Polymorphisms identified for the 5 cases and 5 controls individuals used for sequencing.

<p>For each case, the number in red corresponds to the haplotype number defined with the 35 SNP of the chip surrounding <i>SOX9</i>. For each individual the phases defined in <i>TESCO</i> and <i>SOX9</i> with the detected polymorphisms is reported. Positions were defined from position 9033579 (=1) on the pig draft sequence for <i>SOX9</i> and 9047123 (=1) for TESCO. Five different alleles were detected for <i>SOX9</i> (Genbank Accession numbers: KF422597, KF422598, KF422599, KF422600, KF422601), and 3 for the TESCO (KF422602, KF422603, KF422604).</p

Manhattan plot of genome-wide TDT analysis for sex-reversal phenotype.

<p>For each marker the nominal significance (log(1/p)) is indicated. The dotted and the solid lines correspond to the genome-wide suggestive and significant thresholds respectively. </p

List of the 43 haplotypes defined with the 35 SNP of the chip surrounding <i>SOX9</i>.

<p>The haplotypes were classified according to the p-value obtained for each marker (sharing of the transmitted allele from the most significant SNP to the less significant one). For each marker the preferentially transmitted allele was noted “1”, the alternative allele “0” and the log(1/p) obtained with the TDT analysis was reported. On the right, the frequency of each haplotype among the affected animals is reported (the 3 most frequent ones are indicated in red). The marker shown in red box is the marker closest to the gene <i>SOX9</i>.</p

Log(1/p) values of the SNP localized in the 6Mb-12Mb region on SSC12.

<p>The non-significant markers are presented in grey, suggestive ones in medium grey, the significant SNP in black. The suggestive (dotted line) and significant (solid line) thresholds are indicated in red. The two vertical lines delimit the minimum interval defined by the first and least significant SNP in the region. At the bottom, genes and transcripts annotated in Ensembl (Sscrofa10.2) are reported. </p