玉米籽粒长非编码RNA的调控网络解析

Maize is both a model organism for genetic studies and an important crop for food, fuel and feed. Maize kernels accumulate a large amount of nutritional compounds and metabolites. Understanding the genetic regulation of their synthesis and accumulation will be of great value to maize improvement for nutritional quality. In the last decades, many genes/loci involved in maize kernel development and nutrient accumulation have been characterized using QTL mapping and gene cloning methods. Although the transcriptome profiles of maize suggested more candidate genes and co-expression networks, our understanding of the processes and the gene regulatory networks in maize kernels remain limited. .With the development of technology and significant reduction in the cost of next-generation sequencing (NGS), RNA-seq technology has been successfully used for both SNP detection and eQTL analysis to reveal gene regulatory networks that are active in specific tissues. We have explored the gene expression profiles of the developing maize kernel by RNA sequencing of 368 inbred lines at 15 days after pollination (DAP). Through eQTL analysis, we discovered the gene regulatory networks employed in immature maize kernels under grain filling. The established network was exploited to show its value to better understanding of provitamin A-carotenoid and oil accumulation. .Long non-coding RNAs are the moleculars transferring genetic information, which are different to protein-coding messenger RNAs. The previous studies found that long non-coding RNAs, as an essential part of regulatory network, involved in important biological processes and development. Inspired by these findings, this project will further identify intergenic long non-coding RNAs (lincRNAs) in RNA sequencing data and perform eQTL mapping for lincRNAs. After integration with the gene regulatory network, we will establish a large-scale regulatory network including lincRNAs. Based on this newly inferred network, we will explore the possible regulatory mechanism of nutrient accumulation (particularly for vitamins and oil) mediated by lincRNAs. This may facilitate maize molecular breeding for nutritional quality.

玉米籽粒储藏有各种营养代谢物质，解析籽粒物质积累的调控网络是玉米研究中最具挑战的问题之一。我们已经通过玉米关联群体RNA测序，结合基因表达QTL定位解析了玉米籽粒灌浆期的基因表达调控网络，进而揭示了维生素A原、油分等营养代谢物的网络调控机制，为后续研究奠定了良好的基础。长非编码RNA是一类有别于mRNA的遗传信息分子，已发现很多重要的生长发育过程都有长非编码RNA参与其中，是调控网络中至关重要的组成部分。由此，本项目进一步将拟从RNA测序数据中挖掘lincRNA为出发点，借助lincRNA的表达QTL定位，与已构建的基因表达调控网络完成整合，绘制囊括长非编码RNA的表达调控网络图。进而，利用构建的网络，探索lincRNA影响籽粒营养物质及代谢物（特别是油分、维生素）积累的可能调控机制，为优质玉米分子设计育种提供理论支撑。

长非编码RNA是由真核生物基因组转录产生的一类不同于mRNA的遗传信息分子，在中心法则的多个层面上调控基因的表达。长非编码RNA的调控网络是随着高通量测序技术发展而快速兴起的研究领域，目前对其如何影响玉米籽粒发育和物质积累还知之甚少。本项目利用来源广泛的玉米自交系群体及其高密度SNP图谱，研究了长非编码RNA位点对玉米油分、类胡萝卜素和籽粒大小等数量性状的独立遗传效应。为了避免与其它类型基因重叠所带来的干扰，本项目将研究重点集中在来源于基因间区的lincRNA。结合群体授粉后5天和15天籽粒的表达测序数据，发现绝大多数lincRNA只在部分材料中表达，并且其表达水平高于编码基因，同时也发现玉米与大刍草之间的保守lincRNA表达更高。两个时期籽粒的表达QTL（eQTL）分析显示，相同的表达水平下lincRNA更倾向受到eQTL调控，调控位点与lincRNA本身的距离更远且效应更大，两个时期共同受到调控的lincRNA比例与编码基因相比差异不大。在构建lincRNA表达调控网络的基础上，结合全基因组关联分析以及表达与性状相关分析，发掘了玉米籽粒物质积累等性状的关键lincRNA，为lincRNA作用机理研究以及玉米改良应用提供了候选和相关位点。结合本项目的研究进展和同时期发表的研究工作，表明绝大部分lincRNA可能效应很低或者没有功能，因此规模化发掘候选功能lincRNA是开展深入机理研究的前提。lincRNA表达受到的限制少，具有广泛的变异，数量遗传学方法eQTL定位为lincRNA提供了功能证据。另外，本项目尝试利用m6A-seq等多组学技术，对规模化鉴定功能lincRNA的方法做出了有益的探索。