Abstract
BackgroundThe allotetraploid cotton originated from one hybridization event between an extant progenitor of Gosssypium herbaceum (A1) or G. arboreum (A2) and another progenitor, G. raimondii Ulbrich (D5) 1–1.5 million years ago (Mya). The APETALA2/ethylene-responsive element binding protein (AP2/EREBP) transcription factors constitute one of the largest and most conserved gene families in plants. They are characterized by their AP2 domain, which comprises 60–70 amino acids, and are classified into four main subfamilies: the APETALA2 (AP2), Related to ABI3/VP1 (RAV), Dehydration-Responsive Element Binding protein (DREB) and Ethylene-Responsive Factor (ERF) subfamilies. The AP2/EREBP genes play crucial roles in plant growth, development and biotic and abiotic stress responses. Hence, understanding the molecular characteristics of cotton stress tolerance and gene family expansion would undoubtedly facilitate cotton resistance breeding and evolution research.ResultsA total of 269 AP2/EREBP genes were identified in the G. raimondii (D5) cotton genome. The protein domain architecture and intron/exon structure are simple and relatively conserved within each subfamily. They are distributed throughout all chromosomes but are clustered on various chromosomes due to genomic tandem duplication. We identified 73 tandem duplicated genes and 221 segmental duplicated gene pairs which contributed to the expansion of AP2/EREBP superfamily. Of them, tandem duplication was the most important force of the expansion of the B3 group. Transcriptome analysis showed that 504 AP2/EREBP genes were expressed in at least one tested G. hirsutum TM-1 tissues. In G. hirsutum, 151 non-repeated genes of the DREB and ERF subfamily genes were responsive to different stresses: 132 genes were induced by cold, 63 genes by drought and 94 genes by heat. qRT-PCR confirmed that 13 GhDREB and 15 GhERF genes were induced by cold and/or drought. No transcripts detected for 53 of the 111 tandem duplicated genes in TM-1. In addition, some homoeologous genes showed biased expression toward either A-or D-subgenome.ConclusionsThe AP2/EREBP genes were obviously expanded in Gossypium. The GhDREB and GhERF genes play crucial roles in cotton stress responses. Our genome-wide analysis of AP2/EREBP genes in cotton provides valuable information for characterizing the molecular functions of AP2/EREBP genes and reveals insights into their evolution in polyploid plants.
Highlights
The allotetraploid cotton originated from one hybridization event between an extant progenitor of Gosssypium herbaceum (A1) or G. arboreum (A2) and another progenitor, G. raimondii Ulbrich (D5) 1–1.5 million years ago (Mya)
Genome-wide identification of the AP2/EREBP superfamily in cotton The allotetraploid cotton species appeared about 1–1.5 Mya through the hybridization of a maternal A-genome species and a paternal D-genome species [42]
Excellent candidates for cotton improvement In this paper, we identified some important candidate genes which were highly or specific expressed in some tissues, such as GhDREB77 in fiber maturation, GhDREB2 in −3 dpa ovules involved in fiber initiation (Additional file 12: Figure S8), GhERF77 and GhERF88 in root development, GhERF139D in leaf development and GhRAV1 in fiber elongation (Fig. 5)
Summary
The allotetraploid cotton originated from one hybridization event between an extant progenitor of Gosssypium herbaceum (A1) or G. arboreum (A2) and another progenitor, G. raimondii Ulbrich (D5) 1–1.5 million years ago (Mya). The APETALA2/ethylene-responsive element binding protein (AP2/EREBP) transcription factors constitute one of the largest and most conserved gene families in plants. Members are defined by their AP2/ERF domain, which comprises about 60 to 70 amino acids [1,2,3] They play essential roles in plant growth, development and. The RAV subfamily transcription factors, which possess a single AP2 domain and an additional B3 domain [27], as well as a DNA-binding domain commonly found in other TFs [28], play significant roles in the regulating expression of target genes in response to ethylene, brassinosteroids and environmental stresses [29,30,31,32]. The ERF and DREB subfamily members, which contain a single conserved AP2 domain and comprise the largest groups in the AP2/EREBP superfamily, play critical roles in stress responses and in a variety of other plant processes. A fifth group comprises all other AP2/EREBPs not assigned to the other four groups: there is only one gene (At4g13040) in this group in Arabidopsis [11]
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