RESEARCH-PGR: Deciphering the molecular basis of elite red alder lines and their Frankia alni symbionts

红桤木是一种在太平洋西北部具有重要经济价值的硬木树，超过了占主导地位的软木树种道格拉斯冷杉的年产值。 红桤木用于高质量的橱柜、器皿和把手，并作为生物质/生物燃料作物。它生长在不适宜居住的环境和贫瘠的土地上，这意味着它不会与粮食生产竞争。目前，适合种植的树苗供不应求。随着对其遗传学的更好理解，科学家们将能够培育出生长更快、更不适宜居住的树木。 这将扩大可供种植的面积，并增加木材和生物质燃料的年产量。 此外，红桤木不需要氮肥。它通过利用微生物Frankia为自己提供氮来达到这一目的。树木和微生物之间的关系需要科学研究。 一些Frankia菌株比其他菌株更好，一些树木和微生物菌株的组合非常适合某些环境。本研究旨在了解红桤木的遗传学、土壤类型、Frankia菌株和土壤中的其他细菌如何相互作用以促进树木生长。其结果将是能够开发适合某些环境的新树种，扩大种植以满足不断增长的需求。该项目包括为学生提供培训机会（高中到研究生），并支持针对得不到充分服务的学生的高中暑期创新学院。它促进土著和西班牙裔代表性不足的群体获得研究。红桤木（赤杨邦。），具有重要的经济意义，但在科学上了解其遗传变异及其与固氮共生体Frankia alni的关系方面是一个孤儿。该项目将创建一个基于组学的资源，以此为基础的育种和改良计划，旨在提高对非生物胁迫的耐受性和边缘土地面积的增长。目标是创建以下内容：（1）优良高性能红桤木克隆的从头基因组参考组装，使用PacBio测序和BioNano物理作图，（2）导致最佳树性能和共生的五种Frankia菌株的参考基因组序列和表观基因组标记，使用PacBio测序，使用SMRT分析套件确定表观遗传修饰，（3）一组密集的分子标记，通过使用TASSEL-GBS管道对350个树木品系进行基因分型，能够加速预测育种和改良，以及（4）测量树木基因型、根际微生物组、根转录组、共生体之间的相互作用（和其他内生菌）转录组，以及它们对幼龄树生长良好和边缘土壤的影响，通过根际微生物群落的16 S rRNA调查。该项目包括为服务不足的高中生提供暑期科学推广计划。

Red alder is a hardwood tree of economic importance in the Pacific Northwest, exceeding the annual value of the dominant softwood species Douglas-fir. Red alder is used for quality cabinetry, utensils and handles, and as a biomass/biofuels crop. It grows in inhospitable environments and on unproductive land, meaning that it does not compete with food production. Demand for saplings suitable for planting currently greatly exceeds supply. With better understanding of its genetics, scientists would be able to breed trees that grow faster and in more inhospitable environments. This would expand the area available for growing, and increase the annual yield for timber and biomass fuel. Additionally, red alder does not require nitrogen fertilizers. It achieves this by harnessing Frankia, a microbe, to provide the nitrogen for it. The relationship between the tree and the microbe requires scientific study. Some Frankia strains are better than others, and some combinations of tree and microbial strains are well suited to certain environments. This project seeks to understand how the red alder genetics, soil type, Frankia strain, and other bacteria in the soil interact to promote tree growth. The result will be the ability to develop new tree strains suited to certain environments, to expand planting to meet growing demand. The project includes training opportunities for students (high school through graduate level) and supports a high school summer innovation academy that targets underserved students. It promotes access to research by native and Hispanic underrepresented groups.Red alder (Alnus rubra Bong.), has significant economic importance, yet is an orphan in terms of scientific understanding of its genetic variability and its relationship with its nitrogen-fixing symbiont Frankia alni. This project will create an omics-based resource upon which to base a breeding and improvement program, aimed at improving tolerance to abiotic stresses and growth in marginal land area. Objectives are to create the following: (1) a de novo genome reference assembly of an elite high-performing red alder clone, using PacBio sequencing and BioNano physical mapping, (2) reference genome sequences and epigenomic signatures of the five Frankia strains that result in the best tree performance and symbiosis, using PacBio sequencing with epigenetic modifications determined using the SMRTanalysis suite,(3) a dense set of molecular markers to enable accelerated predictive breeding and improvement, through genotyping of 350 tree lines using the TASSEL-GBS pipeline, and (4) measurements of interactions among tree genotype, rhizosphere microbiome, root transcriptome, symbiont (and other endophyte) transcriptomes, and their impacts on juvenile tree growth on good and marginal soils, through 16s rRNA surveys of rhizosphere microbial communities. The project includes a summer science outreach program for underserved high school students.