Genome-wide Identification and Expression Pattern Analysis of the Kiwifruit GRAS Transcription Factor Family in Response to Salt Stress

Overview

Journal BMC Genomics

Publisher Biomed Central

Specialty Genetics

Date 2024 Jan 3

PMID 38166720

Authors

Ling Zhu

Tuo Yin

Mengjie Zhang

Xiuyao Yang

Jiexin Wu

Hanbing Cai

Na Yang

Xulin Li

Ke Wen

Daming Chen

Hanyao Zhang

Xiaozhen Liu

Affiliations

Soon will be listed here.

Abstract

Background: GRAS is a family of plant-specific transcription factors (TFs) that play a vital role in plant growth and development and response to adversity stress. However, systematic studies of the GRAS TF family in kiwifruit have not been reported.

Results: In this study, we used a bioinformatics approach to identify eighty-six AcGRAS TFs located on twenty-six chromosomes and phylogenetic analysis classified them into ten subfamilies. It was found that the gene structure is relatively conserved for these genes and that fragmental duplication is the prime force for the evolution of AcGRAS genes. However, the promoter region of the AcGRAS genes mainly contains cis-acting elements related to hormones and environmental stresses, similar to the results of GO and KEGG enrichment analysis, suggesting that hormone signaling pathways of the AcGRAS family play a vital role in regulating plant growth and development and adversity stress. Protein interaction network analysis showed that the AcGRAS51 protein is a relational protein linking DELLA, SCR, and SHR subfamily proteins. The results demonstrated that 81 genes were expressed in kiwifruit AcGRAS under salt stress, including 17 differentially expressed genes, 13 upregulated, and four downregulated. This indicates that the upregulated AcGRAS55, AcGRAS69, AcGRAS86 and other GRAS genes can reduce the salt damage caused by kiwifruit plants by positively regulating salt stress, thus improving the salt tolerance of the plants.

Conclusions: These results provide a theoretical basis for future exploration of the characteristics and functions of more AcGRAS genes. This study provides a basis for further research on kiwifruit breeding for resistance to salt stress. RT-qPCR analysis showed that the expression of 3 AcGRAS genes was elevated under salt stress, indicating that AcGRAS exhibited a specific expression pattern under salt stress conditions.

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References

Wang Y, Tang H, DeBarry J, Tan X, Li J, Wang X . MCScanX: a toolkit for detection and evolutionary analysis of gene synteny and collinearity. Nucleic Acids Res. 2012; 40(7):e49. PMC: 3326336. DOI: 10.1093/nar/gkr1293. View

Park J, Nguyen K, Park E, Jeon J, Choi G . DELLA proteins and their interacting RING Finger proteins repress gibberellin responses by binding to the promoters of a subset of gibberellin-responsive genes in Arabidopsis. Plant Cell. 2013; 25(3):927-43. PMC: 3634697. DOI: 10.1105/tpc.112.108951. View

Sufyan M, Daraz U, Hyder S, Zulfiqar U, Iqbal R, Eldin S . An overview of genome engineering in plants, including its scope, technologies, progress and grand challenges. Funct Integr Genomics. 2023; 23(2):119. DOI: 10.1007/s10142-023-01036-w. View

Zhang H, Cao Y, Shang C, Li J, Wang J, Wu Z . Genome-wide characterization of GRAS family genes in Medicago truncatula reveals their evolutionary dynamics and functional diversification. PLoS One. 2017; 12(9):e0185439. PMC: 5612761. DOI: 10.1371/journal.pone.0185439. View

Waseem M, Nkurikiyimfura O, Niyitanga S, Jakada B, Shaheen I, Aslam M . GRAS transcription factors emerging regulator in plants growth, development, and multiple stresses. Mol Biol Rep. 2022; 49(10):9673-9685. DOI: 10.1007/s11033-022-07425-x. View

Ito T, Okada K, Fukazawa J, Takahashi Y . DELLA-dependent and -independent gibberellin signaling. Plant Signal Behav. 2018; 13(3):e1445933. PMC: 5927702. DOI: 10.1080/15592324.2018.1445933. View

Xiong L, Zhu J . Regulation of abscisic acid biosynthesis. Plant Physiol. 2003; 133(1):29-36. PMC: 523868. DOI: 10.1104/pp.103.025395. View

