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

在人口快速增长、耕地和水资源减少的威胁下，为了确保世界粮食供应的安全，必须实施培育下一代高产潜力和气候适应型作物的创新战略。新的研究策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度提高产量潜力。怎样才能达到这个巨大的目标呢？现在人们充分认识到，在产量、抗逆性和水分和养分利用效率方面的遗传潜力的任何进一步改进，都必须依赖于创造复杂基因组结构的能力，从而产生新的生化和生理性状。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。它代表了对植物遗传学中最神秘和相对未开发的概念之一的更近距离的观察和更战略性的检查，即越界变异现象。当来自两个不同亲本的后代都优于（或劣于）双亲时，就会观察到越界变异。该项目利用水稻来测试这一概念，将确定哪些DNA片段或RNA分子导致耐盐和耐低温胁迫的越界性状。本项目将验证水稻双亲本杂交组合中的越界胁迫耐受性表型是两个不同亲本基因组之间理想的洗牌和互补效应导致遗传网络重新连接的结果。将探索建立在调控重组、调控非编码rna （ncRNAs）和DNA甲基化力量基础上的新范式，以了解新基因表达模式介导亲本表型越界的复杂机制。通过整合使用各种下一代DNA测序应用，如基因组测序、mrna测序、ncrna测序和亚硫酸盐测序，该项目将：1)发现在具有新型耐盐表型的种内重组中越界表达的胁迫调节miRNAs/ sirna，以及在具有新型低温或其他耐胁迫属性的种间重组中越界表达的miRNAs/ sirna；2)在重组体及其亲本之间建立mRNA和miRNA/siRNA转录组特征之间的有意义的相关性，以提出在越界分离中如何改变全局基因表达的假设；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，以提出关于表观基因组变化如何改变越界分离中基因调控的假设。该方法将解决以下可能性：a)胁迫耐受表型越界是由于调控基因在其新的遗传背景中由于兼容的调控簇而获得最佳功能，即调控重组；b)重组体中的网络重构是由于偶联或解偶联反式ncrna及其靶调控基因或来自亲本的基因组位点；c)基因组洗牌改变重组体的甲基化谱，导致新的基因表达特征。研究结果将促进我们对遗传和表观遗传网络复杂性的理解，并将其应用于水稻和其他主要谷类作物的抗逆性育种。生成的基因组学数据集将通过包括NCBI和DDBJ的Sequence Read Archive在内的公共数据库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.