RESEARCH-PGR: Adapting Perennial Crops for Climate Change: Graft Transmissible Effects of Rootstocks on Grapevine Shoots

副主任：Daniel Chitwood (Donald Danforth Plant Science Center), Anne Fennell（南达科他州立大学），Jason Londo (USDA-ARS/ Geneva， NY)；Laszlo Kovacs（密苏里州立大学斯普林菲尔德分校）和Misha Kwasniewski（密苏里大学哥伦比亚分校）；高级人员：秦马（南达科他州立大学）、安德鲁·怀亚特（密苏里植物园）、彼得·考辛斯（加利福尼亚州莫德斯托市欧内斯特&胡利奥·加洛酒庄）。长寿的植物是如何应对一年四季不断变化的气候的？多年生植物适应环境变化的机制是什么？植物的地下部分如何促进整个植物水平的响应？在多年生木本作物中，包括葡萄藤和大多数果树和坚果树，嫁接是一种外科手术式的增强，将茎系统（接穗）的茎与根系（砧木）的茎拼接在一起，通常将不同的基因型或物种连接到一个单一的植物中。嫁接使多年生作物的发育、无性系繁殖和分布在新的和多样化的环境中，通过分离芽和根的育种努力。该项目利用嫁接葡萄藤和基因组学，对砧木如何改变接穗表型和可塑性产生系统级的理解。研究结果对国内外葡萄产业和木本作物具有重要意义，促进了对根系对茎系表型影响的基因组基础和遗传结构的理解。综合教育和推广包括在密苏里州和南达科他州的农村和城市地区培训博士后、研究生和本科生研究人员，并与USDA-ARS葡萄遗传学研究单位和行业合作伙伴Ernest & Julio Gallo Winery建立了牢固的合作关系。密苏里植物园和美国植物园计划开展有关可持续农业、作物进化和生物多样性的推广活动。无性繁殖、嫁接的作物物种为了解根系在不同气候条件下调节茎系统表型的能力提供了最佳的研究系统。Grapevine是这项工作的一个特殊模型，具有测序和注释的葡萄参考基因组，野生葡萄品种的参考转录组，用于SNP发现和转录组分析的生物信息学管道，高通量表型方法，以及在不同环境下的研究和生产葡萄园。本项目主要研究葡萄藤根和茎的相互作用：1)在密苏里州现有的一个普通花园研究葡萄园，分析未嫁接和嫁接到三种不同砧木上的普通接穗的年际表型变化；2)加州不同环境下的商业葡萄园，分析环境对根冠沟通的影响；3)建立一个新的分离砧木定位群体，在四个气候带复制并嫁接一个共同接穗，以表征根调节接穗表型的基因型x环境相互作用；4)学术和行业合作伙伴关系，开展广泛的跨学科培训和推广。将生成全面的表型数据（RNAseq、生理、代谢和形态学）。鉴于人们对多年生作物作为可持续农业的重要组成部分的兴趣日益浓厚，本项目提供了对长寿植物表型变异的遗传和环境基础的有价值的深入研究，这是生物学中的一个基本挑战，在作物改良中具有重要应用。该项目产生的数据将为建立遗传x环境相互作用模型和砧木对接穗表型的遗传贡献的系统生物学分析提供前所未有的机会。所有数据将通过长期存储库向公众开放。

PI: Allison Miller (Saint Louis University)CoPIs: Daniel Chitwood (Donald Danforth Plant Science Center), Anne Fennell (South Dakota State University), Jason Londo (USDA-ARS/ Geneva, NY); Laszlo Kovacs (Missouri State University-Springfield), and Misha Kwasniewski (University of Missouri-Columbia);Senior Personnel: Qin Ma (South Dakota State University), Andrew Wyatt (Missouri Botanical Garden), and Peter Cousins (Ernest & Julio Gallo Winery, Modesto, CA). How do long-lived plants cope with a shifting climate, over seasons, and from year to year? What are the mechanisms that enable perennial plants to adjust to environmental changes, and how does the belowground part of the plant contribute to responses at a whole plant level? In perennial woody crops, including grapevine and most fruit and nut trees, grafting is a surgical enhancement that splices together the stem of the shoot system (scion) with the stem of the root system (rootstock), often joining different genotypes or species into a single plant. Grafting enables the development, clonal propagation, and distribution of perennial crops into new and diverse environments by separating breeding efforts for shoots and roots. This project uses grafted grapevines and genomics to produce a systems-level understanding of how rootstocks modify scion phenotype and plasticity. Results have implications for the national and global grape industry, and woody crops in general, by advancing understanding of the genomic basis and genetic architecture of the influence of the root system on shoot system phenotype. Integrated education and outreach include training post-doctoral, graduate, and undergraduate researchers in rural and urban locations in Missouri and South Dakota, bolstered by a strong collaborative relationship with the USDA-ARS Grape Genetics Research Unit and industrial partner Ernest & Julio Gallo Winery. Related outreach activities addressing sustainable agriculture, crop evolution, and biodiversity are planned at the Missouri Botanical Garden and U.S. Botanical Garden. Clonally propagated, grafted crop species provide the optimal study system for understanding the ability of the root system to modulate shoot system phenotypes across variable climates. Grapevine is an exceptional model for this work with a sequenced and annotated V. vinifera reference genome, reference transcriptomes for wild grapevine species, bioinformatic pipelines for SNP discovery and transcriptome analyses, high-throughput phenotyping methods, and research and production vineyards in diverse environments. This project focuses on root and shoot interactions in grapevine leveraging: 1) an existing common garden research vineyard in Missouri, to analyze inter-annual phenotypic variation in a common scion growing ungrafted and also grafted to three different rootstocks; 2) commercial vineyards across disparate environments of California, to assay environmental influences on root-shoot communication; 3) a new segregating rootstock mapping population replicated in four climatic zones and grafted with a common scion, to characterize genotype x environment interactions of scion phenotypes modulated by the root; and 4) academic and industry partnerships, to conduct extensive interdisciplinary training and outreach. Comprehensive phenotypic data (RNAseq, physiological, metabolic, and morphological) will be generated. Given increasing interest in perennial crops as important components of sustainable agriculture, this project offers a valuable in-depth look at genetic and environmental bases of phenotypic variation in in long-lived plants, a fundamental challenge in biology with important applications in crop improvement. Data generated in this project will provide an unprecedented opportunity to produce genetic x environment interaction models and systems biology analysis of the genetic contribution of rootstocks to scion phenotypes. All data will be made accessible to the public through long-term repositories.