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RNA sequencing reveals the complex regulatory network in the maize kernel

Author

Listed:
  • Junjie Fu

    (Institute of Crop Science, Chinese Academy of Agricultural Sciences)

  • Yanbing Cheng

    (Beijing Genomics Institute)

  • Jingjing Linghu

    (National Maize Improvement Center of China, Beijing Key Laboratory of Crop Genetic Improvement, China Agricultural University)

  • Xiaohong Yang

    (National Maize Improvement Center of China, Beijing Key Laboratory of Crop Genetic Improvement, China Agricultural University)

  • Lin Kang

    (Beijing Genomics Institute)

  • Zuxin Zhang

    (National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University)

  • Jie Zhang

    (National Maize Improvement Center of China, Beijing Key Laboratory of Crop Genetic Improvement, China Agricultural University)

  • Cheng He

    (National Maize Improvement Center of China, Beijing Key Laboratory of Crop Genetic Improvement, China Agricultural University)

  • Xuemei Du

    (National Maize Improvement Center of China, Beijing Key Laboratory of Crop Genetic Improvement, China Agricultural University)

  • Zhiyu Peng

    (Beijing Genomics Institute)

  • Bo Wang

    (National Maize Improvement Center of China, Beijing Key Laboratory of Crop Genetic Improvement, China Agricultural University)

  • Lihong Zhai

    (National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University)

  • Changmin Dai

    (Beijing Genomics Institute)

  • Jiabao Xu

    (Beijing Genomics Institute)

  • Weidong Wang

    (National Maize Improvement Center of China, Beijing Key Laboratory of Crop Genetic Improvement, China Agricultural University)

  • Xiangru Li

    (Beijing Genomics Institute)

  • Jun Zheng

    (Institute of Crop Science, Chinese Academy of Agricultural Sciences)

  • Li Chen

    (Beijing Genomics Institute)

  • Longhai Luo

    (Beijing Genomics Institute)

  • Junjie Liu

    (Beijing Genomics Institute)

  • Xiaoju Qian

    (Beijing Genomics Institute)

  • Jianbing Yan

    (National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University)

  • Jun Wang

    (Beijing Genomics Institute)

  • Guoying Wang

    (Institute of Crop Science, Chinese Academy of Agricultural Sciences)

Abstract

RNA sequencing can simultaneously identify exonic polymorphisms and quantitate gene expression. Here we report RNA sequencing of developing maize kernels from 368 inbred lines producing 25.8 billion reads and 3.6 million single-nucleotide polymorphisms. Both the MaizeSNP50 BeadChip and the Sequenom MassArray iPLEX platforms confirm a subset of high-quality SNPs. Of these SNPs, we have mapped 931,484 to gene regions with a mean density of 40.3 SNPs per gene. The genome-wide association study identifies 16,408 expression quantitative trait loci. A two-step approach defines 95.1% of the eQTLs to a 10-kb region, and 67.7% of them include a single gene. The establishment of relationships between eQTLs and their targets reveals a large-scale gene regulatory network, which include the regulation of 31 zein and 16 key kernel genes. These results contribute to our understanding of kernel development and to the improvement of maize yield and nutritional quality.

Suggested Citation

  • Junjie Fu & Yanbing Cheng & Jingjing Linghu & Xiaohong Yang & Lin Kang & Zuxin Zhang & Jie Zhang & Cheng He & Xuemei Du & Zhiyu Peng & Bo Wang & Lihong Zhai & Changmin Dai & Jiabao Xu & Weidong Wang &, 2013. "RNA sequencing reveals the complex regulatory network in the maize kernel," Nature Communications, Nature, vol. 4(1), pages 1-12, December.
    • Handle: RePEc:nat:natcom:v:4:y:2013:i:1:d:10.1038_ncomms3832
    DOI: 10.1038/ncomms3832
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