Genetic determinism, inducible morphology and phenotypic plasticity in the marine bryozoan Èlectra pilosa' (L.)

The marine bryozoan Electra pilosa typically inhabits ephemeral substrata in the intertidal and shallow subtidal, and is probably the ecologically most successful bryozoan species in British waters. Modular organisms like E. pilosa frequently evolve pronounced phenotypic plasticity to cope with the ecological challenges resulting from passive larval dispersal into unpredictable habitats, and temporal variability of the environment colonized by the immobile adult stage. E. pilosa colonies on wave-exposed shores differ morphologically from those found on sheltered shores in possessing numerous long-spined zooids. The present study demonstrates that spine formation in E. pilosa is environmentally inducible by wave-related abrasion by macroalgae; additionally, the spines also have a fortuitous anti-predator effect in discouraging predation by the nudibranchs Adalaria proxima and Polycera quadrilineata. It is suggested that the inducible spines of E. pilosa constitute an adaptation for the protection of feeding polypides in high-energy environments, and that plasticity for the trait is of adaptive value in this organism which exploits a diverse range of habitats. Although a number of traits in this species clearly are subject to considerable phenotypic plasticity, other attributes apparently are highly deterministic, heritable and genotype-specific. Electra pilosa displays pronounced among-genotype variation in colony growth rate, and the present study shows that this variation is due to proximate factors which affect growth rate and covary with genotype. This study also presents the first evidence of senescence at the zooid level in E. pilosa: Zooids deteriorate systematically over time, as indicated by decreasing polypide life spans and increasing polypide regeneration times, but in contrast to this, whole-organism senescence does not appear to occur in this species

Diatom contour analysis using morphological curvature scale spaces

A method for shape analysis of diatoms (single-cell algae with silica shells) based on extraction of features on the contour of the cells by multi-scale mathematical morphology is presented. After building a morphological contour curvature scale space, we present a method for extracting the most prominent features by unsupervised cluster analysis. The number of extracted features matches well with those found visually in 92 % of the 350 diatom images examined

An evaluation of genotyping by sequencing (GBS) to map the <em>Breviaristatum-e (ari-e)</em> locus in cultivated barley

ABSTRACT: We explored the use of genotyping by sequencing (GBS) on a recombinant inbred line population (GPMx) derived from a cross between the two-rowed barley cultivar ‘Golden Promise’ (ari-e.GP/Vrs1) and the six-rowed cultivar ‘Morex’ (Ari-e/vrs1) to map plant height. We identified three Quantitative Trait Loci (QTL), the first in a region encompassing the spike architecture gene Vrs1 on chromosome 2H, the second in an uncharacterised centromeric region on chromosome 3H, and the third in a region of chromosome 5H coinciding with the previously described dwarfing gene Breviaristatum-e (Ari-e). BACKGROUND: Barley cultivars in North-western Europe largely contain either of two dwarfing genes; Denso on chromosome 3H, a presumed ortholog of the rice green revolution gene OsSd1, or Breviaristatum-e (ari-e) on chromosome 5H. A recessive mutant allele of the latter gene, ari-e.GP, was introduced into cultivation via the cv. ‘Golden Promise’ that was a favourite of the Scottish malt whisky industry for many years and is still used in agriculture today. RESULTS: Using GBS mapping data and phenotypic measurements we show that ari-e.GP maps to a small genetic interval on chromosome 5H and that alternative alleles at a region encompassing Vrs1 on 2H along with a region on chromosome 3H also influence plant height. The location of Ari-e is supported by analysis of near-isogenic lines containing different ari-e alleles. We explored use of the GBS to populate the region with sequence contigs from the recently released physically and genetically integrated barley genome sequence assembly as a step towards Ari-e gene identification. CONCLUSIONS: GBS was an effective and relatively low-cost approach to rapidly construct a genetic map of the GPMx population that was suitable for genetic analysis of row type and height traits, allowing us to precisely position ari-e.GP on chromosome 5H. Mapping resolution was lower than we anticipated. We found the GBS data more complex to analyse than other data types but it did directly provide linked SNP markers for subsequent higher resolution genetic analysis

EORNA, a barley gene and transcript abundance database

A high-quality, barley gene reference transcript dataset (BaRTv1.0), was used to quantify gene and transcript abundances from 22 RNA-seq experiments, covering 843 separate samples. Using the abundance data we developed a Barley Expression Database (EORNA*) to underpin a visualisation tool that displays comparative gene and transcript abundance data on demand as transcripts per million (TPM) across all samples and all the genes. EORNA provides gene and transcript models for all of the transcripts contained in BaRTV1.0, and these can be conveniently identified through either BaRT or HORVU gene names, or by direct BLAST of query sequences. Browsing the quantification data reveals cultivar, tissue and condition specific gene expression and shows changes in the proportions of individual transcripts that have arisen via alternative splicing. TPM values can be easily extracted to allow users to determine the statistical significance of observed transcript abundance variation among samples or perform meta analyses on multiple RNA-seq experiments. * Eòrna is the Scottish Gaelic word for Barley.</p