RNA sequencing reveals the complex regulatory network in the maize kernel
RNA sequencing reveals the complex regulatory network in the maize kernel
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DOI：
10.1038/ncomms3832
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发表时间：
2013-12-01
影响因子：
16.6
通讯作者：
Wang, Guoying
中科院分区：
文献类型：
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作者：
Fu, Junjie;Cheng, Yanbing;Wang, Guoying
RNA测序可以同时识别外显子多态性和定量基因表达。在这里，我们报告了 368 个近交系发育中的玉米粒的 RNA 测序，产生了 258 亿个读数和 360 万个单核苷酸多态性。 MaizeSNP50 BeadChip 和 Sequenom MassArray iPLEX 平台均确认了高质量 SNP 的子集。在这些 SNP 中，我们将 931,484 个 SNP 映射到基因区域，每个基因的平均密度为 40.3 个 SNP。全基因组关联研究确定了 16,408 个表达数量性状位点。两步法将 95.1% 的 eQTL 定义为 10 kb 区域，其中 67.7% 包含单个基因。 eQTL与其靶标之间关系的建立揭示了一个大规模的基因调控网络，其中包括31个玉米醇溶蛋白和16个关键内核基因的调控。这些结果有助于我们了解籽粒发育以及提高玉米产量和营养质量。
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.