Large-scale Gene Ontology analysis of plant transcriptome-derived sequences retrieved by AFLP technology

<p>Abstract</p> <p>Background</p> <p>After 10-year-use of AFLP (Amplified Fragment Length Polymorphism) technology for DNA fingerprinting and mRNA profiling, large repertories of genome- and transcriptome-derived sequences are available in public databases for model, crop and tree species. AFLP marker systems have been and are being extensively exploited for genome scanning and gene mapping, as well as cDNA-AFLP for transcriptome profiling and differentially expressed gene cloning. The evaluation, annotation and classification of genomic markers and expressed transcripts would be of great utility for both functional genomics and systems biology research in plants. This may be achieved by means of the Gene Ontology (GO), consisting in three structured vocabularies (<it>i</it>.<it>e</it>. ontologies) describing genes, transcripts and proteins of any organism in terms of their associated cellular component, biological process and molecular function in a species-independent manner. In this paper, the functional annotation of about 8,000 AFLP-derived ESTs retrieved in the NCBI databases was carried out by using GO terminology.</p> <p>Results</p> <p>Descriptive statistics on the type, size and nature of gene sequences obtained by means of AFLP technology were calculated. The gene products associated with mRNA transcripts were then classified according to the three main GO vocabularies. A comparison of the functional content of cDNA-AFLP records was also performed by splitting the sequence dataset into monocots and dicots and by comparing them to all annotated ESTs of Arabidopsis and rice, respectively. On the whole, the statistical parameters adopted for the <it>in silico </it>AFLP-derived transcriptome-anchored sequence analysis proved to be critical for obtaining reliable GO results. Such an exhaustive annotation may offer a suitable platform for functional genomics, particularly useful in non-model species.</p> <p>Conclusion</p> <p>Reliable GO annotations of AFLP-derived sequences can be gathered through the optimization of the experimental steps and the statistical parameters adopted. The Blast2GO software was shown to represent a comprehensive bioinformatics solution for an annotation-based functional analysis. According to the whole set of GO annotations, the AFLP technology generates thorough information for angiosperm gene products and shares common features across angiosperm species and families. The utility of this technology for structural and functional genomics in plants can be implemented by serial annotation analyses of genome-anchored fragments and organ/tissue-specific repertories of transcriptome-derived fragments.</p

ZIEL: Internet-Based Self-Help for Adjustment Problems: Results of a Randomized Controlled Trial

Adjustment Disorder (AjD) represents a healthcare paradox. On the one hand, it is one of the most diagnosed mental disorders worldwide. On the other hand, AjD and its possible treatment options remain a severely neglected field of research. In this context, we developed a self-guided online intervention for adjustment problems, named ZIEL, and tested its efficacy. It is based on and extends a bibliotherapeutic treatment approach for symptoms of AjD. In our study, a total of 98 individuals who had experienced a life event in the last two years, were randomly assigned to care as usual (CAU) or an online intervention group (CAU + online intervention). The primary endpoint was AjD symptom severity measured by Adjustment Disorder-New Module 20 (ADNM-20). Secondary endpoints were depressive symptoms, quality of life and other variables such as satisfaction and usability. Both the intervention and the control group improved comparably well regarding the severity of adjustment disorder symptoms post-treatment. However, participants in the intervention group showed significantly fewer depressive symptoms and a significantly higher quality of life (Cohen's d: 0.89 (BDI) and -0.49 (SF-12)). The intervention was well-received by users with an above average usability rating. Overall, the results suggest that the ZIEL intervention has the promise to contribute to the treatment of AjD and reduce symptom burden by means of a scalable low-barrier approach

From QTL to candidate gene: Genetical genomics of simple and complex traits in potato using a pooling strategy

<p>Abstract</p> <p>Background</p> <p>Utilization of the natural genetic variation in traditional breeding programs remains a major challenge in crop plants. The identification of candidate genes underlying, or associated with, phenotypic trait QTLs is desired for effective marker assisted breeding. With the advent of high throughput -omics technologies, screening of entire populations for association of gene expression with targeted traits is becoming feasible but remains costly. Here we present the identification of novel candidate genes for different potato tuber quality traits by employing a pooling approach reducing the number of hybridizations needed. Extreme genotypes for a quantitative trait are collected and the RNA from contrasting bulks is then profiled with the aim of finding differentially expressed genes.</p> <p>Results</p> <p>We have successfully implemented the pooling strategy for potato quality traits and identified candidate genes associated with potato tuber flesh color and tuber cooking type. Elevated expression level of a dominant allele of the β-carotene hydroxylase (<it>bch</it>) gene was associated with yellow flesh color through mapping of the gene under a major QTL for flesh color on chromosome 3. For a second trait, a candidate gene with homology to a tyrosine-lysine rich protein (TLRP) was identified based on allele specificity of the probe on the microarray. TLRP was mapped on chromosome 9 in close proximity to a QTL for potato cooking type strengthening its significance as a candidate gene. Furthermore, we have performed a profiling experiment targeting a polygenic trait, by pooling individual genotypes based both on phenotypic and marker data, allowing the identification of candidate genes associated with the two different linkage groups.</p> <p>Conclusions</p> <p>A pooling approach for RNA-profiling with the aim of identifying novel candidate genes associated with tuber quality traits was successfully implemented. The identified candidate genes for tuber flesh color (<it>bch</it>) and cooking type (<it>tlrp</it>) can provide useful markers for breeding schemes in the future. Strengths and limitations of the approach are discussed.</p

