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Viehöver, P.

Publications and source records attributed to Viehöver, P..

12 recordsLinked to original sources
bioRxiv2026

Molecular sources of monoterpenoid chemodiversity in the Asteraceae Tanacetum vulgare suggest a new model for the evolution of specialized metabolism

Highly diversified specialized metabolism enables plant communication with pollinators, herbivores, and protectors1-4. Its chemodiversity, under which evenness, richness and variation is summarized5-7, includes many compounds without known function1-4 and presents an evolutionary conundrum about how and what is selected for8,9. Due to its complexity, it is frequently unknown how it is encoded in genomes. To produce population level chemodiversity, the traits need to allow for highly chemodiverse and highly specific individuals in the same population. Here we use metabolomics, transcriptomics, and genomics combined with field analyses and functional assays of monoterpene synthases in the Asteraceae Tanacetum vulgare (tansy) and identify forces which produce high population level chemodiversity: selection for product specificity in enzymes, loss-of-expression alleles, absence variation, and specialized metabolism islands drive individuals towards low chemodiversity while unlinked enzyme loci, expression variation alleles, presence variation, and de novo enzyme evolution enable high individual chemodiversity. Since the molecular data suggests selection for mechanisms that increase chemodiversity itself at the population level, the screening hypothesis which posited plants produce a reservoir of diverse chemicals prior to selection8 should be replaced by a chemodiversity selection hypothesis. The results demonstrate that, in addition to plant protection via individual chemicals with known targeting mechanisms for predators, being different from your neighbors even if you are closely related is likely an important element in plant protection.

plant biology↗
bioRxiv2024

Many transcription factor families have evolutionarily conserved binding motifs in plants

Transcription factors control gene expression during development and in response to a broad range of internal and external stimuli. They regulate promoter activity by directly binding cis- regulatory elements in DNA. The angiosperm Arabidopsis thaliana contains more than 1,500 annotated transcription factors, each containing a DNA-binding domain that is used to define transcription factor families. Analyzing binding motifs of 686 and the binding sites of 335 A. thaliana transcription factors as well as motifs of 92 transcription factors from other plants, we identified a constrained vocabulary of 74 conserved motifs spanning 50 families in plants. Among 21 transcription factor families, we found one core motif for all analyzed members and between 2 and 72% overlapping binding sites. Five families show conservation of the motif along phylogenetic clades. Five families including the C2H2 zinc finger family show high diversity among motifs in plants, suggesting potential for neofunctionalization of duplicated transcription factors based on the motif recognized. For conserved motifs we tested if they remained conserved since at least 450 million years ago by determining the binding motifs of 17 orthologous transcription factors from 11 families in M. polymorpha using amplified DNA affinity purification sequencing. We detected nearly identical binding motifs as predicted from the angiosperm data. Taken together, the results show a large repertoire of overlapping binding sites within a TF family and species and a high degree of binding motif conservation for at least 450 million years. The results indicate more potential for evolution in cis- rather than trans-regulatory elements.

plant biology↗
bioRxiv2024

Regulation of Crassulacean Acid Metabolism at the protein level in the CAM plant Kalanchoë laxiflora

Crassulacean acid metabolism (CAM) is an adaptation to environments where water availability is seasonal or extremely low. It serves to ensure survival and/ or maintain productivity in these adverse environments. CAM has repeatedly evolved although it requires a large and complex set of enzymes and transporters and regulatory processes to control metabolite flux and pools. To test potential regulatory levels, we analyze the CAM plant Kalanchoe laxiflora embedded in the context of available CAM genome and transcriptome sequences. We show that CAM associated transcripts and proteins do not show a binary on/off pattern between day and night in K. laxiflora. Instead, we observe that many CAM plants display shared amino acid changes compared to C3 plants especially in starch metabolism. Phosphoproteomics identifies phosphoproteome changes in K. laxiflora between day and night. Taken together, the analyses demonstrate the CAM photosynthesis is regulated at the levels of transcripts and proteins. One sentence summaryRegulation of CAM cannot be explained by transcript and protein abundance alone but is also dependent on adaptive changes in proteins and posttranslational modifications.

