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

鉴于人口迅速增长、可耕地和水资源不断减少的威胁，为确保世界粮食供应安全，必须实施创新战略，培育下一代高产潜力和气候适应能力强的作物。新的研究战略应创造尚未实现的新的作物性状，以大幅提高边际环境下的产量潜力。如何实现这一宏伟目标？现在充分认识到，产量、胁迫耐受性以及水和养分利用效率的遗传潜力的任何进一步改进将必须依赖于产生导致新的生物化学和生理性状的复杂基因组构型的能力。这个项目代表了使用当代研究工具来解决一个古老的难题。它代表了植物遗传学中最神秘和相对未开发的概念之一，超亲变异现象的更近距离观察和更有战略意义的检查。当来自两个不同亲本的后代比两个亲本都上级（或下级）时，可以观察到超进变异。本项目将以水稻为研究对象，确定哪些DNA片段或RNA分子导致了水稻耐盐和低温胁迫的超亲性状，并验证水稻双亲杂交组合中超亲胁迫耐受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连接的结果这一假设。建立在调节子重组，调节非编码RNA（ncRNA）和DNA甲基化的力量的新范式将被探索，以了解新的基因表达模式介导从亲本表型超越的复杂机制。本项目将综合利用基因组测序、mRNA-Seq测序、ncRNA-Seq测序和亚硫酸氢盐测序等新一代DNA测序技术，实现以下目标：1）发现在具有新的耐盐表型的种内重组体中超亲表达的逆境调节miRNAs/siRNAs，以及在具有新的耐低温或其他逆境特性的种间重组体中超亲表达的逆境调节miRNAs/siRNAs; 2）在重组体及其各自亲本之间建立mRNA和miRNA/siRNA转录组特征之间的有意义的相关性，以发展关于在超亲分离体中如何改变整体基因表达的假设;和3）在重组体及其亲本之间建立转录组特征和基因组甲基化谱之间的有意义的相关性，以发展关于表观基因组变化如何改变基因的假说。超亲分离子的调控。该方法将解决以下可能性：a）胁迫耐受性表型超越是由于调节基因由于其新的遗传背景中的相容调节簇而获得最佳功能，即，调节子重组; B）重组体中的网络重构是由于反式作用ncRNA及其靶调控基因或基因组基因座与任一亲本的偶联或解偶联;和c）基因组改组改变重组体中的甲基化谱，导致新的基因表达特征。结果将推进我们对遗传和表观遗传网络的复杂性的理解，以应用于水稻和其他主要谷类作物的耐胁迫育种。将生成的基因组学数据集将通过公共数据库（包括NCBI和DDBJ的Sequence Read Archive）提供给更广泛的科学界。待鉴定的水稻遗传资源将通过美国农业部水稻遗传资源维护和分配中心提供给其他研究人员。

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.