Implementation of two high through-put techniques in a novel application: detecting point mutations in large EMS mutated plant populations

Background - The establishment of mutant populations together with the strategies for targeted mutation detection has been applied successfully to a large number of organisms including many species in the plant kingdom. Considerable efforts have been invested into research on tomato as a model for berry-fruit plants. With the progress of the tomato sequencing project, reverse genetics becomes an obvious and achievable goal. Results - Here we describe the treatment of Solanum lycopersicum seeds with 1% EMS and the development of a new mutated tomato population. To increase targeted mutant detection throughput an automated seed DNA extraction has been combined with novel mutation detection platforms for TILLING in plants. We have adapted two techniques used in human genetic diagnostics: Conformation Sensitive Capillary Electrophoresis (CSCE) and High Resolution DNA Melting Analysis (HRM) to mutation screening in DNA pools. Classical TILLING involves critical and time consuming steps such as endonuclease digestion reactions and gel electrophoresis runs. Using CSCE or HRM, the only step required is a simple PCR before either capillary electrophoresis or DNA melting curve analysis. Here we describe the development of a mutant tomato population, the setting up of two polymorphism detection platforms for plants and the results of the first screens as mutation density in the populations and estimation of the false-positives rate when using HRM to screen DNA pools. Conclusion - These results demonstrate that CSCE and HRM are fast, affordable and sensitive techniques for mutation detection in DNA pools and therefore allow the rapid identification of new allelic variants in a mutant population. Results from the first screens indicate that the mutagen treatment has been effective with an average mutation detection rate per diploid genome of 1.36 mutation/kb/1000 line

Induced point mutations in the phytoene synthase 1 gene cause differences in carotenoid content during tomato fruit ripening

In tomato, carotenoids are important with regard to major breeding traits such as fruit colour and human health. The enzyme phytoene synthase (PSY1) directs metabolic flux towards carotenoid synthesis. Through TILLING (Targeting Induced Local Lesions IN Genomes), we have identified two point mutations in the Psy1 gene. The first mutation is a knockout allele (W180*) and the second mutation leads to an amino acid substitution (P192L). Plants carrying the Psy1 knockout allele show fruit with a yellow flesh colour similar to the r, r mutant, with no further change in colour during ripening. In the line with P192L substitution, fruit remain yellow until 3 days post-breaker and eventually turn red. Metabolite profiling verified the absence of carotenoids in the W180* line and thereby confirms that PSY1 is the only enzyme introducing substrate into the carotenoid pathway in ripening fruit. More subtle effects on carotenoid accumulation were observed in the P192L line with a delay in lycopene and β-carotene accumulation clearly linked to a very slow synthesis of phytoene. The observation of lutein degradation with ripening in both lines showed that lutein and its precursors are still synthesised in ripening fruit. Gene expression analysis of key genes involved in carotenoid biosynthesis revealed that expression levels of genes in the pathway are not feedback-regulated by low levels or absence of carotenoid compounds. Furthermore, protein secondary structure modelling indicated that the P192L mutation affects PSY1 activity through misfolding, leading to the low phytoene accumulation

Unravelling enzymatic discoloration in potato through a combined approach of candidate genes, QTL, and expression analysis

