title: RNA sequencing reveals the complex regulatory network in the maize kernel.
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.
authors.affiliation: Institute of Crop Science, Chinese Academy of Agricultural Sciences, Beijing 100081, China.
authors.forename: Junjie
authors.initials: J
authors.lastname: Fu
authors.affiliation: Beijing Genomics Institute, Shenzhen 518083, China.
authors.forename: Yanbing
authors.initials: Y
authors.lastname: Cheng
authors.affiliation: National Maize Improvement Center of China, Beijing Key Laboratory of Crop Genetic Improvement, China Agricultural University, Beijing 100193, China.
authors.forename: Jingjing
authors.initials: J
authors.lastname: Linghu
authors.affiliation: National Maize Improvement Center of China, Beijing Key Laboratory of Crop Genetic Improvement, China Agricultural University, Beijing 100193, China.
authors.forename: Xiaohong
authors.initials: X
authors.lastname: Yang
authors.affiliation: Beijing Genomics Institute, Shenzhen 518083, China.
authors.forename: Lin
authors.initials: L
authors.lastname: Kang
authors.affiliation: National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan 430070, China.
authors.forename: Zuxin
authors.initials: Z
authors.lastname: Zhang
authors.affiliation: National Maize Improvement Center of China, Beijing Key Laboratory of Crop Genetic Improvement, China Agricultural University, Beijing 100193, China.
authors.forename: Jie
authors.initials: J
authors.lastname: Zhang
authors.affiliation: National Maize Improvement Center of China, Beijing Key Laboratory of Crop Genetic Improvement, China Agricultural University, Beijing 100193, China.
authors.forename: Cheng
authors.initials: C
authors.lastname: He
authors.affiliation: National Maize Improvement Center of China, Beijing Key Laboratory of Crop Genetic Improvement, China Agricultural University, Beijing 100193, China.
authors.forename: Xuemei
authors.initials: X
authors.lastname: Du
authors.affiliation: Beijing Genomics Institute, Shenzhen 518083, China.
authors.forename: Zhiyu
authors.initials: Z
authors.lastname: Peng
authors.affiliation: National Maize Improvement Center of China, Beijing Key Laboratory of Crop Genetic Improvement, China Agricultural University, Beijing 100193, China.
authors.forename: Bo
authors.initials: B
authors.lastname: Wang
authors.affiliation: National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan 430070, China.
authors.forename: Lihong
authors.initials: L
authors.lastname: Zhai
authors.affiliation: Beijing Genomics Institute, Shenzhen 518083, China.
authors.forename: Changmin
authors.initials: C
authors.lastname: Dai
authors.affiliation: Beijing Genomics Institute, Shenzhen 518083, China.
authors.forename: Jiabao
authors.initials: J
authors.lastname: Xu
authors.affiliation: National Maize Improvement Center of China, Beijing Key Laboratory of Crop Genetic Improvement, China Agricultural University, Beijing 100193, China.
authors.forename: Weidong
authors.initials: W
authors.lastname: Wang
authors.affiliation: Beijing Genomics Institute, Shenzhen 518083, China.
authors.forename: Xiangru
authors.initials: X
authors.lastname: Li
authors.affiliation: Institute of Crop Science, Chinese Academy of Agricultural Sciences, Beijing 100081, China.
authors.forename: Jun
authors.initials: J
authors.lastname: Zheng
authors.affiliation: Beijing Genomics Institute, Shenzhen 518083, China.
authors.forename: Li
authors.initials: L
authors.lastname: Chen
authors.affiliation: Beijing Genomics Institute, Shenzhen 518083, China.
authors.forename: Longhai
authors.initials: L
authors.lastname: Luo
authors.affiliation: Beijing Genomics Institute, Shenzhen 518083, China.
authors.forename: Junjie
authors.initials: J
authors.lastname: Liu
authors.affiliation: Beijing Genomics Institute, Shenzhen 518083, China.
authors.forename: Xiaoju
authors.initials: X
authors.lastname: Qian
authors.affiliation: National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan 430070, China.
authors.forename: Jianbing
authors.initials: J
authors.lastname: Yan
authors.affiliation: Beijing Genomics Institute, Shenzhen 518083, China.
authors.forename: Jun
authors.initials: J
authors.lastname: Wang
authors.affiliation: Institute of Crop Science, Chinese Academy of Agricultural Sciences, Beijing 100081, China.
authors.forename: Guoying
authors.initials: G
authors.lastname: Wang