Identification and expression analysis of chlorophyll a/b binding protein gene family in grape (Vitis vinifera)

Abstract

In higher plants, light capture of chlorophyll a/b binding protein (Lhc) plays a crucial role in the plant's response to adverse environment. So far, the family has not been systematically identified in grapes. In this study, 20 VvLhcs were identified in the grape genome, which were distributed in 13 of 19 grape chromosomes and divided into 7 developing branches. The results of gene duplication analysis showed that 6 VvLhcs formed fragment duplication events, while there was no tandem duplication in VvLhcs. Exon-intron structure analysis showed that they had a wide number of exons. Protein conserved motif analysis showed that VvLhcs contained more similar motif structures in the same phylogenetic branch. The cis-acting elements in the VvLhcs promoter region mainly respond to light, plant hormones and abiotic stresses. In addition, qRT-PCR results showed that different proportions of salt stress and red-blue light affected the expression of VvLhcs and the expression patterns of genes in different grape varieties were different. The results for further study on different grape varieties in different combinations of red and blue light of the Lhc provide a theoretical basis.

Supplementary information: The online version contains supplementary material available at 10.1007/s12298-022-01204-5.

Keywords: Gene family identification; Grape; Lhc; Red-blue light; Salt stress.

Fig. 1

Phylogenetic relationship of grape Lhcs and other plants. The phylogenetic tree was constructed using 20 grape, 21 Arabidopsis, and 20 cassava Lhc proteins sequences

Fig. 2

Schematic representation of VvLhcs. A Based on the total amino acids of 20 VvLhc proteins, the phylogenetic tree was constructed by the adjacency method realized by MEGA software. B Gene structures of the 20 VvLhcs. The exons and introns were marked by yellow rectangles and thin lines, respectively. The untranslated regions (UTRs) were indicated by blue rectangles. C Motifs of the VvLhc proteins were identified using the online MEME program. Different colors boxes represented different motifs

Fig. 3

The distribution of VvLhc on grape chromosomes

Fig. 4

The number of stress-responsive cis-acting elements in the promoter region of each VvLhc

Fig. 5

The expression profiles of VvLhc in 6 different grape organs and tissues. Expression data corresponding to 20 grape VvLhc was retrieved from the international bio-analytic resource for plant biology (BAR) data sets for further analysis. The heat map was generated based on the RPKM (Reads Per Kilobase of exon model per million mapped reads) values that were transformed to log2 (value + 1). Red and blue color gradients indicate an increase or decrease, respectively

Fig. 6

The expression levels of 20 VvLhcs in grape leaves under NaCl treatment. Each value is expressed as the mean ± SD (n = 3, 3 biological replicates × 3 technical replicates). Different lowercase letters represent significant differences (P ≤ 0.05)