TITLE

The distal end of porcine chromosome 6p is involved in the regulation of skatole levels in boars

AUTHOR(S)
Ramos, António M.; Duijvesteijn, Naomi; Knol, Egbert F.; Merks, Jan W. M.; Bovenhuis, Henk; Crooijmans, Richard P. M. A.; Groenen, Martien A. M.; Harlizius, Barbara
PUB. DATE
January 2011
SOURCE
BMC Genetics;2011, Vol. 12 Issue 1, p35
SOURCE TYPE
Academic Journal
DOC. TYPE
Article
ABSTRACT
Background: Boar taint is an unpleasant condition of pork, mainly due to the accumulation of androstenone and skatole in male pigs at onset of puberty. This condition is the cause of considerable economic losses in the pig industry and the most common practice to control it is to castrate male piglets. Because of the economic and animal welfare concerns there is interest in developing genetic markers that could be used in selection schemes to decrease the incidence of boar taint. The Porcine 60 K SNP Beadchip was used to genotype 891 pigs from a composite Duroc sire line, for which skatole levels in fat had been collected. Results: The genome-wide association study revealed that 16 SNPs (single nucleotide polymorphisms) located on the proximal region of chromosome 6 were significantly associated with skatole levels. These SNPs are grouped in three separate clusters located in the initial 6 Mb region of chromosome 6. The differences observed between the homozygote genotypes for SNPs in the three clusters were substantial, including a difference of 102.8 ng/g skatole in melted fat between the homozygotes for the ALGA0107039 marker. Single SNPs explain up to 22% of the phenotypic variance. No obvious candidate genes could be pinpointed in the region, which may be due to the need of further annotation of the pig genome. Conclusions: This study demonstrated new SNP markers significantly associated with skatole levels in the distal region of chromosome 6p. These markers defined three independent clusters in the region, which contain a low number of protein-coding genes. The considerable differences observed between the homozygous genotypes for several SNPs may be used in future selection schemes to reduce skatole levels in pigs
ACCESSION #
62608280

 

Related Articles

  • Not so lost in the genetic crowd. Schork, Nicholas J.; Bansal, Vikas // Nature Genetics;Nov2009, Vol. 41 Issue 11, p1163 

    Two new studies report improved statistics to predict whether an individual participated in a genome-wide association study based on aggregate allele or genotype frequency information. They demonstrate that it may be possible to release summary statistics for a subset of genetic markers in a...

  • Evaluation of approaches for identifying population informative markers from high density SNP Chips. Wilkinson, Samantha; Wiener, Pamela; Archibald, Alan L.; Law, Andy; Schnabel, Robert D.; McKay, Stephanie D.; Taylor, Jeremy F.; Ogden, Rob // BMC Genetics;2011, Vol. 12 Issue 1, p45 

    Background: Genetic markers can be used to identify and verify the origin of individuals. Motivation for the inference of ancestry ranges from conservation genetics to forensic analysis. High density assays featuring Single Nucleotide Polymorphism (SNP) markers can be exploited to create a...

  • Utilization of next-generation sequencing platforms in plant genomics and genetic variant discovery. Deschamps, Stéphane; Campbell, Matthew A. // Molecular Breeding;Apr2010, Vol. 25 Issue 4, p553 

    Genome-wide variant detection within a species is the primary initial step towards linking genotypic variation and phenotypes. The conversion of these genetic variants (the most prevalent of these being single-nucleotide polymorphisms or SNPs) into genetic markers is particularly important in...

  • CYP3A5*3, CYP3A4*1B and MDR1 C3435T genotype distributions in Ecuadorians. Sinués, Blanca; Vicente, Jorge; Fanlo, Ana; Mayayo-Sinués, Esteban; González-Andrade, Fabricio; Sánchez-Q, Dora; Martínez-Jarreta, Begoña // Disease Markers;2008, Vol. 24 Issue 6, p325 

    Polymorphisms in CYP3A genes, such as CYP3A5} and CYP3A4, as well as in the MDR1 gene, which encodes for P-glycoprotein, have been implicated as genetic markers in several disorders. Differences in the frequency distribution of the allelic variants CYP3A5*3, CYP3A4*1B, and MDR1 3435T have been...

  • Polimorfismo g.37190613 G>A del gen ELMO1 en población mexicana, marcador potencial para la patología clínico-quirúrgica. Topete-González, Luz Rosalba; Ramirez-Garcia, Sergio Alberto; Charles-Niño, Claudia; Villa-Ruano, Nemesio; Mosso-González, Clemente; Dávalos-Rodríguez, Nory Omayra // Cirugia y Cirujanos;jul/ago2014, Vol. 82 Issue 4, p402 

    Background: ELMO1 is a gene located at locus 7p14.2-14.1 that codifies a regulatory protein involved in fibrogenesis, cell migration, phagocytosis and apoptosis. This gene presents a single nucleotide polymorphism, which appears to be linked with the development of diabetic nephropathy....

  • PeakSeeker: a program for interpreting genotypes of mononucleotide repeats. Thompson, James M.; Salipante, Stephen J. // BMC Research Notes;2009, Vol. 2, p1 

    Background: Mononucleotide repeat microsatellites are abundant, highly polymorphic DNA sequences, having the potential to serve as valuable genetic markers. Use of mononucleotide microsatellites has been limited by their tendency to produce "stutter", confounding signals from insertions and...

  • CrypticIBDcheck: an R package for checking cryptic relatedness in nominally unrelated individuals. Nembot-Simo, Annick; Graham, Jinko; McNeney, Brad // Source Code for Biology & Medicine;2013, Vol. 8 Issue 1, p1 

    Background: In population association studies, standard methods of statistical inference assume that study subjects are independent samples. In genetic association studies, it is therefore of interest to diagnose undocumented close relationships in nominally unrelated study samples. Results: We...

  • The BCL-2 promoter (−938C>A) polymorphism does not predict clinical outcome in chronic lymphocytic leukemia. Kaderi, M. A.; Norberg, M.; Murray, F.; Merup, M.; Sundström, C.; Roos, G.; Åleskog, A.; Karlsson, K.; Axelsson, T.; Tobin, G.; Rosenquist, R. // Leukemia (08876924);Feb2008, Vol. 22 Issue 2, p339 

    The (−938C>A) polymorphism in the promoter region of the BCL-2 gene was recently associated with inferior time to treatment and overall survival in B-cell chronic lymphocytic leukemia (CLL) patients displaying the −938A/A genotype and may thus serve as an unfavorable genetic marker...

  • A Genetic Association Study of Single Nucleotide Polymorphisms in FGFR1OP2/wit3.0 and Long-Term Atrophy of Edentulous Mandible. Suwanwela, Jaijam; Jaehoon Lee; Lin, Audrey; Ucer, T. Cemal; Devlin, Hugh; Sinsheimer, Janet; Garrett, Neal R.; Nishimura, Ichiro // PLoS ONE;2011, Vol. 6 Issue 1, p1 

    Background: After dental extraction, the external surface of alveolar bone undergoes resorption at various rates, and a group of patients develop excessive jawbone atrophy. Oral mucosa overlying the atrophied jawbone is unusually thin; therefore, we have hypothesized that excessive jawbone...

Share

Other Topics