2012 Annual Report
1a.Objectives (from AD-416):
Objective 1. Initiate an integrated cranberry genetics and genetic improvement plan to develop enhanced germplasm and superior new cultivars of cranberry adapted for a short growing season climate with superior productivity, increased disease resistance, enhanced nutritional characteristics, improved environmental adaptation (especially cold tolerance), and more uniform ripening with excellent berry color. Evaluate field performance and quality under current commercial conditions as well as under enhanced production systems utilizing new IPM and water management technologies.
Objective 2. Initiate an innovative and integrated research program to characterize current insect pest damage of the cranberry crops, develop efficacious and economical insect Integrated Pest Management (IPM) strategies for cranberry production systems, and respond to emerging insect pests. Evaluate field performance under current commercial conditions as well as under enhanced production systems utilizing new cranberry varieties and new water management technologies.
1b.Approach (from AD-416):
For Objective 1, novel phenotypic variation will be identified, genetically characterized, mapped on the cranberry genome, and key genes incorporated into breeding stocks that are well-adapted for commercial growers. DNA polymorphisms and molecular tools will be developed to improve the efficiency of cranberry breeding. Methods for accurately phenotyping traits of importance will be developed and promising genetic selections will be tracked in commercial production systems that include up-to-date IPM and water management technologies.
For Objective 2, novel pest management strategies will be developed and evaluated including, but not limited to, biological controls, host pest resistances, reduced risk chemicals, and cultural practices. Pest biologies will be studied to develop models for making optimal control decisions directly applicable to commercial production systems. Environmental impact of climate change, emerging water management issues and their application to new cranberry cultivars will be incorporated into reduced-risk pest management strategies developed and evaluated in commercial production systems.
Objective 1: The USDA-ARS Cranberry Genetics Laboratory (CGGL) is currently developing molecular tools useful for breeding and genetics studies in Vaccinium. Simple sequence repeats (SSR) and single nucleotide polymorphic (SNP) markers are being developed using next generation sequencing data. These markers will facilitate cultivar development through genetic mapping. Thousands of SSRs are being developed for the genetic mapping of important traits in cranberry. Additionally, sequencing efforts have yielded the complete plastid and mitochondria genomes of cranberry through bioinformatic approaches.
Developed SSR markers are also being used for the genetic characterization of cultivated and natural plant germplasm and the discovery of best parental combinations in cranberry for controlled crosses prioritization. Cultivated and wild cranberry genotypes are continually being collected around the U.S. We are evaluating and comparing the genetic diversity of several cranberry collections, for example the USDA-ARS National Clonal Germplasm Repository (NCGR). Genetic information gained from examining cranberry collections together with information from a genetic survey of cultivated and wild cranberries conducted in Wisconsin allowed the designation and conservation of appropriate genotypes for several of the most important cranberry cultivars.
Objective 2: Research has focused on elements of integrated pest management (IPM) and arthropod biology that facilitate reduced pesticide use in U.S. cranberries. Thousands of arthropod specimens collected in spring floods have been analyzed to reveal the diversity and abundance of pests physically removed from beds during flood events. The first ever 3-species mating disruption program was tested on four marshes in Wisconsin. The species targeted represent the top three pests of Wisconsin cranberries. Additionally, eight years of pheromone-baited trap-catch counts were analyzed to illuminate the historic flight patterns for these pests. The cranberry flea beetle has recently emerged as a major pest of Wisconsin cranberries, so an experiment was initiated to show that a single well-timed June soil-drench could replace three late-summer foliar sprays. Since soil-drench treatments would need to be applied where the beetle larvae are feeding underground, we conducted a study to determine isotopically where the beetles are overwintering. The temperature-specific growth rates of Sparganothis fruitworm, the most ubiquitous pest of U.S. cranberries, were empirically isolated. In the marshlands of Wisconsin, the 15N signatures of wild cranberry populations are being determined, forming the basis of in-depth investigations of cranberry trophic structure.
A new invasive species, the spotted wing Drosophila, has been reported in Wisconsin. This Asian pest has caused major fruit crop losses on the East and West Coasts. In a collaborative study that focused on the susceptibility of ripe, under-ripe, over-ripe, and damaged cranberry fruit, the threat to cranberries has been characterized.
Simple Sequence Repeat (SSR) fingerprinting in cranberry. Cranberries are an economically important fruit crop derived from a North American native species. Twelve SSR markers were used to assess the genetic diversity of 164 samples of 21 different cranberry cultivars, 11 experimental hybrids, and 6 representative accessions of wild species. Genetic cluster analysis, based on 117 SSR alleles, differentiated the major cranberry cultivars. However, some cranberry cultivar sub-clone variants and mislabeled samples were observed. Consensus genetic profiles identified the most likely clonal representatives of several important cranberry cultivars (e.g., ‘Ben Lear’, ‘Howes’, and ‘Stevens’). The markers were further used to confirm putative parents of several hybrid progenies. The long-term goal of our studies is to identify, preserve, and utilize unique genetic materials to breed improved cranberries. This accomplishment marks progress to identify unique genetic materials and attaining this goal will help growers maintain sustainability under changing economic and environmental conditions.
Removal of arthropods during spring flooding. Among the arthropods, the most abundant group was the beetles, which were represented by 18 families and totaled over 1,300 individuals/acre. While the white grubs and June beetles, weevils, and wireworms/click-beetles are significant pests and thus good to eliminate, the rove beetles and ground beetles are largely predaceous and probably eat many pests. The total number of arthropods removed per-acre from the beds was approximately 2,127 specimens. As a result of this research, grower interest in and adoption of flooding as a pest control tactic have increased markedly. Since flooding replaces the pre-bloom insecticide application, flooding effectively eliminates one of the annual sprays applied by growers. With the elimination of one spray, growers reduce insecticide application by which in turn increases their profits and reduces the ecological footprint of cranberry production.
Cranberry plastid genome sequence. The American cranberry is a commercially important fruit crop species. A fundamental requirement for breeding improved cranberry varieties is the accumulation of cranberry genetic information. We used next-generation sequencing technologies and deciphered the complete cranberry chloroplast (i.e., photosynthetic machinery) deoxyribonucleic acid (DNA) code. We isolated plastid-specific sequences of ‘HyRed’ via comparisons with complete plastid sequences of several species available at the National Center for Biotechnology (NCBI) database. We reconstructed a 176kb cranberry plastid sequence, and compared it to the sequence of 30 other species. The cranberry plastid genome sequence will be useful during breeding high yielding varieties for adapted cold and other environmental stresses. Additionally, cranberry chloroplast information will help understand evolutionary aspects of the species that could have important implications for breeding. The chloroplast DNA code of cranberry will also be useful as a model to researchers to study other closely related species such as blueberry.
Zalapa, J.E., Simon, P.W., Hummer, K.E., Bassil, N.V., Senalik, D.A., Zhu, H., Mccown, B.H., Zeldin, E., Speers, J., Hyman, J. 2012. Mining and validation of pyrosequenced simple sequence repeats (SSRs) from American cranberry (Vaccinium macrocarpon Ait.). Theoretical and Applied Genetics. 124(1):87-96.
Zalapa, J.E., Cuevas, H.E., Steffan, S.A., Simon, P.W., Senalik, D.A., Zhu, H., Mccown, B., Zeldin, E., Harbut, R. 2012. Using next generation sequencing approaches for the isolation of simple sequence repeats (SSR) in the plant sciences. American Journal of Botany. 99(2):193-208.