Comparative physical mapping of segments of the genome of Brassica oleracea var. alboglabra that are homoeologous to sequenced regions of chromosomes 4 and 5 of Arabidopsis thaliana

Abstract

SummaryDue to their relatedness to Arabidopsis thaliana (Arabidopsis), the cultivated Brassica species represent the ®rst group of crops with which to evaluate comparative genomics approaches to understanding biological processes and manipulating traits. We have constructed a high-quality binary BAC library (JBo) from genomic DNA of Brassica oleracea var. alboglabra, in order to underpin such investigations. Using the Arabidopsis genome sequence and clones from the JBo library, we have analysed aspects of gene conservation and microsynteny between a 222 kb region of the genome of Arabidopsis and homoeologous segments of the genome of B. oleracea. All 19 predicted genes tested were found to hybridize to clones in the JBo library, indicating a high level of gene conservation. Further analyses and physical mapping with the BAC clones identi®ed allowed us to construct clone contig maps and analyse in detail the gene content and organization in the set of paralogous segments identi®ed in the genome of B. oleracea. Extensive divergence of gene content was observed, both between the B. oleracea paralogous segments and between them and their homoeologous segment within the genome of Arabidopsis. However, the genes present show highly conserved collinearity with their orthologues in the genome of Arabidopsis. We have identi®ed one example of a Brassica gene in a non-collinear position and one rearrangement. Some of the genes not present in the discernible homoeologous regions appear to be located elsewhere in the B. oleracea genome. The implications of our ®ndings for comparative map-based cloning of genes from crop species are discussed.

Comparative Sequence Analysis Reveals Extensive Microcolinearity in the Lateral Suppressor Regions of the Tomato, Arabidopsis, and Capsella Genomes

“…Similarly, comparative studies of soybean and Arabidopsis (Grant et al, 2000) as well as tomato and Arabidopsis (Ku et al, 2000) have confirmed the presence of large duplicated segments in the Arabidopsis genome. Comparative analysis of duplicated segments in the Arabidopsis and Brassica genomes has revealed that they show differences in gene repertoire; however, the order of the genes that are in common in both regions was found to be very similar or identical (The Arabidopsis Genome Initiative, 2000; Blanc et al, 2000;O'Neill and Bancroft, 2000). The same pattern was observed in the duplicated region of the Arabidopsis genome studied here (Figure 2).…”

“…These data indicate that the duplication event of the region harboring gene C most likely took place before the progenitors of Arabidopsis and Capsella diverged. Comparative physical mapping studies using Arabidopsis and Brassica oleracea also revealed that another duplication event in the Arabidopsis genome predates the divergence of the progenitors of those two species (O'Neill and Bancroft, 2000). Similarly, comparative studies of soybean and Arabidopsis (Grant et al, 2000) as well as tomato and Arabidopsis (Ku et al, 2000) have confirmed the presence of large duplicated segments in the Arabidopsis genome.…”

“…The same pattern was observed in the duplicated region of the Arabidopsis genome studied here (Figure 2). The results of a comparison of the gene arrangement in triplicated Brassica segments among each other and with the corresponding regions in Arabidopsis suggested that differences in gene repertoire are caused by deletions of genes (The Arabidopsis Genome Initiative, 2000;O'Neill and Bancroft, 2000). The same conclusion was reached when it was established that a region of tomato chromosome 2 showed conservation of gene repertoire and order with four different segments of the Arabidopsis genome (Ku et al, 2000).…”

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).…”

Simple Sequence Repeat-Based Comparative Genomics Between Brassica rapa and Arabidopsis thaliana: The Genetic Origin of Clubroot Resistance

“…Since the DNA sequences of homologous genes in the related taxa are quite similar, clones have been extensively used as RFLP markers to elucidate the genomic colinearity between species . The degree of genomic conservation has been elucidated by comparative linkage mapping, and conserved genomic segments have been identified by micro-and macrosynteny studies in various Brassica species (Cavell et al 1998;Lagercrantz 1998;O'Neill and Bancroft 2000;Ryder et al 2001). However, because of the high rate of genomic segment replication, RFLP has been shown at times to detect more than one locus in Brassica genomes (Lagercrantz and Lydiate 1996).…”