on the horse genome: Permutation sequences including all repeat motifs of two to five bases with at least 15 and up to 30 repeats were generated for the search of EquCab2.0. We then employed a stand-alone BLAST with the Blastn mode (ftp://ftp.ncbi.nih.gov/ blast/executable/) with maximum e-values of e )6 to e )10 for alignment of the permutated SSRs with di-, tri-, tetra-or pentanucleotide sequences. The maximum number of repeat motifs was set at 30 for two to four bases and at 15 for five bases.PCR-primers: Primer pairs were designed using PRIMER3 (version 0.4.0,

The availability of a high-quality draft sequence of the horse makes known the physical location of microsatellites. The aim of the present study was to establish a highly polymorphic minimal screening set of microsatellite markers for horses (MSSH) annotated on the horse genome assembly EquCab2.0. We have used the previously reported linkage and radiation hybrid maps and have extended these marker sets by filling in gaps as noted from annotation on the horse sequence. This MSSH covers all autosomes and the X chromosome with 322 evenly spaced microsatellites whose positions were determined on the horse genome assembly (EquCab2.0). The average chromosomal distance among markers amounts to 7.44 Mb. The characteristics established for this microsatellite set were the number of alleles, the observed heterozygosity (HET), and the polymorphism information content (PIC) for Hanoverian warmblood (HW) and several German coldblood horse breeds (CB). The average number of alleles was 7.3 and 8.0 in HW and CB, respectively. HET was at 71% for HW and CB, PIC at 65% (HW) and 67% (CB). This MSSH allows scanning of the whole horse genome at close to 7-to 10-Mb resolution.

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