Effect of Light Intensity on Gene Expression in Hypocotyl during the Elongation in a Leaf-Yellowing Mutant of Pepper (Capsicum annuum L.)

Light is vital for plant growth and development, and the germination of many plant seeds and the development of seedlings are very sensitive to the light environment. Under no or low light conditions, pepper seedlings will accelerate the elongation of the hypocotyl to obtain light. To elucidate the molecular mechanism by which light regulates hypocotyl elongation in pepper, RNA sequencing was performed to analyze the hypocotyls and cotyledons of the yellowing mutant R24 under three different light intensity treatments. A total of 35,341 gene were identified; moreover, during the treatment, 9695 new genes and 13,123 differentially expressed genes (DEGs) were observed, respectively. Some genes related to brassino-lide receptor protein kinase BRI1, light capture proteins LHCA and LHCB, and auxin response factor may regulate the response of hot pepper cotyledons and hypocotyls to different light intensity. KEGG functional enrichment analysis revealed that the most abundant pathways were phenylpropane biosynthesis, plant hormone signal transduction, and carbon metabolism. This study provides a valuable reference for understanding the molecular mechanism of pepper’s response to different light intensities at the seedling stage and for improving the local light environment to overcome the hypocotyl elongation of pepper crop under low light conditions.