Identification of candidate genes controlling cucumber hypocotyl elongation under low light stress based on BSA-seq and RNA-seq.

• Low light stress induced hypocotyl elongation in cucumber. • The candidate region of hypocotyl elongation under low light was mapped on Chr 2 by BSA-seq. • Low light regulate the expression of auxin related genes. Cucumber (Cucumis sativus L.) is cultivated worldwide and is known to be photophilic and thermophilic. Low light stress (LLS) in winter and spring in Northern and early spring in Southern China has a severe impact on the growth and development of greenhouse cucumbers. However, the molecular regulatory mechanisms of LLS in cucumbers remain unclear, which seriously limits the development of cucumber breeding under LLS. In this study, we investigated hypocotyl differences in two cucumber lines grown under LLS and normal (CK) condition. Under LLS, the activities of ascorbate peroxidase (APX), superoxide dismutase (SOD), peroxidase (POD), and malondialdehyde (MDA) declined tovarying degrees compared with CK, and Y8 showed a relatively small decline. The hypocotyl length of the F 2 population is a quantitative trait controlled by multiple genes under LLS conditions. The candidate region for hypocotyl elongation under LLS was mapped to chromosome 2 using bulk segregant analysis sequencing (BSA-seq). In addition, transcriptome analysis revealed 2786 differentially expressed genes (DEGs), of which 871 DEGs were specifically identified between Y5 and Y8 under LLS. Among these DEGs, 12 DEGs were involved in plant hormone signal transduction. Association analysis of the BSA-Seq and RNA-Seq results suggested that 36 DEGs were as candidate genes. Furthermore, three TFs (NAC, MYB and C2H2) may be considered the most likely candidate genes of hypocotyl elongation under LLS. Our results provide comprehensive understandings of the mechanism of hypocotyl elongation under LLS, and contribute to foundation for cloning the genes involved in hypocotyl elongation under LLS. [ABSTRACT FROM AUTHOR]