A molecular makeover: histone switches drive salt tolerance in peas
image: Histone modification profiles in pea seedlings analyzed by ChIP-Seq.
Credit: Horticulture Research
A new study has decoded how pea plants respond to salt stress through precise epigenetic reprogramming. Researchers created the first genome-wide map of four major histone modifications—H3K4me3, H3K27me3, H3K9ac, and H3K9me2—and uncovered their role in regulating gene expression and metabolic responses under saline conditions. Notably, they discovered a previously unreported bivalent chromatin state (H3K9ac-H3K27me3) linked to both development and stress adaptation. By integrating transcriptomic and metabolomic data, the team showed that these histone marks orchestrate the expression of genes involved in phenylpropanoid biosynthesis, a key stress-response pathway. This work not only reveals new layers of gene regulation in legumes but also opens doors for crop improvement strategies.
Salt stress is one of the most pressing challenges in global agriculture, affecting nearly one-fifth of cultivated land and over half of irrigated areas. Excess salinity disrupts water balance, causes toxic ion buildup, and triggers oxidative stress, ultimately impairing plant growth. Peas (Pisum sativum L.), despite their historical significance in genetics and wide agricultural use, are highly sensitive to salt. While histone modifications have been shown to influence stress responses in model species like Arabidopsis and rice, their specific roles in peas remain largely unknown. Due to these gaps in understanding, there is an urgent need to explore how histone marks regulate gene activity and metabolism in salt-stressed pea plants.
In a study (DOI: 10.1093/hr/uhae259) published in Horticulture Research on September 16, 2024, scientists from Jianghan University unveiled the first comprehensive epigenomic map of the pea genome under salt stress. Using ChIP-seq, RNA-seq, and metabolomic profiling, the team charted the distribution and regulatory functions of four histone modifications. The research revealed a novel chromatin feature—H3K9ac-H3K27me3 bivalency—and demonstrated how histone modifications reshape gene expression and metabolic networks. This integrative study provides critical insights into the epigenetic architecture behind salt stress responses in legumes.
The researchers analyzed the pea genome to understand how histone modifications control gene activity under stress. They profiled four key marks—H3K4me3, H3K27me3, H3K9ac, and H3K9me2—and found that over 80% of the genome is associated with epigenetic signals. Particularly, H3K4me3 and H3K9ac were linked to high gene expression, while H3K27me3 correlated with repression. Intriguingly, they discovered a new bivalent chromatin state—where the activating H3K9ac and repressive H3K27me3 marks coexist—found primarily in gene promoters related to stress and hormone signaling. Under salt stress, the levels of H3K4me3 and H3K27me3 increased, while H3K9ac sharply declined. This shift coincided with the differential expression of 2,396 genes, with 1,034 likely modulated by histone changes. Further, metabolomic analysis revealed a surge in compounds from the phenylpropanoid pathway, which plays a vital role in plant defense. The expression of 25 genes in this pathway was directly linked to histone modification dynamics. Genes such as PAL, C4H, 4CL, and CCR exhibited expression changes that matched histone modification shifts. The combined data paint a detailed picture of how histone codes translate environmental signals into genetic and metabolic responses in pea.
“This study provides a rare, integrative view of how histone modifications govern plant responses to environmental stress,” said Prof. Xiaoyun Liu, senior author of the study. “The discovery of the H3K9ac-H3K27me3 bivalent state is particularly exciting—it represents a unique regulatory mechanism that has not been observed in other plant species. By linking epigenetic regulation to metabolic adaptation, we're now closer to understanding how crops can naturally withstand harsh conditions, and how we might harness these insights to improve future varieties.”
The study's findings offer powerful new tools for breeding salt-tolerant crops. By pinpointing key histone modifications and their influence on gene expression and metabolite production, researchers can now target epigenetic markers to enhance stress resilience. The novel H3K9ac-H3K27me3 bivalent state could serve as a biomarker for selecting or engineering stress-adaptive traits. Additionally, the research highlights the importance of integrating epigenomics, transcriptomics, and metabolomics in agricultural innovation. As soil salinity worsens globally, understanding these chromatin-based defense strategies in crops like pea may prove vital for sustaining food security under changing climate conditions.
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References
DOI
Original Source URL
https://doi.org/10.1093/hr/uhae259
Funding information
This work was supported by The Major Special Funding Plan for the Construction of First Class Disciplines at Jianghan University (2023XKZ018), Hubei Provincial Natural Science Foundation (2023AFB427).
About Horticulture Research
Horticulture Research is an open access journal of Nanjing Agricultural University and ranked number one in the Horticulture category of the Journal Citation Reports ™ from Clarivate, 2023. The journal is committed to publishing original research articles, reviews, perspectives, comments, correspondence articles and letters to the editor related to all major horticultural plants and disciplines, including biotechnology, breeding, cellular and molecular biology, evolution, genetics, inter-species interactions, physiology, and the origination and domestication of crops.