Programme

• Maize genomics and bio-informatics
  
• Breeding
• Phenotyping and gene function
• CRISPR and transgene technologies
• Environmental responses

Wednesday 18th September        

Thursday 19th September  

Friday 20th September  

Prof. dr. Klaas Vandepoele

Vlaams instituut voor Biotechnologie, University of Gent (Belgium)

Title: A map of integrated cis-regulatory elements enhances gene regulatory analysis in maize

​Cis-regulatory elements (CREs) are non-coding DNA sequences that modulate the expression of genes. Their identification is critical to study the transcriptional regulation of genes controlling key traits that govern plant  growth and development. They are also crucial components for the delineation of gene regulatory networks , which are sets of regulatory interactions between transcription factors (TFs) and target genes. In maize, CREs have been profiled using different computational and experimental methods, but the extent to which these methods complement each other in identifying functional CREs remains unclear. Here, we report the data-driven integration of different maize CRE profiling methods to optimize the capture of experimentally-confirmed TF binding sites, resulting in maps of integrated CREs (iCREs) showing increased levels of completeness and precision. We combined the iCREs with gene expression data under drought conditions to perform motif enrichment and infer drought-specific GRNs. Mining these GRNs revealed previously characterized and novel candidate regulators of maize drought response. By studying the transposable elements (TEs) overlapping with iCREs, we identified few TE superfamilies, displaying typical epigenetic features of regulatory DNA, that are involved in wiring specific TF - target gene regulatory interactions. Overall, our study showcases the integration of different omics data sources to generate a high-quality collection of CREs, together with their applicability to better characterize gene regulation in the complex maize genome.

Prof. dr. Xiangnan Li

Northeast Institute of Geography and Acroecology, Chinese Academy of Sciences (China)

Title: Microbial induced tolerance of maize to abiotic stress.

Saline-alkali soils significantly hinder crop growth and yield, posing a serious challenge to sustainable agriculture. Bio-organic fertilizers have emerged as a promising approach to enhance soil quality and boost plant productivity. However, more research is needed to fully understand their potential to alleviate crop stress caused by salinity.

In this study, a 20-year field experiment was conducted to investigate the long-term effects of organic and chemical fertilizers on maize yield, soil chemistry, and microbial community in saline-alkali soils. The experiment used a split-plot design with two levels of organic fertilizer in the main plot and an orthogonal arrangement of nitrogen (N), phosphorus (P), and potassium (K) fertilizers in the subplots. Based on the comparison of grain yield stability, specific microbe was selected and used to establish a synthetic microbial community, to assess the role of rhizosphere microorganisms in mitigating salinity-alkali stress in maize.

The study revealed that applying organic fertilizers, compared to chemical fertilizers alone, increased maize yield and yield stability. Organic fertilizers enhanced soil quality by increasing soil organic matter, as well as available N, P, and K levels. Additionally, organic fertilizers significantly altered soil microbial community structure, increasing the α-diversity index and modifying β-diversity. This led to a higher relative abundance of key genera, such as Flavobacterium, Lysobacter, and Sphingomonas, and shifted the prevalence of nutrient cycling-related genes, potentially enhancing denitrification, carbon, and P cycling.

Variance decomposition analysis indicated that the improvement in maize yield and stability was primarily driven by soil biological characteristics. To identify key contributing genera, random forest analysis was employed, leading to the construction of a synthetic bacterial community (SynCom). SynCom was found to mitigate Na⁺ accumulation in maize leaves, promote photosynthetic carbon assimilation and antioxidant capacity, and ultimately enhance maize yield under saline-alkali conditions. Furthermore, SynCom increased the atrazine and tryptophol contents in soil, altering bacterial diversity and composition in saline-alkali soils.

In conclusion, this study demonstrated the potential of bio-organic fertilizers to improve the biological properties of saline-alkali soils and promote crop stress tolerance. The findings also provide a potential way to the resistant cultivation in maize.

Prof. dr. Nils Stein

Leibniz Institute of Plant Genetics and Crop Plants Research (Germany)

Title: Everything a Maize researcher always wanted to know about Barley

Barley and maize do not compare in their economic importance, however, both species since long play an important role as genetic models in research. In the absence of high-quality genome sequences, there was very limited interest in comparative analyses involving both species. With the genomic revolution and the easy access to pangenomes of both species as well as their respective close relatives it is possibly time to reconsider: could barley and maize researchers take advantage of a better understanding of the respective other research objectives?
I will review the status of genome/pangenome research in barley as well as the available genetic and genomic tools and resources to foster discussions about opportunities of bringing maize and barley research into closer contact.

Dr. Christopher Topp

Donald Danforth Plant Science Center, St. Louis (USA)

Title: Strengthening the foundation of maize agriculture through rational design of root systems

Actualizing maize root system ideotypes toward more sustainable crop production has been hindered by a gap in understanding the genetic basis of root traits and their interactions with the environment. A lack of adequate phenotyping tools to measure root system complexity has contributed to this gap by limiting full exploration of the phenotype space. I will describe our efforts to develop more effective root phenotyping tools in controlled environments and in the field, and to use them in large-scale genome-wide association and other genetic studies, which has allowed us to identify genes that control traits potentially advantageous to root system function. I will describe some of these genes and what we know so far about their performance in the field. Along with several recent discoveries by colleagues, our collective understanding of the genetic basis of maize root system architecture has leapt forward in recent years. With concomitant advances in gene editing and plant transformation, we are on the cusp of rational design and testing of root systems and their actual, rather than theorized, functions. Near-term challenges are to determine how to best leverage this knowledge for future climate and cropping system goals. For example, can we increase the compatibility of maize root systems with cover or relay crops? Can we manipulate root systems to shift the edaphic food web to reduce nitrogen loss and pollution, and to sequester carbon? The time is now to move our basic research discoveries into real-world solutions.

Dr. Ellen Slaman

​​Vlaams instituut voor Biotechnologie, University of Gent (Belgium)

Title: Advancing Maize Genome Editing with a Rapid Protoplast Prototyping Platform

CRISPR-mediated genome editing has enabled researchers to introduce targeted indels at nearly any desired position in the genome. After a decade of CRISPR research, new applications are moving away from targeted mutagenesis and towards precision engineering, such as base editing and prime editing. While these tools hold significant promise for plant research, they are often developed in mammalian systems and do not always easily translate to our favorite crops. To keep plant research in step with this rapidly advancing field, high-throughput screening systems with quick turnaround times are essential. Here, we combine protoplast transfections with high-throughput imaging techniques to significantly improve Cas12a-mediated adenosine base editing. Using this screening approach along with our extensive collection of genome editing parts and straightforward cloning system (available at vectorvault.vib.be), we increased base editing activity from nearly undetectable levels to over 65% in maize protoplast pools. This setup is being extended to additional technologies and species. For example, we have systematically tested numerous experimental conditions for prime editing. This work showcases how high-throughput strategies can advance genome editing applications, making cutting-edge technology more accessible for plant science.