Untangling the molecular mechanisms underlying adaptive difference between autopolyploid and its diploid ancestor: A case study of Hordeum bulbosum species

多倍化被认为是物种形成和基因组进化的主要力量。尽管研究取得了巨大的进展，但关于多倍体进化的遗传后果的许多基本问题仍然没有得到解答，特别是在生态学、生理学和进化方面，可能促进全基因组复制后物种形成的分子机制。对异源多倍体的分子研究揭示了多倍体化引起的结构和功能变化是多倍体成功的关键，其可以通过杂交或基因组加倍或两者的组合来诱导。基因组加倍的效果只能用二倍体和同源多倍体来检验。以往的研究表明，基因组加倍比杂交对植物的抗逆性有更大的影响。对人工合成同源多倍体的研究表明，同源多倍体比二倍体具有更强的抗逆性。然而，我们仍然缺乏证据表明观察到的转录和基因组变化实际上导致自然种群中同源多倍体的更大适应。MicroRNA不仅在基因组加倍过程中调控基因表达，而且在各种逆境胁迫反应中发挥重要作用，导致异源多倍体适应不同的环境条件。然而，同源多倍体中的miRNAs相对于其二倍体如何响应环境变化的研究很少。虽然在人工合成的同源多倍体中报道了有限的或没有基因组重组和结构的变化，但这些多倍体中发生了甲基化变化，这可能有助于生态和生理新奇。然而，甲基化模式的变化并不总是伴随着基因组加倍。目前还不清楚为什么在特定的植物系统中观察到这种效果，而不是在others.Hordeum bulbosum有二倍体和同源四倍体细胞型，是一个很好的模式系统的同源倍性研究。我们将使用创新的分子和实验方法来验证这一假设，即天然同源四倍体经历了重大的遗传和表观遗传变化，通过增加适应性来促进进化。具体目标是：1）揭示在转录组，蛋白质组和miRNA水平上解释二倍体和同源多倍体之间适应性差异的分子基础; 2）确定基因组加倍本身诱导的甲基化变化是否促进同源多倍体适应，以及这些变化是否与不同的生态型有关; 3）培养学生在分子生物学和进化方面的新的跨学科性。这项研究的结果将揭示多倍体在应对环境变化的适应性作用，将提供新的知识的多倍体本身的物种形成的作用，并将在实践和理论上的兴趣，因为产生的知识可用于多倍体育种。

Polyploidization has been proposed as a major force for speciation and genome evolution. Despite enormous research progress, many basic questions concerning the genetic consequences of polyploid evolution remain unanswered, specifically molecular mechanisms that might promote speciation after whole-genome duplication, especially in ecology, physiology, and evolution.Molecular studies of allopolyploids have revealed structural and functional changes caused by polyploidization as the key to the success of polyploids, which might be induced by either hybridization or genome doubling or a combination of both. The effect of genome doubling can only be examined using diploids and autopolyploids. Previous studies suggested that genome doubling has a greater influence on stress tolerance than hybridization. Some studies on synthetic autopolyploids showed that an autopolyploid has a stronger stress tolerance than its diploid. However, we still lack evidence that observed transcriptional and genomic changes actually lead to greater adaptation of autopolyploids, in natural populations. MicroRNAs not only play an important role in regulating gene expression during genome doubling but also in various stresses response, resulting in allopolyploids that adapt to different environmental conditions. However, how miRNAs in autopolyploids respond relative to its diploid to environmental changes has rarely been studied. Although limited or no changes on genome reorganization and structure were reported in synthetic autopolyploids, methylation changes in these polyploids occurred, which may contribute to ecological and physiological novelty. However, changes to methylation patterns do not always accompany genome doubling. It is unclear why the effect was observed in particular plant systems but not in others.Hordeum bulbosum has both diploid and autotetraploid cytotypes, and is an excellent model system for autoployploidy studies. We will use innovative molecular and experimental approaches to test the hypothesis that natural autotetraploids have experienced major genetic and epigenetic changes to promote evolution via increased adaptability. Specific objectives are: 1) to reveal the molecular basis to explain the adaptive difference between diploid and autopolyploid at the transcriptome, proteome, and miRNA levels; 2) to determine if methylation changes induced by genome doubling per se promote autopolyploid adaption, and if these are linked to different ecotypes; 3) to train students in novel interdisciplinarity both in molecular biology and evolution. The outcome of this study will reveal the adaptive role of polyploidy in response to environmental changes, will provide novel knowledge on the role of polyploidy per se on speciation, and will be of both practical and theoretical interest since the generated knowledge can be used in polyploidy breeding.