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De novo transcriptome sequencing of pakchoi (Brassica rapa L. chinensis) reveals the key genes related to the response of heat stress

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Abstract

Pakchoi is an important vegetable grown in worldwide that prefers a cool climate, and its growth is severely affected by high temperatures in the summer. Little is known for the molecular regulatory mechanisms of high-temperature stress in pakchoi. The limited availability of gene sequence has greatly affected molecular breeding and functional genomic analysis. In this study, we conducted comprehensive analyses for heat treatment in pakchoi by RNA-Seq. Finally, 64.29 million clean reads containing 32,666 unigenes with an N50 length of 1405 bp, and a total length of 33.39 Mb were identified. Overall, 11,024 SSRs located in 8404 unigenes were obtained; these findings will be very useful for molecular assisted breeding. Totally, 1220 differentially expressed genes (DEGs) were detected between the high-temperature group (TH) and the control (CK), among which 699 DEGs were up-regulated and 521 were down-regulated. The enrichment analysis indicated that 12 GO subcategories and 9 KEGG pathways were enriched significantly (P value <0.05). Finally, six DEGs were validated by qRT-PCR, and the results further verified the reliability of RNA-Seq. Herein, we present the first comprehensive characterization of heat-treated pakchoi using transcriptome analysis. Several important genes that respond to high temperature were identified, and their roles in heat stress responses are discussed. In conclusion, our study represents a fully characterised pakchoi transcriptome. In addition, it provides the important resources for future genomic and genetic studies of pakchoi under heat stress.

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Acknowledgments

This study was funded by the National Key Science and Technology Supporting Program of China (Grant No. 2013BAD01B04-11) and by the Jiangsu agricultural science and technology innovation fund of China [Grant No. CX (13) 2004]. We also thank Genepioneer Biotechnologies for their help with the bioinformatics analyses.

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Authors and Affiliations

  1. State Key Laboratory of Crop Genetics & Germplasm Enhancement, Nanjing Agricultural University, Nanjing, 210095, China

    Hai Xu, Bo Song & Jinfeng Chen

  2. Institute of Vegetable Crops, Jiangsu Academy of Agricultural Sciences, Nanjing, 210014, China

    Hai Xu, Longzheng Chen, Bo Song, Xiaoxue Fan & Xihan Yuan

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  1. Hai Xu
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  2. Longzheng Chen
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  3. Bo Song
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  4. Xiaoxue Fan
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  6. Jinfeng Chen
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Correspondence to Jinfeng Chen.

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Communicated by W. Zhou.

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Xu, H., Chen, L., Song, B. et al. De novo transcriptome sequencing of pakchoi (Brassica rapa L. chinensis) reveals the key genes related to the response of heat stress. Acta Physiol Plant 38, 252 (2016). https://doi.org/10.1007/s11738-016-2269-5

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  • DOI: https://doi.org/10.1007/s11738-016-2269-5

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