Additional file 3: of eQTL discovery and their association with severe equine asthma in European Warmblood horses

Association of DEXI and NSUN2 gene expression to RAO disease status. Html output of an R markdown document. The file contains two multiple logistic regressions and one simple logistic regression showing the association between DEXI gene expression and disease status. Multiple logistic regression with known confounders as independent variables, and the simple logistic regression only has the independent variable of interest (DEXI or NSUN2 gene expression) as the single covariate. An R markdown document that generated this html file is available on GitHub: https://github.com/VCMason . (HTML 844 kb

Additional file 4: of eQTL discovery and their association with severe equine asthma in European Warmblood horses

Association of ATF7IP2, and GLIPR1L2 gene expression to RAO disease status. Html output of an R markdown document. The file contains one multiple logistic regression for each gene ATF7IP2, and GLIPR1L2. These models quantify the association between gene expression in ATF7IP2, or GLIPR1L2 and disease status. Four significant surrogate variables were calculated for the HDE treatment by SVA and therefore none were included in the model. An R markdown document that generated this html file is available on GitHub: https://github.com/VCMason . (HTML 866 kb

Additional file 2: of eQTL discovery and their association with severe equine asthma in European Warmblood horses

Linear mixed models jointly modeling MCK and HDE. Linear mixed models with random intercepts for each individual model the association between the top fifteen RAO associated SNPs that were also eSNPs in either MCK or HDE (chr13.32843309, chr13.32844446, chr13.33460982, chr13.33502488, chr28.3692072, chr21.52625145) and the gene expression of the genes they regulated (DEXI, NSUN2, ATF7IP2, GLIPR1L2) with reduced maximum likelihood (REML) and maximum likelihood (ML). An R markdown document that generated this html file is available on GitHub: https://github.com/VCMason . (HTML 5545 kb

Additional file 5: Figure S2. of Co-expression network analysis of duplicate genes in maize (Zea mays L.) reveals no subgenome bias

Co-expression divergence in terms of shortest network path, edge connectivity of a duplicate pair, and local clustering coefficient. (A) WGD duplicates had significantly shorter path edges than inserted and tandem duplicate genes. (B) WGD duplicates had significantly higher edge connectivity than inserted and tandem duplicate genes. (C) Maize1 and maize2 genes had significantly lower local clustering coefficient than non-syntenic genes (usually generated by inserted and tandem duplications). (D) and (E) Shortest network path and edge connectivity of a duplicate pair were associated with synonymous mutation rate (dS). (PDF 740 kb

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

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

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

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

GWAS plots for the IAR phenotype displaying results for the 52,583 SNPs that passed quality control.

<p>(A) standard chi-square based association test without permutations; (B) standard association test after 10,000 t-max permutations, and (C) mixed-model test. The SNPs are plotted according to their position on each chromosome (x-axis) and association with the IAR phenotype (y-axis). Significance is given as the −log₁₀ of the uncorrected (A and C) or corrected (B) <i>P</i>-value. The genome-wide significance threshold is log₁₀<i>P</i>>5 or log₁₀<i>EMP2</i>>1. 5.</p

Equine <i>FKBP6</i> organization and splicing.

<p>(A) <i>FKBP6</i> genomic (left) and cDNA (right) according to ENSEMBL (<a href="http://www.ensembl.org/index.html" target="_blank">http://www.ensembl.org/index.html</a>); (B) <i>FKBP6</i> splice variants in stallion testis and sperm according to this study; (C) RT-PCR with combinations of <i>FKBP6</i> exon primers to determine alternative splicing in testis (T), normal sperm (S) and IAR sperm (I). Arrows show PCR products for alternative splice variants.</p