Illustration of maize and teosinte roots intertwining in a flooded field.

Unlocking Waterlogging Tolerance: How a Nicaraguan Teosinte Could Revolutionize Maize Breeding

Mira Elwood in Science & Nature December 2025 • 4 min read.

"Genetic analysis reveals Zea nicaraguensis's unique potential to enhance maize resilience in flood-prone environments."

For years, breeders have sought ways to bolster maize crops against the devastating effects of waterlogging. Now, a newly discovered teosinte (a close relative of maize) called Zea nicaraguensis, found in the Pacific Coastal regions of Nicaragua, is showing incredible promise. This plant can thrive in flooded conditions that would typically destroy maize crops, opening new avenues for genetic improvement.

The key to unlocking this potential lies in understanding the genetic relationship between Zea nicaraguensis and other Zea species, including maize. Teosintes, native to Mexico and Central America, are invaluable resources for studying maize genetics, evolution, and breeding. They offer traits that have been lost or diminished in cultivated maize, such as disease resistance and, in this case, waterlogging tolerance.

This article delves into research that uses cutting-edge genetic analysis to classify Zea nicaraguensis and explore its close relationship with other teosintes, especially Zea luxurians. By examining RAPD markers and ITS sequences, scientists are gaining insights into how this Nicaraguan teosinte can be used to breed maize varieties that are far more resilient to waterlogged environments.

Decoding the DNA: RAPD and ITS Sequence Analysis

Illustration of maize and teosinte roots intertwining in a flooded field.

To determine the genetic placement of Zea nicaraguensis, scientists employed two powerful techniques: Randomly Amplified Polymorphic DNA (RAPD) and Internal Transcribed Spacer (ITS) sequence analysis. RAPD uses random DNA fragments to identify genetic differences, while ITS focuses on specific regions of ribosomal DNA. Together, they provide a comprehensive view of genetic relationships.

The RAPD analysis generated a massive dataset of 5,303 fragments using 136 primers, with a high polymorphism rate of 84.86%. This vast genetic diversity underscores the potential for unique traits within the Zea genus. UPGMA analysis, a method for grouping organisms based on genetic similarity, revealed two major clusters within Zea:

Section Luxuriantes: Includes Zea diploperennis, Zea luxurians, Zea perennis, and Zea nicaraguensis.
Section Zea: Includes various maize subspecies such as Zea mays ssp. mexicana, Zea mays ssp. parviglumis, Zea mays ssp. huehuetenangensis, and cultivated maize (Zea mays ssp. mays).

ITS sequence analysis corroborated these findings. The lengths of the ITS regions varied slightly among the Zea taxa, but a significant number of variable sites were identified within the ITS1 and ITS2 regions. Phylogenetic trees constructed using neighbor-joining (NJ) and maximum parsimony (MP) methods confirmed the relationships suggested by the RAPD data, firmly placing Zea nicaraguensis within the section Luxuriantes and highlighting its close relationship to Zea luxurians.

A Genetic Key to Flood-Resilient Maize

The convergence of evidence from both RAPD and ITS sequence analyses strongly indicates that Zea nicaraguensis is more closely related to Zea luxurians than to other teosintes or cultivated maize. This is not merely a taxonomic distinction; it has profound implications for maize breeding. Knowing the precise genetic placement of Zea nicaraguensis allows breeders to strategically utilize its unique traits.

The waterlogging tolerance of Zea nicaraguensis is linked to its ability to form root aerenchyma (air spaces in the roots) and adventitious roots, allowing it to thrive in oxygen-depleted environments. Transferring these traits into cultivated maize could create varieties capable of withstanding prolonged flooding, a critical adaptation given increasing climate variability.

While further research is needed to fully understand the mechanisms underlying waterlogging tolerance and to optimize breeding strategies, Zea nicaraguensis represents a significant step forward. It provides a vital genetic resource for enhancing maize resilience and ensuring food security in regions vulnerable to flooding. As climate change continues to pose challenges to agriculture, unlocking the potential of wild relatives like Zea nicaraguensis will be essential for creating crops that can thrive in a changing world.

