Transcriptome analysis of wild soybean (Glycine soja) under salt stress and identification of salt-responsive genes.

Background: Soil salinity has been a serious threat to agricultural production worldwide, including soybeans. Glycine soja, the wild ancestor of cultivated soybeans, harbors high genetic diversity and possesses attractive rare alleles.

Objective: We conducted a transcriptome analysis of G. soja subjected to salt stress to profile the transcriptomes and identify salt-responsive genes.

Methods: G. soja was subjected to salt stress at 0, 24, and 48 h. RNA was sequenced using the Illumina NovaSeq 6000 platform. Transcriptome sequencing was used to identify differentially expressed genes (DEGs) and differential alternative splicing genes (DASGs) and to analyze alterations in salt-responsive genes.

Results: A total of 249 and 1890 DEGs were identified at 24 and 48 h under salt stress, respectively. Among the DEGs, 45 and 252 transcription factors, including bHLH, MYB, and WRKY, were identified at 24 and 48 h, respectively. Additionally, 602 and 1850 DASGs were identified at 24 and 48 h, respectively. For DASGs, significant GO term enrichments included 'mRNA processing', 'Chromatin organization', 'Nucleus', and 'Transcription cofactor activity' at 48 h. The KEGG pathways, 'Spliceosome' and the 'mRNA surveillance pathway', were significantly enriched in DASGs at 48 h. Salt-responsive genes were identified in DEGs and/or DASGs, specifically GsJ3, GsACA12, GsACA13, GsHSFA2-like, and GsHSF30-like.

Conclusion: Through the analysis of DEGs, DASGs, and transcription factor predictions, we identified key factors involved in the salt stress response and tolerance of G. soja, which could contribute to salt-tolerant soybean cultivar through genetic engineering strategies.