Molecular characterisation of the SNAKESKIN mutation in Arabidopsis

Screening of an En element population of Arabidopsis thaliana resulted in the identification of a mutant known as snakeskin (sks) in which the epidermal cell-cell linkages appear to be significantly perturbed (Marchant and Bennett, unpublished results). As a result of the breakdown of epidermal cell-to-cell linkages there are changes in epidermal cell architecture and distribution. These include alterations in pavement epidermal cell shape, stomatal distribution and trichome morphology. The defect in epidermal cell-to-cell adhesion may be a consequence of reduced cell expansion resulting in increased cell division as a compensation mechanism. This results in altered stomatal index and density and reduced root and hypocotyl elongation. A change in the ability of a cell to expand may be attributed to defects in cell wall composition or to the cytoskeleton that determines where the cell wall components arc localised during expansion. The sks mutant was found to have changes in its cellulose, xyloglucan and pectin fractions of the cell wall resulting in defects in cell wall adhesion, strength and expansion. To gain a greater understanding of the sks mutation the molecular basis of the SKS gene map based cloning was undertaken employing a combination of SSLPs, InDels and SNP markers. The SKS gene was found to be located on the bottom arm of chromosome 1 on BAC clone TIl 111. SALK insert lines have been utilised in a candidate gene approach in addition to fine mapping the mutation with SNP markers

Special features of RAD Sequencing data:implications for genotyping

Restriction site-associated DNA Sequencing (RAD-Seq) is an economical and efficient method for SNP discovery and genotyping. As with other sequencing-by-synthesis methods, RAD-Seq produces stochastic count data and requires sensitive analysis to develop or genotype markers accurately. We show that there are several sources of bias specific to RAD-Seq that are not explicitly addressed by current genotyping tools, namely restriction fragment bias, restriction site heterozygosity and PCR GC content bias. We explore the performance of existing analysis tools given these biases and discuss approaches to limiting or handling biases in RAD-Seq data. While these biases need to be taken seriously, we believe RAD loci affected by them can be excluded or processed with relative ease in most cases and that most RAD loci will be accurately genotyped by existing tools

Molecular characterisation of the SNAKESKIN mutation in Arabidopsis

Screening of an En element population of Arabidopsis thaliana resulted in the identification of a mutant known as snakeskin (sks) in which the epidermal cell-cell linkages appear to be significantly perturbed (Marchant and Bennett, unpublished results). As a result of the breakdown of epidermal cell-to-cell linkages there are changes in epidermal cell architecture and distribution. These include alterations in pavement epidermal cell shape, stomatal distribution and trichome morphology. The defect in epidermal cell-to-cell adhesion may be a consequence of reduced cell expansion resulting in increased cell division as a compensation mechanism. This results in altered stomatal index and density and reduced root and hypocotyl elongation. A change in the ability of a cell to expand may be attributed to defects in cell wall composition or to the cytoskeleton that determines where the cell wall components arc localised during expansion. The sks mutant was found to have changes in its cellulose, xyloglucan and pectin fractions of the cell wall resulting in defects in cell wall adhesion, strength and expansion. To gain a greater understanding of the sks mutation the molecular basis of the SKS gene map based cloning was undertaken employing a combination of SSLPs, InDels and SNP markers. The SKS gene was found to be located on the bottom arm of chromosome 1 on BAC clone TIl 111. SALK insert lines have been utilised in a candidate gene approach in addition to fine mapping the mutation with SNP markers.EThOS - Electronic Theses Online ServiceGBUnited Kingdo

Cell adhesion in Arabidopsis thaliana is mediated by ECTOPICALLY PARTING CELLS 1 – a glycosyltransferase (GT64) related to the animal exostosins

