Yeisoo Yu, Ph.D. - US grants

Full-length complementary DNA (FLcDNA) sequences are crucial for accurate annotation and future functional characterization of the genes in the maize genome. This project will generate approximately 30,000 FLcDNA sequences focusing on reproductive development and stress-induced transcripts. A commercial library in a Gateway-compatible backbone built using RNA from 13 organs types (from inflorescence primordia to immature seeds), highly enriched for full-length cDNA representation by cap and tail selection, will be normalized to increase representation of rare transcripts. A new library from additional floral developmental stages, embryo, scutellum, and 7-day seedlings with stress inducer treatments will be made using the same methods.

Candidate clones for finishing will be picked based on (1) 360,000 5' and 3' Expressed Sequence Tag (EST) assemblies generated in this project by alignment to publicly available ESTs, FLcDNAs and genomic sequences of rice and maize, and (2) hybridization of RNA from specific reproductive stages to 360,000 filter-arrayed clones in order to enrich rare transcripts. Iterative primer walking will be employed on each candidate FLcDNA, and a transposon method will also be utilized to complete finish larger insert and difficult clones with phred 40 quality.

The outcomes from the project to be delivered to the community include: (1) 360,000 5' and 3' ESTs from 180,000 presumptive FLcDNAs, (2) 30,000 FLcDNA clones and sequences, and (3) FLcDNA annotation, including available stage-specificity of expression and possible mapping information, and a web-based genome browser.

The maize FLcDNA resources will have a wide variety of potential uses from functional studies towards understanding gene evolution during cereal diversification, and exploration of gene regulatory networks involved in plant reproduction and environmental stresses.

Availability of project outcomes
A web-based display will be created at http://www.genome.arizona.edu to provide access to the project results and project progress. All biological resources including clones, amplified libraries, and high-density filters will also make publicly available through BAC/EST resource center at Arizona Genomics Institute (www.genome.arizona.edu/order).

PI: Rod A. Wing (University of Arizona)
CoPIs: Steven D. Rounsley and Yeisoo Yu (University of Arizona)

The objective of this project is to generate and analyze a reference genome sequence of the West African cultivated rice Oryza glaberrima (CG14). The reference sequence will be generated using a minimum tiling path of bacterial artificial chromosome (BAC) clones selected from an existing NSF-funded O. glaberrima physical map, which encompasses the entire genome. DNA from these clones will be purified, pooled and sequenced using 454/Roche GSFLX Titanium and paired-end pyrosequencing technologies. A standardized annotation process will be applied across the whole genome taking advantage of the well-curated annotation for the Asian cultivated rice species - Oryza sativa. In addition, customized analyses targeted at specific biological questions will be performed. The genome sequence and its annotation will be accessible via public databases, such as GenBank and Gramene (www.gramene.org).

The broader impacts of this project are two-fold. First, since the world's rice-dependent population is expected to double in the next 25 years, rice breeders are faced with the challenge of doubling rice yields with less land and water, and with poorer soils. Obtaining the genome of the African cultivated rice, O. glaberrima, is the first step towards understanding the differences between the two cultivated species, how each has adapted to their particular environments, and how each may benefit the other to be grown in more diverse and often harsh environments. The genome sequence produced by this research project will be a resource utilized by biologists and rice breeders as a component in efforts towards improving worldwide rice production. This project also offers several research training opportunities for postdoctoral scientists and students at all levels. First, students and postdoctoral researchers will be trained to perform research using cutting edge genomics research technologies such as next generation sequencing, physical mapping, de novo assembly of large plant genomes, genome annotation and comparative evolutionary genomics. Their research results will be disseminated through peer review publications and at local and international meetings. Project personnel will serve as mentors for all training activities and will meet regularly with each student and postdoc to ensure they are on track and getting the most out of their research experience. In addition, the project has partnered with Biotechnology, Agronomy and Plant Science programs at Pima Community College (Tucson AZ), and the Life Science Undergraduate Biology Research Program at University of Arizona to provide undergraduate students with summer research internships. These students will also have an opportunity to apply for the BRAVO program (http://www.ubrp.arizona.edu/) which allows them to perform research abroad for a minimum of 10 weeks. The project has research partnerships in Benin (West Africa), China, Colombia, France, Japan, the Philippines, and Taiwan, all suitable locations for a 10 week international research experience.
Finally, the project will participate in the University of Arizona's KEYS program (K-12 Engaging Youth in Science; http://www.bio5.org/training/trainingHigh.php) which provides six week summer research internships for advanced high school students.