Abstract
Cotton is sensitive to waterlogging stress, which usually results in stunted growth and yield loss. To date, the molecular mechanisms underlying the responses to waterlogging in cotton remain elusive. Cotton was grown in a rain-shelter and subjected to 0 (control)-, 10-, 15- and 20-d waterlogging at flowering stage. The fourth-leaves on the main-stem from the top were sampled and immediately frozen in liquid nitrogen for physiological measurement. Global gene transcription in the leaves of 15-d waterlogged plants was analyzed by RNA-Seq. Seven hundred and ninety four genes were up-regulated and 1018 genes were down-regulated in waterlogged cotton leaves compared with non-waterlogged control. The differentially expressed genes were mainly related to photosynthesis, nitrogen metabolism, starch and sucrose metabolism, glycolysis and plant hormone signal transduction. KEGG (Kyoto Encyclopedia of Genes and Genomes) analysis indicated that most genes related to flavonoid biosynthesis, oxidative phosphorylation, amino acid metabolism and biosynthesis as well as circadian rhythm pathways were differently expressed. Waterlogging increased the expression of anaerobic fermentation related genes, such as alcohol dehydrogenase (ADH), but decreased the leaf chlorophyll concentration and photosynthesis by down-regulating the expression of photosynthesis related genes. Many genes related to plant hormones and transcription factors were differently expressed under waterlogging stress. Most of the ethylene related genes and ethylene-responsive factor-type transcription factors were up-regulated under water-logging stress, suggesting that ethylene may play key roles in the survival of cotton under waterlogging stress.
Highlights
Waterlogging is a well-known abiotic stress that can severely damage crop production worldwide
The gene sequences of G. hirsutum genome were used as reference to align and identify the sequencing reads
Our data showed that many genes with potential roles in carbohydrate metabolism, nitrogen metabolism and photosynthesis were down-regulated; in ethylene synthesis and perception, regulation of transcription and glycolysis were significantly up-regulated in cotton under waterlogging stress
Summary
Waterlogging is a well-known abiotic stress that can severely damage crop production worldwide. It usually occurs in areas with high rainfall and/or poor drainage [1]. Low oxygen is known to be a serious factor in the adverse effects of waterlogging [2]. Agricultural Scientific and Technological Innovation Project of Shandong Academy of Agricultural Sciences (CXGC2016C04)
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