An EST-enriched Comparative Map of Brassica oleracea and Arabidopsis thaliana

Abstract

A detailed comparative map of Brassica oleracea and Arabidopsis thaliana has been established based largely on mapping of Arabidopsis ESTs in two Arabidopsis and four Brassica populations. Based on conservative criteria for inferring synteny, "one to one correspondence" between Brassica and Arabidopsis chromosomes accounted for 57% of comparative loci. Based on 186 corresponding loci detected in B. oleracea and A. thaliana, at least 19 chromosome structural rearrangements differentiate B. oleracea and A. thaliana orthologs. Chromosomal duplication in the B. oleracea genome was strongly suggested by parallel arrangements of duplicated loci on different chromosomes, which accounted for 41% of loci mapped in Brassica. Based on 367 loci mapped, at least 22 chromosomal rearrangements differentiate B. oleracea homologs from one another. Triplication of some Brassica chromatin and duplication of some Arabidopsis chromatin were suggested by data that could not be accounted for by the one-to-one and duplication models, respectively. Twenty-seven probes detected three or more loci in Brassica, which represent 25.3% of the 367 loci mapped in Brassica. Thirty-one probes detected two or more loci in Arabidopsis, which represent 23.7% of the 262 loci mapped in Arabidopsis. Application of an EST-based, cross-species genomic framework to isolation of alleles conferring phenotypes unique to Brassica, as well as the challenges and opportunities in extrapolating genetic information from Arabidopsis to Brassica and to more distantly related crops, are discussed.Arabidopsis thaliana, a weed-like member of the Cruciferae family (tribe Sisymbrieae), offers many advantages for basic and applied plant research. These features include small stature, short life cycle, small genome size (2n=10, estimated physical genome size of 100-120 Mb), low frequency of repetitive sequences (∼10% of the nuclear genome; Leutwiler et al. 1984), and prolific seed production. These features, combined with research of the past several decades yielding many mutants, efficient transformation systems, detailed genetic and physical maps, the availability of several P1, YAC, and BAC libraries, and 36,569 public ESTs (http:// www.cbc.umn.edu/ResearchProjects/Arabidopsis), make A. thaliana an ideal model for further molecular and genetic study (Meyerowitz and Somerville 1994). A multinational genome research initiative aiming to completely sequence the Arabidopsis genome by year 2004 (The Multinational Science Steering Committee 1997) is ahead of schedule. Such an accomplishment will undoubtedly create new scientific challenges and opportunities. One of the core issues will be how to apply the information obtained from the Arabidopsis genome project to the improvement of the world's leading crops.The genus Brassica (tribe Brassiceae), including many important crops, is in the same taxonomic family as Arabidopsis thaliana. Such a close relationship suggests that crop plants of the genus Brassica will be among the earliest beneficiaries of a complete sequence of Ara...

Complexities of Chromosome Landing in a Highly Duplicated Genome: Toward Map-Based Cloning of a Gene Controlling Blackleg Resistance in Brassica napus

“…Such duplications within the diploid Brassica genomes have been described in previous mapping studies and suggest recent evolution of the diploid genomes from a common polyploid ancestor (Lagercrantz 1998;Lan et al 2000;O'Neill and Bancroft 2000;Parkin et al 2002). The majority of markers, linked to the blackleg resistance locus, were localized on two Southern analysis of flanking markers BNID7804T7 and est148G3 in segregating populations derived from Shiralee and Cresor (DH12075).…”

Development of an integrated approach for evaluation of 2‐D gel image analysis: Impact of multiple proteins in single spots on comparative proteomics in conventional 2‐D gel/MALDI workflow

“…Although the genome of cauliflower has not been fully sequenced, there are significant amounts of Brassica sequence information. In addition, cauliflower and Arabidopsis typically share over 85% nucleotide sequence identity in coding regions [35][36][37]. Therefore, it is not surprising that using the green plant database (including Arabidopsis) as was done for this study, we did not find even small numbers of good mass spectra that failed to result in an identification.…”

Genome-wide comparative analysis of the transposable elements in the related species Arabidopsis thaliana and Brassica oleracea

“…In support of this view is the finding that a high percentage (Ϸ48%) of T-DNA insertions in A. thaliana are knockouts (41). On the other hand, the B. oleracea genome was recently reported to be the product of a triplication event after its divergence from A. thaliana (25)(26)(27). Such an event would have produced numerous safe havens for TE insertions because of functional redundancy.…”

“…Although A. thaliana and B. oleracea diverged from a common ancestor Ϸ15-20 million years ago (1), the B. oleracea genome at Ϸ600 Mb is almost 5-fold larger (24). Recent studies indicate that the B. oleracea genome has expanded through triplication since its divergence from Arabidopsis (25)(26)(27). However, genome triplication cannot fully explain the genome size difference between the two species.…”