About this Article -

This article was crafted using a human-AI hybrid and collaborative approach. AI assisted our team with initial drafting, research insights, identifying key questions, and image generation. Our human editors guided topic selection, defined the angle, structured the content, ensured factual accuracy and relevance, refined the tone, and conducted thorough editing to deliver helpful, high-quality information.See our About page for more information.

This article is based on research published under:

DOI-LINK: 10.1371/journal.pone.0016728, Alternate LINK

Title: Rapd And Internal Transcribed Spacer Sequence Analyses Reveal Zea Nicaraguensis As A Section Luxuriantes Species Close To Zea Luxurians

Subject: Multidisciplinary

Journal: PLoS ONE

Publisher: Public Library of Science (PLoS)

Authors: Pei Wang, Yanli Lu, Mingmin Zheng, Tingzhao Rong, Qilin Tang

Published: 2011-04-15

Everything You Need To Know

What is Zea nicaraguensis and why is it important?

The term *Zea nicaraguensis* refers to a newly discovered teosinte species found in Nicaragua. Teosintes are close relatives of maize and are invaluable resources for studying maize genetics, evolution, and breeding. *Zea nicaraguensis* is particularly interesting because it exhibits waterlogging tolerance, a trait that could significantly improve maize's ability to survive in flooded conditions. Its discovery offers a new avenue for enhancing the resilience of maize crops in challenging environments, specifically those prone to flooding.

Why is waterlogging tolerance significant?

The significance of *Zea nicaraguensis* lies in its potential to enhance maize's tolerance to waterlogging. This is crucial because waterlogging can devastate maize crops, leading to significant yield losses. By identifying and utilizing the genes responsible for this tolerance in *Zea nicaraguensis*, breeders can develop maize varieties that can withstand flooded conditions. This could have a profound impact on food security and agricultural sustainability in regions susceptible to flooding. The genetic analysis of *Zea nicaraguensis* helps to understand how to use it for maize breeding purposes.

How are RAPD and ITS sequence analyses used?

RAPD (Randomly Amplified Polymorphic DNA) and ITS (Internal Transcribed Spacer) sequence analysis are two molecular techniques used to study the genetic relationships between different *Zea* species, including *Zea nicaraguensis*. RAPD uses random DNA fragments to identify genetic differences, while ITS focuses on specific regions of ribosomal DNA. These techniques provide a comprehensive view of the genetic relationships. By comparing the genetic profiles of *Zea nicaraguensis* with other *Zea* species, scientists can determine its genetic placement and understand how closely it is related to cultivated maize and other teosintes such as *Zea luxurians*.

What is the significance of Zea nicaraguensis being closely related to Zea luxurians?

The genetic analysis revealed that *Zea nicaraguensis* is more closely related to *Zea luxurians* than to cultivated maize. This close relationship is significant because it suggests that *Zea nicaraguensis* shares a common ancestor with *Zea luxurians*, potentially inheriting similar traits. Understanding this relationship allows breeders to strategically introduce the waterlogging tolerance genes from *Zea nicaraguensis* into maize through crossbreeding. This targeted approach is more efficient and effective than random breeding, as it allows breeders to focus on specific traits, such as waterlogging tolerance, improving the process of maize crop improvement.

What are the broader implications of this research?

The implications of these findings are far-reaching. By understanding the genetic makeup and relationships of *Zea nicaraguensis*, scientists can develop maize varieties that are more resilient to waterlogged conditions. This is particularly important in regions where flooding is a common problem. The ability to breed flood-tolerant maize could significantly reduce crop losses, increase food production, and enhance the sustainability of agriculture. The utilization of *Zea nicaraguensis* in maize breeding represents a significant step toward more climate-resilient agriculture.