Full-Length Transcriptome Sequencing Reveals the Impact of Cold Stress on Alternative Splicing in Quinoa

Abstract

Quinoa is a cold-resistant and nutrient-rich crop. To decipher the cold stress response of quinoa, the full-length transcriptomes of the cold-resistant quinoa variety CRQ64 and the cold-sensitive quinoa variety CSQ5 were compared. We identified 55,389 novel isoforms and 6432 novel genes in these transcriptomes. Under cold stress, CRQ64 had more differentially expressed genes (DEGs) and differentially alternative splicing events compared to non-stress conditions than CSQ5. DEGs that were specifically present only in CRQ64 were significantly enriched in processes which contribute to osmoregulation and ROS homeostasis in plants, such as sucrose metabolism and phenylpropanoid biosynthesis. More genes with differential alternative splicing under cold stress were enriched in peroxidase functions in CRQ64. In total, 5988 transcription factors and 2956 long non-coding RNAs (LncRNAs) were detected in this dataset. Many of these had altered expression patterns under cold stress compared to non-stress conditions. Our transcriptome results demonstrate that CRQ64 undergoes a wider stress response than CSQ5 under cold stress. Our results improved the annotation of the quinoa genome and provide new insight into the mechanisms of cold resistance in quinoa.

Leaf and shoot apical meristem transcriptomes of quinoa (Chenopodium quinoaWilld.) in response to photoperiod and plant development

“…We found a surprisingly high number of novel transcripts (57,342), including algorithmic artifacts, splice variants, and genes specifically transcribed under our experimental conditions. Similar results were reported in a recent study by Zheng et al . (2022), where >50,000 novel transcripts were discovered under cold stress, including splicing variants and 5′ or 3′ extensions or truncations.…”

Long-term cold, freezing and drought: overlapping and specific regulatory mechanisms and signal transduction in tea plant (Camellia sinensis (L.) Kuntze)

“…TTL1 regulates the transcript levels of several dehydration-responsive genes, such as CBF2 , ERD1 (early response to dehydration 1), ERD3 , and COR15a ( Rosado et al., 2006 ; Lakhssassi et al., 2012 ). Our results indicate that jasmonic acid, brassinosteroid-, and the ABA-signaling pathways are consistently upregulated during long-term stress, which is partly consistent with recent studies on woody plants ( Wisniewski et al., 2014 ; Estravis-Barcala et al., 2019 ; He et al 2019; Zheng et al., 2022 ). It is suggested that a highly variable interaction between different hormone signal transduction pathways takes place, leading to a complex transcriptional landscape in response to abiotic stress.…”

“…Additionally, DUF567 encodes a protein of unknown function ( Nabi et al., 2020 ), GRAS , and GIF1 (GIF1/2/3), which regulate root and shoot development ( Tian et al., 2004 ; Zhang et al., 2018 ; Liu et al., 2020 ). Corresponding with our results, cold and drought induce transcription factors of an ABA-dependent response, such as members of the basic-domain leucine zipper ( bZIP ) family, the MYB family, and the WRKY family ( Li et al., 2019 ; Zhou et al., 2019 ; Zheng et al., 2022 ).…”

Full-length transcriptome sequencing provides insights into alternative splicing under cold stress in peanut

“…In agreement with other plant species, the predominant AS events were IR in peanut. The number of IR events was decreased after cold treatment, while ES was significantly increased in both of the peanut cultivars; similar results were also found in quinoa and other plants ( Zheng et al., 2022a , b ). In addition, our transcriptome data showed that more DEGs were identified in cold-sensitive cultivar (ZH12) than in cold-tolerant cultivar (SLH), while more AS events were found in SLH compared to ZH12.…”