Despite the fact that several hundred glycosyltransferases have been identified from sequencing of plant genomes, the biological functions of only a handful have been established to date. A Poplar glycosyltransferase 64 (GT64) family member that is differentially expressed during the cell division and elongation phases of cambial growth was identified from previously generated transcript profiling of cambium tissues. The predicted Poplar GT64 protein has a closely related Arabidopsis homolog ECTOPICALLY PARTING CELLS (EPC1). Mutation of the EPC1 gene, one of three Arabidopsis GT64 family members, results in plants with a dramatically reduced growth habit, defects in vascular formation and reduced cell–cell adhesion properties in hypocotyl and cotyledon tissues. Secondary growth is enhanced in epc1 hypocotyl tissues and it is proposed that this results from the abnormal cell–cell adhesion within the cortical parenchyma cell layers. Loss of cell–cell contacts within cotyledon and leaf tissues is also proposed to account for vascular patterning defects and the fragile nature of epc1 tissues. The EPC1 protein thus plays a critical role during plant development in maintaining the integrity of organs via cell–cell adhesion, thereby providing mechanical strength and facilitating the movement of metabolites throughout the plant

Data from: Special features of RAD Sequencing data: implications for genotyping

RAD Sequencing (RAD-Seq) is an economical and efficient method for SNP discovery and genotyping. As with other sequencing-by-synthesis methods, RAD-Seq produces stochastic count data and requires sensitive analysis to develop or genotype markers accurately. We show that there are several sources of bias specific to RAD-Seq that are not explicitly addressed by current genotyping tools, namely restriction fragment bias, restriction site heterozygosity and PCR GC content bias. We explore the performance of existing analysis tools given these biases and discuss approaches to limiting or handling biases in RAD-Seq data. While these biases need to be taken seriously, we believe RAD loci affected by them can be excluded or processed with relative ease in most cases, and that most RAD loci will be accurately genotyped by existing tools

Davey2012_MolEcol_Dryad_Submission.tar

Scripts and data files required to replicate figures and calculations for associated paper. Details in DESCRIPTION.md file, included in archive

Data from: Sturgeon conservation genomics: SNP discovery and validation using RAD sequencing

Caviar-producing sturgeons belonging to the genus Acipenser are considered to be one of the most endangered species groups in the world. Continued overfishing in spite of increasing legislation, zero catch quotas and extensive aquaculture production have led to the collapse of wild stocks across Europe and Asia. The evolutionary relationships among Adriatic, Russian, Persian and Siberian sturgeons are complex because of past introgression events and remain poorly understood. Conservation management, traceability and enforcement suffer a lack of appropriate DNA markers for the genetic identification of sturgeon at the species, population and individual level. This study employed RAD sequencing to discover and characterize single nucleotide polymorphism (SNP) DNA markers for use in sturgeon conservation in these four tetraploid species over three biological levels, using a single sequencing lane. Four population meta-samples and eight individual samples from one family were barcoded separately before sequencing. Analysis of 14.4 Gb of paired-end RAD data focused on the identification of SNPs in the paired-end contig, with subsequent in silico and empirical validation of candidate markers. Thousands of putatively informative markers were identified including, for the first time, SNPs that show population-wide differentiation between Russian and Persian sturgeons, representing an important advance in our ability to manage these cryptic species. The results highlight the challenges of genotyping-by-sequencing in polyploid taxa, while establishing the potential genetic resources for developing a new range of caviar traceability and enforcement tools

Genomic-assisted identification of genes involved in secondary growth in Arabidopsis utilising transcript profiling of poplar wood-forming tissues

Despite the importance of secondary growth in plants, relatively few genes regulating this process have been identified to date. By using data from detailed transcript profiling of the poplar wood-forming tissues, 150 genes that are differentially expressed within the zone of secondary growth were identified. In order to determine the possible function of these poplar genes, potential Arabidopsis thaliana orthologs were identified and gene knockout lines anal- ysed. Three selection filters were used to identify the most likely orthologous genes using poplar and Arabidopsis sequence comparisons, expression pro- filing in secondary thickened Arabidopsis hypocotyls and global expression analysis of Arabidopsis tissues. Three genes encoding AtCSLA2 (At5g22740), the AtGUT1 GT47 glycosyltransferase (At1g27440) and a protein with no proposed function AtUNKA (At4g27435) were selected for further detailed analysis of their role in secondary growth in Arabidopsis. The presented genome-based approach using both poplar and Arabidopsis systems provides powerful means towards assigning biological functions to enzymes with poorly understood biochemical activity, such as AtCSLA2 and AtGUT1, as well as for proteins with no known function

mec12-0761_DRYAD entry

mec12-0761_DRYAD entr