Haplotype inference from unphased SNP data in heterozygous polyploids based on SAT

<p>Abstract</p> <p>Background</p> <p>Haplotype inference based on unphased SNP markers is an important task in population genetics. Although there are different approaches to the inference of haplotypes in diploid species, the existing software is not suitable for inferring haplotypes from unphased SNP data in polyploid species, such as the cultivated potato (<it>Solanum tuberosum</it>). Potato species are tetraploid and highly heterozygous.</p> <p>Results</p> <p>Here we present the software SATlotyper which is able to handle polyploid and polyallelic data. SATlo-typer uses the Boolean satisfiability problem to formulate Haplotype Inference by Pure Parsimony. The software excludes existing haplotype inferences, thus allowing for calculation of alternative inferences. As it is not known which of the multiple haplotype inferences are best supported by the given unphased data set, we use a bootstrapping procedure that allows for scoring of alternative inferences. Finally, by means of the bootstrapping scores, it is possible to optimise the phased genotypes belonging to a given haplotype inference. The program is evaluated with simulated and experimental SNP data generated for heterozygous tetraploid populations of potato. We show that, instead of taking the first haplotype inference reported by the program, we can significantly improve the quality of the final result by applying additional methods that include scoring of the alternative haplotype inferences and genotype optimisation. For a sub-population of nineteen individuals, the predicted results computed by SATlotyper were directly compared with results obtained by experimental haplotype inference via sequencing of cloned amplicons. Prediction and experiment gave similar results regarding the inferred haplotypes and phased genotypes.</p> <p>Conclusion</p> <p>Our results suggest that Haplotype Inference by Pure Parsimony can be solved efficiently by the SAT approach, even for data sets of unphased SNP from heterozygous polyploids. SATlotyper is freeware and is distributed as a Java JAR file. The software can be downloaded from the webpage of the GABI Primary Database at <url>http://www.gabipd.org/projects/satlotyper/</url>. The application of SATlotyper will provide haplotype information, which can be used in haplotype association mapping studies of polyploid plants.</p

The Transcriptome of Compatible and Incompatible Interactions of Potato (Solanum tuberosum) with Phytophthora infestans Revealed by DeepSAGE Analysis

Late blight, caused by the oomycete Phytophthora infestans, is the most important disease of potato (Solanum tuberosum). Understanding the molecular basis of resistance and susceptibility to late blight is therefore highly relevant for developing resistant cultivars, either by marker-assissted selection or by transgenic approaches. Specific P. infestans races having the Avr1 effector gene trigger a hypersensitive resistance response in potato plants carrying the R1 resistance gene (incompatible interaction) and cause disease in plants lacking R1 (compatible interaction). The transcriptomes of the compatible and incompatible interaction were captured by DeepSAGE analysis of 44 biological samples comprising five genotypes, differing only by the presence or absence of the R1 transgene, three infection time points and three biological replicates. 30.859 unique 21 base pair sequence tags were obtained, one third of which did not match any known potato transcript sequence. Two third of the tags were expressed at low frequency (<10 tag counts/million). 20.470 unitags matched to approximately twelve thousand potato transcribed genes. Tag frequencies were compared between compatible and incompatible interactions over the infection time course and between compatible and incompatible genotypes. Transcriptional changes were more numerous in compatible than in incompatible interactions. In contrast to incompatible interactions, transcriptional changes in the compatible interaction were observed predominantly for multigene families encoding defense response genes and genes functional in photosynthesis and CO2 fixation. Numerous transcriptional differences were also observed between near isogenic genotypes prior to infection with P. infestans. Our DeepSAGE transcriptome analysis uncovered novel candidate genes for plant host pathogen interactions, examples of which are discussed with respect to possible function

The GABI Primary Database: GABIPD - Integration of Plant &#x27;Omics&#x27;-Data in Gene Context

GabiPD (&#x22;http://www.gabipd.org/&#x22;:http://www.gabipd.org/) at the Max Planck Institute of Molecular Plant Physiology constitutes a repository and analysis platform of genomic, transcriptomic, proteomic, and metabolomic plant data provided by the GABI community (Ria&#xf1;o-Pach&#xf3;n et al., 2009). Beside the data, current versions of useful tools are being made accessible via GabiPD, such as MapMan (Usadel et al., 2005) and SATlotyper (Neigenfind et al., 2008). Access to GabiPD is provided via either the web interface or WebServices.&#xd;&#xa;&#xd;&#xa;In GabiPD, twenty different plant species are currently represented with the model plant A. thaliana on top followed by the crop plants S. tuberosum and H. vulgare. Innovative user interfaces allow interactive access to the different data types, e.g. (i) GreenCards to all text-based information, like sequences and comparative SNP information (e.g., Pajerowska-Mukhtar et al., 2009) (ii) YAMB to comparative genetic maps, (iii) MapManWeb to gene expression or metabolite profiling data mapped onto pathways, or (iv) 2DGelViewer to annotated 2DE gel images. All data types (e.g., clones, protein spots, gene expression data) in GabiPD are pointing to the central Gene GreenCard, where gene information is retrieved from genome annotation projects or UniGene sets (provided by NCBI). With the Gene GreenCards, we provide MapMan and Gene Ontology annotations and ortholog information (currently only between _A. thaliana_ and _O. sativa ssp. japonica_). Recently, a new graphical representation of transcripts was integrated displaying gene structure (untranslated regions, start and stop codons and exon-exon junctions). Protein domains as well as ESTs, are mapped on the transcript displays. In order to ease the transfer of knowledge from model to crop plants, we have performed similarity-based mappings between closely related species, i.e., _O. sativa ssp. japonica_ and _H. vulgare_. By the integration of complex data in a framework of existing knowledge, GabiPD provides new insights and allows for new interpretations of plant data.&#xd;&#xa;This work is/was supported by the BMBF (GABI grants 0312272, 0313112, 0315046).&#xd;&#xa;&#xd;&#xa;Neigenfind J et al. (2008) Haplotype inference from unphased SNP data in heterozygous polyploids based on SAT. _BMC Genomics_ 9:356.&#xd;&#xa;&#xd;&#xa;Pajerowska-Mukhtar K et al. (2009) Single nucleotide polymorphisms in the allene oxide synthase 2 gene are associated with field resistance to late blight in populations of tetraploid potato cultivars. _Genetics_, doi:&#x22;10.1534/genetics.108.094268&#x22;:http://dx.doi.org/10.1534/genetics.108.094268&#xd;&#xa;&#xd;&#xa;Riano-Pachon DM et al. (2009) GabiPD: The GABI Primary Database - a plant integrative &#x2018;omics&#x2019; database. _Nucleic Acids Research_ 37(Database issue):D954-9, DOI &#x22;10.1093/nar/gkn611&#x22;:http://dx.doi.org/10.1093/nar/gkn611&#xd;&#xa;&#xd;&#xa;Usadel B et al (2006) PageMan: an interactive ontology tool to generate, display, and annotate overview graphs for profiling experiments. _BMC Bioinformatics_ 7:535.&#xd;&#xa

