Submitted to: In Vitro Biology
Publication Type: Abstract only
Publication Acceptance Date: 4/12/2006
Publication Date: 6/3/2006
Citation: Havey, M.J. 2006. Allium genomics: Exploiting model plants for analyses of enormous nuclear genomes [Abstract]. In Vitro Biology. Available: http://www.sivb.org/2005A_p1.pdf. Interpretive Summary:
Technical Abstract: Enormous genomic resources have been developed for the grasses, culminating with the complete genomic sequence of rice and reduced-representation sequencing of maize. These extensive resources may be applicable to other major groups of monocots outside of the grasses. The order Asparagales (carries the Alliums and asparagus) and the commelinids (carries the grasses) are sister monophyletic groups within the monocots. The Alliaceae (onion, garlic, leek, chive, bunching onion, among others) is the second most economically important family in the monocots, following only the Poaceae. The huge nuclear genomes of the Alliaceae are major constraints to the development of genomic resources. We sequenced asparagus and onion BACs and revealed high densities of retroelements and transposons with few open-reading frames. We also observed little synteny on the recombinational and sequence levels among asparagus, onion, and rice, as might be expected given that the Asparagales and commelinids split at least 130 million years ago. Nevertheless, genomic resources developed for the grasses are useful for translational genomics of the Alliums. Occasionally physically linked sequences in rice show genetic linkage in onion and this microsynteny across shorter genomic regions aids in the identification and mapping of candidate genes. Single-copy expressed regions in the rice genome show significant similarities and share most introns with coding regions in onion, allowing the development of PCR-based markers carrying indels or single nucleotide polymorphisms to evaluate for associations between candidate genes and economically important traits.