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

Cornell University, Ithaca NY

Investigators

Abstract

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.