Genome-wide identification, characterization analysis and expression profiling of auxin-responsive GH3 family genes in wheat (Triticum aestivum L.)

Auxin affects many aspects of plant growth and development by regulating the expression of auxin-responsive genes. As one of the three major auxin-responsive families the Gretchen Hagen3 (GH3) gene family maintains hormonal homeostasis by conjugating excess indole-3-acetic acid (IAA), salicylic acid (SA), and jasmonic acid (JA) to amino acids during hormone and stress-related signaling. Although some work has been carried out the functions of wheat GH3 (TaGH3) family genes in response to abiotic stresses (including salt stress and osmotic stress) are largely unknown. Access to the complete wheat genome sequence permits genome-wide studies on TaGH3s. We performed a systematic identification of the TaGH3 gene family at the genome level and detected 36 members on 14 wheat chromosomes. Many of the genes were segmentally duplicated and Ka/Ks and inter-species synthetic analyses indicated that polyploidization was the contributor to the increased number of TaGH3 members. Phylogenetic analyses revealed that TaGH3 proteins could divided into three major categories (TaGH3-I, TaGH3-II, and TaGH3-III). Diversified cis-elements in the promoters of TaGH3 genes were predicted as essential players in regulating TaGH3 expression patterns. Gene structure and motif analyses indicated that most TaGH3 genes have relatively conserved exon/intron arrangements and motif compositions. Analysis of multiple transcriptome data sets indicated that many TaGH3 genes are responsive to biological and abiotic stresses and possibly have important functions in stress response. qRT-PCR analysis revealed that TaGH3s were induced by salt and osmotic stresses. Customized annotation results revealed that TaGH3s were widely involved in phytohormone response, defense, growth and development, and metabolism. Overall, our work provides a comprehensive insight into the TaGH3 family members, and a basis for the further study of their biological functions in wheat.