Comprehensive analysis of cotton AMT genes and functional analysis of the GhAMT1.4a in nitrogen metabolism

Ammonium (NH₄⁺) serves as the primary nitrogen (N) source for many plants and is mainly transported within plants via ammonium transporters (AMTs). N use efficiency (NUE) depends on AMT-mediated ammonium uptake and allocation, followed by efficient assimilation. Although AMT proteins have been studied in various plant species, their functions in cotton remain poorly understood. Here, we systematically identified 84 AMT genes in four Gossypium species, including 14 members each in the diploids G. raimondii and G. arboreum and 28 members each in the allotetraploids G. hirsutum and G. barbadense. Phylogenetic and structural analyses classified these genes into AMT1 and AMT2 clades and revealed conserved motif composition and exon–intron organization within subfamilies. Duplication analyses indicated that segmental duplication was the primary force driving the expansion of GhAMT gene family. Transcriptomic profiling and qRT-PCR showed that multiple GhAMTs respond to cold, heat, salt, and drought stresses, with GhAMT1.4a exhibiting broad tissue expression and strong induction under NH₄⁺ or nitrate (NO₃⁻) treatments. Furthermore, virus-induced gene silencing of GhAMT1.4a reduced N content and total N accumulation in cotton. These findings provide insights into the potential roles of GhAMT genes in cotton N metabolism and NUE, and establish a foundation for future functional studies and agronomic improvement.