ABI Innovation: Barcoding-Free Multiplexing: Leveraging Combinatorial Pooling for High-Throughput Sequencing

University Of California-Riverside, Riverside CA

Investigators

Abstract

The University of California, Riverside is awarded a grant to develop an innovative sequencing protocol for hierarchical (i.e., BAC-by-BAC) genome sequencing of large eukaryotic genomes. At the core of the protocol is the ability to solve a set of hard computational questions, which are the focus of the research plan. The computational challenges require the study of novel combinatorial optimization problems, the development of innovative time- and space-efficient algorithms, and ultimately the implementation and deployment of user-friendly web-based software tools. The new combinatorial sequencing protocol is going to be tested to the cowpea genome. Cowpea Vigna unguiculata, also known as China bean or black-eyed pea, is one of the most important food legume crops in the semi-arid tropics covering Asia, Africa, and Central and South America. A drought-tolerant and warm-weather crop, cowpeas are well-adapted to the drier regions of the tropics, where other food legumes do not perform well. Its modest genome size makes it an excellent candidate to demonstrate the utility of our protocol. We expect the final assembly to provide a sufficient depth of knowledge to support most downstream applications including map-based cloning of trait determinants, development of markers for marker-assisted breeding, microarray development for gene expression studies and analysis of synteny with related species. This project will advance sequencing techniques for complex genomes, using cowpea, an essential food source in developing countries. Software tools and the assembled data will be placed into the public domain, which will benefit researchers and the public worldwide, and potentially lead to new international and industrial collaborations. This project will directly support one graduate students in a highly interdisciplinary environment, building on UCR's strengths in Computer Science and Agricultural Sciences. Undergraduates will have opportunities to participate in research through a Research Experiences for Undergraduates (REU) site at UCR, a collaboration with a nearby community college, and a new US Department of Education Title V Hispanic Serving Institution grant (UCR is an accredited HSI). More details and information about this project will be available at http://www.cs.ucr.edu/~stelo/dbi.htm