A QTL for number of teats shows breed specific effects on number of vertebrae in pigs: Bridging the gap between molecular and quantitative genetics

Modern breeding schemes for livestock species accumulate a large amount of genotype and phenotype data which can be used for genome-wide association studies (GWAS). Many chromosomal regions harboring effects on quantitative traits have been reported from these studies, but the underlying causative mutations remain mostly undetected. In this study, we combine large genotype and phenotype data available from a commercial pig breeding scheme for three different breeds (Duroc, Landrace, and Large White) to pinpoint functional variation for a region on porcine chromosome 7 affecting number of teats (NTE). Our results show that refining trait definition by counting number of vertebrae (NVE) and ribs (RIB) helps to reduce noise from other genetic variation and increases heritability from 0.28 up to 0.62 NVE and 0.78 RIB in Duroc. However, in Landrace, the effect of the same QTL on NTE mainly affects NVE and not RIB, which is reflected in reduced heritability for RIB (0.24) compared to NVE (0.59). Further, differences in allele frequencies and accuracy of rib counting influence genetic parameters. Correction for the top SNP does not detect any other QTL effect on NTE, NVE, or RIB in Landrace or Duroc. At the molecular level, haplotypes derived from 660K SNP data detects a core haplotype of seven SNPs in Duroc. Sequence analysis of 16 Duroc animals shows that two functional mutations of the Vertnin (VRTN) gene known to increase number of thoracic vertebrae (ribs) reside on this haplotype. In Landrace, the linkage disequilibrium (LD) extends over a region of more than 3 Mb also containing both VRTN mutations. Here, other modifying loci are expected to cause the breed-specific effect. Additional variants found on the wildtype haplotype surrounding the VRTN region in all sequenced Landrace animals point toward breed specific differences which are expected to be present also across the whole genome. This Landrace specific haplotype contains two missense mutations in the ABCD4 gene, one of which is expected to have a negative effect on the protein function. Together, the integration of largescale genotype, phenotype and sequence data shows exemplarily how population parameters are influenced by underlying variation at the molecular level.</p

Three Blind Mice, See How They Run: A Critique of Behavioral Research With Animals

Animal research has been a traditionally accepted and respected part of modern psychology from its earliest days. The prevalent view of animals in contemporary psychology has origins far more basic than the scientific method. Its roots are deeply imbedded in Judaeo-Christian culture, a tradition which postulates a wide gulf between humankind and the animal world. The Darwinian revolution and the ethological outlook it fostered, while of immense biological significance, has for the most part been neglected by modern American comparative psychologists in favor of a positivistic-behaviorist orientation with a heavy reliance upon laboratory experimentation. In recent years, opposition to animal research (some of it rational, some not) has experienced a profound resurgence. Psychologists have received a disproportionate share of the criticism considering the relatively small numbers of animals sacrificed in psychology laboratories. In this paper, I propose to review this development, critically examine the response of orthodox psychology to it, and offer suggestions for improvement