Recipient Organization
UNIVERSITY OF PUERTO RICO
AVE PONCE DE LEON
SAN JUAN,PR 00918-1000
Performing Department
Biology
Non Technical Summary
This AGFEI proposal seeks to strengthen research capability in plant pathology, plant-microbe interactions and plant biology in the Department of Biology at the University of Puerto Rico - Río Piedras. Puerto Rico and Hawaii face unique disease and pest challenges to agriculture as tropical US jurisdictions and islands. The equipment requested includes compound and dissecting microscopes, a fluorometer and spectrophotometer to measure DNA and RNA, and a computer for genomic and metagenomic data analysis. The requested equipment will be used for research, teaching and outreach in the Mycology Laboratory at the UPR Río Piedras and the Herbarium and Zoology Museum. The proposed equipment will strengthen existing, successful research and teaching programs and help strengthen collaborations with other institutions in Puerto Rico, Hawaii and ARS.
Animal Health Component
10%
Research Effort Categories
Basic
90%
Applied
10%
Developmental
(N/A)
Goals / Objectives
1. Strengthen research capability in plant pathology, plant-microbe interactions and plant biology in the Department of Biology at the University of Puerto Rico - Río Piedras;2. Strengthen collaborations, student training and outreach in these fields;3. Acquire equipment for research, which will also be used for teaching and outreach: a research brightfield/fluorescence microscope, a fluorometer and spectrophotometer to measure DNA and RNA, and a computer for genomic and metagenomic data analysis. Funds are also requested for a compound microscope and a dissection microscope for research, teaching and outreach at the UPR Río Piedras Herbarium and Zoology Museum.
Project Methods
Initial research projects and relevance of the proposed equipmentLECANICILLIA FUNGI AS PATHOGENS OF COFFEE LEAF RUST. Coffee leaf rust is a serious disease that limits coffee production worldwide. The pathogen Hemileia vastatrix It arrived in Puerto Rico in 1989 and in Hawaii in 2020. (Because of its geographic isolation, Hawaii had escaped the pathogen until last year.) Control is mainly through spraying with fungicides and planting resistant varieties. In recent years, coffee leaf rust has become more serious in Central Americaand Puerto Rico. Recombination has apparently produced new genotypes able to overcome previously resistant cultivars of coffee.Lecanicillium fungi include pathogens of rust fungi (that is, they are fungi that parasitize other fungi), as well as insects. They were previously classified as Verticillium, but recent molecular systematics studies have divided them into species of Lecanicillium, Simplicillium and Akanthomyces. They may have potential for biological control of coffee leaf rust and other rust diseases. Previous studies have not been successful at using them to attack rust pathogens, but these studies did not identify the fungi accurately and thus may have chosen the wrong organisms to use or combined different species with different effects without realizing it.Importance of proposed equipment: The acquisition of the Qubit fluorometer and Nanodrop spectrophotometer would allow measurement of DNA quantity and quality (necessary for PCR and for DNA sequencing on Illumina NGS platforms) and the Mac Pro computer will allow assembly of contigs of DNA (a very computationally intense process that would take too long on a standard desktop or laptop computer).GENETIC DIVERSITY OF COFFEE LEAF RUST. The coffee leaf rust pathogen Hemileia vastatrix was found in Puerto Rico in 1989 and in Hawaii in 2020, as noted above. It is unclear how many independent introductions occurred, where the inoculum came from, and whether there is genetic recombination in local populations. These questions can be answered by sequencing variable loci from H. vastatrix collections from Puerto Rico and Hawaii. This is a proposed project in collaboration with Lisa Keith (USDA-ARS Daniel K. Inouye U.S. Pacific Basin Agricultural Research Center, Hilo, HI) and Luz Serrato, TARS (mentioned above).ADAPTING COFFEE PLANTS TO HEAT, DROUGHT AND CLIMATE CHANGE. Like many crops, coffee cultivation is threatened by climate change. Many areas currently used for coffee are predicted to become too hot or dry in the coming decades, in Puerto Ricoand worldwide. Development of new cultivars is the main way to increase resistance of coffee plants to heat, drought and disease, but it is a slow process. Manipulating the microbial