ARS | Publication request: APPLIED GENOMICS IN THE PLANT MONOCOT ORDER ASPARAGALES

Submitted to: Meeting Abstract
Publication Type: Abstract Only
Publication Acceptance Date: October 15, 2004
Publication Date: November 30, 2004
Citation: Martin, W., Havey, M.J., Jakse, J., Mccallum, J. 2004. Applied genomics in the plant monocot order asparagales. Meeting Abstract.

Technical Abstract: Onion (Allium cepa) is a member of the monocot order Asparagales, a monophyletic group sister to the class Commelinanae (carries the grasses). Genomic resources and syntenic relationships are well established for the grasses. However, the extent of synteny between onion, as a representative of the Asparagales, and the grasses is unknown. Single pass sequencing reactions from a normalized cDNA library of onion produced 11,008 unique ESTs. Onion ESTs were selected that showed high similarities to non-duplicated, expressed regions of the rice genome. Primers were designed after alignment of the onion EST and rice EST and genomic sequences and single onion amplicons were sequenced to confirm similarities with the original sequences. These amplicons were subsequently screened for SNPs, indels, and microsatellites. A comparative linkage map of expressed sequences in onion and rice revealed no obvious synteny on the recombinational level. This lack of synteny between onion and rice supports the development of genomic resources for major monocot plants outside of the grasses. Our goal is to use genomic approaches to enhance the health functionality of onion. Onion bulbs accumulate fructans, a soluble dietary fiber associated with lower rates of colorectal cancers. Higher fructan concentrations in bulbs show significant correlations with higher pungency, longer dormancy, and greater antiplatelet activity. Genetic mapping revealed one major region on onion chromosome 5 significantly affecting the accumulation of fructans. Because of onion's enormous nuclear genome, the development of a genomic model for the Alliums and the identification and mapping of candidate genes will be important tools for the cloning of loci controlling health-enhancing, flavor, and production characteristics of onion.