Schematic of the IAR–associated region in ECA13p.

<p>(A) A G-banded ideogram of ECA13 (ISCNH, 1997) showing the cytogenetic location of the IAR associated region; (B) Statistical significance values for 721 ECA13 SNPs analyzed for genome wide association using chi-square; yellow shade highlights the IAR-associated ∼3.9 Mb region; (C) Sequence map of chr13:8,000,000–11,900,000 showing all ENSMBL annotated genes in the region; <i>TRIM56</i> and <i>FKBP6</i> are highlighted. (D) A graph showing chi-square test −log₁₀(<i>P</i>) values for 10 significant SNPs: 1–8027172, 2–8382955, 3–8977804, 4–8987922, 5–9034435, 6–9034502, 7–9183989, 8–10894213, 9–11043916 (black circles), and 10–11044175 (red circle); the seven SNPs above the grey line showed moderate significance also in mixed model; (E) Confidence interval LD blocks; (F) Solid spine LD blocks; blocks with significant permuted <i>P</i>-values (<i>P</i><0.0005) for association with IAR are highlighted yellow; red diamonds represent D′ values equal to 1, lower values of D′ are presented in blue and white; the ∼306 kb highly associated haplotype in both LD analyses is in a red box.</p

Distribution and expression of mapped RNA sequence tags in the horse genome.

<p><b>Mb</b>–megabase-pair; <b>AC</b>–average coverage; <b>Mt</b>–mitochondrial genome; map information for horse chromosomes was retrieved from Ensemb (<a href="http://www.ensembl.org/index" target="_blank">http://www.ensembl.org/index</a>. html); * includes known and novel protein coding, miRNA, rRNA, snRNA, snoRNA and Misc RNA genes.</p

Summary statistics for mapped RNA sequence tags

<p>: (<b>a</b>) Comparison of mapped tags (AC≥1) between the two sperm samples; (<b>b</b>) Proportions of tags with very high (AC≥100), high (10</p

Monoallelic expression of equine <i>FKBP6</i>.

<p>gDNA and cDNA sequences from testis and sperm of two heterozygous control stallions.</p

ECAY transcripts in stallion sperm.

<p>Agarose gel images showing RT-PCR amplicons of 7 ECAY genes and transcripts in stallion sperm.</p

Inbreeding coefficients (diagonal boxes) and genetic relationship coefficients of and among the seven affected stallions calculated from i) pedigree data in bold (upper triangle of the matrix) and from ii) SNP genotyping data in normal font (lower triangle of the matrix).

<p>Stallion code names correspond to the codes in the 5-generation pedigree (<a href="http://www.plosgenetics.org/article/info:doi/10.1371/journal.pgen.1003139#pgen.1003139.s001" target="_blank">Figure S1</a>).</p>*<p>The diagonal boxes in <b><i>bold italics with %</i></b> that should correspond to self-to-self genetic relationship ( = 1) have been used to show inbreeding coefficients for each of the 7 stallions.</p

Structural and functional annotations for mRNAs and ESTs with the highest AC values by RNA-seq.

<p>Structural and functional annotations for mRNAs and ESTs with the highest AC values by RNA-seq.</p

Venn diagram of transcripts detected in stallion sperm and testes by microarray analysis (SNR ≥2).

<p>Venn diagram of transcripts detected in stallion sperm and testes by microarray analysis (SNR ≥2).</p

Comparison of RNA-seq data with current equine gene models:

<p>(a) <i>PKM2</i> showing 9 <i>in silico</i> prediction sites, of which two are positioned 5′ upstream to exon 1; (b) <i>CRISP3</i> with 3 <i>in silico</i> prediction sites, all located 5′ upstream to exon 1; (c) <i>PRM1</i> and <i>TNP2</i> cluster (the protamine cluster) with 12 <i>in silico</i> prediction sites of which only two align with <i>PRM1</i> and <i>TNP2</i> exons. Black boxes with numbers –exons in current gene models; blue boxes –very highly expressed tags (AC≥100); red boxes–highly expressed tags (10</p

<i>FKBP6</i> exon 4 genotype frequencies across horse breeds: Thoroughbred, TB (n = 145); Quarter Horse, QH (n = 56); other breeds (21 breeds; n = 64; 1 to 8 individuals each).

<p>The IAR susceptibility genotype AAAA is in bold italics.</p