community associated with plant roots has been used to increase resistance to heat and drought in several annual crops and could work with coffee as well. The proposed experiments will sample coffee seedlings from different locations, test them for resistance to heat and drought, and sequence the microbiomes of the most resistant (and control plants as well). Importance of proposed equipment: This will be done with Illumina sequencing. The NanoDrop and Qubit fluorometer are needed to quantify and determine quality of DNA extracted for amplification and sequencing. The iMacPro computer is needed to run metagenomics programs such as QIIME that are too memory-intensive to run on standard desktops and laptops.MECHANISMS OF RESISTANCE TO PATHOGENS IN THE COFFEE BERRY BORER. The coffee berry borer (CBB) Hypothenemus hampei is the most destructive insect pest of coffee worldwide. It has been in Puerto Rico since 2007 and Hawaii since 2010. One of the most widely-used control measures is application of the entomopathogenic fungus Beauveria bassiana, usually in form of Mycotrol® or Botaniguard®. Strains of B. bassiana from Puerto Rico vary widely in virulence to the CBB. PhD student Jéssica Torres wants to explore mechanisms of resistance to B. bassiana in the CBB. She would like to compare gene expression in CBBs infected by a virulent strain of B. bassiana, a less virulent strain and uninfected control CBBs. The method is RNAseq transciptome analysis. This information may suggest more effective methods to control the CBB. Importance of proposed equipment: As above, this will be done with Illumina sequencing. The NanoDrop and Qubit fluorometer are needed to quantify and determine quality of DNA extracted for amplification and sequencing. The iMacPro computer is needed to run the analyses.FUNGAL PATHOGENS CAUSING COFFEE FRUIT ROT. Coffee fruit rot is a common and costly but largely unstudied disease in Puerto Rico and Hawaii. The literature says that pathogens that attack green coffee fruits only occur in Africa at high elevations, but we have shown this is not true. PhD student Maylin Caldwell is studying coffee fruit rot and the pathogens that cause it. Importance of proposed equipment: The pathogens are identified by DNA sequencing, so again, theNanoDrop, Qubit fluorometer and iMacPro computer would greatly facilitate her project.GENETIC DIVERSITY OF VANILLA. A collaboration with a local startup company, Vainilla Castañer LLC is studying genetic diversity in Vanilla planifolia plants in Puerto Rico and elsewhere. Vanilla was an important crop in Puerto Rico from the early 1900s until 1950, when disease wiped it out (Bayman et al., 2018). Vainilla Castañer LLC aims to reestablish the crop as a source of additional revenue for farmers in Puerto Rico and as an attraction for agrotourism. However, it is not clear what plants are best to grow. Disease-resistant hybrids were developed by the USDA in Puerto Rico the early twentieth century, but have since been lost. We will sequence variable genes from a collection of Vanilla planifolia plants to determine if the lost hybrids can be recovered and to distinguish local plants from imports from Mexico and Florida, with the goal of identifying which genotypes will be most productive under local conditions. Importance of proposed equipment: The NanoDrop and Qubit fluorometer are needed to quantify and determine quality of DNA extracted for amplification and sequencing. The MacPro computer is needed to assemble DNA sequences and run phylogenetic analysis programs that are too memory-intensive to run on our standard desktops and laptops.INTERACTIONS OF MITES WITH PLANTS. Graduate student Ahmetsaí Cruz is doing thesis research on plant mites. Mites are very small; identification is based on morphology of anatomical structures less than 1mm in size. The Olympus microscope will be an essential to Ahmetsaí's ability to identify them.MYCORRHIZAL INTERACTIONS OF ORCHIDS. Orchid seeds do not germinate in nature without help from mycorrhizal fungi, which provide nutrients. Many orchids maintain mycorrhizal relationships throughout their lives, while others do not. The role of the distribution of mycorrhizal fungi in determining the distribution of orchids is still not fully understood. Graduate student Normandie González is studying this relationship in the tropical epiphytic orchid Psychilis. Her project would be facilitated by the NanoDrop spectrophotometer to measure DNA for PCRs, the iMacPro computer for phylogenetic analyses, and both microscopes.