Comparative analysis of growth, physiological and transcriptomic response revealed mechanisms of waterlogging tolerance of hot pepper (Capsicum annuum var. conoides)

Waterlogging-sensitive ('ZHC1') and waterlogging-tolerant ('ZHC2') hot peppers were selected from three years of field investigation. 'ZHC2' could keep growing under waterlogging conditions, its lateral roots were distributed near the water surface, and its stem base grew many adventitious roots and rapidly formed aerenchyma. The chlorophyll content was stable, and the contents of carotenoid and amino acid were significantly greater in 'ZHC2' than in 'ZHC1' under both waterlogging stress and recovery conditions. However, waterlogging stress led to in-root decay and a significant increase in malondialdehyde content of 'ZHC1'. Using transcriptome analysis, we correlated the functions of many waterlogging-responsive differentially expressed genes closely with the pathways for reactive oxygen species production, lutein synthesis, auxin signal transduction, and amino acid synthesis, which were consistent with the above growth and physiological data (adventitious root formation and the contents of malondialdehyde, carotenoids and amino acids). Some novel candidate genes related to waterlogging tolerance were also detected. This work provides new insights into waterlogging-tolerant mechanisms and valuable clues for breeding of waterlogging-tolerant peppers.