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

PI: Herbert Aldwinckle（康奈尔大学）合作PI: Marcela Yepes（康奈尔大学），Keithanne Mockaitis（印第安纳大学），Aleksey Zimin（马里兰大学）和James Yorke（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，使它们极易受到气候变化模式带来的疾病和压力的影响。在拉丁美洲和非洲部分地区，栽培咖啡目前面临的毁灭性疾病和发育压力正在以惊人的速度降低产量和质量，并给小农户带来经济损失。因此，迫切需要努力提高咖啡的抗病性和农艺性状，以适应气候变化的压力，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，因为它含有四个基因组拷贝，这是两个祖先物种杂交的遗产，它们产生了咖啡。这些额外的拷贝现在使测序过程复杂化。栽培阿拉比卡咖啡及其祖先物种的完整基因组序列的可用性有望使在自然种群和用于育种的种群中更容易发现额外的遗传多样性。实验的重点将是发现对导致目前咖啡锈病流行的真菌菌株的抗性基因变异，以及对咖啡浆果蛀虫的抗性。咖啡浆果蛀虫是一种新抵达美国的害虫，其种群在高温下不断扩大。目前的资助旨在(i)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、搭建和注释，并对其假定的二倍体亲本（C. eugenioides和C. canephora）的基因组进行高质量组装；（ii）建立DNA序列资源，用于检测高杂合育种和自然群体的基因组多态性。（iii）生成和分析转录组序列资源，丰富了不同胁迫下叶、果和花基因表达的综合图谱。广泛的基因分型和转录组分析结合精细的表型分型，对阿拉比卡咖啡的高级育种和自然群体进行分析，将确定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。这笔资金将用于鉴定单核苷酸多态性、小索引、拷贝数变异和存在/缺失变异，这将为将该属未开发的基因组多样性转化为咖啡育种计划提供必要的手段，而不会损害对消费者和美国咖啡行业至关重要的理想质量性状。该项目还将为作物基因组学社区的目标做出重要贡献，即开发更多高质量的基因组资源，用于系统发育多样性多倍体基因组的进化和遗传学研究，以更好地了解多倍体如何影响作物基因型和进化适应性。为了促进生物学、数学和计算机科学的研究和教育，这项资助将为合作院校的研究生、研究生、本科生和高中学生提供培训机会。将开发基于网络的咖啡基因组学教育资源和年度研讨会，以帮助促进生物信息学和分子基因组工具在学术和科学研究计划中的使用，并向咖啡育种者展示基于基因组学的工具的实用性。国际咖啡和植物基因组学社区将通过国际咖啡基因组学网络（ICGN）网站（http://www.coffeegenome.org）广泛获取该项目的结果，该网站将链接到其他已经收集咖啡信息的公共网站，包括由美国国家科学基金会资助的开源数据库。康奈尔大学是ICGN的创始成员，并积极支持该网络的秘书处国际生物多样性。

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.