Wang Jia, Yu Huihui, Weng Xiaoyu, Xie Weibo, Xu Caiguo, Li Xianghua, Xiao Jinghua, Zhang Qifa
National Key Laboratory of Crop Genetic Improvement, National Center of Plant Gene Research, Huazhong Agricultural University, Wuhan 430070, PR China.
J Exp Bot. 2014 Mar;65(4):1069-79. doi: 10.1093/jxb/ert464. Epub 2014 Jan 13.
The ability to reveal the regulatory architecture of genes at the whole-genome level by constructing a regulatory network is critical for understanding the biological processes and developmental programmes of organisms. Here, we conducted an eQTL-guided function-related co-expression analysis to identify the putative regulators and construct gene regulatory network. We performed an eQTL analysis of 210 recombinant inbred lines (RILs) derived from a cross between two indica rice lines, Zhenshan 97 and Minghui 63, the parents of an elite hybrid, using data obtained by hybridizing RNA samples of flag leaves at the heading stage with Affymetrix whole-genome arrays. Making use of an ultrahigh-density single-nucleotide polymorphism bin map constructed by population sequencing, 13 647 eQTLs for 10 725 e-traits were detected, comprising 5079 cis-eQTLs (37.2%) and 8568 trans-eQTLs (62.8%). The analysis revealed 138 trans-eQTLs hotspots, each of which apparently regulates the expression variations of many genes. Co-expression analysis of functionally related genes within the framework of regulator-target relationships outlined by the eQTLs led to the identification of putative regulators in the system. The usefulness of the strategy was demonstrated with the genes known to be involved in flowering. We also applied this strategy to the analysis of QTLs for yield traits, which also suggested likely candidate genes. eQTL-guided co-expression analysis may provide a promising solution for outlining a framework for the complex regulatory network of an organism.
通过构建调控网络在全基因组水平揭示基因调控结构的能力，对于理解生物体的生物学过程和发育程序至关重要。在此，我们进行了一项基于表达数量性状基因座（eQTL）的功能相关共表达分析，以鉴定潜在的调控因子并构建基因调控网络。我们利用在抽穗期将剑叶RNA样本与Affymetrix全基因组芯片杂交获得的数据，对由两个籼稻品系珍汕97和明恢63（一个优良杂交种的亲本）杂交产生的210个重组自交系（RIL）进行了eQTL分析。利用通过群体测序构建的超高密度单核苷酸多态性bin图谱，检测到10725个表达性状的13647个eQTL，其中包括5079个顺式eQTL（37.2%）和8568个反式eQTL（62.8%）。该分析揭示了138个反式eQTL热点，每个热点显然调控许多基因的表达变异。在eQTL勾勒出的调控因子-靶标关系框架内对功能相关基因进行共表达分析，从而鉴定出该系统中的潜在调控因子。已知参与开花的基因证明了该策略的有效性。我们还将此策略应用于产量性状QTL的分析，这也提示了可能的候选基因。基于eQTL的共表达分析可能为勾勒生物体复杂调控网络的框架提供一个有前景的解决方案。
