Translational Genomics of Onion for Prioritized Pest Resistances (J. Craig Venter Institute, INC.)
Vegetable Crops Research Unit
2011 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.
Normalized complementary deoxyribonucleic acid (cDNA) libraries were synthesized from equal amounts of Ribonucleic acids (RNA) from leaves, roots, immature bulbs, and unopened umbles from two onion populations: doubled haploid 5225B and inbred OH-1. These two cDNA libraries were prepared for sequencing using the 454 platform and 1.25 plates of sequence was generated from each library. There were 1,779,892 reads yielding 554,061,316 bases of sequence for 5225B and 1,820,460 reads yielding 604,685,381 bases for OH-1. In total, 3.6 million reads yielded 1,158 megabasepairs of onion sequence. These cDNA sequences assembled into 48,459 sequences of an average length of 1315.5 bases. Single nucleotide polymorphisms are being identified in these cDNA sequences for genetic mapping. Progress on this research is monitored by quarterly conference calls.