Probing into the Role of Regulatory RNA, DNA Methylation and Associated Network Rewiring in Transgressive Segregation for Stress Tolerance in Rice

鉴于人口快速增长以及耕地和水资源减少的威胁，为了确保世界粮食供应的安全，必须实施培育下一代具有高产潜力和气候适应性的作物的创新战略。新的研究战略应该创造尚未实现的新的作物性状，以便在边际环境下大幅提高产量潜力。如何才能实现这个宏伟的目标呢？现在人们充分认识到，在产量、抗逆性以及水分和养分利用效率的遗传潜力方面的任何进一步改进，都必须依赖于创造复杂基因组配置的能力，从而产生新的生化和生理性状。这个项目代表了现代研究工具的使用来解决一个古老的谜题。它代表了对植物遗传学中最神秘和相对未被开发的概念之一--越级变异现象--的更仔细的观察和更具战略性的检查。当来自两个不同亲本的后代高于(或低于)双亲时，就会观察到超亲变异。利用水稻来测试这一概念，该项目将确定哪些DNA片段或RNA分子导致耐盐度和低温胁迫的超亲性状。该项目将检验这样一种假设，即水稻双亲杂交组合的超亲耐逆表型是两个不同亲本基因组之间理想的改组和互补效应导致遗传网络重新布线的结果。将探索建立在调节子重组、调控非编码RNA(NcRNAs)和DNA甲基化能力基础上的新范式，以了解新的基因表达模式介导亲本表型违规的复杂机制。通过综合使用各种下一代DNA测序应用程序，如基因组-Seq、mRNA-Seq、ncRNA-Seq和亚硫酸盐-Seq，本项目将：1)发现胁迫调节的miRNAs/siRNAs，它们在具有新的耐盐性表型的种内重组体中反式表达，以及在具有新的低温或其他逆境耐性属性的种间重组体中反式表达；2)在重组体及其各自的亲本之间建立有意义的mRNAs和miRNA/siRNA转录体特征之间的相关性，从而为全球基因表达如何在海侵分离体中的改变提供假说；3)在转录组特征和重组体及其双亲之间的基因组甲基化特征之间建立有意义的关联，以发展关于表基因组变化如何改变侵入式分离体中的基因调控的假说。该方法将解决以下可能性：a)逆境耐受表型越轨是由于调控基因在其新的遗传背景中获得最佳功能，因为它们在新的遗传背景中具有相容的调控簇，即调节子重组；b)重组体中的网络重组是由于反式作用的ncRNAs与其目标调控基因或来自父母的基因组位点的耦合或解偶联；以及c)基因组改组改变重组体中的甲基化特征，导致新的基因表达特征。结果将促进我们对遗传和表观遗传网络的错综复杂的理解，从而应用于水稻和其他主要谷类作物的抗逆性育种。将生成的基因组数据集将通过公共数据库，包括NCBI和DDBJ的序列读取档案，提供给更广泛的科学界。待鉴定的水稻遗传库存将通过美国农业部水稻遗传库存维护和分配中心向其他研究人员提供。

To ensure the safety of the world's food supply given the threats of rapid population growth and declining arable land and water resources, innovative strategies for breeding the next generation of high-yield potential and climate-resilient crops will have to be implemented. New research strategies should create novel crop traits that have not yet been achieved in order to substantially enhance yield potential under marginal environments. How can this enormous goal be attained? It is now fully appreciated that any further improvements in genetic potential for yield, stress tolerance and water and nutrient use efficiency will have to rely on the ability to create complex genomic configurations that lead to novel biochemical and physiological traits. This project represents the use of contemporary research tools to solve an old puzzle. It represents a closer look and more strategic examination of one of the most enigmatic and relatively unexploited concepts in plant genetics, the phenomenon of transgressive variation. Transgressive variation is observed when progeny derived from two divergent parents are superior (or inferior) to both parents. Using rice to test the concept, this project will determine which DNA segments or RNA molecules cause transgressive traits for salinity and low temperature stress tolerance.This project will test the hypothesis that transgressive stress tolerance phenotypes in biparental cross combinations of rice are the consequences of ideal shuffling and complementation effects between two divergent parental genomes leading to genetic network rewiring. New paradigms built upon the power of regulon restructuring, regulatory non-coding RNAs (ncRNAs), and DNA methylation will be explored to understand the intricate mechanisms by which novel gene expression patterns mediate transgression from parental phenotypes. By integrated use of various next-generation DNA sequencing applications such as genome-Seq, mRNA-Seq, ncRNA-Seq, and bisulfite-Seq, this project will: 1) discover stress-regulated miRNAs/siRNAs that are transgressively expressed in intraspecific recombinants with novel salt tolerance phenotypes, and those that are transgressively expressed in interspecific recombinants with novel low temperature or other stress tolerance attributes; 2) establish meaningful correlations between mRNA and miRNA/siRNA transcriptome signatures among recombinants and their respective parents to evelop hypotheses on how global gene expression is altered in transgressive segregants; and 3) establish meaningful correlations between transcriptome signatures and genome methylation profiles between recombinants and their parents to develop hypotheses on how epigenomic changes alter gene regulation in transgressive segregants. The approach will address the possibilities that: a) stress tolerance phenotypic transgression is due to regulatory genes that acquired optimal function because of compatible regulatory clusters in their new genetic background, i.e., regulon restructuring; b) network reconfiguration in recombinants is due to coupling or uncoupling of trans-acting ncRNAs and their target regulatory genes or genomic loci from either parents; and c) genome shuffling alters the methylation profiles in recombinants leading to novel gene expression signatures. Outcomes will advance our understanding of the intricacies of genetic and epigenetic networks towards applications to stress tolerance breeding in rice and other major cereal crops. The genomics datasets to be generated will be made available to the broader scientific community through public data repositories including the Sequence Read Archive of NCBI and DDBJ. The rice genetic stocks to be characterized will be made available to other researchers through the USDA rice genetic stock maintenance and distribution center.