Comparative transcriptome analysis reveals the molecular regulation underlying the adaptive mechanism of cherry (Cerasus pseudocerasus Lindl.) to shelter covering

Abstract Background Rain-shelter covering is widely applied during cherry fruit development in subtropical monsoon climates with the aim of decreasing the dropping and cracking of fruit caused by excessive rainfall. Under rain-shelter conditions, the characteristics of the leaves and fruit of the cherry plant may adapt to the changes in the microclimate. However, the molecular mechanism underlying such adaptation remains unclear, although clarifying it may be helpful for improving the yield and quality of cherry under rain-shelter conditions.Results To better understand the regulation and adaptive mechanism of cherry under rain-shelter covering, 38,621 and 3,584 differentially expressed genes were identified with the combination of Illumina HiSeq and single-molecule real-time sequencing in leaves and fruits, respectively, at three developmental stages. Among these, key genes, such as those encoding photosynthetic-antenna proteins ( Lhca and Lhcb ) and photosynthetic electron transporters (PsbP , PsbR , PsbY , and PetF ), were upregulated following the application of rain-shelter covering, leading to increased efficiency of light utilization. The mRNA levels of genes involved in carbon fixation, namely, rbcL and rbcS , were clearly increased in comparison to those under shelter-free conditions, giving rise to improved CO 2 utilization. Furthermore, the transcription levels of genes involved in chlorophyll ( hemA , hemN , and chlH ) and carotenoid synthesis ( crtB , PDS , crtISO , and lcyB ) in the sheltered leaves peaked earlier than those in the unsheltered leaves, thereby promoting organic matter accumulation in leaves. Remarkably, the expression levels of key genes involved in the metabolic pathways of phenylpropanoid ( PAL , C4H , and 4CL ) and flavonoid ( CHS , CHI , F3’H , DFR , and ANS ) in the sheltered fruits were also upregulated earlier than those in the shelter-free fruits, conducive to an increase in anthocyanin content in the fruits.Conclusions According to the physiological indicators and transcriptional expression levels of related genes, the adaptive regulation mechanism of cherry plants was systematically revealed. These findings can help understand the effect of rain-shelter covering on Chinese cherry cultivation in rainy regions.