Development of Genomic and Genetic Tools for Foxtail Millet, and Use of These Tools in the Improvement of Biomass Production for Bioenergy Crops
Investigators: J.L. Bennetzen and K.M. Devos
Institution: University of Georgia
Non-Technical Summary: Foxtail millet, Setaria italica, has the full set of attributes that will make it a model plant for basic and applied studies, particularly for its close relatives like switchgrass, an important bioenergy crop. Foxtail millet has small and simple chromosomes that will be sequenced this year by the DOE’s Joint Genome Institute (JGI). This sequence will enormously enhance further study and understanding of the genetic basis of biomass production, but it will only be fully useful if additional technologies are developed for use in foxtail millet. This proposal describes experiments to improve the genetic and genomic toolkit for foxtail millet, and thus assist with the assembly of the foxtail millet genomic sequence, anchor the sequence to the genetic map and lay the foundation for future molecular, developmental, physiological and genetic studies.
Objectives: The objectives of this proposal are 1) to construct a >12X redundant clone (BAC) library from foxtail millet inbred Yugu1 DNA, the DNA that will be sequenced by JGI; 2) to sequence the ends of the BACs so these data can help in the assembly and annotation of the complete foxtail millet genome sequence; 3) to confirm the assembly and detailed annotation, 4) to generate a new and large mapping population from the cross of Yugu1 foxtail millet with its wild progenitor, Setaria viridis, 5) to sequence the S. viridis genome with next-generation technology to find single nucleotide polymorphism (SNP) markers, and 6) to construct a >1000 marker genetic map from the new crossing population using these SNPs.
Approach: The approaches in this project include BAC library construction (obj. 1) and sequencing of the ends of these BACs (obj. 2), both using standard genomic technologies. The assembly and annotation of the complete foxtail millet genome sequence (obj. 3) will use these data, in collaboration with JGI, to provide an ordered and informative coverage, emphasizing the high throughput expertise of the JGI group and the manual confirmation skills of the UGA group. Population construction and marker analysis (objectives 4 and 6) in the mapping study will be by routine genetic/genomic approaches, but the identification of useful SNP markers (obj. 5) will involve ‘next generation’ DNA sequencing technologies that generate huge quantities of data but also require new informatic mining tools that the UGA groups will utilize and adapt.
Name: J.L. Bennetzen