# Genome-Wide Identification Analysis of the MAPKKK Gene Family in Cotton and Its Role in Development and Stress Response

## TL;DR

This study explores the role of MAPKKK genes in cotton, focusing on their function in development and resistance to plant diseases.

## Contribution

The paper provides the first comprehensive analysis of the MEKK subfamily of MAPKKK genes in cotton and their role in stress responses.

## Key findings

- Genome-wide analysis identified 660 MAPKKK genes in four cotton species, categorized into three subfamilies.
- WGD events were found to be the main driver of MAPKKK gene expansion in cotton.
- Expression profiling revealed distinct roles of MAPKKK genes in stress adaptation and immune homeostasis.

## Abstract

Mitogen-activated protein kinase kinase kinases (MAPKKKs) are pivotal upstream regulators of MAPK cascades, integrating signals that coordinate plant development and stress responses. However, the specific functions of MAPKKKs, particularly within the MEKK subfamily, in mediating cotton resistance to Verticillium wilt and Fusarium wilt remain poorly characterized. To address this, we conducted a systematic, cross-species analysis of the MAPKKK family in four key cotton species: Gossypium arboreum, Gossypium barbadense, Gossypium hirsutum, and Gossypium raimondii. Genome-wide identification and phylogenetic analysis revealed 660 MAPKKK genes, classifying them into the MEKK, Raf, and ZIK subfamilies. Evolutionary analysis indicated that Whole-Genome Duplication (WGD) events were the primary driver of family expansion. Promoter cis-element and Gene Ontology (GO) enrichment analyses implicated these genes in hormone signaling and stress adaptation. Expression profiling demonstrated functional modularity, with distinct members responding specifically to cold stress or cooperatively to drought and salt stresses. Upon pathogen infection, members diverged into regulatory modules associated with immune homeostasis, tissue-specific defense, and core signaling potentially governing systemic acquired resistance (SAR). The temporal expression patterns of core candidate genes were validated by qRT-PCR. This study provides, for the first time, a comprehensive evolutionary and functional framework for the MEKK subfamily within the cotton MAPKKK family. It reveals the conserved and divergent roles of this subfamily in stress adaptation and identifies key candidate genes for breeding disease-resistant cotton varieties.