Time-Course Transcriptomics Analysis Reveals Molecular Mechanisms of Salt-Tolerant and Salt-Sensitive Cotton Cultivars in Response to Salt Stress

Salt stress is an environmental factor that limits plant seed germination, growth, and survival. We performed a comparative RNA sequencing transcriptome analysis during germination of the seeds from two cultivars with contrasting salt tolerance responses. A transcriptomic comparison between salt-tolerant cotton cv Jin-mian 25 and salt-sensitive cotton cv Su-mian 3 revealed both similar and differential expression patterns between the two genotypes during salt stress. The expression of genes related to aquaporins, kinases, reactive oxygen species (ROS) scavenging, trehalose biosynthesis, and phytohormone biosynthesis and signaling that include ethylene (ET), gibberellin (GA), abscisic acid (ABA), jasmonic acid (JA), and brassinosteroid (BR) were systematically investigated between the cultivars. Despite the involvement of these genes in cotton's response to salt stress in positive or negative ways, their expression levels were mostly similar in both genotypes. Interestingly, a PXC2 gene (Ghir_D08G025150) was identified, which encodes a leucine-rich repeat receptor-like protein kinase (LRR-RLK). This gene showed an induced expression pattern after salt stress treatment in salt-tolerant cv Jin-mian 25 but not salt-sensitive cv Su-mian 3. Our multifaceted transcriptome approach illustrated a differential response to salt stress between salt-tolerant and salt-sensitive cotton.