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<jats:title>SUMMARY</jats:title><jats:p>Alternative splicing (AS) of pre‐mRNAs increases the diversity of transcriptome and proteome and plays fundamental roles in plant development and stress responses. However, the prevalent changes in AS events and the regulating mechanisms of plants in response to pathogens remain largely unknown. Here, we show that AS changes are an important mechanism conferring cotton immunity to <jats:italic>Verticillium dahliae</jats:italic> (<jats:italic>Vd</jats:italic>). <jats:italic>GauSR45a</jats:italic>, encoding a serine/arginine‐rich RNA binding protein, was upregulated expression and underwent AS in response to <jats:italic>Vd</jats:italic> infection in <jats:italic>Gossypium australe</jats:italic>, a wild diploid cotton species highly resistant to <jats:italic>Vd</jats:italic>. Silencing <jats:italic>GauSR45a</jats:italic> substantially reduced the splicing ratio of <jats:italic>Vd</jats:italic>‐induced immune‐associated genes, including <jats:italic>GauBAK1</jats:italic> (<jats:italic>BRI1‐associated kinase 1</jats:italic>) and <jats:italic>GauCERK1</jats:italic> (chitin elicitor receptor kinase 1). GauSR45a binds to the <jats:italic>GAAGA</jats:italic> motif that is commonly found in the pre‐mRNA of genes essential for PTI, ETI, and defense. The binding between GauSR45a and the <jats:italic>GAAGA</jats:italic> motif in the pre‐mRNA of <jats:italic>BAK1</jats:italic> was enhanced by two splicing factors of GauU2AF35B and GauU1‐70 K, thereby facilitating exon splicing; silencing either <jats:italic>AtU2AF35B</jats:italic> or <jats:italic>AtU1‐70 K</jats:italic> decreased the resistance to <jats:italic>Vd</jats:italic> in transgenic <jats:italic>GauSR45a</jats:italic> Arabidopsis. Overexpressing the short splicing variant of <jats:italic>BAK1GauBAK1.1</jats:italic> resulted in enhanced Verticillium wilt resistance rather than the long one <jats:italic>GauBAK1.2</jats:italic>. <jats:italic>Vd</jats:italic>‐induced far more AS events were in <jats:italic>G. barbadense</jats:italic> (resistant tetraploid cotton) than those in <jats:italic>G. hirsutum</jats:italic> (susceptible tetraploid cotton) during <jats:italic>Vd</jats:italic> infection, indicating resistance divergence in immune responses at a genome‐wide scale. We provided evidence showing a fundamental mechanism by which GauSR45a enhances cotton resistance to <jats:italic>Vd</jats:italic> through global regulation of AS of immunity genes.</jats:p>

<jats:title>SUMMARY</jats:title><jats:p>Salinity is frequently mentioned as a major constraint in worldwide agricultural production. Lint percentage (LP) is a crucial yield‐component in cotton lint production. While the genetic factors affect cotton yield in saline soils are still unclear. Here, we employed a recombinant inbred line population in upland cotton (<jats:italic>Gossypium hirsutum</jats:italic> L.) and investigated the effects of salt stress on five yield and yield component traits, including seed cotton yield per plant, lint yield per plant, boll number per plant, boll weight, and LP. Between three datasets of salt stress (E1), normal growth (E2), and the difference values dataset of salt stress and normal conditions (<jats:italic>D</jats:italic>‐value), 87, 82, and 55 quantitative trait loci (QTL) were detectable, respectively. In total, five QTL (<jats:italic>qLY‐Chr6‐2</jats:italic>, <jats:italic>qBNP‐Chr4‐1</jats:italic>, <jats:italic>qBNP‐Chr12‐1</jats:italic>, <jats:italic>qBNP‐Chr15‐5</jats:italic>, <jats:italic>qLP‐Chr19‐2</jats:italic>) detected in both in E1 and <jats:italic>D</jats:italic>‐value were salt related QTL, and three stable QTL (<jats:italic>qLP‐Chr5‐3</jats:italic>, <jats:italic>qLP‐Chr13‐1</jats:italic>, <jats:italic>qBW‐Chr5‐5</jats:italic>) were detected both in E1 and E2 across 3 years. Silencing of nine genes within a stable QTL (<jats:italic>qLP‐Chr5‐3</jats:italic>) highly expressed in fiber developmental stages increased LP and decreased fiber length (FL), indicating that multiple minor‐effect genes clustered on Chromosome 5 regulate LP and FL. Additionally, the difference in LP caused by <jats:italic>Gh_A05G3226</jats:italic> is mainly in transcription level rather than in the sequence difference. Moreover, silencing of salt related gene (<jats:italic>GhDAAT</jats:italic>) within <jats:italic>qBNP‐Chr4‐1</jats:italic> decreased salt tolerance in cotton. Our findings shed light on the regulatory mechanisms underlining cotton salt tolerance and fiber initiation.</jats:p>