Genome-wide identification of Gossypium INDETERMINATE DOMAIN genes and their expression profiles in ovule development and abiotic stress responses

Abstract

Abstract Background INDETERMINATE DOMAIN (IDD) transcription factors form one of the largest and most conserved gene families in plant kingdom and play important roles in various processes of plant growth and development, such as flower induction in term of flowering control. Till date, systematic and functional analysis of IDD genes remained infancy in cotton. Results In this study, we identified total of 162 IDD genes from eight different plant species including 65 IDD genes in Gossypium hirsutum. Phylogenetic analysis divided IDDs genes into seven well distinct groups. The gene structures and conserved motifs of GhIDD genes depicted highly conserved exon-intron and protein motif distribution patterns. Gene duplication analysis revealed that among 142 orthologous gene pairs, 54 pairs have been derived by segmental duplication events and four pairs by tandem duplication events. Further, Ka/Ks values of most of orthologous/paralogous gene pairs were less than one suggested the purifying selection pressure during evolution. Spatiotemporal expression pattern by qRT-PCR revealed that most of the investigated GhIDD genes showed higher transcript levels in ovule of seven days post anthesis, and upregulated response under the treatments of multiple abiotic stresses. Conclusions Evolutionary analysis revealed that IDD gene family was highly conserved in plant during the rapid phase of evolution. Whole genome duplication, segmental as well as tandem duplication significantly contributed to the expansion of IDD gene family in upland cotton. Some distinct genes evolved into special subfamily and indicated potential role in the allotetraploidy Gossypium hisutum evolution and development. High transcript levels of GhIDD genes in ovules illustrated their potential roles in seed and fiber development. Further, upregulated responses of GhIDD genes under the treatments of various abiotic stresses suggested them as important genetic regulators to improve stress resistance in cotton breeding.

Keywords

• Upland cotton
• IDD transcription factor
• Gene duplication
• Collinearity
• Spatiotemporal expression
• Abiotic stresses