REMARKABLE SELECTIVE CONSTRAINTS ON EXONIC DINUCLEOTIDE REPEATS

Long dinucleotide repeats found in exons present a substantial mutational hazard: mutations at these loci occur often and generate frameshifts. Here, we provide clear and compelling evidence that exonic dinucleotides experience strong selective constraint. In humans, only 18 exonic dinucleotides have repeat lengths greater than six, which contrasts sharply with the genome‐wide distribution of dinucleotides. We genotyped each of these dinucleotides in 200 humans from eight 1000 Genomes Project populations and found a near‐absence of polymorphism. More remarkably, divergence data demonstrate that repeat lengths have been conserved across the primate phylogeny in spite of what is likely considerable mutational pressure. Coalescent simulations show that even a very low mutation rate at these loci fails to explain the anomalous patterns of polymorphism and divergence. Our data support two related selective constraints on the evolution of exonic dinucleotides: a short‐term intolerance for any change to repeat length and a long‐term prevention of increases to repeat length. In general, our results implicate purifying selection as the force that eliminates new, deleterious mutants at exonic dinucleotides. We briefly discuss the evolution of the longest exonic dinucleotide in the human genome—a 10 x CA repeat in fibroblast growth factor receptor‐like 1 (FGFRL1)—that should possess a considerably greater mutation rate than any other exonic dinucleotide and therefore generate a large number of deleterious variants.     

Association between COMT SNP variation and timidity in Golden and Labrador Retrievers

Timidity in dogs is a trait with high heritability. However, the relevant genetic factors and markers associated with this condition are largely unknown. The function of the catechol‐O‐methyl transferase (COMT) gene has been found to be associated with human fearful or anxious emotions, and the COMT:p.Val158Met polymorphism locus is significantly related to anxious behavior. In the present study, the correlation between timidity and four single nucleotide polymorphism (SNP) variations (C.‐1666C>G c.39A>G, c.216G>A, c.482G>A) of the COMT gene was investigated in dogs. The evaluation was based on the dog courage assessment assay and a genotype and haplotype analysis in Labrador Retrievers (LR) and Golden Retrievers (GR). The principal components analysis factor structure of the courage phenotype was invariant between LR and GR. Sex, breed and age had no statistically significant effect on the timidity of the dogs. All SNP loci detected were in Hardy–Weinberg equilibrium. The c.39A>G locus was removed in the subsequent association analysis due to the significant difference between LR and GR in genotype distributions. Intriguingly, the genotypes and haplotypes of the COMT gene were significantly and highly correlated with the timidity of LR and GR. The A alleles of the COMT:c.216G>A and c.482G>A loci appeared to play a dominant role in the timid behavior of the dogs. This result supports and broadens the warrior/worrier hypothesis and will have important implications for the understanding of the evolution of temperament in dogs. Additionally, the results provide predictive genetic markers for temperament in dogs.     

A polymorphism in the porcine miR‐208b is associated with microRNA biogenesis and expressions of SOX‐6 and MYH7 with effects on muscle fibre characteristics and meat quality

MicroRNAs (miRNAs) encoded by the myosin heavy chain (MHC) genes are muscle‐specific miRNAs (myomiRs) and regulate the expression of MHC isoforms in skeletal muscle. These miRNAs have been implicated in muscle fibre types and their characteristics by affecting the heterogeneity of myosin. In pigs, miR‐208b and miR‐499 are embedded in introns of MYH7 and MYH7b respectively. Here, we identified a novel single nucleotide polymorphism (SNP) in intron 30 of MYH7 by which porcine miR‐208b is encoded. Based on the association study using a total of 487 pigs including Berkshire (n = 164), Landrace (n = 121) and Yorkshire (n = 202), the miR‐208b SNP (g.17104G>A) had significant effects on the proportions of types I and IIb fibre numbers (P < 0.010) among muscle fibre characteristics and on drip loss (P = 0.012) in meat quality traits. Moreover, the SNP affected the processing of primary miR‐208b into precursor miR‐208b with a marginal trend towards significance (P = 0.053), thereby leading to significant changes in the levels of mature miR‐208b (P = 0.009). These SNP‐dependent changes in mature miR‐208b levels were negatively correlated with the expression levels of its target gene, SOX‐6 (P = 0.038), and positively associated with the expression levels of its host gene, MYH7 (P = 0.046). Taken together, our data suggest that the porcine miR‐208b SNP differentially represses the expression of SOX‐6 by regulating miRNA biogenesis, thereby affecting the expression of MYH7 and the traits of muscle fibre characteristics and meat quality.     

Mapping markers linked to porcine salmonellosis susceptibility

The goal of this study was to identify pig chromosomal regions associated with susceptibility to salmonellosis. Genomic DNA from pig reference populations with differences in susceptibility to Salmonella enterica serovar Choleraesuis as quantified by spleen and liver bacterial colonization at day 7 post-infection (dpi; Van Diemen et al. 2002 ) was used. These samples belonged to the offspring of a sire thought to be heterozygous for genes involved in susceptibility to salmonellosis. Amplified fragment length polymorphism (AFLP) markers were created and used to determine associations with spleen or bacterial counts at 7 dpi. To position linked markers, two mapping populations, the Roslin and Uppsala PiGMaP pedigrees were used to create an integrated map which included the AFLP markers associated with salmonellosis. Twenty-six AFLP markers located in 14 different chromosomal regions in the porcine genome were found to be significantly associated with susceptibility (Chi-square P  < 0.05). More than one linked marker was found on chromosomes 1, 7, 13, 14 and 18. It is likely that these regions contain genes involved in Salmonella susceptibility. Regions on chromosomes 1, 7 and 14 were significantly associated with Salmonella counts in the liver and regions on chromosomes 11, 13 and 18 with counts in spleen. The identification of these chromosomal regions highlights specific areas to search for candidate genes that may be involved in innate or adaptive immunity. Further investigation into these chromosomal regions would be useful to improve our understanding of host responses to infection with this widespread pathogen.     

