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. 2022 Aug 29;12(9):1340.
doi: 10.3390/life12091340.

Genome-Wide Identification and Expression Analyses of the Chitinase Gene Family in Response to White Mold and Drought Stress in Soybean (Glycine max)

Peiyun Lv  1 , Chunting Zhang  1 , Ping Xie  1 , Xinyu Yang  1 , Mohamed A El-Sheikh  2 , Daniel Ingo Hefft  3 , Parvaiz Ahmad  4 , Tuanjie Zhao  1 , Javaid Akhter Bhat  1
Affiliations

Genome-Wide Identification and Expression Analyses of the Chitinase Gene Family in Response to White Mold and Drought Stress in Soybean (Glycine max)

Peiyun Lv et al. Life (Basel). .

Abstract

Chitinases are enzymes catalyzing the hydrolysis of chitin that are present on the cell wall of fungal pathogens. Here, we identified and characterized the chitinase gene family in cultivated soybean (Glycine max L.) across the whole genome. A total of 38 chitinase genes were identified in the whole genome of soybean. Phylogenetic analysis of these chitinases classified them into five separate clusters, I-V. From a broader view, the I-V classes of chitinases are basically divided into two mega-groups (X and Y), and these two big groups have evolved independently. In addition, the chitinases were unevenly and randomly distributed in 17 of the total 20 chromosomes of soybean, and the majority of these chitinase genes contained few introns (≤2). Synteny and duplication analysis showed the major role of tandem duplication in the expansion of the chitinase gene family in soybean. Promoter analysis identified multiple cis-regulatory elements involved in the biotic and abiotic stress response in the upstream regions (1.5 kb) of chitinase genes. Furthermore, qRT-PCR analysis showed that pathogenic and drought stress treatment significantly induces the up-regulation of chitinase genes belonging to specific classes at different time intervals, which further verifies their function in the plant stress response. Hence, both in silico and qRT-PCR analysis revealed the important role of the chitinases in multiple plant defense responses. However, there is a need for extensive research efforts to elucidate the detailed function of chitinase in various plant stresses. In conclusion, our investigation is a detailed and systematic report of whole genome characterization of the chitinase family in soybean.

Keywords: Glycine max L.; PR proteins; chitinase; genome-wide; plant stresses.

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Conflict of interest statement

The authors declare no conflict of interest.

Figures

Figure 1
Figure 1
Phylogenetic analysis and chromosomal distribution of chitinase genes identified in the soybean genome.
Figure 2
Figure 2
Exon–intron analysis of chitinase genes of soybean. Graphic representation of the gene models of 38 GmChis genes identified from Glycine max. L genome revealed presence of varied numbers of introns. Exons are shown as red boxes and introns are shown as black lines.
Figure 3
Figure 3
Predicted 3D structures and transmembrane helix (TM) of 10 randomly selected soybean chitinase proteins, two from each class I–V, from top to bottom.
Figure 4
Figure 4
Syntenic relationships of among A. thaliana and G. max L. chitinase genes are indicated in different colors. Synteny relationships were lined by Circos (http://circos.ca/ (accessed on 23 December 2019)).
Figure 5
Figure 5
Expression analysis of ten randomly selected chitinase genes (two from each of the five classes) of the soybean ate 6, 12, 24 and 48 h after the inoculation of white mold pathogen (Sclerotinia sclerotiorum) and drought stress treatment. Three biological replicates were used to calculate error bars, based on standard error.
See this image and copyright information in PMC

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