Marchler-Bauer A, Bo Y, Han L, He J, Lanczycki C, Lu S . CDD/SPARCLE: functional classification of proteins via subfamily domain architectures. Nucleic Acids Res. 2016; 45(D1):D200-D203. PMC: 5210587. DOI: 10.1093/nar/gkw1129. View

Di Laurenzio L, Malamy J, Pysh L, Helariutta Y, Freshour G, Hahn M . The SCARECROW gene regulates an asymmetric cell division that is essential for generating the radial organization of the Arabidopsis root. Cell. 1996; 86(3):423-33. DOI: 10.1016/s0092-8674(00)80115-4. View

10.

Itoh H, Ueguchi-Tanaka M, Sato Y, Ashikari M, Matsuoka M . The gibberellin signaling pathway is regulated by the appearance and disappearance of SLENDER RICE1 in nuclei. Plant Cell. 2002; 14(1):57-70. PMC: 150551. DOI: 10.1105/tpc.010319. View

11.

Stuurman J, Jaggi F, Kuhlemeier C . Shoot meristem maintenance is controlled by a GRAS-gene mediated signal from differentiating cells. Genes Dev. 2002; 16(17):2213-8. PMC: 186665. DOI: 10.1101/gad.230702. View

12.

Zhang J, Liao J, Ling Q, Xi Y, Qian Y . Genome-wide identification and expression profiling analysis of maize AP2/ERF superfamily genes reveal essential roles in abiotic stress tolerance. BMC Genomics. 2022; 23(1):125. PMC: 8841118. DOI: 10.1186/s12864-022-08345-7. View

13.

Li Z, Zhong F, Guo J, Chen Z, Song J, Zhang Y . Improving Wheat Salt Tolerance for Saline Agriculture. J Agric Food Chem. 2022; 70(48):14989-15006. DOI: 10.1021/acs.jafc.2c06381. View

14.

Cantalapiedra C, Hernandez-Plaza A, Letunic I, Bork P, Huerta-Cepas J . eggNOG-mapper v2: Functional Annotation, Orthology Assignments, and Domain Prediction at the Metagenomic Scale. Mol Biol Evol. 2021; 38(12):5825-5829. PMC: 8662613. DOI: 10.1093/molbev/msab293. View

15.

Van De Velde K, Ruelens P, Geuten K, Rohde A, Van Der Straeten D . Exploiting DELLA Signaling in Cereals. Trends Plant Sci. 2017; 22(10):880-893. DOI: 10.1016/j.tplants.2017.07.010. View

16.

Zhang S, Li X, Fan S, Zhou L, Wang Y . Overexpression of HcSCL13, a Halostachys caspica GRAS transcription factor, enhances plant growth and salt stress tolerance in transgenic Arabidopsis. Plant Physiol Biochem. 2020; 151:243-254. DOI: 10.1016/j.plaphy.2020.03.020. View

17.

Pilkington S, Crowhurst R, Hilario E, Nardozza S, Fraser L, Peng Y . A manually annotated Actinidia chinensis var. chinensis (kiwifruit) genome highlights the challenges associated with draft genomes and gene prediction in plants. BMC Genomics. 2018; 19(1):257. PMC: 5902842. DOI: 10.1186/s12864-018-4656-3. View

18.

Mannu J, Latha A, Rajagopal S, Lalitha H, Muthurajan R, Loganathan A . Whole genome sequencing of ASD 16 and ADT 43 to identify predominant grain size and starch associated alleles in rice. Mol Biol Rep. 2022; 49(12):11743-11754. DOI: 10.1007/s11033-022-07935-8. View

19.

Zhang D, Iyer L, Aravind L . Bacterial GRAS domain proteins throw new light on gibberellic acid response mechanisms. Bioinformatics. 2012; 28(19):2407-11. PMC: 3463117. DOI: 10.1093/bioinformatics/bts464. View

20.

Marchler-Bauer A, Lu S, Anderson J, Chitsaz F, Derbyshire M, DeWeese-Scott C . CDD: a Conserved Domain Database for the functional annotation of proteins. Nucleic Acids Res. 2010; 39(Database issue):D225-9. PMC: 3013737. DOI: 10.1093/nar/gkq1189. View