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United States Department of Agriculture

Agricultural Research Service

Research Project: ALGORITHMS AND EXPLORATIONS OF WILD AND DOMESTIC POTATOES FOR GENOME DISCOVERY AND GENETIC IMPROVEMENT

Location: Crop Improvement & Utilization Research

2011 Annual Report


1a.Objectives (from AD-416)
The objective of this cooperative research project is to develop methodologies to explore large and repetitive plant genomes. The initial focus will be on comparisons of the diploid wild potato (Solanum bulbocastanum) with the tetraploid cultivated potato (S. tuberosum). The haploid genomes of each are estimated to be ~900 Mbp.


1b.Approach (from AD-416)
Genomic sequence information will be generated with Ilumina’s next generation sequencing technologies and analyzed in silico to identify potential subsequences to use as molecular markers and identify genes and sequences of interest for applied agronomic improvement. Assembled contigs will also be used to compare wild and domestic potato. This comparison may result in the development of single nucleotide polymorphisms (SNPs) that can be used as molecular markers by breeders. Identification of selected subsequences and novel genes will enable their isolation. Wet lab testing will be used to validate the utility of these subsequences and should enable the development of sequences that can be applied to the molecular genetic improvement of potato. Using standard Agrobacterium-mediated transformation, appropriate transgenes vectors will be constructed and the sequences mobilized into potatoes. Resulting transgenic lines will be examined for function, efficacy and to demonstrate proof of principle. We anticipate that this novel approach, if successful, will be applicable to the improvement of other plant species. Documents Non Funded Cooperative Agreement with University of Houston.


3.Progress Report

The wild potato relative (Solanum bulbocastanum) has been the ongoing subject of next generation sequencing with an Illumina Genome analyzer and to date 16 Gigabytes of sequence or roughly 16x genome coverage has been obtained for analysis. The potato genome sequence version 1 has recently been published by the Plant Genome Sequencing Consortium. This sequence is now available and will facilitate analysis and assembly of an S. bulbocastanum genomic sequences.

Zebra chip is an important emerging disease of potatoes in the United States caused by the vascular infection of potato plants with Candidatus Liberibacter solanacearum which is spread by a psyllid (Bactericera cockerelli Sulc ) vector. Potato plants either asymptomatic or infected with the Candidatus as well as the psyllid vector with and without the Candidatus have been analyzed by Illumina sequencing. This data will be analyzed to verify the presence of pathogen sequences in a large and complex background.

The agreement was monitored by regular (monthly) electronic communications and telephone conversations between participants, and included personal meetings.


Last Modified: 10/1/2014
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