Deciphering the genetics of pig complex traits through QTL mapping and positional candidate cloing

Abstract

Most traits in livestock are controlled by multiple genes and are therefore called genetically complex traits. In this thesis, we firstly report the molecular characterization and evaluation of the porcine SOX9 gene as a positional candidate for inguinal/scrotal hernia. The SOX9 gene was assigned to SSC12p13-p14 by FISH and RH-panel analysis. Four polymorphisms were detected and genotyped. Association analyses between the SOX9 gene and pig hernia inguinalis/scrotalis showed that the 18-bp deletion at 223 bp of the 5'UTR had a significant effect on hernia inguinalis/scrotalis in pig (p<0.05). A protein factor binding specifically to the 18-bp-deletion allele was detected using electrophoretic mobility shift assay (EMSA). Further transfection assays showed that the deletion leads to a dramatic increase in the transcription activation compared to the insertion. We propose that this deletion creates a potential binding site of a transcription factor to enhance SOX9 expression level which might contribute to pig inguinalis/scrotalis through its functions on the development of the male gonad, collagen metabolism and apoptosis.In the present thesis, we also performed a genome-wide scan to identify quantitative trait loci (QTLs) affecting the traits associated with teat number. A total of 151 microsatellites were genotyped for 560 F2 pigs in a White Duroc×Erhualian intercross. Linear regression method was used to map QTL via QTL Express. Four genome-wide significant QTLs for total teat number (TTN) were detected on SSC4, SSC7, SS12 and SSC13. Four chromosomal regions prominently affecting the teat number of right side (RTN) were identified on SSC3, SS7, SSC12 and SSC15, while only two significant QTLs related to left teat number (LTN) were found on SSC7 and SSC12. The estimated additive effects indicated that Erhualian alleles at the most significant QTLs had positive additive effects compared with the Duroc alleles, except for one QTL on SSC7 at which White Duroc alleles showed increasing teat numbers.