Genome-wide characterization of the GRF family and their roles in response to salt stress in Gossypium

Abstract

Background Cotton ( Gossypium spp.) is the most important world-wide fiber crop but salt stress limits cotton production in coastal and other areas. Growth regulation factors (GRFs) play regulatory roles in response to salt stress, but their roles have not been studied in cotton under salt stress. Results We identified 19 GRF genes in G. raimondii , 18 in G. arboreum , 34 in G. hirsutum and 45 in G. barbadense , respectively. These GRF genes were phylogenetically analyzed leading to the recognition of seven GRF clades. GRF genes from diploid cottons ( G. raimondii and G. arboreum ) were largely retained in allopolyploid cotton, with subsequent gene expansion in G. barbadense relative to G. hirsutum . Most G. hirsutum GRF ( GhGRF ) genes are preferentially expressed in young and growing tissues. To explore their possible role in salt stress, we used qRT-PCR to study expression responses to NaCl treatment, showing that five GhGRF genes were down-regulated in leaves. RNA-seq experiments showed that seven GhGRF genes exhibited decreased expression in leaves under NaCl treatment, three of which ( GhGRF3 , GhGRF4 , and GhGRF16 ) were identified by both RNA-seq and qRT-PCR. We also identified six and three GRF genes that exhibit decreased expression under salt stress in G. arboreum and G. barbadense , respectively. Consistent with its lack of leaf withering or yellowing under the salt treatment conditions, G. arboreum had better salt tolerance than G. hirsutum and G. barbadense . Our results suggest that GRF genes are involved in salt stress responses in Gossypium . Conclusion In summary, we identified candidate GRF genes that were involved in salt stress responses in cotton.

Genome-Wide Identification and Characterization of the Abiotic-Stress-Responsive GRF Gene Family in Diploid Woodland Strawberry (Fragaria vesca)

“…The downstream targets of AtGRF1 and AtGRF3 are involved in defense response and disease resistance, which indicates that AtGRF1 and AtGRF3 play primary roles in the coordination of plant growth and defense signals [ 20 ]. Expression patterns of GhGRF1A , GhGRF1D , and GhGRF17D in cotton change in response to salt stress [ 24 ]. Under shade stress, all GmGRF genes are significantly down-regulated in soybean [ 25 ].…”

Genome-wide identification and expression analysis of the growth regulating factor (GRF) family in Jatropha curcas

“…QLQ domain is an important protein-protein interaction domain, whereas WRC domain is a kind of plant-specific motif, which is mainly responsible for the interaction between transcription factors and DNA [2]. Since the first GRF family gene, namely OsGRF1, is isolated and functionally studied in rice [3], many GRF genes have been identified and characterized in a variety of plant species such as tomato, soybean, rice, cotton, streptophyta and Arabidopsis [2,[4][5][6][7].…”

Characterization of cotton ARF factors and the role of GhARF2b in fiber development

“…Raw RNA-Seq data were downloaded from the NCBI Sequence Read Archive ( https://www.ncbi.nlm.nih.gov/bioproject/PRJNA248163 ) [ 42 ], including G. hirsutum seed, root, stem, leaf, torus, petal, stamen, ovary, calyx, ovule (− 3 dpa, − 1 dpa, 0 dpa, 1 dpa, 3 dpa, 5 dpa, 10 dpa, 20 dpa, 25dpa, 35dpa) and fiber (5 dpa, 10 dpa, 20 dpa, 25dpa). The method of gene expression analyses based on transcriptome was same to our previous study [ 69 ]. Differentially expressed genes were determined based on the following criteria: more than two-fold change and p -value less than 0.05.…”

“…All cotton samples were ground in liquid nitrogen and total RNAs of these cotton tissues were extracted using the RNAprep pure plant kit (TIANGEN, Shanghai, China) following the manufacturer’s protocol. The method of qRT-PCR analyses was same to our previous study [ 69 ]. The forward and reverse primers of specific gene for quantitative real-time PCR (qRT-PCR) analyses, were designed using the Primer5 software (Additional file 3 : Table S1).…”