Identification of R-Gene homologous DNA fragments genetically linked to disease resistance loci in Arabidopsis thaliana

Disease resistance in plants is a desirable economic trait. A number of disease resistance genes from various plant species have been cloned so far. The gene products of some of these can be distinguished by the presence of an N-terminal nucleotide binding site and a C-terminal stretch of leucine-rich repeats. Although these gene products are structurally related, the DNA sequences are poorly conserved. Only parts of the nucleotide binding site share enough DNA identity to design primers for polymerase chain reaction amplification of related DNA sequences. Such primers were used to amplify different resistance-gene-like (RGL) DNA fragments from Arabidopsis thaliana accessions Landsberg erecta and Columbia. Almost all cloned DNA fragments were genetically closely linked with known disease resistance loci. Most RGL fragments were found in a clustered or dispersed multi-copy sequence organization, supporting the supposed correlation of RGL sequences and disease resistance loci

Host- and stage-dependent secretome of the arbuscular mycorrhizal fungus Rhizophagus irregularis

Arbuscular mycorrhizal fungi form the most wide‐spread endosymbiosis with plants. There is very little host‐specificity in this interaction, however host preferences as well as varying symbiotic efficiencies have been observed. We hypothesize that secreted proteins (SPs) may act as fungal effectors to control symbiotic efficiency in a host‐dependent manner. Therefore, we studied whether AM fungi adjust their secretome in a host‐ and stage‐dependent manner to contribute to their extremely wide host‐range. We investigated the expression of SP‐encoding genes of Rhizophagus irregularis in three evolutionary distantly‐related plant species, Medicago truncatula, Nicotiana benthamiana and Allium schoenoprasum. In addition we used laser microdissection in combination with RNAseq to study SP expression at different stages of the interaction in Medicago. Our data indicate that most expressed SPs show roughly equal expression levels in the interaction with all three host plants. In addition, a subset shows significant differential expression depending on the host plant. Furthermore, SP expression is controlled locally in the hyphal network in response to host dependent cues. Overall, this study presents a comprehensive analysis of the R. irregularis secretome, which now offers a solid basis to direct functional studies on the role of fungal SPs in AM symbiosis

Biochemical and Molecular Analysis of Pink Tomatoes: Deregulated Expression of the Gene Encoding Transcription Factor SlMYB12 Leads to Pink Tomato Fruit Color1[W][OA]

The color of tomato fruit is mainly determined by carotenoids and flavonoids. Phenotypic analysis of an introgression line (IL) population derived from a cross between Solanum lycopersicum ‘Moneyberg’ and the wild species Solanum chmielewskii revealed three ILs with a pink fruit color. These lines had a homozygous S. chmielewskii introgression on the short arm of chromosome 1, consistent with the position of the y (yellow) mutation known to result in colorless epidermis, and hence pink-colored fruit, when combined with a red flesh. Metabolic analysis showed that pink fruit lack the ripening-dependent accumulation of the yellow-colored flavonoid naringenin chalcone in the fruit peel, while carotenoid levels are not affected. The expression of all genes encoding biosynthetic enzymes involved in the production of the flavonol rutin from naringenin chalcone was down-regulated in pink fruit, suggesting that the candidate gene underlying the pink phenotype encodes a regulatory protein such as a transcription factor rather than a biosynthetic enzyme. Of 26 MYB and basic helix-loop-helix transcription factors putatively involved in regulating transcription of genes in the phenylpropanoid and/or flavonoid pathway, only the expression level of the MYB12 gene correlated well with the decrease in the expression of structural flavonoid genes in peel samples of pink- and red-fruited genotypes during ripening. Genetic mapping and segregation analysis showed that MYB12 is located on chromosome 1 and segregates perfectly with the characteristic pink fruit color. Virus-induced gene silencing of SlMYB12 resulted in a decrease in the accumulation of naringenin chalcone, a phenotype consistent with the pink-colored tomato fruit of IL1b. In conclusion, biochemical and molecular data, gene mapping, segregation analysis, and virus-induced gene silencing experiments demonstrate that the MYB12 transcription factor plays an important role in regulating the flavonoid pathway in tomato fruit and suggest strongly that SlMYB12 is a likely candidate for the y mutation

