Identification and Analysis of the <i>MIR399</i> Gene Family in Grapevine Reveal Their Potential Functions in Abiotic Stress

Jingjing Liu; Yi Ren; Yan Sun; Yonggang Yin; Bin Han; Lipeng Zhang; Yue Song; Zhen Zhang; Yuanyuan Xu; Dongying Fan; Junpeng Li; Huaifeng Liu; Chao Ma

doi:10.3390/ijms25052979

International Journal of Molecular Sciences (Mar 2024)

Identification and Analysis of the <i>MIR399</i> Gene Family in Grapevine Reveal Their Potential Functions in Abiotic Stress

Jingjing Liu,
Yi Ren,
Yan Sun,
Yonggang Yin,
Bin Han,
Lipeng Zhang,
Yue Song,
Zhen Zhang,
Yuanyuan Xu,
Dongying Fan,
Junpeng Li,
Huaifeng Liu,
Chao Ma

Affiliations

Jingjing Liu: Key Laboratory of Special Fruits and Vegetables Cultivation Physiology and Germplasm Resources Utilization of Xinjiang Production and Construction Corps, Department of Horticulture, Agricultural College of Shihezi University, Shihezi 832003, China
Yi Ren: College of Landscape and Horticulture, Yunnan Agricultural University, Kunming 650201, China
Yan Sun: Changli Research Institute of Fruit Trees, Hebei Academy of Agricultural and Forestry Sciences, Changli 066600, China
Yonggang Yin: Changli Research Institute of Fruit Trees, Hebei Academy of Agricultural and Forestry Sciences, Changli 066600, China
Bin Han: Changli Research Institute of Fruit Trees, Hebei Academy of Agricultural and Forestry Sciences, Changli 066600, China
Lipeng Zhang: Key Laboratory of Special Fruits and Vegetables Cultivation Physiology and Germplasm Resources Utilization of Xinjiang Production and Construction Corps, Department of Horticulture, Agricultural College of Shihezi University, Shihezi 832003, China
Yue Song: Shanghai Collaborative Innovation Center of Agri-Seeds, School of Agriculture and Biology, Shanghai Jiao Tong University, Shanghai 200240, China
Zhen Zhang: Shanghai Collaborative Innovation Center of Agri-Seeds, School of Agriculture and Biology, Shanghai Jiao Tong University, Shanghai 200240, China
Yuanyuan Xu: Shanghai Collaborative Innovation Center of Agri-Seeds, School of Agriculture and Biology, Shanghai Jiao Tong University, Shanghai 200240, China
Dongying Fan: Shanghai Collaborative Innovation Center of Agri-Seeds, School of Agriculture and Biology, Shanghai Jiao Tong University, Shanghai 200240, China
Junpeng Li: Shanghai Collaborative Innovation Center of Agri-Seeds, School of Agriculture and Biology, Shanghai Jiao Tong University, Shanghai 200240, China
Huaifeng Liu: Key Laboratory of Special Fruits and Vegetables Cultivation Physiology and Germplasm Resources Utilization of Xinjiang Production and Construction Corps, Department of Horticulture, Agricultural College of Shihezi University, Shihezi 832003, China
Chao Ma: Shanghai Collaborative Innovation Center of Agri-Seeds, School of Agriculture and Biology, Shanghai Jiao Tong University, Shanghai 200240, China

DOI: https://doi.org/10.3390/ijms25052979
Journal volume & issue: Vol. 25, no. 5
p. 2979

Abstract

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MiR399 plays an important role in plant growth and development. The objective of the present study was to elucidate the evolutionary characteristics of the MIR399 gene family in grapevine and investigate its role in stress response. To comprehensively investigate the functions of miR399 in grapevine, nine members of the Vvi-MIR399 family were identified based on the genome, using a miRBase database search, located on four chromosomes (Chr 2, Chr 10, Chr 15, and Chr 16). The lengths of the Vvi-miR399 precursor sequences ranged from 82 to 122 nt and they formed stable stem–loop structures, indicating that they could produce microRNAs (miRNAs). Furthermore, our results suggested that the 2 to 20 nt region of miR399 mature sequences were relatively conserved among family members. Phylogenetic analysis revealed that the Vvi-MIR399 members of dicots (Arabidopsis, tomato, and sweet orange) and monocots (rice and grapevine) could be divided into three clades, and most of the Vvi-MIR399s were closely related to sweet orange in dicots. Promoter analysis of Vvi-MIR399s showed that the majority of the predicted cis-elements were related to stress response. A total of 66.7% (6/9) of the Vvi-MIR399 promoters harbored drought, GA, and SA response elements, and 44.4% (4/9) of the Vvi-MIRR399 promoters also presented elements involved in ABA and MeJA response. The expression trend of Vvi-MIR399s was consistent in different tissues, with the lowest expression level in mature and young fruits and the highest expression level in stems and young leaves. However, nine Vvi-MIR399s and four target genes showed different expression patterns when exposed to low light, high light, heat, cold, drought, and salt stress. Interestingly, a putative target of Vvi-MIR399 targeted multiple genes; for example, seven Vvi-MIR399s simultaneously targeted VIT_213s0067g03280.1. Furthermore, overexpression of Vvi_MIR399e and Vvi_MIR399f in Arabidopsis enhanced tolerance to drought compared with wild-type (WT). In contrast, the survival rate of Vvi_MIR399d-overexpressed plants were zero after drought stress. In conclusion, Vvi-MIR399e and Vvi-MIR399f, which are related to drought tolerance in grapevine, provide candidate genes for future drought resistance breeding.

Published in International Journal of Molecular Sciences

ISSN: 1661-6596 (Print); 1422-0067 (Online)
Publisher: MDPI AG
Country of publisher: Switzerland
LCC subjects: Science: Biology (General); Science: Chemistry
Website: http://www.mdpi.com/journal/ijms

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