GabiPD: The GABI Primary Database - a plant integrative &#x2018;omics&#x2019; database

The GABI Primary Database, GabiPD (http://www.gabipd.org/), was established in the frame of the German initiative for Genome Analysis of the Plant Biological System (GABI). The goal of GabiPD is to collect, integrate, analyse and visualise primary information from GABI projects. GabiPD constitutes a repository and analysis platform for a wide array of heterogeneous data from high-throughput experiments in several plant species. Data from different &#x2018;omics&#x2019; fronts are incorporated (i.e., genomics, transcriptomics, proteomics and metabolomics), originating from 14 different model or crop species. We have developed the concept of GreenCards for text based retrieval of all data types in GabiPD (e.g., clones, genes, mutant lines). All data types point to a central Gene GreenCard, where gene information is integrated from genome projects or NCBI UniGene sets. The centralised Gene GreenCard allows visualising ESTs aligned to annotated transcripts as well as displaying identified protein domains and gene structure. Moreover GabiPD makes available interactive genetic maps from potato and barley, and 2DE-gels from Arabidopsis thaliana and Brassica napus. Gene expression and metabolic profiling data can be visualised through MapManWeb. By the integration of complex data in a framework of existing knowledge, GabiPD provides new insights and allows for new interpretations of the data

Single Nucleotide Polymorphisms in the Allene Oxide Synthase 2 Gene Are Associated With Field Resistance to Late Blight in Populations of Tetraploid Potato Cultivars

The oomycete Phytophthora infestans causes late blight, the most relevant disease of potato (Solanum tuberosum) worldwide. Field resistance to late blight is a complex trait. When potatoes are cultivated under long day conditions in temperate climates, this resistance is correlated with late plant maturity, an undesirable characteristic. Identification of natural gene variation underlying late blight resistance not compromised by late maturity will facilitate the selection of resistant cultivars and give new insight in the mechanisms controlling quantitative pathogen resistance. We tested 24 candidate loci for association with field resistance to late blight and plant maturity in a population of 184 tetraploid potato individuals. The individuals were genotyped for 230 single nucleotide polymorphisms (SNPs) and 166 microsatellite alleles. For association analysis we used a mixed model, taking into account population structure, kinship, allele substitution and interaction effects of the marker alleles at a locus with four allele doses. Nine SNPs were associated with maturity corrected resistance (P < 0.001), which collectively explained 50% of the genetic variance of this trait. A major association was found at the StAOS2 locus encoding allene oxide synthase 2, a key enzyme in the biosynthesis of jasmonates, plant hormones that function in defense signaling. This finding supports StAOS2 as being one of the factors controlling natural variation of pathogen resistance

Heat map of the log-fold change values of sample groups R1, r1 and ORF45 at 1 dpi and 3 dpi compared to 0 dpi.

<p>Shown is the result of a hierarchical cluster analysis using 406 unitags with significant expression changes in the incompatible interactions (R1) at 3 dpi compared to 0 dpi. Two regions with preferential up or down regulation in the incompatible interaction are shown enlarged with the tag annotation given on the right side. NA: Tag with no matching target sequence.</p

Differential expression of known defense response genes in compatible and incompatible interactions analysed by hierarchical cluster analysis.

<p>The heat map of the log-fold change values of sample groups R1, r1 and ORF45 at 1 dpi and 3 dpi versus 0 dpi is shown. Unitags matching to twenty four transcripts were selected based on allocation to the gene ontology term “defense response” (GO:0006952). The annotation and the corresponding unigene number are shown on the right. Significance of the pair wise comparisons between R1, r1 and ORF45 sample groups is indicated by * (FDR≤0.05), ** (FDR≤0.01) and *** (FDR≤0.001).</p

Expression patterns of tags StET010753 and StET009643 matching the tomato transaldolase isoforms ToTAL1 (PotTAL1) and ToTAL2, respectively.

<p>Tag StET10753 is weakly up regulated in the R1 and r1 plants but not in the ORF45 plants at three days post inoculation. Tag StET009643 shows clear up regulation only in the R1 plants one day after inoculation. Transcript levels are shown as mean tag counts/million of six (R1 and r1 plants), three (ORF45 plants at 0 dpi and 2 dpi) and two (ORF45 plants at 3 dpi) independent samples. Bars indicate the standard deviation according to the Poisson distribution.</p