Identification of candidate genes controlling porcine female reproductive traits

Breeding programs have been used to improve livestock performance by selecting for traits of economic importance. However, as traits for prolificacy tend to have a low heritability, are sex limited and are expressed only in mature animals, improvement has been slow. The chromosomal locations that control these traits for which there is a continuum between high and low performing animals, are termed Quantitative Trait Loci (QTL). Three-generation pedigrees, in which the founders were Meishan and Large White purebred pigs, were used to identify QTL for female reproductive performance. The Chinese Meishan is one of the most prolific pig breeds known, farrowing up to five more piglets per litter than the European commercial Large White breed. However, the Meishan is not commercially viable in Europe due to its poor growth rate and high carcass fat content. Therefore, including the beneficial alleles from the Meishan into the Large White breed is of commercial relevance. QTL for ovulation rate, teat number, age at puberty and uterine capacity have been mapped to chromosome 8 (SSC8) in earlier studies. The aim of this study was to focus specifically on SSC8 and to identify and test candidate genes for the QTL. The genotypes of twenty markers on SSC8 were combined with data collected on the reproductive performance of 220 F2 females. QTL for the related traits of litter size and prenatal survival were identified at the distal end of the q arm. The beneficial alleles at these QTL seem to be from the Meishan and that is consistent with the fact that this breed delivers larger litter sizes through higher levels of prenatal survival at a given ovulation rate. The QTL for prenatal survival was defined as a region of about 30 cM and therefore contains many positional candidate genes, but only a few of these have been mapped in pigs. Human chromosome 4 (HSA4) shares extensive homology to SSC8. A gene map of SSC8 was developed by radiation hybrid mapping in order to align the human genome sequence of HSA4 with the QTL and thus identify comparative positional candidate genes. The resulting comparative map revealed extensive conservation of synteny and gene order. One positional candidate gene, secreted phosphoprotein 1 (SPPJ), is also a physiological candidate gene as the protein is involved in porcine embryo implantation and maintenance of pregnancy. A copy of SPPJ ( 10 kb) from both Meishan and Large White origin was sequenced to identify candidate causal variation. A total of 97 variants, including single nucleotide polymorphisms (SNPs) and sequence insertions and deletions were found. Three of the SNPs would result in non-synonymous amino acid changes. Expression of SPPJ is controlled mainly by posttranslational modification and for one of these SNPs the Meishan allele encodes a serine, which would be phosphorylated and the Large White allele encodes a proline, which would not. To test whether the variation at this particular locus resulted in differences in litter size, the SNP was genotyped over 2974 pigs of varying breed origin. No association was identified between genotypes at this locus and litter size. Evidence for genetic variation associated with litter size in or close to the SPPJ gene comes from two other independent studies in which SPP1 was used as the genetic marker. Future work could therefore involve typing further candidate SNPs in the SPPJ gene to identify whether there is a causative mutation in this gene. Furthermore, (li1-i(n21 nn tcn,1 (n anc rrii1A hp tcti1 frr '211cl ,ri,firn