Transcriptome analysis of Chongyi wild mandarin, a wild species more cold-tolerant than Poncirus trifoliata, reveals key pathways in response to cold

Abstract

Much effort has been made on the dissection of cold response in citrus, but relevant study in wild germplasm has been rare. Based on the result of the membership function value analysis with 12 physiological indexes, we reported a wild citrus germplasm, Chongyi wild mandarin (Citrus reticulata), which was more cold-tolerant than a cold-hardy rootstock, Poncirus trifoliata. To gain an overview of transcriptome changes under cold, leaves of Chongyi wild mandarin were sampled at 0, 1, 5 d after 0 °C treatment, and sequenced using an Illumina sequencing platform. Totally, 3921 and 5995 differentially expressed genes (DEGs) were identified in 1 d and 5 d, respectively. And then, RNA-seq results were further validated via real-time quantitative PCR with 17 DEGs. Many DEGs related to various cold signaling pathways were identified, especially those related to brassinosteroid cascade. Around 10 % of the total DEGs were transcription factors from 67 families, suggesting that transcriptional regulation, both C-repeat/dehydration responsive element-binding factor-dependent/independent pathways, was crucial for the cold tolerance of Chongyi wild mandarin. Our data also revealed that the transcriptional levels of many DEGs related to anti-oxidant enzymes and osmoprotectants metabolism were altered, which were consistent with the results of physiological experiments. Moreover, a number of DEGs involved in ABA, BR, GA metabolisms were isolated. Accordingly, the levels of ABA and BR were significantly increased under cold, but GAs were decreased. Taken together, this work provided a comprehensive view of physiological and transcriptional alterations in cold response of Chongyi wild mandarin.