The Potential Impact of Genomes for Allium Crop Improvement

Onion (Allium cepa L.) is the most economically important monocot outside of the grasses and is a member of the family Alliaceae in the order Asparagales. The Asparagales are a monophyletic order sister to the Commelinanae, which carries the grasses, palms, and bananas. These two important groups of monocots separated at least 130 million years ago and show little synteny at the recombinational and sequence levels. Onion differs from the grasses for other important genomic characteristics, including an enormous diploid genome, lower GC content of coding regions, and unique telomeric sequences. Expressed sequence tags (ESTs) have proven useful for the development of molecular markers and identification of candidate genes in the Alliums. Sequencing from a variety of cDNA libraries will yield a larger sample of expressed regions in the Allium genomes. Pilot sequencing of onion BACs revealed low gene densities with long tracts of degenerated transposable elements. Reduced representation sequencing of onion genomic DNA will provide sequences that can be compared with ESTs to monitor coverage of expressed regions. Molecular markers can be developed from these genomic and expressed sequences for comparative mapping among the Alliums, as well as marker-facilitated selection.