Crop Genomics Research: Instrumentation for High-Throughput Processing of Samples

University Of California-Davis, Davis CA

Investigators

Abstract

0070371 PI: Thea A. Wilkins Title: Crop Genomics Research: Instrumentation for High-throughput Processing of Samples Project Abstract The need for genetic diversity, increased productivity, and improved food and fiber quality in the improvement of crop plants to offset a narrow germplasm base, yield plateaus and rising production costs has never been greater. Geneticists have been hard at work developing the tools and resources to improve crop plants using molecular approaches to augment traditional breeding programs and implement strategies for bioengineering elite cultivars. The introduction of innovative instrumentation that mechanizes labor-intensive procedures using robotics has revolutionized the study of genomes. The impact of such high-throughput processing on the study of large, complex genomes as those found in crop species is enormous, leading to an unprecedented investment in Plant Genome Initiatives by government agencies. Robotic equipment pivotal to high-throughput processing will nucleate the formation of a genomics facility that provides core services in support of genome projects. The equipment includes Genetix's Q-Bot, a unique multi-tasking, fully automated robot that specializes in high speed, high accuracy picking and spotting of clones in microtiter plates onto filters (macroarrays) and microarrays in high density gridded arrays. The high capacity HiGro orbital shaker optimizes the growth of bacterial cultures in microtiter plates in support of Q-Bot operations and high-throughput sequencing efforts. Studies on the structure and function of crop genomes that hinge on Q-Bot-mediated tasks encompass two major areas of endeavor related to physical mapping and analysis of gene function. BAC libraries, both existing and soon-to-be constructed, will be picked and arrayed on high density filters for distribution to the research community. BAC filters serve to fingerprint BAC clones and assemble BAC contigs for the purpose of preparing a sequence-ready physical map for beans, cotton, lettuce, rice, and diploid and tetraploid wheat. Such filters will also facilitate map-based cloning of important agronomic genes, including submergence tolerance in rice, vernalization in wheat, and cotton fiber genes. The Q-Bot will also speed up the gene discovery process in EST projects and facilitate the study of gene function. Macro- and microarrays will be used to study differential gene expression in response to a host of environmental, physiological and developmental stimuli to identify key gene functions in crop productivity, including nutritional seed quality (walnuts), stress (rice and wheat) and disease (Arabidopsis and lettuce) responses, and yield and fiber quality (cotton). The crop genomics consortium will develop tools and resources in service of the scientific community for global distribution, and in so doing, evolve as a major center and focal point for activities to harness genomics in the development of novel germplasm with enhanced food and fiber quality in major crop species. Training of students and postdoctoral fellows in high-throughput technology will be an integral part of research and teaching activities offered by the group.