Gene, phenotype and function: GLABROUS1 and resistance to herbivory in natural populations of Arabidopsis lyrata

The molecular genetic basis of adaptive variation is of fundamental importance for evolutionary dynamics, but is still poorly known. Only in very few cases has the relationship between genetic variation at the molecular level, phenotype and function been established in natural populations. We examined the functional significance and genetic basis of a polymorphism in production of leaf hairs, trichomes, in the perennial herb Arabidopsis lyrata. Earlier studies suggested that trichome production is subject to divergent selection. Here we show that the production of trichomes is correlated with reduced damage from insect herbivores in natural populations, and using statistical methods developed for medical genetics we document an association between loss of trichome production and mutations in the regulatory gene GLABROUS1. Sequence data suggest that independent mutations in this regulatory gene have provided the basis for parallel evolution of reduced resistance to insect herbivores in different populations of A. lyrata and in the closely related Arabidopsis thaliana. The results show that candidate genes identified in model organisms provide a valuable starting point for analysis of the genetic basis of phenotypic variation in natural populations.     

Patterns of clonal diversity in three species of sub-arctic willow (Salix lanata, Salix lapponum and Salix herbacea)

Sub-arctic willow scrub is an endangered habitat in Britain, and typically occurs on steep crags inaccessible to grazing animals. These willows can reproduce both sexually and asexually, although the relative importance of each is unknown. Knowledge of reproductive mode is important for the design of grazing management and restoration programmes. Accordingly, clonality was assessed in the largest stand of sub-arctic willow scrub in the UK, focusing on Salix lanata and S. lapponum. Little evidence of clonal growth was detected; most individuals possessed distinct multi-locus genotypes. Thus despite the capacity for vegetative reproduction, and seedlings being rarely observed, sexual reproduction is the predominant means of perpetuation and dispersal at this site. We also examined clonal growth in a common willow species (Salix herbacea) that occupies a different habitat type (exposed mountain tops and ridges). Multiple individuals shared identical genotypes up to 7 m apart, suggesting an important role for clonal growth in local patch formation in this species.     

Characterization of AFLP Markers Associated with Growth in the Kuruma Prawn, <Emphasis Type="Italic">Marsupenaeus japonicus</Emphasis>, and Identification of a Candidate Gene

Growth rate of the Kuruma prawn, Marsupenaeus japonicus is an important economic trait, with larger animals commanding higher market prices. To identify gene markers associated with growth, a genetic map of a full-sib F₂ intercross family of M. japonicus has previously been generated and quantitative trait loci (QTL) influencing weight, total length, and carapace length were identified. In this study, amplified fragment length polymorphism (AFLP) markers associated with the major QTL region, contributing 16% to phenotypic variation, were characterized. Flanking sequence has been obtained and allelic variants responsible for segregation patterns of these markers have been identified. The genomic sequence surrounding the AFLP band 7.21a, residing under the QTL peak, contains a gene sequence homologous to the elongation of very long chain fatty acids-like (ELOVL) protein family. A full-length mRNA (ELOVL-MJ) encoding this protein was isolated from M. japonicus, representing both the first ELOVL gene in crustacea and the first candidate gene identified via QTL studies in crustacea.     

Design, synthesis and structure-activity relationships of (indo-3-yl) heterocyclic derivatives as agonists of the CB1 receptor. Discovery of a clinical candidate

We report an expansion of the structure-activity relationship (SAR) of a novel series of indole-3-heterocyclic CB1 receptor agonists. Starting from the potent but poorly soluble lead, 1, a rational approach was taken in order to balance solubility, hERG activity and potency while retaining the desired long duration of action within the mouse tail flick test. This led to the discovery of compound 38 which successfully progressed into clinical development.     

Association of Mc1r variants with ecologically relevant phenotypes in the European ocellated lizard, Lacerta lepida

A comprehensive knowledge on the genetic basis of coloration is crucial to understand how new colour phenotypes arise and how they contribute to the emergence of new species. Variation in melanocortin‐1 receptor (Mc1r), a gene that has been reported as a target for repeated evolution in a wide range of vertebrate taxa, was assessed in European ocellated lizards (Lacerta lepida) to search for associations with melanin‐based colour phenotypes. Lacerta lepida subspecies’ distribution is associated with the three major bio‐climatic regions in the Iberian Peninsula. A nonconserved and derived substitution (T162I) was associated with the L. l. nevadensis phenotype (prevalence of brown scales). Another substitution (S172C) was associated with the presence of black scales in both L. l. lepida and L. l. iberica, but no mutations were found to be associated with the higher proportion of black in L. l. iberica. Extensive genotyping of Mc1r along the contact zone between L. l. nevadensis and L. l. lepida revealed low gene flow (only two hybrids detected). The implications of these findings are discussed in the context of previous knowledge about the evolutionary history of ocellated lizards.     

