Research-PGR: unlocking the genetic and epigenetic basis of cereal crop adaptation to acidic soil regions

This federal Project Grant award from the National Science Foundation's Biological Sciences program (CFDA 47.074) provides $2,000,000 to Cold Spring Harbor Laboratory (CSHL) for a project titled "Unlocking the Genetic and Epigenetic Basis of Cereal Crop Adaptation to Acidic Soil Regions." The project aims to identify genetic and epigenetic mechanisms that contribute to aluminum (Al) tolerance in major cereal crops like maize and sorghum, which is crucial for improving crop resilience on the widespread acidic soils globally. Key activities include leveraging multi-omics data, single-cell transcriptomics, gene editing, and field testing to explore the MATE family of transporters involved in Al tolerance. A sub-award to the Donald Danforth Plant Science Center will support data analysis, integration, and informatics for the project. The award period runs from Apr 1, 2024 to Mar 31, 2027.

Abstract

In a climate that is rapidly transitioning into much harsher crop cultivation conditions, resilience becomes vital for sustainable food production and security across the globe. Acidic soils with low PH are widespread globally and common in tropical and sub-tropical regions, where food security is a challenge. Aluminum (AL) toxicity, a significant abiotic stress on acidic soils, damages root systems and enhances crop susceptibility to drought and mineral deficiencies. Previous studies have shown that genes in the multidrug and toxic compound extrusion (MATE) family of membrane transporters play an important role in AL tolerance in sorghum and maize while others strongly implicate epigenetic variation in DNA methylation and histone modification in AL tolerance in various plant species. This project will take a multi-omics approach to identify and explore variation in AL tolerance at both the genetic and epigenetic levels, using AL tolerance as a paradigm to connect gene regulation to abiotic stress tolerance in cereals. IT is expected that this project will have significant impacts for facilitating translation of findings from maize and sorghum genetics/epigenetics and genomics research to develop more effective breeding strategies targeting adaptation to broader abiotic stress conditions. With respect to training and outreach, in addition to the training of project students and postdoctoral scientists, the project will develop a module on translational genomics focusing on AL tolerance that will be included in the long-running cereal genomics workshop held at cold spring harbor lab. Homologous genes in the MATE family of membrane transporters play an important role in AL tolerance in sorghum (SBMATE) and maize (ZMMATE1) by mediating release of AL detoxifying citrate into the rhizosphere. Studies have shown that AL-induced expression of SBMATE is not just localized to the root apex, which is the site of AL toxicity and tolerance, but also very specifically to the epidermal and cortical cells in the distal transition zone. This project will leverage single-cell transcriptomics technologies that will provide the spatial resolution necessary to discover novel AL tolerance genes by associating epigenetic responses with cell-specific gene expression. Candidate regulatory elements will be functionally validated using gene editing and mutant analyses and AL tolerance phenotypes will be evaluated in controlled conditions and in the field on well-characterized acidic soils. All project outcomes will be made available and broadly distributed through deposition at the appropriate long-term data repositories and stock centers. This award reflects NSF's statutory mission and has been deemed worthy of support through evaluation using the foundation's intellectual merit and broader impacts review criteria.- subawards are planned for this award.