Genome-wide identification and expression pattern analysis of the kiwifruit GRAS transcription factor family in response to salt stress

Ling Zhu; Tuo Yin; Mengjie Zhang; Xiuyao Yang; Jiexin Wu; Hanbing Cai; Na Yang; Xulin Li; Ke Wen; Daming Chen; Hanyao Zhang; Xiaozhen Liu

doi:10.1186/s12864-023-09915-z

Genome-wide identification and expression pattern analysis of the kiwifruit GRAS transcription factor family in response to salt stress

BMC Genomics. 2024 Jan 2;25(1):12. doi: 10.1186/s12864-023-09915-z.

Authors

Ling Zhu¹, Tuo Yin¹, Mengjie Zhang², Xiuyao Yang¹, Jiexin Wu², Hanbing Cai¹, Na Yang², Xulin Li², Ke Wen², Daming Chen³, Hanyao Zhang⁴, Xiaozhen Liu⁵

Affiliations

¹ Key Laboratory for Forest Resources Conservation and Utilization in the Southwest Mountains of China, Ministry of Education, Southwest Forestry University, Kunming, 650224, China.
² Key Laboratory of Biodiversity Conservation in Southwest China, National Forest and Grassland Administration, Southwest Forestry University, Kunming, 650224, Yunnan Province, China.
³ Research Institute of Agriculture Ecological in Hot Areas, Yunnan Academy of Agricultural Science, Yuan Mou, Yunnan, 651300, China.
⁴ Key Laboratory for Forest Resources Conservation and Utilization in the Southwest Mountains of China, Ministry of Education, Southwest Forestry University, Kunming, 650224, China. zhanghanyao@swfu.edu.cn.
⁵ Key Laboratory of Biodiversity Conservation in Southwest China, National Forest and Grassland Administration, Southwest Forestry University, Kunming, 650224, Yunnan Province, China. 15198729095@swfu.edu.cn.

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.

Keywords: Expression patterns; GRAS transcription factors; Genome-wide analysis; Kiwifruit; Salt stress; Transcriptome.

MeSH terms

Gene Expression Profiling
Gene Expression Regulation, Plant
Genome, Plant*
Phylogeny
Plant Breeding
Plant Proteins / metabolism
Salt Tolerance
Stress, Physiological / genetics
Transcription Factors* / genetics
Transcription Factors* / metabolism

Substances

Transcription Factors
Plant Proteins