plant biology↗
bioRxiv2023

Pangenome of cultivated beet and crop wild relatives reveals parental relationships of a tetraploid wild beet

Most crop plants, including sugar beet (Beta vulgaris subsp. vulgaris), suffer from domestication bottlenecks and low genetic diversity caused by extensive selection for few traits. However, crop wild relatives (CWRs) harbour useful traits relevant for crop improvement, including enhanced adaptation to biotic and abiotic stresses. Especially polyploids are interesting from an evolutionary perspective as genes undergo reorganisation after the polyploidisation event. Through neo-and subfunctionalisation, novel functions emerge, which enable plants to cope with changing environments and extreme/harsh conditions. Particularly in the face of climate change, specific stress and pathogen resistances or tolerances gain importance. To introduce such traits into breeding material, CWRs have already been identified as an important source for sustainable breeding. The identification of genes underlying traits of interest is crucial for crop improvement. For beets, the section Corollinae contains the tetraploid species Beta corolliflora (2n=4x=36) that harbours salt and frost tolerances as well as a wealth of pathogen resistances. The number of beneficial traits of B. corolliflora is increased compared to those of the known diploids in this section (all 2n=2x=18). Nevertheless, neither the parental relationships of B. corolliflora have been resolved, nor are genomic resources available to steer sustainable, genomics-informed breeding. To benefit from the resources offered by polyploid beet wild relatives, we generated a comprehensive pangenome dataset including B. corolliflora, Beta lomatogona, and Beta macrorhiza, as well as a more distant wild beet Patellifolia procumbens (2n=2x=18). Joined analyses with publicly available genome sequences of two additional wild beets allowed the identification of genomic regions absent from cultivated beet, providing a sequence database harbouring traits relevant for future breeding endeavours. In addition, we present strong evidence for the parental relationship of the B. corolliflora wild beet as an autotetraploid emerging from B. macrorhiza.

genomics↗
bioRxiv2023

Homoeologous non-reciprocal translocation explains a major QTL for seed lignin content in oilseed rape (Brassica napus L.)

Oilseed rape is a major oil crop and a valuable protein source for animal and human nutrition. Lignin is a non-digestible, major component of the seed coat with negative effect on sensory quality, bioavailability and usage of oilseed rapes protein. Hence, seed lignin reduction is of economic and nutritional importance. In this study, the major QTL for reduced lignin content found on chromosome C05 in the DH population SGDH14 x Express 617 was further examined. SGDH14 had lower seed lignin content than Express 617. Harvested seeds from a F2 population of the same cross were additionally field tested and used for seed quality analysis. The F2 population showed a bimodal distribution for seed lignin content. F2 plants with low lignin content had thinner seed coats compared to high lignin lines. Both groups showed a dark seed colour with a slightly lighter colour in the low lignin group indicating that a low lignin content is not necessarily associated with yellow seed colour. Mapping of genomic long-reads from SGDH14 against the Express 617 genome assembly revealed a homoeologous non-reciprocal translocation (HNRT) in the confidence interval of the major QTL for lignin content. A homologous A05 region is duplicated and replaced the C05 region in SGDH14. As consequence several genes located in the C05 region were lost in SGDH14. Thus, a HNRT was identified in the major QTL region for reduced lignin content in the low lignin line SGDH14. The most promising candidate gene related to lignin biosynthesis on C05, PAL4, was deleted. Key messageA homoeologous non-reciprocal translocation was identified in the major QTL for seed lignin content in the low lignin line SGDH14. The lignin biosynthetic gene PAL4 was deleted.

genomics↗
bioRxiv2022

Mapping-by-sequencing reveals genomic regions associated with seed quality parameters in Brassica napus

