Analysis of a database of DNA profiles of 734 hybrid tea rose varieties

Over 10,000 Hybrid Tea rose varieties have been described. The large number of varieties and the size of the reference collections may cause problems in DUS (Distinctiveness, Uniformity, and Stability) testing. Molecular markers may help to solve these problems by providing high power to identify and recognise seedling-derived varieties based on unique genotypes, while grouping mutants into groups with identical marker scores. Here we describe the use of a set of 11 rose microsatellite markers to generate a database of molecular profiles of Hybrid Tea varieties. The data were analysed with respect to reproducibility, discriminative power, genetic (sub) structure, and correlation between molecular and DUS characteristics. The use of the markers in the DUS context is discussed with respect to the options 2 and 3 as they were formulated by the UPOV-BMT working group. It is concluded that an option 3 approach (granting of PBR based on distinctness observed with molecular markers) is feasible for ros

In search of genetic diversity in Rosa foetida Hermann in Iran

Rosa foetida is a dense, erect shrub with bright yellow or scarlet flowers with a yellowish reverse petal. It is most abundant in South West Asia. In Iran R. foetida occurs mainly in the mountainous North and West regions. The species is the origin of the strong yellow color in hybrid roses, which was introduced into modern cultivars in 1900 through a single species hybridization event. In this study we have used 10 microsatellite markers to determine diversity in Rosa foetida accessions collected across Iran. To our surprise, nearly all samples collected were of the same genotype, even when collected at different sites. Only four different genotypes have been detected in total. The results are discussed in relation to breeding system, human influence and overall gene pool statu

Grazing as a conservation management tool:Responses of voles to grazer species and densities

Grazing is a widely applied conservation management tool, but the optimal regime for biodiversity conservation is still unknown. The effects of grazers on small mammals are not yet fully understood and mostly restricted to studies which compare grazed with ungrazed areas. We determined the effect of different livestock grazers and densities and a rotation regime, on voles in a conservation area in The Netherlands. We used a 7-year grazing experiment with horse and cattle grazing at two densities namely 0.5 and 1 animal ha(-1) (equivalent to 0.4 and 0.8 LSU), including a rotation regime i.e. 1 year summer grazing with 1 cattle ha(-1) followed by 1 ungrazed year. We recorded vole activity signs as a measure for presence (i.e. presence of burrow entrances, droppings, runways and plant clippings) in circular 2 m(2) plots along transects. Low grazer densities, regardless of species, corresponded to higher vole presence. Vole presence tended to be greater with cattle grazing than with horse grazing, but the difference was not significant. The increase in vole presence was greater in the rotation regime than with low or high density cattle grazing. The different vole activity signs provided similar results to each other with the exception of burrow entrances, suggesting that this measure is less accurate in predicting vole presence. Hence, voles clearly responded to the different grazing regimes. Our results have high relevance for conservation, in particular in systems where small mammals contribute to important ecological processes (e.g. bioturbation, seed dispersal) and play a crucial role in the survival of (iconic) higher trophic level taxa such as raptors or mammalian predators. In such systems, conservation management may best implement low-density cattle or rotation grazing. (C) 2018 Gesellschaft fur Okologie. Published by Elsevier GmbH. All rights reserved

Genomic sequencing and microsatellite marker development for Boswellia papyrifera, an economically important but threatened tree native to dry tropical forests

Microsatellite (or simple sequence repeat, SSR) markers are highly informative DNA markers often used in conservation genetic research. Next-generation sequencing enables efficient development of large numbers of SSR markers at lower costs. Boswellia papyrifera is an economically important tree species used for frankincense production, an aromatic resinous gum exudate from bark. It grows in dry tropical forests in Africa and is threatened by a lack of rejuvenation. To help guide conservation efforts for this endangered species, we conducted an analysis of its genomic DNA sequences using Illumina paired-end sequencing. The genome size was estimated at 705 Mb per haploid genome. The reads contained one microsatellite repeat per 5.7 kb. Based on a subset of these repeats, we developed 46 polymorphic SSR markers that amplified 2-12 alleles in 10 genotypes. This set included 30 trinucleotide repeat markers, four tetranucleotide repeat markers, six pentanucleotide markers and six hexanucleotide repeat markers. Several markers were cross-transferable to Boswellia pirrotae and B. popoviana. In addition, retrotransposons were identified, the reads were assembled and several contigs were identified with similarity to genes of the terpene and terpenoid backbone synthesis pathways, which form the major constituents of the bark resin

