Genomic Resources for Asparagales

Enormous genomic resources have been developed for plants in the monocot order Poales; however, it is not known how useful these resources will be for other economically important monocots. Asparagales are a monophyletic order sister to class Commelinanae that carries Poales, and is the second most economically important monocot order. Development of genomic resources for and their application to Asparagales are challenging because of huge nuclear genomes and the relatively long generation times required to develop segregating families. We synthesized a normalized eDNA library of onion (Allium cepa) and produced II ,008 unique expressed sequence tags (ESTs) for comparative genomic analyses of Asparagales and Poales. Alignments of onion ESTs, Poales ESTs, and genomic sequences from rice were used to design oligonucleotide primers amplifying genomic regions from asparagus, garlic, and onion. Sequence analyses of these genomic regions revealed microsatellites, insertions/deletions, and single nucleotide polymorphisms for comparative mapping of rice and Asparagales vegetables. Initial mapping revealed no obvious synteny at the recombinationallevel between onion and rice, indicating that genomic resources developed for Poales may not be applicable to the monocots as a whole. Genomic analyses of Asparagales would greatly benefit from EST sequencing and deep-coverage, large-insert genomic libraries of representative small-genome model species within the higher and lower Asparagales, such as asparagus and orchid, respectively

Crop Registration: The Pathway to Public Access of Plant Genetic Materials to Build Crops for the Future

Starting in 1926 and continuing for 80+ yr, 11,241 crop genetic materials have been registered as of 31 Dec. 2008. The crop registration process is an important pathway to publically describe and document new and useful genetic materials and to incorporate these into the public domain via the National Plant Germplasm System (NPGS). Crop Registration materials are now searchable via the Germplasm Resources Information Network (GRIN) and demand for registered materials remains strong with more than 9150 registered accessions distributed in the past 26 yr by the NPGS. Guidelines continue to evolve to accommodate global factors effecting germplasm exchange such as Intellectual Property Rights (IPR) and international treaties (i.e., The International Treaty on Genetic Resources for Food and Agriculture). Together with (i) the advent of the new Journal of Plant Registrations; (ii) the facilitated search capabilities of GRIN; (iii) the development and definition of genetic materials needing registration (cultivars, germplasm, genetic stocks, parental lines, and mapping populations); and (iv) the recognition and allowance of IPR rights: the registration of crops is a healthy viable dynamic registration system to meet the needs of breeders over the next 80 yr

A Unique Set of 11,008 Onion Expressed Sequence Tags Reveals Expressed Sequence and Genomic Differences between the Monocot Orders Asparagales and Poales

Enormous genomic resources have been developed for plants in the monocot order Poales; however, it is not clear how representative the Poales are for the monocots as a whole. The Asparagales are a monophyletic order sister to the lineage carrying the Poales and possess economically important plants such as asparagus, garlic, and onion. To assess the genomic differences between the Asparagales and Poales, we generated 11,008 unique ESTs from a normalized cDNA library of onion. Sequence analyses of these ESTs revealed microsatellite markers, single nucleotide polymorphisms, and homologs of transposable elements. Mean nucleotide similarity between rice and the Asparagales was 78% across coding regions. Expressed sequence and genomic comparisons revealed strong differences between the Asparagales and Poales for codon usage and mean GC content, GC distribution, and relative GC content at each codon position, indicating that genomic characteristics are not uniform across the monocots. The Asparagales were more similar to eudicots than to the Poales for these genomic characteristics