# Morphological characterization and RNA sequencing reveal adaptive strategies of Coix lacryma-jobi L. under waterlogging stress during the jointing stage

## TL;DR

This study explores how Coix lacryma-jobi L. adapts to waterlogging stress by analyzing its morphological changes and gene expression patterns.

## Contribution

The study identifies specific genes and molecular mechanisms involved in waterlogging tolerance in Coix lacryma-jobi L.

## Key findings

- Waterlogging caused significant morphological changes and reduced growth parameters by 14.4–21.8%.
- Adventitious root formation increased by 76.6% as an adaptive response.
- RNA-Seq identified 207 differentially expressed genes linked to photosynthesis, carbohydrate dynamics, and signaling pathways.

## Abstract

Coix lacryma-jobi L. is a vital medicinal and dual-purpose crop in Guizhou, requiring optimal cultivation conditions to preserve its therapeutic properties. Waterlogging stress significantly reduces its productivity, yet the underlying molecular mechanisms remain poorly understood.

We investigated the species’ adaptive responses using controlled waterlogging experiments on potted plants. Morphological alterations and key growth parameters (culm diameter, plant height, dry biomass) were quantified. We performed transcriptomic profiling by RNA-Seq to identify differentially expressed genes (DEGs). To elucidate the functional implications of these DEGs, we conducted systematic enrichment analyses using the clusters of orthologous groups (COG), Gene Ontology (GO), and Kyoto Encyclopedia of Genes and Genomes (KEGG) databases. Expression patterns of candidate genes were validated using Quantitative Real-Time Reverse Transcription Polymerase Chain Reaction (qRT-PCR).

Flooded plants exhibited significant morphological changes, with key growth parameters decreasing by 14.4–21.8%. A pronounced adaptive response was a 76.6% increase in adventitious root formation. RNA-Seq revealed 207 DEGs (133 upregulated, 74 downregulated). Enrichment analyses indicated these DEGs were predominantly involved in photosynthetic processes, carbohydrate dynamics, and signaling pathways. qRT-PCR confirmed consistent expression patterns for six candidate genes associated with photosynthesis and carbohydrate metabolism. These findings demonstrate that Coix lacryma-jobi L. activates coordinated molecular responses, including photosynthetic efficiency adjustment and metabolic pathway remodeling, to enhance waterlogging tolerance. This work identifies critical genetic components governing waterlogging adaptation, providing molecular markers for developing stress-tolerant cultivars through targeted breeding.