RNA-Seq analysis reveals potential salt- and drought stress tolerance-associated genes in advanced long-day onion breeding lines.

Onion production is negatively influenced by abiotic stresses, including drought and salinity. A transcriptome investigation of long-day onion breeding lines was performed to understand the transcriptional basis of abiotic stress tolerance in onion and identify genes that are involved in tolerance. A total of 11,410 differentially expressed genes (DEGs) under drought, salinity, and combined drought + salinity were identified in this study; among these genes, 6281 were upregulated, and 5129 were downregulated. Transcriptome analysis revealed different biological processes under individual and combined stress conditions. The salinity- and drought-associated genes regulated in tolerant breeding lines were associated with different biological processes, including transport, carbohydrate metabolism, protein modifications, and transcriptional regulation. A total of 1422 DEGs were identified in the U24 breeding line under salinity stress, and 1048 DEGs were identified in the U17 breeding line under drought and salinity stress. The transcriptomic results revealed the greatest increase in the expression of the chaperone binding (CHAP), superoxide dismutase (SOD), WRKY transcription factor 41 (WRKY), 36.4 kDa proline-rich protein-like (KDA), and aquaporin PIP2-7 (AQP) genes, which may have conferred tolerance in long-day onion breeding lines under drought, salinity, and combined stresses. The findings of this study will help researchers develop breeding strategies for tolerance to multiple abiotic stresses in onion.