Quantitative and qualitative differences in celiac disease epitopes among durum wheat varieties identified through deep RNA-amplicon sequencing

BACKGROUND: Wheat gluten is important for the industrial quality of bread wheat (Triticum aestivum L.) and durum wheat (T. turgidum L.). Gluten proteins are also the source of immunogenic peptides that can trigger a T cell reaction in celiac disease (CD) patients, leading to inflammatory responses in the small intestine. Various peptides with three major T cell epitopes involved in CD are derived from alpha-gliadin fraction of gluten. Alpha-gliadins are encoded by a large multigene family and amino acid variation in the CD epitopes is known to influence the immunogenicity of individual gene family members. Current commercial methods of gluten detection are unable to distinguish between immunogenic and non-immunogenic CD epitope variants and thus to accurately quantify the overall CD epitope load of a given wheat variety. Such quantification is indispensable for correct selection of wheat varieties with low potential to cause CD. RESULTS: A 454 RNA-amplicon sequencing method was developed for alpha-gliadin transcripts encompassing the three major CD epitopes and their variants. The method was used to screen developing grains on plants of 61 different durum wheat cultivars and accessions. A dedicated sequence analysis pipeline returned a total of 304 unique alpha-gliadin transcripts, corresponding to a total of 171 ‘unique deduced protein fragments’ of alpha-gliadins. The numbers of these fragments obtained in each plant were used to calculate quantitative and quantitative differences between the CD epitopes expressed in the endosperm of these wheat plants. A few plants showed a lower fraction of CD epitope-encoding alpha-gliadin transcripts, but none were free of CD epitopes. CONCLUSIONS: The dedicated 454 RNA-amplicon sequencing method enables 1) the grouping of wheat plants according to the genetic variation in alpha-gliadin transcripts, and 2) the screening for plants which are potentially less CD-immunogenic. The resulting alpha-gliadin sequence database will be useful as a reference in proteomics analysis regarding the immunogenic potential of mature wheat grains

Monitoringonderzoek proefverkweldering Noard-Fryslân Bûtendyks : Tussenrapportage 2004

Gegevens betreffende: vernatting en grondwatersamenstelling, verzilting (bodemvochtigheid en saliniteit), vegetatie-ontwikkeling, ganzen en broedvogels. Gezamenlijk onderzoek van: Altenburg & Wymenga, koeman en bijkerk, Rijksuniversiteit Groningen, en Alterra-Texe

QualitySNPng: a user-friendly SNP detection and visualization tool

QualitySNPng is a new software tool for the detection and interactive visualization of single-nucleotide polymorphisms (SNPs). It uses a haplotype-based strategy to identify reliable SNPs; it is optimized for the analysis of current RNA-seq data; but it can also be used on genomic DNA sequences derived from next-generation sequencing experiments. QualitySNPng does not require a sequenced reference genome and delivers reliable SNPs for di- as well as polyploid species. The tool features a user-friendly interface, multiple filtering options to handle typical sequencing errors, support for SAM and ACE files and interactive visualization. QualitySNPng produces high-quality SNP information that can be used directly in genotyping by sequencing approaches for application in QTL and genome-wide association mapping as well as to populate SNP arrays. The software can be used as a stand-alone application with a graphical user interface or as part of a pipeline system like Galaxy. Versions for Windows, Mac OS X and Linux, as well as the source code, are available fro

Genotype calling in tetraploid species from bi-allelic marker data using mixture models

