Genome-Wide Identification and Expression Analysis of SnRK2 Gene Family in Dormant Vegetative Buds of Liriodendron chinense in Response to Abscisic Acid, Chilling, and Photoperiod

Abstract

Protein kinases play an essential role in plants' responses to environmental stress signals. SnRK2 (sucrose non-fermenting 1-related protein kinase 2) is a plant-specific protein kinase that plays a crucial role in abscisic acid and abiotic stress responses in some model plant species. In apple, corn, rice, pepper, grapevine, Arabidopsis thaliana, potato, and tomato, a genome-wide study of the SnRK2 protein family was performed earlier. The genome-wide comprehensive investigation was first revealed to categorize the SnRK2 genes in the Liriodendron chinense (L. chinense). The five SnRK2 genes found in the L. chinense genome were highlighted in this study. The structural gene variants, 3D structure, chromosomal distributions, motif analysis, phylogeny, subcellular localization, cis-regulatory elements, expression profiles in dormant buds, and photoperiod and chilling responses were all investigated in this research. The five SnRK2 genes from L. chinense were grouped into groups (I-IV) based on phylogeny analysis, with three being closely related to other species. Five hormones-, six stress-, two growths and biological process-, and two metabolic-related responsive elements were discovered by studying the cis-elements in the promoters. According to the expression analyses, all five genes were up- and down-regulated in response to abscisic acid (ABA), photoperiod, chilling, and chilling, as well as photoperiod treatments. Our findings gave insight into the SnRK2 family genes in L. chinense and opened up new study options.

Keywords: SnRK2 kinase family; abscisic acid; chilling; photoperiod; qRT-PCR.

Figure 1

This schematic flow depicts the experimental setup. The various box designs and color schemes represent different modes of treatment and sampling.

Figure 2

The SnRK2 gene distribution on the chromosomes of L. chinense serves as a scaffold. The chromosomal/scaffold numbers are found at the top of each chromosome. The names of each LcSnRK2 gene are displayed on the left side of each chromosome. The bars on the scaffold/chromosomes represent the SnRK2 genes.

Figure 3

A phylogenetic analysis of SnRK2 proteins from Liriodendron chinense (5), Arabidopsis thaliana (11), Solanum lycopersicum (8), Capsicum annuum (9), Solanum tuberosum (8), Vitis vinifera (8), Zea mays (10), Oryza sativa (10), and Malus domestica was carried out using the maximum likelihood method (9). There are four groups of SnRK2 proteins: I, II, III, and IV, each of which is represented by a different color.

Figure 4

L. chinense’s SnRK2 family gene structure and motif analysis: (A) Based on phylogenetic relationships and domain identification, the SnRK2s were classified into four groups. Gene structure for SnRK2 (B). The blue horizontal line denotes exon regions, while the green horizontal line denotes intron regions. (C) Conserved motif compositions were found in L. chinense SnRK2s. Various color boxes represent numerous motifs.

Figure 5

SnRK2 family 3D structures displaying functional sites.

Figure 6

Cis-regulatory elements (CREs) found in the promoters of SnRK2 genes. (A) The positional distribution of the projected CREs on the SnRK2 promoters is shown by vertical bars. Five SnRK2 genes’ promoter sequences (2500 bp) were examined using PlantCARE. In this legend, each cis-color element is represented: (B) Hormones, stress, growth and biological processes, and sensitive metabolic components are linked to the distribution of cis-elements in the promoters of SnRK2 genes. The detected cis-elements are displayed in colored boxes.

Figure 7

The distribution of cis-regulatory elements (CREs) in the promoters of SnRK2 genes is based on their hypothesized roles. The four different types of CREs are (A) hormone-responsive CREs, (B) stress-responsive CREs, (C) growth and biological process-responsive CREs, and (D) metabolic-responsive CREs.

Figure 8

The expression of LchiSnRK2s by qRT-PCR in dormant buds of L. chinense at the seedling stage under different photoperiods (long day (P-LD) and short-day (P-SD)), chilling, various abscisic acid concentrations (ABA-10 µM and ABA-100 µM), and chilling as well as photoperiod (C + P-LD, C + P-SD). The Least Significant Difference (LSD) test indicates a significant (p ≤ 0.05) difference between the control and all conditions. * = Showed significant differences and ns = Showed non-significant differences.