RNA sequencing reveals the complex regulatory network in the maize kernel

• Published in: Nature communications Vol. 4; no. 1; p. 2832
• Main Authors: Fu, Junjie, Cheng, Yanbing, Linghu, Jingjing, Yang, Xiaohong, Kang, Lin, Zhang, Zuxin, Zhang, Jie, He, Cheng, Du, Xuemei, Peng, Zhiyu, Wang, Bo, Zhai, Lihong, Dai, Changmin, Xu, Jiabao, Wang, Weidong, Li, Xiangru, Zheng, Jun, Chen, Li, Luo, Longhai, Liu, Junjie, Qian, Xiaoju, Yan, Jianbing, Wang, Jun, Wang, Guoying
• Format: Journal Article
• Language: English
• Published: London Nature Publishing Group UK 17.12.2013; Nature Publishing Group
• Subjects: 38/43; 38/91; 631/208/514/1949; 631/449/2491; Corn; Gene expression; Gene mapping; Genomes; Genomics; Humanities and Social Sciences; multidisciplinary; Nutritive value; Science; Science (multidisciplinary); Beijing China; China
• ISSN: 2041-1723; 2041-1723
• DOI: 10.1038/ncomms3832

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. Determining the link between gene polymorphisms and phenotypic traits is the subject of intense research in agricultural plant science. In this study, Fu et al . conduct RNA sequencing in maize kernels to determine gene polymorphisms, which may aid future research aiming to improve the nutritional value of maize.