2010 Annual Report
1a.Objectives (from AD-416)
We will significantly increase the numbers of robust single nucleotide polymorphisms (SNPs) and develop a high through-put genotyping platform for onion. Workshops will be held at regional and national Allium meetings.
1b.Approach (from AD-416)
Develop a detailed genetic map for onion:
Identify simple single nucleotide polymorphisms (SNPs) in onion;
Develop high throughput SNP genotyping platform for onion; and
Develop workshops for public and private-sector researchers, students, and regional grower and consumer groups for onion to illustrate the usefulness of genomics to solve high-priority research goals.
Onion tissues were delivered for isolation of Ribonucleic acid (RNA) for cDNA library synthesis. Leaves, roots, immature umbels, and immature bulbs were harvested from onion inbreds B5225B and OH-1, frozen in liquid nitrogen, and shipped to J. Craig Venter Institute, Inc. (JCVI). At JCVI, RNA was isolated from each of these tissues and quality and quantity were established. Equal molar amounts of RNA of each inbred were used for construction of normalized cDNA libraries. The RNAs were provided to a company for synthesis of the normalized cDNAs.
JCVI was experiencing relatively low sequence output from their 454 sequencing machines. We worked with a company to identify the problem, which was due to problems when a poly-T primer was used to synthesize the cDNAs. An interrupted primer worked well and expected levels of sequence were produced. Project is monitored by conference calls every two months.