84 tomato accessions - Exploring genetic variation in the tomato (Solanum section Lycopersicon) clade by whole-genome sequencing

84 tomato accessions - Genetic variation in the tomato clade was explored by sequencing a selection of 84 tomato accessions and related wild species representative for the Lycopersicon, Arcanum, Eriopersicon and Neolycopersicon group. In addition, we present a reconstruction of three new reference genomes in support of our comparative genome analyses. This comparative analysis elucidates species specific chromosome structural differences. Furthermore, sequence diversity in commercial breeding lines appears extremely low, indicating the dramatic genetic erosion of crop tomatoes. For wild species the SNP frequency increases 20 folds to more than 10 million SNPs. Our study unequivocally illustrates the need for multiple reference genomes in support of tomato comparative genomics and Solanum genome evolution studies. Comparative sequence alignment reveals group, species, and accession specific polymorphisms within domestication syndrome genes, which are explanatory for characteristic fruit traits and growth habit in tomato accessions. Using gene models from the annotated Heinz reference genome, we observe a bias in dN/dS ratio in domestication syndrome genes compared to a random set of genes which probably is the result of a positive selection. Based on whole genome SNP information, we unambiguously resolved the phylogenetic placement for each accession in the four main groups in the Lycopersicon clade using Maximum Likelihood analyses. Phylogenetic relationships appear correlated with habitat and mating type and point to the occurrence of geographical races within these groups and thus are of practical importance for introgressive hybridization breeding

84 tomato accessions - Exploring genetic variation in the tomato (Solanum section Lycopersicon) clade by whole-genome sequencing

84 tomato accessions - Genetic variation in the tomato clade was explored by sequencing a selection of 84 tomato accessions and related wild species representative for the Lycopersicon, Arcanum, Eriopersicon and Neolycopersicon group. In addition, we present a reconstruction of three new reference genomes in support of our comparative genome analyses. This comparative analysis elucidates species specific chromosome structural differences. Furthermore, sequence diversity in commercial breeding lines appears extremely low, indicating the dramatic genetic erosion of crop tomatoes. For wild species the SNP frequency increases 20 folds to more than 10 million SNPs. Our study unequivocally illustrates the need for multiple reference genomes in support of tomato comparative genomics and Solanum genome evolution studies. Comparative sequence alignment reveals group, species, and accession specific polymorphisms within domestication syndrome genes, which are explanatory for characteristic fruit traits and growth habit in tomato accessions. Using gene models from the annotated Heinz reference genome, we observe a bias in dN/dS ratio in domestication syndrome genes compared to a random set of genes which probably is the result of a positive selection. Based on whole genome SNP information, we unambiguously resolved the phylogenetic placement for each accession in the four main groups in the Lycopersicon clade using Maximum Likelihood analyses. Phylogenetic relationships appear correlated with habitat and mating type and point to the occurrence of geographical races within these groups and thus are of practical importance for introgressive hybridization breeding

Genome sequence and analysis of the tuber crop potato.

Potato (Solanum tuberosum L.) is the world's most important non-grain food crop and is central to global food security. It is clonally propagated, highly heterozygous, autotetraploid, and suffers acute inbreeding depression. Here we use a homozygous doubled-monoploid potato clone to sequence and assemble 86% of the 844-megabase genome. We predict 39,031 protein-coding genes and present evidence for at least two genome duplication events indicative of a palaeopolyploid origin. As the first genome sequence of an asterid, the potato genome reveals 2,642 genes specific to this large angiosperm clade. We also sequenced a heterozygous diploid clone and show that gene presence/absence variants and other potentially deleterious mutations occur frequently and are a likely cause of inbreeding depression. Gene family expansion, tissue-specific expression and recruitment of genes to new pathways contributed to the evolution of tuber development. The potato genome sequence provides a platform for genetic improvement of this vital crop