Mining the Core Genes Being Tolerant to Cadmium in Wild Soybean by WGCNA

doi:10.13560/j.cnki.biotech.bull.1985.2024-1113

Abstract

Abstract:

Objective Wild soybean has characteristics of tolerance to stress, gradually becoming a germplasm resource for improved cultivated soybeans. It is significant to clarify the molecular regulation mechanism of tolerance to cadmium in wild soybeans and provide a basis for cultivating tolerant soybean varieties. Method In this study, 200 wild soybeans in eastern Hebei were used as experimental materials. Wild soybean seedlings were treated with Hoagland nutrient solution containing 75 mol/L CdCl₂, and the dry weight of the seedlings was measured. Transcriptome sequencing was performed on Cd-tolerant wild soybean R and sensitive material S at 24 h and 48 h under Cd treatment, respectively. KEGG and GO enrichment analyses were performed on differentially expressed genes (DEGs), and weighted gene co-expression network analysis (WGCNA) was used to detect Cd-tolerant core genes. Result The 200 wild soybean seedlings have shown remarkable differences under stress. Compared with the control, the shoot dry weight and root dry weight of seedlings under cadmium treatment significantly reduced. Transcriptome analysis showed that 6 443 and 4 496 DEGs were identified in R and S materials, respectively. GO and KEGG analyses found that these DEGs were enriched in photosynthesis and stress response pathways. Combined with WGCNA, the key turquoise and blue modules were significantly correlated with cadmium tolerance in wild soybeans. According to the connectivity and functional annotation of the genes in the module, it was predicted that 8 genes, such as LOC114376469, LOC114412091, LOC114388638, and LOC114399512 may play a role in the process of cadmium stress in wild soybean. Conclusion Two specific modules related to the tolerance of wild soybean to cadmium are identified, and LOC114376469, LOC114412091, LOC114388638, and LOC114399512 are screened to be the core genes related to the tolerance of wild soybean to cadmium.

Key words: wild soybean, Cd stress, WGCNA, core gene

ZHU Li-juan, ZHANG Kai, WEN Xiao-lei, CHU Jia-hao, SHI Feng-yu, WANG Yan-li. Mining the Core Genes Being Tolerant to Cadmium in Wild Soybean by WGCNA[J]. Biotechnology Bulletin, 2025, 41(8): 124-136.

Figures/Tables 11

Table 1 Description analysis of wild soybean seedlings under Cd treatment

性状 Trait	全距 Range	最小值 Min	最大值 Max	平均值 Average	标准差 Standard deviation
SDW-CK1 （g）	0.090	0.006	0.096	0.017	0.008
SDW-Cd1 （g）	0.049	0.001	0.050	0.013	0.005
RDW-CK1 （g）	0.043	0.002	0.045	0.007	0.005
RDW-Cd1 （g）	0.029	0.001	0.030	0.005	0.003
RSR-CK1	1.265	0.149	1.414	0.373	0.151
RSR-Cd1	2.037	0.077	2.114	0.404	0.225
CTC-SDW1	1.643	0.199	1.842	0.802	0.212
CTC-RDW1	2.363	0.146	2.509	0.848	0.315
CTC-RSR1	3.332	0.165	3.497	1.122	0.467
SDW-CK2 （g）	0.082	0.007	0.089	0.016	0.008
SDW-Cd2 （g）	0.059	0.002	0.061	0.014	0.007
RDW-CK2 （g）	0.056	0.002	0.058	0.006	0.005
RDW-Cd2 （g）	0.031	0.001	0.032	0.005	0.003
RSR-CK2	1.411	0.158	1.569	0.364	0.167
RSR-Cd2	1.180	0.062	1.242	0.365	0.165
CTC-SDW2	3.570	0.166	3.736	0.877	0.438
CTC-RDW2	2.500	0.014	2.514	0.856	0.342
CTC-RSR2	2.824	0.039	2.863	1.068	0.428
D1	1.05	0.14	1.19	0.459	0.147
D2	1.14	0.02	1.16	0.512	0.181

Fig. 1 Correlation analysis of dry weight of wild soybean seedlings under two repetitions*, ** and *** indicate extremely significant correlaton at 0.05, 0.01 and 0.001 levels, respectively

Fig. 2 Cadmium tolerant, sensitive wild soybean seedlings

Fig. 3 Analysis of transcriptome sequencing dataA: PCA analysis. B: Correlation test among samples. C: Heat map of DEGs. R0, R24, R48, S0, S24, and S48 indicate 0, 24, and 48 h under Cd stress in R and S. The same below

Fig. 4 Analysis of DEGs of R and S in wild soybean under cadmium stressA: Number of DEGs. B: Venn diagram of DEGs in R at different time. C: Venn diagram of DEGs in S at different time. D: Venn diagram of DEGs in R and S at 24 h under treatment. E: Venn diagram of DEGs in R and S at 48 h under treatment

Fig. 5 GO enrichment analysisA, B: GO enrichment analysis of DEGs in R at 24 h (A) and 48 h (B). C, D: GO enrichment analysis of DEGs in S at 24 h (C) and 48 h (D)

Fig. 6 KEGG enrichment analysiA, B: KEGG enrichment analysis of DEGs in R at 24 h (A) and 48 h (B) under stress. C, D: KEGG enrichment analysis of DEGs in S at 24 h (C) and 48 h (D) under stress

Fig. 7 WGCNA enrichment analysis of DEGs in wild soybean under Cd stressA: Co-expression module division. B: Gene module eigenvalue connectivity heat map. C: Blue module co-expresses the regulatory network. D: Turquoise module co-expresses the regulatory network

Table 2 Functional annotation of 8 WGCNA hub genes

关键基因 Gene ID	基因功能注释 Gene function	同源基因 Orthologs
LOC114375809	Glutamine synthetase leaf isozyme， chloroplastic-like	Glyma 13G210800v4
LOC114376496	Protein DETOXIFICATION 42-like	Glyma 13G339800v4
LOC114377985	Stromal 70 kD heat shock-related protein， chloroplastic-like	Glyma 12G166200v4
LOC114387053	Phosphoglycerate kinase， cytosolic-like	Glyma 15G261900v4
LOC114388638	Heat shock 70 kD protein 14-like	Glyma 15G014400v4
LOC114399512	Magnesium-chelatase subunit ChlH， chloroplastic-like	Glyma 19G139300v4
LOC114406715	Magnesium-chelatase subunit ChlH， chloroplastic-like	Glyma 03G137000v4
LOC114412091	FAM10 family protein At4g22670-like	Glyma 05G051600v4

Fig. 8 RT-qPCR analysis of candidate genes for cadmium tolerance in wild soybean

Fig. 9 Prediction of protein interaction proteins encoded by cadmium-tolerant hub gene in wild soybean

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