Identification and comparative analysis of Histidine phosphotransfer (HP) genes reveal their role in cotton development and stress tolerance

Abstract

Histidine phosphotransfer (HP) genes are involved in cytokinin signaling and stress responses in Arabidopsis and rice. However, HP genes have not been reported in Gossypium species. Here, we comprehensively identified 224 HP genes in 17 plant species. The phylogenetic analysis classified HP genes into six clades. Gene structure and protein motif analysis of GhHP genes demonstrated well-conserved intron/exon and motif configuration within the same group. Chromosomal location outcomes indicated the mapping of 25 GhHP genes on 14 chromosomes, with the maximum number of genes on chromosome D06. Numerous cis-regulatory elements related to phytohormones, abiotic stress, growth, light responsiveness, meristem expression, and flavonoid biosynthesis were predicted in the promoter regions of GhHP genes. Sequence logos exhibited a highly conserved pattern of amino acids in the Gossypium species. Gene duplication depicts that gene loss or addition occurs mainly through segmental or whole-genome duplication. Further, collinearity analysis identified 90 and 33 orthologous gene pairs in G. hirsutum and G. barbadense, respectively. Ghi-miRN530, Ghi-miRN1478, and Ghi-miRN1478 targeted GhHP9, GhHP19, and GhHP23, respectively. The GhHP genes (GhHP7, GhHP9, and GhHP21) exhibited preferential expression in roots. Further, GhHP genes (GhHP13 and GhHP23) were significantly upregulated under abiotic stress (cold, heat, PEG, and salt) with few exceptions, indicating their significant role in the root and abiotic stress responses. Our research provides a substantial understanding of GhHP genes and offers a foundation for further investigation of HP genes for cotton breeding.