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Background  Chlorophyll (Chl) is a vital photosynthetic pigment involved in capturing light energy and energy conversion. In this study, the color conversion of inner-leaves from green to yellow in the new wucai ( Brassica campestris  L.) cultivar W7–2 was detected under low temperature. The W7–2 displayed a normal green leaf phenotype at the seedling stage, but the inner leaves gradually turned yellow when the temperature was decreased to 10 °C/2 °C (day/night), This study facilitates us to understand the physiological and molecular mechanisms underlying leaf color changes in response to low temperature.    Results  A comparative leaf transcriptome analysis of W7–2 under low temperature treatment was performed on three stages (before, during and after leaf color change) with leaves that did not change color under normal temperature at the same period as a control. A total of 67,826 differentially expressed genes (DEGs) were identified. Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway and Gene Ontology (GO) analysis revealed that the DEGs were mainly enriched in porphyrin and Chl metabolism, carotenoids metabolism, photosynthesis, and circadian rhythm. In the porphyrin and chlorophyll metabolic pathways, the expression of several genes was reduced [i.e.  magnesium chelatase subunit H  ( CHLH )] under low temperature. Almost all genes [i.e.  phytoene synthase  ( PSY )] in the carotenoids (Car) biosynthesis pathway were downregulated under low temperature. The genes associated with photosynthesis [i.e.  photosystem II oxygen-evolving enhancer protein 1  ( PsbO )] were also downregulated under LT. Our study also showed that  elongated hypocotyl5  ( HY5 ), which participates in circadian rhythm, and the metabolism of Chl and Car, is responsible for the regulation of leaf color change and cold tolerance in W7–2.    Conclusions  The color of inner-leaves was changed from green to yellow under low temperature in temperature-sensitive mutant W7–2. Physiological, biochemical and transcriptomic studies showed that HY5 transcription factor and the downstream genes such as  CHLH  and  PSY , which regulate the accumulation of different pigments, are required for the modulation of leaf color change in wucai under low temperature.    Supplementary Information  The online version contains supplementary material available at 10.1186/s12870-021-03218-9.

bmc plant biology

Comparative transcriptome analysis reveals that chlorophyll metabolism contributes to leaf color changes in wucai (Brassica campestris L.) in response to cold