Rapeseed (Brassica napus L.) is an important oil crop and harbours the potential to serve as a highly productive source of protein. This protein exhibits an excellent amino acid composition and has a high nutritional value for humans. Seed protein content (SPC) and seed oil content (SOC) are two complex quantitative and polygenic traits which are negatively correlated and assumed to be controlled by additive and epistatic effects. A reduction of seed glucosinolate (GSL) content is desired as GSLs cause a stringent and bitter taste. The goal here was the identification of genomic intervals relevant for seed GSL content and SPC/SOC. Mapping-by-sequencing (MBS) revealed 30 and 15 new and known genomic intervals associated with seed GSL content and SPC/SOC, respectively. Within these intervals we identified known but also so far unknown putatively causal genes and sequence variants. A 4 bp insertion in the MYB28 homolog on C09 shows a significant correlation with a reduction in seed GSL content. This study provides insights into the genetic architecture and potential mechanisms underlying seed quality traits, which will enhance future breeding approaches in B. napus.

genomics↗
bioRxiv2021

Transcriptomic analysis of temporal shifts in berry development between two grapevine cultivars of the Pinot family reveals potential ripening-regulative genes

BackgroundGrapevine cultivars of the Pinot family represent clonally propagated mutants with major phenotypic and physiological differences, such as different colour or shifted ripening time, as well as changes in important viticultural traits. Specifically, the cultivars Pinot Noir (PN) and Pinot Noir Precoce (PNP, early ripening) flower at the same time, but vary in the beginning of berry ripening (veraison) and, consequently, harvest time. In addition to genotype, seasonal climatic conditions (i.e. high temperatures) also affect ripening times. To reveal possible regulatory genes that affect the timing of veraison onset, we investigated differences in gene expression profiles between PN and PNP throughout berry development with a closely meshed time series and over two separate years. ResultsThe difference in the duration of berry formation between PN and PNP was quantified to be approximately two weeks under the growth conditions applied, using plant material with a proven PN and PNP clonal relationship. Clusters of co-expressed genes and differentially expressed genes (DEGs) were detected which reflect the shift in the timing of veraison onset. Functional annotation of these DEGs fit to observed phenotypic and physiological changes during berry development. In total, we observed 3,342 DEGs in 2014 and 2,745 DEGs in 2017 between PN and PNP, with 1,923 DEGs across both years. Among these, 388 DEGs were identified as veraison-specific and 12 were considered as berry ripening time regulatory candidates. The expression profiles revealed two candidate genes for ripening time control which we designated VviRTIC1 and VviRTIC2 (VIT_210s0071g01145 and VIT_200s0366g00020, respectively). These genes likely contribute the phenotypic differences observed between PN and PNP. ConclusionsMany of the 1,923 DEGs show highly similar expression profiles in both cultivars if the patterns are aligned according to developmental stage. In our work, putative genes differentially expressed between PNP and PN which could control ripening time as well as veraison-specific genes were identified. We point out connections of these genes to molecular events during berry development and discuss potential candidate genes which may control ripening time. Two of these candidates were observed to be differentially expressed in the early berry development phase. Several down-regulated genes during berry ripening are annotated as auxin response factors / ARFs. Conceivably, general changes in auxin signaling may cause the earlier ripening phenotype of PNP.

developmental biology↗
bioRxiv2020

RNA-Seq Time Series of Vitis vinifera Bud Development Reveals Correlation of Expression Patterns with the Local Temperature Profile

Plants display sophisticated mechanisms to tolerate challenging environmental conditions and need to manage their ontogenesis in parallel. Here, we set out to generate an RNA-Seq time series dataset throughout grapevine (Vitis vinifera) early bud development. The expression of the developmental regulator VviAP1 served as an indicator for progress of development. We investigated the impact of changing temperatures on gene expression levels during the time series and detected a correlation between increased temperatures and a high expression level of genes encoding heat-shock proteins. The data set also allowed the exemplary investigation of expression patterns of genes from three transcription factor (TF) gene families, namely MADS-box, WRKY, and R2R3-MYB genes. Inspection of the expression profiles from all three TF gene families indicated that a switch in the developmental program takes place in July which coincides with increased expression of the bud dormancy marker gene VviDRM1.

plant biology↗
bioRxiv2020

Genome sequences of both organelles of the grapevine rootstock cultivar 'Börner'