The antimalarial ferroquine: from bench to clinic

Ferroquine (FQ, SSR97193) is currently the most advanced organo-metallic drug candidate and about to complete phase II clinical trials as a treatment for uncomplicated malaria. This ferrocene-containing compound is active against both chloroquine-susceptible and chloroquine-resistant Plasmodium falciparum and P. vivax strains and/or isolates. This article focuses on the discovery of FQ, its antimalarial activity, the hypothesis of its mode of action, the current absence of resistance in vitro and recent clinical trials.     

Fingerprinting,embryo type and geographic differentiation in mango (<Emphasis Type="Italic">Mangifera indica</Emphasis> L., Anacardiaceae) with microsatellites

We report the sequence and variability parameters of 16 microsatellite primer pairs obtained from two mango (Mangifera indica L.) genomic libraries after digestion of DNA of the cultivar Tommy Atkins with HaeIII and RsaI and enrichment in CT repeats. Although no significant differences were recorded between the two libraries in the informativeness of the markers obtained, the RsaI library was shown to be more useful than the HaeIII taking into account the efficiency of the library and the feasibility of clone sequencing. The polymorphism revealed by those microsatellites was evaluated in a collection of 28 mango cultivars of different origins. A total of 88 fragments were detected with the 16 simple sequence repeats (SSRs) with an average of 5.5 bands/SSR. Two primer pairs amplified more than a single locus. The mean expected and observed heterozygosities over the 14 single-locus SSRs averaged 0.65 and 0.69 respectively. The total value for the probability of identity was 2.74 × 10⁻⁹. The SSRs studied allowed the unambiguous identification of all the mango genotypes studied and this discrimination can be carried out with just three selected microsatellites. UPGMA cluster analysis and Principal coordinates analysis group the genotypes according to their origin and their classification as monoembryonic or polyembryonic types reflecting the pedigree of the cultivars and the movement of mango germplasm. The results demonstrate the usefulness of microsatellites for studies on identification, variability, germplasm conservation, domestication and movement of germplasm in mango.     

Bioinformatics approaches and resources for single nucleotide polymorphism functional analysis

Since the initial sequencing of the human genome, many projects are underway to understand the effects of genetic variation between individuals. Predicting and understanding the downstream effects of genetic variation using computational methods are becoming increasingly important for single nucleotide polymorphism (SNP) selection in genetics studies and understanding the molecular basis of disease. According to the NIH, there are now more than four million validated SNPs in the human genome. The volume of known genetic variations lends itself well to an informatics approach. Bioinformaticians have become very good at functional inference methods derived from functional and structural genomics. This review will present a broad overview of the tools and resources available to collect and understand functional variation from the perspective of structure, expression, evolution and phenotype. Additionally, public resources available for SNP identification and characterisation are summarised.     

Evaluation of Candidate Gene Effects for Beef Backfat via Bayesian Model Selection

Candidate gene approaches provide tools for exploring and localizing causative genes affecting quantitative traits and the underlying variation may be better understood by determining the relative magnitudes of effects of their polymorphisms. Diacyglycerol O-acyltransferase 1 (DGAT1), fatty acid binding protein (heart) 3 (FABP3), growth hormone 1 (GH1), leptin (LEP) and thyroglobulin (TG) have been previously identified as genes contributing to genetic control of subcutaneous fat thickness (SFT) in beef cattle. In the present research, Bayesian model selection was used to evaluate effects of these five candidate genes by comparing competing non-nested models and treating candidate gene effects as either random or fixed. The analyses were implemented in SAS to simplify the programming and computation. Phenotypic data were gathered from a F₂ population of Wagyu × Limousin cattle. The five candidate genes had significant but varied effects on SFT in this population. Bayesian model selection identified the DGAT1 model as the one with the greatest model probability, whether candidate gene effects were considered random or fixed, and DGAT1 had the greatest additive effect on SFT. The SAS codes developed in the study are freely available and can be downloaded at: http://www.ansci.wsu.edu/programs/.Mention of a proprietary product does not constitute a guarantee or warranty of the product by USDA, Montana AES, or the authors and does not imply its approval to the exclusion of other products that may also be suitable.