title: Genome-wide association study reveals novel loci for litter size and its variability in a Large White pig population.
abstract: BACKGROUND
  In many traits, not only individual trait levels are under genetic control, but also the variation around that level. In other words, genotypes do not only differ in mean, but also in (residual) variation around the genotypic mean. New statistical methods facilitate gaining knowledge on the genetic architecture of complex traits such as phenotypic variability. Here we study litter size (total number born) and its variation in a Large White pig population using a Double Hierarchical Generalized Linear model, and perform a genome-wide association study using a Bayesian method.
  
  
  RESULTS
  In total, 10 significant single nucleotide polymorphisms (SNPs) were detected for total number born (TNB) and 9 SNPs for variability of TNB (varTNB). Those SNPs explained 0.83 % of genetic variance in TNB and 1.44 % in varTNB. The most significant SNP for TNB was detected on Sus scrofa chromosome (SSC) 11. A possible candidate gene for TNB is ENOX1, which is involved in cell growth and survival. On SSC7, two possible candidate genes for varTNB are located. The first gene is coding a swine heat shock protein 90 (HSPCB = Hsp90), which is a well-studied gene stabilizing morphological traits in Drosophila and Arabidopsis. The second gene is VEGFA, which is activated in angiogenesis and vasculogenesis in the fetus. Furthermore, the genetic correlation between additive genetic effects on TNB and on its variation was 0.49. This indicates that the current selection to increase TNB will also increase the varTNB.
  
  
  CONCLUSIONS
  To the best of our knowledge, this is the first study reporting SNPs associated with variation of a trait in pigs. Detected genomic regions associated with varTNB can be used in genomic selection to decrease varTNB, which is highly desirable to avoid very small or very large litters in pigs. However, the percentage of variance explained by those regions was small. The SNPs detected in this study can be used as indication for regions in the Sus scrofa genome involved in maintaining low variability of litter size, but further studies are needed to identify the causative loci.
authors.affiliation: Animal Breeding and Genomics Center, Wageningen University, P.O. Box 338, 6700, Wageningen, AH, The Netherlands. ewa.sell.kubiak@gmail.com.
authors.forename: E
authors.initials: E
authors.lastname: Sell-Kubiak
authors.affiliation: Topigs Norsvin Research Center B.V, P.O. Box 43, 6640, Beuningen, AA, The Netherlands. naomi.duijvesteijn@topigsnorsvin.com.
authors.forename: N
authors.initials: N
authors.lastname: Duijvesteijn
authors.affiliation: Topigs Norsvin Research Center B.V, P.O. Box 43, 6640, Beuningen, AA, The Netherlands. marcos.lopes@topigsnorsvin.com.
authors.forename: M S
authors.initials: MS
authors.lastname: Lopes
authors.affiliation: Department of Molecular Biology and Genetics, Aarhus University, P.O. Box 50, 8830, Tjele, Denmark. luc.janss@mbg.au.dk.
authors.forename: L L G
authors.initials: LL
authors.lastname: Janss
authors.affiliation: Topigs Norsvin Research Center B.V, P.O. Box 43, 6640, Beuningen, AA, The Netherlands. egbert.knol@topigsnorsvin.com.
authors.forename: E F
authors.initials: EF
authors.lastname: Knol
authors.affiliation: Animal Breeding and Genomics Center, Wageningen University, P.O. Box 338, 6700, Wageningen, AH, The Netherlands. piter.bijma@wur.nl.
authors.forename: P
authors.initials: P
authors.lastname: Bijma
authors.affiliation: Animal Breeding and Genomics Center, Wageningen University, P.O. Box 338, 6700, Wageningen, AH, The Netherlands. han.mulder@wur.nl.
authors.forename: H A
authors.initials: HA
authors.lastname: Mulder
mesh_terms: D000818:Animals; D001499:Bayes Theorem; D033481:Chromosomes, Mammalian / Q000235:genetics; D056426:Genetic Loci; D055106:Genome-Wide Association Study / Q000379:methods / Q000662:veterinary*; D018841:HSP90 Heat-Shock Proteins / Q000235:genetics; D016014:Linear Models; D008098:Litter Size; D020641:Polymorphism, Single Nucleotide; D034421:Sus scrofa / Q000235:genetics*; D013552:Swine; D042461:Vascular Endothelial Growth Factor A / Q000235:genetics
chemical_list: D018841:HSP90 Heat-Shock Proteins; D042461:Vascular Endothelial Growth Factor A