RNA sequencing reveals the complex regulatory network in the maize kernel

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, Xiangru Li, Jun Zheng, Li Chen, Longhai Luo, Junjie Liu, Xiaoju Qian, Jianbing Yan (), Jun Wang () and Guoying Wang ()
Additional contact information
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

Nature Communications, 2013, vol. 4, issue 1, 1-12

Abstract: 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.

Date: 2013
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DOI: 10.1038/ncomms3832

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