<i>UCN3</i> mRNA secondary structure predicted by Mfold on a partial sequence of 81 bp surrounding four coding SNPs.

<div><p>A: mRNA secondary structure for haplotype <i>CTTC</i>.</p> <p>B: mRNA secondary structure for haplotype <i>TCGA</i>.</p></div

Genomic organization and haplotype analysis in the bovine <i>CRHR2</i> gene.

<div><p>Coding exons are marked by black boxes.</p> <p>Pairwise linkage disequilibrium relationship for 5 mutations is illustrated based on r² measurements.</p> <p>The mutation g.2072A>B represents AAFC03056271.1:<i>g.33947-33964TGAATCCAGCCTGAGTTG>CTTTGTCTTGAG</i>.</p></div

Genomic organization and haplotype analysis in the bovine <i>UCN3</i> gene.

<div><p>Noncoding exon 1, partial non-conding exon 2 and 3′untranslated region are marked by white boxes and coding exon 2 by a black box.</p> <p>Pairwise linkage disequilibrium relationship for 12 mutations is illustrated based on r² measurements.</p> <p>The mutation g.8272A>B represents AAFC03043460.1:<i>g.8272-8281AATAATAAAT>GGAGC</i>.</p></div

Distribution of CNVRs found in autosomes of porcine genome.

<p>X axis indicates the 18 autosomes, Y axis the length of each chromosome, and the black frames the different chromosomes. The green bars (left border of each chromosome) represent copy number loss regions and the red bars (right border of each chromosome) represent copy number gain regions.</p

Gene symbols, GenBank references, amplicons and SNPs discovered in the present study.

<p>*Number in brackets is the length of forward or reverse primer for the amplicon.</p

Linkage disequilibrium analysis for markers in the bovine <i>ABCA1</i>, <i>APOE</i> and <i>SCARB1</i> genes.

<p>Pairwise linkage disequilibrium relationship for these SNPs are based on r² measurements.</p

raw SNP data_Rahmani sheep

raw SNP data_Rahmani shee

Identification of genetic networks related to RCT pathway via Akaiki Information Criterion based model comparison.

<p>A1, B1 and C1 are genetic networks previously reported by Jiang et al. (2009 with permission), while A2, B2 and C2 are newly identified networks in the present study for KPH, REA and SFD, respectively. The x-axis and y-axis represent actual and predicted trait (genotypic) values. The numbers in arrows represent substitution effects of one type of genotypes or allele for another one. In the graph, AIC  =  computed AIC value for a specific model, say A1, and Δ =  the difference of AIC values, say, between model A1 and the base model A0. The AIC values for the three base models, A0, B0 and C0, were −424.15, 132.2, and −653.61, respectively.</p

CN values predicted and observed near three gene loci.

<p>The left pictures are CN values estimated from at least 5 individuals in different breeds using the qPCR method. X axis means different pig breeds (TC = Tongcheng; MS = Meishan; NJ = Neijiang; JH = Jinhua; PZ = Penzhou; LW = LargeWhite; DU = Duroc; LR = Landrace). Y axis means the CN values. The cycles indicate CN values for each individual. The right histograms describe the predicted and observed CN values in four Tongcheng pigs. CN gain in these four gene loci was predicted. <b>(A) (B)</b> and <b>(C)</b> The left pictures showed that CN was increased in most individuals in a large range for 2–12. Also, the same trend was observed for CN gain between predicted and observed events in three Tongcheng pigs according to the right histograms.</p

Neighbor-Joining tree relating the 94 individuals.

<p>The tree was constructed using allele sharing distances averaged over 46,850 SNPs. Different colors in labels represent the origin of breed individuals. S, R, C, P, and T represent Suffolk, Rambouillet, Columbia, Polypay, and Targhee sheep breeds, respectively. The meanings of S, R, C, P, and T are same in the following figures.</p