Enzymatic discoloration (ED) of potato tubers was investigated in an attempt to unravel the underlying genetic factors. Both enzyme and substrate concentration have been reported to influence the degree of discoloration and as such this trait can be regarded as polygenic. The diploid mapping population C × E, consisting of 249 individuals, was assayed for the degree of ED and levels of chlorogenic acid and tyrosine. Using this data, Quantitative Trait Locus (QTL) analysis was performed. Three QTLs for ED have been found on parental chromosomes C3, C8, E1, and E8. For chlorogenic acid a QTL has been identified on C2 and for tyrosine levels, a QTL has been detected on C8. None of the QTLs overlap, indicating the absence of genetic correlations between these components underlying ED, in contrast to earlier reports in literature. An obvious candidate gene for the QTL for ED on Chromosome 8 is polyphenol oxidase (PPO), which was previously mapped on chromosome 8. With gene-specific primers for PPO gene POT32 a CAPS marker was developed. Three different alleles (POT32-1, -2, and -3) could be discriminated. The segregating POT32 alleles were used to map the POT32 CAPS marker and QTL analysis was redone, showing that POT32 coincides with the QTL peak. A clear correlation between allele combinations and degree of discoloration was observed. In addition, analysis of POT32 gene expression in a subset of genotypes indicated a correlation between the level of gene expression and allele composition. On average, genotypes having two copies of allele 1 had both the highest degree of discoloration as well as the highest level of POT32 gene expression

Synchronization of developmental, molecular and metabolic aspects of source–sink interactions

Plants have evolved a multitude of strategies to adjust their growth according to external and internal signals. Interconnected metabolic and phytohormonal signalling networks allow adaption to changing environmental and developmental conditions and ensure the survival of species in fluctuating environments. In agricultural ecosystems, many of these adaptive responses are not required or may even limit crop yield, as they prevent plants from realizing their fullest potential. By lifting source and sink activities to their maximum, massive yield increases can be foreseen, potentially closing the future yield gap resulting from an increasing world population and the transition to a carbon-neutral economy. To do so, a better understanding of the interplay between metabolic and developmental processes is required. In the past, these processes have been tackled independently from each other, but coordinated efforts are required to understand the fine mechanics of source–sink relations and thus optimize crop yield. Here, we describe approaches to design high-yielding crop plants utilizing strategies derived from current metabolic concepts and our understanding of the molecular processes determining sink development.Research in the authors’ laboratories was supported by the following grants: the cassava source–sink (CASS) project of the Bill and Melinda Gates Foundation (to A.R.F., H.E.N., M.S. and U.S.); the ERA-CAPs project SourSi (to A.R.F. and L.J.S.); the BIO2015-3019-EXP grant from the Spanish Ministry of Economy, Industry and Competitiveness and the PCIN-2017-032 CONCERT-JAPAN project financed by the Ministry of Science, Innovation and Universities (to S.P.); Australian Research Council DP180103834 (to Y.L.R.); the US National Science Foundation (grant no. IOS-1457183); the Agriculture and Food Research Initiative (AFRI; grant no. 2017-67013-26158) from the USDA National Institute of Food and Agriculture (to M.T.); the Finnish Centre of Excellence in Molecular Biology of Primary Producers (Academy of Finland CoE program 2014–2019; grant no. 271832); the Gatsby Foundation (grant no. GAT3395/PR3); the University of Helsinki (grant no. 799992091); the European Research Council Advanced Investigator Grant SYMDEV (grant no. 323052; to Y.H.); the BMBF (grant no. 031B0191); the DFG (SPP1530: WA3639/1-2, 2-1); and the Max-Planck-Society (to V.W.). We additionally thank D. Ko and R. Ruonala for their comments on the manuscript

Sequencing the Potato Genome: Outline and First Results to Come from the Elucidation of the Sequence of the World’s Third Most Important Food Crop

Potato is a member of the Solanaceae, a plant family that includes several other economically important species, such as tomato, eggplant, petunia, tobacco and pepper. The Potato Genome Sequencing Consortium (PGSC) aims to elucidate the complete genome sequence of potato, the third most important food crop in the world. The PGSC is a collaboration between 13 research groups from China, India, Poland, Russia, the Netherlands, Ireland, Argentina, Brazil, Chile, Peru, USA, New Zealand and the UK. The potato genome consists of 12 chromosomes and has a (haploid) length of approximately 840 million base pairs, making it a medium-sized plant genome. The sequencing project builds on a diploid potato genomic bacterial artificial chromosome (BAC) clone library of 78000 clones, which has been fingerprinted and aligned into ~7000 physical map contigs. In addition, the BAC-ends have been sequenced and are publicly available. Approximately 30000 BACs are anchored to the Ultra High Density genetic map of potato, composed of 10000 unique AFLPTM markers. From this integrated genetic-physical map, between 50 to 150 seed BACs have currently been identified for every chromosome. Fluorescent in situ hybridization experiments on selected BAC clones confirm these anchor points. The seed clones provide the starting point for a BAC-by-BAC sequencing strategy. This strategy is being complemented by whole genome shotgun sequencing approaches using both 454 GS FLX and Illumina GA2 instruments. Assembly and annotation of the sequence data will be performed using publicly available and tailor-made tools. The availability of the annotated data will help to characterize germplasm collections based on allelic variance and to assist potato breeders to more fully exploit the genetic potential of potat