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RNA-Seq reveals differential expression patterns of genes associated with carotenoid accumulation in loquat

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Abstract

Loquat (Eriobotrya japonica Lindl.) cultivars can be classified as yellow- and white-fleshed based on fruit color. The pulps of yellow-fleshed cultivars appear yellow because of high contents of carotenoids, while the pulps of white-fleshed cultivars appear ivory white due to the lack of carotenoid accumulation. To elucidate the genes associated with the carotenoid accumulation, de novo assembly of the fruit transcriptome in three loquat cultivars having different pulp colors, including ‘Golden nugget’ (yellow pulp), ‘Jiefangzhong’ (yellow pulp), and ‘Baiyu’ (white pulp), at breaker stage, was conducted in this study. By RNA-seq, a total of 11.92 Gb clean data was obtained, and 51,934 unigenes were assembled and annotated. Based on BLAST search, 26,447 unigenes had a hit in at least one of the protein and nucleotide databases used in the present study. Swiss-Port annotation and Clusters of Orthologous Group were assigned for 16,679 and 13,986 unigenes, respectively. Moreover, Gene Ontology enrichment analysis classified 18,842 unigenes into 53 functional groups, which largely detected in biological process category, followed by cellular component category and molecular function category. We detected 3438 differentially expressed genes using Reads Per kb per Million reads method. Of these genes, six were identified as carotenoid accumulation-related genes. Our study revealed a certain relationship between carotenoid accumulation and expression patterns of carotenogenic genes.

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Acknowledgements

This research was partially supported by Guangzhou Science and Technology Program key projects (201504010028).

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Authors and Affiliations

  1. State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, South China Agricultural University, Guangzhou, 510642, China

    Ting-ting Zheng, Zhi-ke Zhang, Muhammad Qasim Shahid, Wei-ling Wei, Shun-quan Lin & Xiang-hui Yang

  2. Department of Field Crops, Faculty of Agricultural and Natural Science, Abant İzzet Baysal University, Bolu, Turkey

    Faheem Shehzad Baloch

  3. Fujian Provincial Key Laboratory of Ecology-Toxicological Effects and Control Techniques of Emerging Contaminants, Putian University, Putian, 351100, China

    Jin-cheng Wu

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  1. Ting-ting Zheng
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  2. Zhi-ke Zhang
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Correspondence to Shun-quan Lin or Xiang-hui Yang.

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Communicated by M Stobiecki.

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Zheng, Tt., Zhang, Zk., Shahid, M.Q. et al. RNA-Seq reveals differential expression patterns of genes associated with carotenoid accumulation in loquat. Acta Physiol Plant 39, 168 (2017). https://doi.org/10.1007/s11738-017-2463-0

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