A genome-wide association study points out the causal implication of SOX9 in the sex-reversal phenotype in XX pigs

Among farm animals, pigs are known to show XX sex-reversal. In such cases the individuals are genetically female but exhibit a hermaphroditism, or a male phenotype. While the frequency of this congenital disease is quite low (less than 1%), the economic losses are significant for pig breeders. These losses result from sterility, urogenital infections and the carcasses being downgraded because of the risk of boar taint. It has been clearly demonstrated that the SRY gene is not involved in most cases of sex-reversal in pigs, and that autosomal recessive mutations remain to be discovered. A whole-genome scan analysis was performed in the French Large-White population to identify candidate genes: 38 families comprising the two non-affected parents and 1 to 11 sex-reversed full-sib piglets were genotyped with the PorcineSNP60 BeadChip. A Transmission Disequilibrium Test revealed a highly significant candidate region on SSC12 (most significant p-value<4.65.10(-10)) containing the SOX9 gene. SOX9, one of the master genes involved in testis differentiation, was sequenced together with one of its main regulatory region Tesco. However, no causal mutations could be identified in either of the two sequenced regions. Further haplotype analyses did not identify a shared homozygous segment between the affected pigs, suggesting either a lack of power due to the SNP properties of the chip, or a second causative locus. Together with information from humans and mice, this study in pigs adds to the field of knowledge, which will lead to characterization of novel molecular mechanisms regulating sexual differentiation and dysregulation in cases of sex reversal

A genome scan for QTL affecting resistance to Haemonchus contortus in sheep

Gastrointestinal nematodes are one of the main health issues in sheep breeding. To identify loci affecting the resistance to Haemonchus contortus, a genome scan was carried out using 1,275 Romane × Martinik Black Belly backcross lambs. The entire population was challenged with Haemonchus contortus in 2 consecutive experimental infections, and fecal egg counts (FEC) and packed cell volumes were measured. A subgroup of 332 lambs with extreme FEC was necropsied to determine the total worm burden, length of female worms, sex ratio in the worm population, abomasal pH, and serum and mucosal G immunoglobulins (IgG) responses. Pepsinogen concentration was measured in another subset of 229 lambs. For QTL detection, 160 microsatellite markers were used as well as the Illumina OvineSNP50 BeadChip that provided 42,469 SNP markers after quality control. Linkage, association, and joint linkage and association analyses were performed with the QTLMAP software. Linkage disequilibrium (LD) was estimated within each pure breed, and association analyses were carried out either considering or not the breed origin of the haplotypes. Four QTL regions on sheep chromosomes (OAR)5, 12, 13, and 21 were identified as key players among many other QTL with small to moderate effects. A QTL on OAR21 affecting pepsinogen concentration exactly matched the pepsinogen (PGA5) locus. A 10-Mbp region affecting FEC after the 1st and 2nd infections was found on OAR12. The SNP markers outperformed microsatellites in the linkage analysis. Taking advantage of the LD helped to refine the locations of the QTL mapped on OAR5 and 13

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

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