Identification of candidate genes involved in salt stress response at germination and seedling stages by QTL mapping in upland cotton

Salinity is a major abiotic stress at critical stages of seed germination and seedling establishment. Germination rate (GR) and field emergence rate (FER) are the key traits that determine the basic number of plants stand under field conditions. To explore molecular mechanisms in upland cotton under salt stress, a population of 177 recombinant inbred lines (RILs) and their parents were evaluated for seed germination traits (GP, germination potential; GR; FW, fresh weight; DW, dry weight; GL, germinal length) and seedling traits (FER; SH, seedling height; NL, Number of main stem leaves) in 2016-2018. Based on the linkage map contained 2,859 single nucleotide polymorphism (SNP) and simple sequence repeats (SSR) markers, traits under salt stress (E1) and normal condition, (E2) and the converted relative index (R-value) of three years' trials were used to map quantitative trait loci (QTL). A total of three QTL and two clusters were detected as salt-tolerant QTL. Three QTL (qGR-Chr4-3, qFER-Chr12-3, qFER-Chr15-1) were detected under salt stress and R-value, which explained phenotypic variance of 9.62%-13.67%, and 4.2%-4.72%, 4.75%-8.96%, respectively. Two clusters (Loci-Chr4-2 and Loci-Chr5-4) harboring the QTL for four germination traits (GR, FER, GL, NL) and six seedling traits (GR, FER, DW, FW, SH, NL) were detected related under salt stress. A total of 691 genes were found in the candidate QTL or clusters. Among them, four genes (Gh_A04G1106, Gh_A05G3246, Gh_A05G3177, Gh_A05G3266) showed expression changes between sensitive and tolerant lines under salt stress, and were assigned as candidate genes in response to salt stress. The consistent salt-tolerance QTL identified in both germination and seedling stages will facilitate new information for cotton breeding. Overall design: RNA-seq profiles of five time points after 150 mM NaCl treatment in two upland cotton varieties.