Biology subjects

Groh, S.

Publications and source records attributed to Groh, S..

4 recordsLinked to original sources

bioRxiv2026

Genome-wide association study in a maize diversity panel dissects the genetic basis of lignocellulosic recalcitrance

Lignocellulosic biomass is an abundant, renewable resource for the production of biorenewable products. Its efficient utilization is largely hindered by the inherent recalcitrance of lignocellulose to degradation. Natural genetic variation in biomass saccharification efficiency and lignocellulose components across diverse maize germplasm provides a powerful resource to dissect the genetic basis of lignocellulosic recalcitrance. Here, we performed high-throughput profiling of lignocellulosic components and saccharification efficiency in mature stalks across a diverse panel of 239 field grown maize inbred lines, and identified extensive natural variation in biomass properties. Saccharification efficiency was strongly positively associated with matrix glucose content, moderately positively associated with the arabinose-to-xylose (Ara:Xyl) molar ratio and crystalline cellulose content, whereas saccharification efficiency was strongly negatively associated with xylose and lignin content. Genome-wide association studies (GWAS) were conducted to identify single nucleotide polymorphisms (SNPs) associated with saccharification efficiency and lignocellulosic components. Numerous significant single nucleotide polymorphisms (SNPs) were identified, defining 79 quantitative trait loci (QTLs) across all 10 maize chromosomes. The presence of pleiotropic SNPs and the extensive co-localization of QTLs for multiple traits highlight the complex genetic architecture and shared genetic basis of maize biomass properties. Our study reveals substantial natural variation in maize biomass digestibility and identifies multiple novel genetic loci underlying variation in saccharification efficiency and lignocellulose components.

plant biology↗

bioRxiv2026

ZmPMI3 phosphomannose isomerase kinetics is associated with natural variation of watersoluble carbohydrate content in mature maize stem

Mature maize stems accumulate substantial amounts of water-soluble carbohydrates (WSC) providing an accessible carbon pool for industrial bioconversion. However, the genetic factors controlling WSC reserves under field conditions remain poorly resolved. In this study, we quantified total WSC including glucose, fructose, sucrose contents in the internode below the first ear of a genetically diverse maize panel at physiological maturity and associated trait variation with genome-wide SNP data. The panel displayed extensive variation in stem WSCs content, with values ranging up to 50.4 % of dry weight. Genome-wide association mapping identified 20 quantitative trait loci associated with individual sugars or total WSC content. One fructose associated region contained two adjacent gene annotations predicted to encode fragments of a phosphomannose isomerase. Sequence comparison, cDNA amplification and protein structure prediction supported a unified gene model, here designated as ZmPMI3. Biochemical characterization showed ZmPMI3 catalyzes the reversible conversion between mannose-6-phosphate and fructose-6-phosphate, a central reaction in carbohydrate metabolism. Natural protein haplotypes with distinct kinetic properties were identified correlating with significant differences in stem WSC content. Together, these findings identify ZmPMI3 as a candidate contributor to natural variation in maize stem carbohydrate reserves, potentially through altered hexose-phosphate partitioning.

plant biology↗

bioRxiv2020

Morc3 silences endogenous retroviruses by enabling Daxx-mediated H3.3 incorporation

Endogenous retroviruses (ERVs) comprise a significant portion of mammalian genomes. Although, specific ERV loci feature regulatory roles for host gene expression, most ERV integrations are transcriptionally repressed by Setdb1 mediated H3K9me3 and DNA methylation. However, the protein network which regulates deposition of these chromatin modifications is still incompletely understood. Here, we performed a genome-wide sgRNA screen for genes involved in ERV silencing and identified the GHKL ATPase protein Morc3 as top scoring hit. Morc3 knock-out cells display de-repression, reduced H3K9me3 and increased chromatin accessibility of distinct ERV classes. We found that the GHKL ATPase domain of Morc3 is critical for ERV silencing, since mutants which cannot bind ATP, or which are defective in ATP hydrolysis cannot rescue the Morc3 ko phenotype. Proteomic analysis revealed that Morc3 mutant protein which cannot bind ATP fails to interact with the H3.3 chaperone Daxx. This interaction depends on Morc3 SUMOylation, as Daxx lacking the SUMO interaction domain shows reduced association with Morc3. Notably, in Morc3 ko cells, we observed strongly reduced H3.3 on Morc3 binding sites. Thus, our data demonstrate Morc3 as critical regulator of Daxx-mediated H3.3 incorporation to ERV regions.

molecular biology↗

bioRxiv2019

Pre-marked chromatin and transcription factor co-binding shape the pioneering activity of Foxa2.

Pioneer transcription factors (PTF) can recognize their binding sites on nucleosomal DNA and trigger chromatin opening for recruitment of other non-pioneer transcription factors. However, critical properties of PTFs are still poorly understood, such as how these transcription factors selectively recognize cell type-specific binding sites and under which conditions can they can initiate chromatin remodelling. Here we show that early endoderm binding sites of the paradigm PTF Foxa2 are epigenetically primed by low levels of active chromatin modifications in embryonic stem cells (ESC). Priming of these binding sites is supported by preferential recruitment of Foxa2 to endoderm binding sites compared to lineage-inappropriate binding sites, when ectopically expressed in ESCs. We further show that binding of Foxa2 is required for chromatin opening during endoderm differentiation. However, increased chromatin accessibility was only detected on binding sites which are synergistically bound with other endoderm transcription factors. Thus, our data suggest that binding site selection of PTFs is directed by the chromatin environment and that chromatin opening requires collaboration of PTFs with additional transcription factors.

genomics↗