Temperature modulation of behavioural thresholds controlling male moth sex pheromone response specificity

ABSTRACT. The response specificity of male Oriental fruit moths, Grapholita molesta (Busck) and pink bollworm moths, Pectinophora gossypiella (Saunders), to different blends and doses of pheromone is altered dramatically by temperature. When acclimated and tested in a flight tunnel at 20^oC males of both species exhibit a high degree of specificity, with peak response levels occurring to a narrow range of blend-dose combinations close to the natural blend. When tested at 26^oC, however, males exhibit a significantly lower degree of specificity, with peak response occurring to a broader range of treatments. The change in response specificity results from shifts in behavioural threshold effects influencing plume orientation and initiation of upwind flight, as well as from arrestment of upwind flight, occurring later in the flight sequence. The observed changes in male behaviour suggest that the effect of temperature is directly on neural pathways involved in the perception of odour, and not simply the result of an increase in motor activity or a significant change in the release rate of the pheromone. The results support the threshold hypothesis for pheromone perception (Roelofs, 1978) as a general principle in the Lepidoptera, but also show that the degree of response specificity can be significantly affected by temperature.     

Characterization of the erythrocyte superoxide dismutase allozymes in the deer Cervus elaphus

The cDNA sequences for Cu,Zn superoxide dismutase from two Cervus elaphus subspecies, North American wapiti and European red deer, were determined. The derived amino acid sequences showed two differences: residue 8 was Leu in wapiti and Met in red deer and residue 25 was His in wapiti and Asn in red deer. The extra positive charge at position 25 in the wapiti isoform accounted for its greater mobility towards the cathode during non-denaturing electrophoresis, a procedure widely used in the genetic analysis of deer. There was no difference in specific activity between the two Cu,Zn superoxide dismutase isoforms, but the wapiti isoform was slightly more susceptible to heat denaturation.     

Phylogenetic analysis and evolution of the genusJuglans (Juglandaceae) as determined from nuclear genome RFLPs

RFLPs were studied in 13Juglans species to determine phylogenetic relationships inJuglans. Allele frequency data were used to generate genetic distance matrices and fragment data were used to generate genetic distances based upon shared-fragments and to perform parsimony analysis. Although similar cluster analyses result from analysing allelic and shared-fragment distance, the two types of distance values displayed variable correspondence with each other. Parsimony analysis produced a tree similar to distance data trees, but with additional phylogenetic resolution agreeing with previous systematic studies. All analyses indicate an ancient origin ofJ. regia, previously considered a recently derived species.     

Biochemical and genetic analysis of variant C of caprine αs2-casein (Capra hircus)

Two alleles, A and B, were previously described at the goat α_s2-casein locus. Isoelectric focusing allowed us to subdivide the former one in two new alleles, called A and C. Although α_s2-casein C cannot actually be distinguished from its A counterpart by starch or polyacrylamide gel electrophoresis, it differs from the previous allele by a single substitution Lys (A)/Ile (C) at position 167, which was confirmed at the nucleotide level. The frequencies of the three α_s2-casein alleles A, B and C were estimated to be 0.85, 0.04 and 0.11 in the French dairy breeds ‘Alpine’ and ‘Saanen’.     

High herkogamy but low reciprocity characterizes isoplethic populations of Jasminum malabaricum,a species with stigma‐height dimorphism

• Studies of floral polymorphisms have focused on heterostyly, while stigma‐height dimorphism has received considerably less attention. Few studies have examined the reproductive biology of species with stigma‐height dimorphism to understand how factors influencing mate availability and pollen transfer are related to morph ratios in populations.
• Floral morphological traits, especially herkogamy and reciprocity, pollinator visitation, breeding system and spatiotemporal mate availability, are known to affect inter‐morph pollination and morph ratios in species with stigma‐height dimorphism. In this study, we investigated the presence of stigma‐height dimorphism and estimated morph ratios in four naturally occurring populations of Jasminum malabaricum. We quantified morph‐ and population‐specific differences in the abovementioned factors in these populations to understand the observed morph ratios.
• The positions of anthers and stigmas were characteristic of stigma‐height dimorphism, the first report of this polymorphism in the genus. All study populations were isoplethic, implying equal fitness of both morphs. Herkogamy was higher in the short‐styled morph, while reciprocity was higher between the long‐styled stigma and short‐styled anthers. Long‐ and short‐tongued pollinators were common floral visitors, and we observed no differences between morphs in spatiotemporal mate availability or pollinator visitation. Neither morph exhibited self‐ or heteromorphic incompatibility.
• The short‐styled stigma had lower reciprocity but likely receives sufficient inter‐morph pollen from long‐tongued pollinators, and also by avoiding self‐pollination due to higher herkogamy. These results highlight the importance of sufficient effective pollinators and floral morphological features, particularly herkogamy, in maintaining isoplethy in species with stigma‐height dimorphism.