Unlocking the secrets of nitrogen use in potatoes

Bellaterra (Barcelona), 4 November 2024 - In a world where food security is increasingly threatened by climate change and the population growth, researchers are turning to genetic solutions to enhance crop resilience. A recent study led by Salomé Prat, a CSIC researcher at CRAG has unveiled groundbreaking findings on the role of the StCDF1 gene in nitrogen use efficiency in potatoes (Solanum tuberosum), a staple food for millions of people.

The study published in New Phytologist in collaboration with the group of Christian Bachem from the University of Wageningen (WUR), expands the role of StCDF1 beyond its previously known function as a central regulator of day length tuberization. Tuber formation is an adaptive strategy of potato plants for winter survival and is triggered by shorter day lengths and cooler temperatures perceived by the plant as the approach of winter.

Maroof Ahmed Shaikh, first author of the study, notes, “Integration of these environmental signals encourages tuber formation.  These organs stay dormant in the soil over winter and wake up in spring to form a new plant. We often notice this awakening at home when older potatoes begin to sprout.”

In wild potatoes, tuber formation is strictly dependent on short days. However, modern cultivars carry mutations in a locus called earliness that allows them to escape this strict control. This adaptation took place after potatoes were introduced to Europe, resulting in early-maturing varieties that carry one or more copies of these alleles. These naturally occurring mutations enhance the stability of the StCDF1 factor, a key player in the day length pathway that modulates the expression of SP6A, a member of the FLOWERING LOCUS T family and a main tuberization signal.

Enhancing nitrogen utilization through genetic innovations

The findings reveal that StCDF1 not only acts as an upstream regulator of the tuberization pathway but also directly controls the expression of several genes involved in nitrogen assimilation and transport. Through a combination of DNA binding and gene expression studies, researchers observed that StCDF1 binds the promoter region of Nitrate Reductase (StNR), an enzyme that catalyses the rate-limiting step in nitrate reduction within the cell. Surprisingly, potatoes possess a single gene copy for StNR, unlike most plants that have several copies allowing them greater efficiency in nitrate utilization.

The research employed advanced techniques, including DAP-seq (DNA Affinity Purification and sequencing), to identify the direct targets of StCDF1. This method revealed DNA recognition peaks in several nitrogen responsive genes.

Knock-down lines of StCDF1, which reduced transcript levels, showed improved performance under nitrogen-limiting conditions due to the lifted repression of StNR. With StCDF1 silenced, the potato plants could express more StNR, leading to better nitrogen utilization. Additionally, the discovery of polymorphisms in the StNR regulatory region indicates that these genetic variations may have evolved in early potato cultivars as a compensatory mechanism, helping these plants adapt to the adverse effects of StCDF1 stabilization, thereby enhancing their nitrogen assimilation capabilities.

Salomé Prat emphasized the significance of these findings, stating, “The novelty of our research lies in uncovering StCDF1's dual role in regulating both tuberization and the nitrogen assimilation pathways. This insight reveals new genetic and molecular targets for enhancing nitrogen utilization in potatoes.”

Implications for sustainable agriculture

The implications of this research are profound, contributing to the broader goal of sustainable agriculture. The study provides molecular targets that can be used for breeding climate-smart potato varieties requiring less nitrate inputs for high tuber production. Breeders could leverage this knowledge to develop potato varieties less dependent on chemical fertilizers.

In conclusion, this study not only enriches our understanding of potato biology but also serves as a ray of hope for sustainable agriculture, demonstrating the power of plant science in addressing global challenges. By harnessing genetic advancements, the agricultural sector can move towards more resilient and environment friendly practices, ensuring food security for future generations.

Reference Article:

Maroof Ahmed Shaikh, Lorena Ramírez-Gonzales, José M. Franco-Zorrilla, Evyatar Steiner, Marian Oortwijn, Christian W.B. Bachem, Salomé Prat. StCDF1: A “jack of all trades” clock output with a central role in regulating potato nitrate reduction activity. New Phytologist, https://doi.org/10.1111/nph.20186

About the authors and funding of the study: This work was supported by the ERA CAPS 647 HotSol project funded by the Netherlands Organization for Scientific Research (NWO project 648 849.13.001), the FlowerPot project, and by the Division for Earth and Life Sciences ALW 649 financial aid from the NWO. Work within the Salomé Prat group was financed by the European H2020- 650 SFS-862858 ADAPT project. Maroof Ahmed Shaikh was supported by a pre-doctoral contract from the ADAPT 651 project. Lorena Ramírez-Gonzales received a fellowship from FONDECYT-CONCYTEC, Lima, Peru (grant no. 652 090-2016-FONDECYT). Work in José M. Franco-Zorrilla's group was funded by the Spanish Ministry for 653 Science and Innovation grant PID2020-119451GB-I00.

About the Centre for Research in Agricultural Genomics (CRAG): CRAG is a centre that forms part of the CERCA system of research centres of the Government of Catalonia (Spain), and which was established as a partnership of four institutions: the Spanish National Research Council (CSIC), the Institute for Agri-Food Research and Technology (IRTA), the Autonomous University of Barcelona (UAB) and the University of Barcelona (UB). CRAG’s research spans from basic research in plant and farm animal molecular biology, to applications of molecular approaches for breeding of species important for agriculture and food production in close collaboration with industry. In 2020, CRAG was recognized for the second time as a "Severo Ochoa Centre of Excellence” by the Spanish Ministry of Economy and Competitiveness.

About New Phytologist: New Phytologist is a leading international journal focusing on high quality, original research across the broad spectrum of plant sciences, from intracellular processes through to global environmental change. The journal is owned by the New Phytologist Foundation, a non-profit organisation dedicated to the promotion of plant science. https://www.newphytologist.org/

Materials:

• 1_image potatoes.jpg: Experiment with potato plants (Credit: CRAG).
• 2_authors.jpg: On the left Salomé Prat, who led the study, and on the right Maroof Ahmed Shaikh, first author of the study (Credit: CRAG).
• 3_authors.jpg: On the left Salomé Prat, who led the study, and on the right Maroof Ahmed Shaikh, first author of the study (Credit: CRAG).
• 4_infographic_ENG.jpg: Schematic summary of the study (Credit: CRAG).

Materials can be downloaded here: https://t.ly/m2y9y

For more information and interviews:

Muriel Arimon

Communication Department

Centre for Research in Agricultural Genomics (CRAG)

+34 93 563 66 00 Ext 3033

+34 600 008 159

email: muriel.arimon@cragenomica.es