ABR-PG: Developing Advanced Genomic Tools to Accelerate Linkage of Structural & Functional Diversity in Coffee

皮埃尔：赫伯特·奥尔德温克尔(康奈尔大学)合作伙伴：Marcela Yepes(康奈尔大学)，Keithanne Mockaitis(印第安纳大学)，Aleksey Zimin(马里兰大学)和James York(马里兰大学)咖啡是地球上最有价值和最广泛消费的作物之一。然而，栽培品种的多样性非常有限。栽培咖啡品种缺乏遗传多样性，这使得它们极易受到气候变化模式带来的疾病和压力的影响。种植咖啡目前面临的毁灭性疾病和发展压力正在以惊人的速度降低拉丁美洲和非洲部分地区的产量和质量，并给小农户带来经济损失。因此，迫切需要努力提高抗病能力和农艺性状以适应气候变化压力，而拥有完整的基因组序列是咖啡育种的一个非常重要的工具。阿拉比卡咖啡是一个复杂的物种，因为它包含四个基因组副本，这是两个起源于咖啡的祖先物种杂交的遗产。这些额外的拷贝现在使测序过程变得复杂。种植的阿拉比卡咖啡及其祖先物种的完整基因组序列的获得，预计将使在自然种群和用于育种的种群中更容易发现更多的遗传多样性。实验将集中在发现对导致当前咖啡锈病流行的真菌菌株的抗性的遗传变异，以及对咖啡浆果害虫的抗性。咖啡浆果害虫是一种新传入美国的害虫，其种群在高温下正在扩大。目前的资助目标是：(I)在高质量的二倍体亲本(C.eugenioides和C.canephora)基因组组装的辅助下，对阿拉比卡咖啡(异源四倍体阿拉比卡咖啡)的基因组进行测序、组装、支架和注释，(Ii)建立一个DNA序列资源，用于检测高度杂合育种和自然群体的基因组多态性，以及(Iii)建立和分析转录组序列资源，丰富了在不同胁迫下叶片、浆果和花中基因表达的全面图谱。广泛的基因分型和转录组分析，结合对阿拉比卡先进育种群体和自然群体的精细表型分析，将确定导致重要农艺性状表型变异的基因及其等位基因。这项研究将产生第一个高度详细的数据集，将与适应相关的咖啡性状的基因型和表型之间的关系联系起来，为分子辅助咖啡育种提供基础。这笔赠款将导致识别单核苷酸多态、小Indels、拷贝数变异和存在/缺失变异，这将提供必要的手段，将该属未开发的基因组多样性转化为咖啡育种计划，而不会危及对消费者和美国咖啡业至关重要的理想质量特征。该项目还将对作物基因组学社区的目标做出重要贡献，即为进化和遗传学研究开发更多高质量的基因组资源，研究系统发育多样化的多倍体基因组，以更好地了解多倍体如何影响作物的基因型和进化适应性。为了促进跨越生物、数学和计算机科学的研究和教育，这笔赠款将支持合作伙伴机构为学生提供研究生、研究生、本科生和高中水平的培训机会。将开发关于咖啡基因组学的网络教育资源和年度研讨会，以帮助促进在学术和科学研究项目中使用生物信息学和分子基因组学工具，并向咖啡育种者演示基于基因组学工具的效用。项目成果将通过国际咖啡基因组学网络(http://www.coffeegenome.org)，)网站(ICGN)广泛向国际咖啡和植物基因组学社区开放，该网站将链接到其他已经管理咖啡信息的公共网站，包括由国家科学基金会资助的开源管理数据库。康奈尔大学是ICGN的创始成员，并与该网络的秘书处生物大学国际积极支持。

PI: Herbert Aldwinckle (Cornell University)Co-PIs: Marcela Yepes (Cornell University), Keithanne Mockaitis (Indiana University), Aleksey Zimin (University of Maryland), and James Yorke (University of Maryland)Coffee is one of the most valuable and widely consumed crops on earth. Yet, the diversity of cultivated varieties is very limited. The lack of genetic diversity in cultivated coffee varieties makes them extremely vulnerable to diseases and stress brought on by variable weather patterns. The devastating disease and developmental stresses that cultivated coffee is currently facing are reducing yield and quality at an alarming rate in parts of Latin America and Africa, and bringing economic ruin to small-holder farmers. Efforts are therefore urgently needed to improve disease resistance and agronomic traits for adaptation to climate change pressures, and having complete genome sequences is a very important tool for coffee breeding. Arabica coffee is a complex species because it contains four copies of its genome, a legacy of the cross between two ancestral species that gave rise to coffee. These additional copies now complicate the sequencing process. The availability of complete genome sequences for cultivated Arabica coffee and its ancestral species is expected to make it easier to find additional genetic diversity in natural populations and in populations used for breeding. Experiments will focus on discovery of genetic variation for resistance to the fungal strains responsible for the current coffee rust epidemic, and resistance to the coffee berry borer, an insect pest newly arrived in the US, and whose population is expanding in elevated temperatures. The current grant aims at (i) sequencing, assembling, scaffolding, and annotating the genome of Arabica coffee (the allotetraploid Coffea arabica), assisted by high quality assemblies of the genomes of its putative diploid parents (C. eugenioides and C. canephora), (ii) building a DNA sequence resource for detection of genomic polymorphism in highly heterozygous breeding and natural populations, and (iii) generating and analyzing transcriptome sequence resources enriched for comprehensive profiles of gene expression in leaves, berries and flowers exposed to different stresses. Broad genotyping and transcriptome analyses combined with refined phenotyping performed on advanced breeding and natural populations of C. arabica will identify the genes and their alleles responsible for phenotypic variation in important agronomic traits. The research will generate the first highly detailed datasets that associate relationships between genotype and phenotype for coffee traits relevant to adaptation, furnishing a basis for molecular-assisted coffee breeding. This grant will lead to the identification of single nucleotide polymorphisms, small indels, copy number variants, and present/absent variants that will provide the essential means to translate the unexploited genomic diversity of the genus into coffee breeding programs without jeopardizing desirable quality traits critical to consumers and the US coffee industry. The project will also contribute importantly to the crop genomics community goals of developing more high-quality genomic resources for research of phylogenetically diverse polyploid genomes for evolutionary and genetics studies to gain better understanding of how polyploidy affects the crop genotype and evolutionary fitness. To promote research and education spanning biology, mathematics and computer sciences, this grant will support training opportunities for students at postgraduate, graduate, undergraduate and high school levels hosted at collaborating partner institutions. Web-based educational resources and annual workshops on coffee genomics will be developed to help promote the use of bioinformatics and molecular-genomic tools in academic and scientific research programs, as well as to demonstrate to coffee breeders the utility of genomics-based tools. The project results will be widely accessible to the international coffee and plant genomics community through the International Coffee Genomics Network (ICGN) website (http://www.coffeegenome.org), which will link to other public websites that have already curated coffee information, including open source curated databases funded by NSF. Cornell University is founding member of ICGN and supports actively with Bioversity International, the secretariat of the network.