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A genome-wide association study reveals a novel candidate gene for sperm motility in pigs

Diniz, D.B., Lopes, M.S., Broekhuijse, M.L.W.J., Lopes, P.S., Harlizius, B., Guimarães, S.E.F., Duijvesteijn, N., Knol, E.F., Silva, F.F.
Animal reproduction science 2014 v.151 no.3-4 pp. 201-207
Sus scrofa, boars, chromosomes, genes, genetic improvement, genome-wide association study, genomics, genotyping, marker-assisted selection, mitochondria, proteins, puberty, quantitative trait loci, semen, single nucleotide polymorphism, sperm motility, spermatozoa, translation (genetics)
Sperm motility is one of the most widely used parameters in order to evaluate boar semen quality. However, this trait can only be measured after puberty. Thus, the use of genomic information appears as an appealing alternative to evaluate and improve selection for boar fertility traits earlier in life. With this study we aimed to identify SNPs with significant association with sperm motility in two different commercial pig populations and to identify possible candidate genes within the identified QTL regions. We performed a single-SNP genome-wide association study using genotyped animals from a Landrace-based (L1) and a Large White-based (L2) pig populations. For L1, a total of 602 animals genotyped for 42,551 SNPs were used in the association analysis. For L2, a total of 525 animals genotyped for 40,890 SNPs were available. After the association analysis, a false discovery rate q-value ≤0.05 was used as the threshold for significant association. No SNPs were significantly associated with sperm motility in L1, while six SNPs on Sus scrofa chromosome 1 (position 117.26–119.56Mb) were significant in L2. The mitochondrial methionyl-tRNA formyltransferase (MTFMT) gene, which affects translation efficiency of proteins in sperm cells, was identified as a putative candidate gene. The significant markers identified in this study may be useful to enhance the genetic improvement of sperm motility by selection of boars at an earlier age under a marker assisted selection strategy.