A Novel Stable QTL in Chromosome A04 for Salt Tolerance at the Seed Germination Stage of Upland Cotton via a Resequencing-Based High-Density Genetic Map

Key message Two candidate genes GhGASA1 and GhADC2 playing negative roles by modulating the GA and PA signaling pathway, respectively, were identified in a major QTL for germination under salt stress.The successful transition of a seed into a seedling is the prerequisite for plant propagation and crop yield. Germination is a vulnerable stage in a plant’s life cycle which is strongly affected by environmental conditions, such as salinity. In this study, we identified a novel stable quantitative trait locus (QTL) qRGR-A04-1 associated with relative germination rate (RGR) after treatment with salt stress based on a high-density genetic map under phytotron and filed conditions, with LOD values of 6.65-16.83 and 6.11-12.63% of phenotypic variations in all five environment tests. Two candidate genes with significantly differential expression between two parents were finally identified through RNA-seq and qRT-PCR analyses. Further functional analyses showed that GhGASA1- and GhADC2-overexpression lines were more sensitive to salt stress than wild-type in Arabidopsis through regulating the transcript levels of gibberellic acid (GA) and polyamine (PA) -related genes implicating in GA and PA biosynthesis with reducing the accumulation of GA and PA under salt stress, respectively. Virus-induced gene silencing analysis showed that TRV:GASA1 and TRV:ADC2 displayed more tolerant to salt stress by increasing the expression of GA-synthesis genes and decreasing the H2O2 content, respectively. Taken together, our results suggested that QTL qRGR-A04-1 and its harbored two genes, GhGASA1 and GhADC2, were promising candidates for salt tolerance improvement in cotton.