Genomic long reads of the interspecific grapevine rootstock cultivar Borner (Vitis riparia GM183 x Vitis cinerea Arnold) were used to assemble its chloroplast and mitochondrion genome sequences. We annotated 133 chloroplast and 172 mitochondrial genes including the RNA-editing sites. The organellar genomes were maternally inherited to Borner from Vitis riparia.

plant biology↗
bioRxiv2020

High contiguity de novo genome sequence assembly of Trifoliate yam (Dioscorea dumetorum) using long read sequencing

Trifoliate yam (Dioscorea dumetorum) is one example of an orphan crop, not traded internationally. Post-harvest hardening of the tubers of this species starts within 24 hours after harvesting and renders the tubers inedible. Genomic resources are required for D. dumetorum to improve breeding for non-hardening varieties as well as for other traits. We sequenced the D. dumetorum genome and generated the corresponding annotation. The two haplophases of this highly heterozygous genome were separated to a large extent. The assembly represents 485 Mbp of the genome with an N50 of over 3.2 Mbp. A total of 35,269 protein-encoding gene models as well as 9,941 non-coding RNA genes were predicted and functional annotations were assigned.

genomics↗
bioRxiv2019

A Partially Phase-Separated Genome Sequence Assembly of the Vitis Rootstock 'Börner' (Vitis riparia x Vitis cinerea) and its Exploitation for Marker Development and Targeted Mapping

Grapevine breeding becomes highly relevant due to upcoming challenges like climate change, a decrease in the number of available fungicides, increasing public concern about plant protection, and the demand for a sustainable production. Downy mildew caused by Plasmopara viticola is one of the most devastating diseases worldwide of cultivated Vitis vinifera. Therefore, in modern breeding programs genetic marker technologies and genomic data are used to develop new cultivars with defined and stacked resistance loci. Potential sources of resistance are wild species of American or Asian origin. The interspecific hybrid of Vitis riparia Gm 183 x V. cinerea Arnold, available as the rootstock cultivar Borner, carries several relevant resistance loci. We applied next generation sequencing to enable the reliable identification of simple sequence repeats (SSR) and also generated a draft genome sequence assembly of Borner to access genome wide sequence variations in a comprehensive and highly reliable way. These data were used to cover the Borner genome with genetic marker positions. A subset of these marker positions was used for targeted mapping of the P. viticola resistance locus, Rpv14, to validate the marker position list. Based on the reference genome sequence PN40024, the position of this resistance locus can be narrowed down to less than 0.5 Mbp on chromosome 5.

genomics↗
bioRxiv2019

Characterization of genes and alleles involved in the control of flowering time in grapevine

Grapevine (Vitis vinifera) is one of the most important perennial crop plants in worldwide. Understanding of developmental processes like flowering, which impact quality and quantity of yield in this species is therefore of high interest. This gets even more important when considering some of the expected consequences of climate change. Earlier bud burst and flowering, for example, may result in yield loss due to spring frost. Berry ripening under higher temperatures will impact wine quality. Knowledge of interactions between a genotype or allele combination and the environment can be used for the breeding of genotypes that are better adapted to new climatic conditions. To this end, we have generated a list of more than 500 candidate genes that may play a role in the timing of flowering. The grapevine genome was exploited for flowering time control gene homologs on the basis of functional data from model organisms like A. thaliana. In a previous study, a mapping population derived from early flowering GF.GA-47-42 and late flowering Villard Blanc was analyzed for flowering time QTLs. In a second step we have now established a workflow combining amplicon sequencing and bioinformatics to follow alleles of selected candidate genes in the F1 individuals and the parental genotypes. Allele combinations of these genes in individuals of the mapping population were correlated with early or late flowering phenotypes. Specific allele combinations of flowering time candidate genes within and outside of the QTL regions for flowering time on chromosome 1, 4, 14, 17, and 18 were found to be associated with an early flowering phenotype. In addition, expression of many of the flowering candidate genes was analyzed over consecutive stages of bud and inflorescence development indicating functional roles of these genes in the flowering control network.

genetics↗