<p>Abstract</p> <p>Background</p> <p>Automated genotype calling in tetraploid species was until recently not possible, which hampered genetic analysis. Modern genotyping assays often produce two signals, one for each allele of a bi-allelic marker. While ample software is available to obtain genotypes (homozygous for either allele, or heterozygous) for diploid species from these signals, such software is not available for tetraploid species which may be scored as five alternative genotypes (aaaa, baaa, bbaa, bbba and bbbb; nulliplex to quadruplex).</p> <p>Results</p> <p>We present a novel algorithm, implemented in the R package fitTetra, to assign genotypes for bi-allelic markers to tetraploid samples from genotyping assays that produce intensity signals for both alleles. The algorithm is based on the fitting of several mixture models with five components, one for each of the five possible genotypes. The models have different numbers of parameters specifying the relation between the five component means, and some of them impose a constraint on the mixing proportions to conform to Hardy-Weinberg equilibrium (HWE) ratios. The software rejects markers that do not allow a reliable genotyping for the majority of the samples, and it assigns a missing score to samples that cannot be scored into one of the five possible genotypes with sufficient confidence.</p> <p>Conclusions</p> <p>We have validated the software with data of a collection of 224 potato varieties assayed with an Illumina GoldenGate™ 384 SNP array and shown that all SNPs with informative ratio distributions are fitted. Almost all fitted models appear to be correct based on visual inspection and comparison with diploid samples. When the collection of potato varieties is analyzed as if it were a population, almost all markers seem to be in Hardy-Weinberg equilibrium. The R package fitTetra is freely available under the GNU Public License from <url>http://www.plantbreeding.wur.nl/UK/software_fitTetra.html</url> and as Additional files with this article.</p

Global-change effects on early-stage decomposition processes in tidal wetlands – implications from a global survey using standardized litter

Tidal wetlands, such as tidal marshes and mangroves, are hotspots for carbon sequestration. The preservation of organic matter (OM) is a critical process by which tidal wetlands exert influence over the global carbon cycle and at the same time gain elevation to keep pace with sea-level rise (SLR). The present study assessed the effects of temperature and relative sea level on the decomposition rate and stabilization of OM in tidal wetlands worldwide, utilizing commercially available standardized litter. While effects on decomposition rate per se were minor, we show strong negative effects of temperature and relative sea level on stabilization, as based on the fraction of labile, rapidly hydrolyzable OM that becomes stabilized during deployment. Across study sites, OM stabilization was 29 % lower in low, more frequently flooded vs. high, less frequently flooded zones. Stabilization declined by ∼ 75 % over the studied temperature gradient from 10.9 to 28.5 ∘C. Additionally, data from the Plum Island long-term ecological research site in Massachusetts, USA, show a pronounced reduction in OM stabilization by > 70 % in response to simulated coastal eutrophication, confirming the potentially high sensitivity of OM stabilization to global change. We therefore provide evidence that rising temperature, accelerated SLR, and coastal eutrophication may decrease the future capacity of tidal wetlands to sequester carbon by affecting the initial transformations of recent OM inputs to soil OM

Generation and analysis of expressed sequence tags in the extreme large genomes Lilium and Tulipa

Background Bulbous flowers such as lily and tulip (Liliaceae family) are monocot perennial herbs that are economically very important ornamental plants worldwide. However, there are hardly any genetic studies performed and genomic resources are lacking. To build genomic resources and develop tools to speed up the breeding in both crops, next generation sequencing was implemented. We sequenced and assembled transcriptomes of four lily and five tulip genotypes using 454 pyro-sequencing technology. Results Successfully, we developed the first set of 81,791 contigs with an average length of 514 bp for tulip, and enriched the very limited number of 3,329 available ESTs (Expressed Sequence Tags) for lily with 52,172 contigs with an average length of 555 bp. The contigs together with singletons covered on average 37% of lily and 39% of tulip estimated transcriptome. Mining lily and tulip sequence data for SSRs (Simple Sequence Repeats) showed that di-nucleotide repeats were twice more abundant in UTRs (UnTranslated Regions) compared to coding regions, while tri-nucleotide repeats were equally spread over coding and UTR regions. Two sets of single nucleotide polymorphism (SNP) markers suitable for high throughput genotyping were developed. In the first set, no SNPs flanking the target SNP (50 bp on either side) were allowed. In the second set, one SNP in the flanking regions was allowed, which resulted in a 2 to 3 fold increase in SNP marker numbers compared with the first set. Orthologous groups between the two flower bulbs: lily and tulip (12,017 groups) and among the three monocot species: lily, tulip, and rice (6,900 groups) were determined using OrthoMCL. Orthologous groups were screened for common SNP markers and EST-SSRs to study synteny between lily and tulip, which resulted in 113 common SNP markers and 292 common EST-SSR. Lily and tulip contigs generated were annotated and described according to Gene Ontology terminology. Conclusions Two transcriptome sets were built that are valuable resources for marker development, comparative genomic studies and candidate gene approaches. Next generation sequencing of leaf transcriptome is very effective; however, deeper sequencing and using more tissues and stages is advisable for extended comparative studies