Comparative Transcriptome Analysis of Salt-Tolerant and -Sensitive Soybean Cultivars under Salt Stress

Soil salinity is a major limiting factor in soybean (Glycine max (L.) Merr.) yield in Xinjiang, China. Therefore, breeding soybean to tolerate highly saline soils is crucial to improve its yield. To explore the molecular mechanisms underlying the response of soybean to salt stress, we performed a comparative transcriptome analysis of root and leaf samples collected from two local soybean cultivars. The salt-tolerant cultivar ‘Xin No. 9’ (X9) showed higher photosynthetic activity than the salt-sensitive cultivar ‘Xinzhen No. 9’ (Z9) under salt stress. In total, we identified 13,180 and 13,758 differential expression genes (DEGs) in X9 and Z9, respectively, of which the number of DEGs identified in roots was much higher than that in leaves. We constructed the co-expression gene modules and conducted Gene Ontology (GO) term and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway enrichment analyses. The results suggested there were distinct differences in the mechanisms of response to salt stress between the two soybean cultivars; i.e., the salt-tolerant cultivar X9 exhibited alterations in fundamental metabolism, whereas the salt-sensitive cultivar Z9 responded to salt stress mainly through the cell cycle. The possible crosstalk among phytohormone signaling, MAPK signaling, phenylpropanoid biosynthesis, starch and sucrose metabolism, and ribosome metabolism may play crucial roles in the response to salt stress in soybean. Our results offered a comprehensive understanding of the genes and pathways involved in the response to salt stress in soybean and provided valuable molecular resources for future functional studies and the breeding of soybean varieties with enhanced tolerance to salinity.