Identification and Expression Analysis of WD40 Gene Family in Grape

doi:10.13560/j.cnki.biotech.bull.1985.2025-0274

Abstract

Abstract:

Objective The WD40 superfamily is widely present in eukaryotes and serves as a basic subunit of protein complexes. WD40 proteins play important regulatory roles in plant development and physiology. This study aims to analyze the sequence structure and physicochemical properties of VvWD40 gene family members in grapes, understand the role of grape WD40 genes in fruit development, and provide genetic resources for grape molecular breeding. Method Based on the grape genome information, bioinformatics methods were used to identify the VvWD40 family, and to analyze the physicochemical properties, chromosomal distribution, gene structure, conserved protein structures, phylogenetic evolution, cis-acting elements in the promoter, and tissue expression characteristics of the family members. Further, transcriptome and RT-qPCR were combined to analyze the expression patterns of VvWD40 genes in different developmental stages of ‘Zaoheibao’ grapes. Result A total of 86 WD40 genes were identified in the grape genome and classified into 7 groups through phylogenetic analysis. A total of 12 pairs of collinear gene pairs were identified in the grape. Ka/Ks analysis indicated that they mainly experienced purifying selection during evolution. The cis-acting element analysis showed that the VvWD40 gene family contained hormone and stress response cis-acting elements, which were closely related to grape fruit development. Among them, VvWD40-62/84 contained flavonoid-synthezing elements, suggesting that they might be related to anthocyanin synthesis. The expression profiles of 4 different stages of ‘Zaoheibao’ grape were analyzed, and it was found that most VvWD40 were expressed during fruit development. The expressions of 8 genes during the development of ‘Zaoheibao’ grape were verified by RT-qPCR. The expressions of VvWD40-34/49 genes were relatively low at the early stage of grape fruit development and the highest at the mature stage, indicating that these two genes might play a key role in the color change process of grape fruit development. Conclusion The 86 VvWD40 genes are identified, which are unevenly distributed on 19 chromosomes. Most VvWD40 show significant expression variations during grape fruit development, suggesting their important roles in grape growth and development.

Key words: Vitis vinifera L., WD40 gene, gene family, bioinformatics analysis, fruit development, expression analysis

ZHANG Gao-xiang, WU Yu-bi, GUO Ya-jing, JI Wei, YANG Zhong-yi. Identification and Expression Analysis of WD40 Gene Family in Grape[J]. Biotechnology Bulletin, 2026, 42(3): 324-337.

Figures/Tables 12

Table 1 Primer information

基因 Gene	正向引物 Forward primer （5′‒3′）	反向引物 Reverse primer （5′‒3′）
WD40-3	F： TTGGAAGGACACGAGAAACC	R： GGATACCTGCCACACCTTAATC
WD40-9	F： GACTTCCTCAAGAGCTCCATAAA	R： GTCCAAGCTCAAGCAAGAAAC
WD40-27	F： GTTCCTTCGATGAGACCGTTAG	R： GAGCCATCACGATTGAAATTGG
WD40-34	F： CAGTTTAGAGAGCGGCAAGAA	R： GTCCGTACAGCCATGTCATTAG
WD40-42	F： AGTGCCAGCAAGGATTCTAC	R： TCTAGGCTGCAACTCCAAAC
WD40-49	F： GTGAGGACTCAAAGGTGTATGT	R： GGACTCCAGCTCACACAATTA
WD40-51	F： CGTGCGATCTCTCGTGTATT	R： GCTCTTTCCCTCAGCATCATA
WD40-77	F： CTGACTCGCCACAGGAATATC	R： CTTTCACCGACCAGACATAGAG
EF1α	F： GAACTGGGTGCTTGATAGGC	R： ACCAAAATATCCGGAGTAAAAGA

Fig. 1 Evolutionary treeof VvWD40 gene family

Fig. 2 Chromosome position of VvWD40 gene family

Fig. 3 Analysis of the motif (A), domain (B) , and gene structure (C) of the VvWD40 gene family

Fig. 4 Cis-acting elements analysis in VvWD40 gene family promoter

Fig. 5 Intersection analysis of cis-acting elements of VvWD40 gene family

Fig. 6 Correlation analysis of codons in the VvWD40 gene family

Fig. 7 Analysis of VvWD40 gene expressions in different tissues and different periods of grape

Fig. 8 Collinearity analysis of VvWD40 gene family

Fig. 9 Analysis of selective pressure on the VvWD40 gene family

Fig. 10 Protein interaction network analysis (A), GO functional annotation (B), and KEGG enrichment analysis of the VvWD40 gene family

Fig. 11 Analysis of the expression pattern of the VvWD40 gene family and RT-qPCR verificationEL33: The berries are still firm and green. EL35: The berries start to color and increase in size. EL36: The berries have a medium content of soluble solids. EL38: The berries are ready for harvest and fully mature. Different lowercase letters indicate significant differences (P<0.05)

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