Genetic and physical mapping inBrassica diploid species of a gene cluster defined inArabidopsis thaliana

Abstract

We report the genetic and physical analysis by pulse field gel electrophoresis (PFGE) in three Brassica diploid genomes for a cluster of five genes characterized in a selected segment of 15 kb on chromosome 3 of Arabidopsis thaliana, encoding a Bradyrhizobium CycJ homologue (At1), a rat p67 translation factor homologue (At2), an Em-like (early methionine) protein (At3), chlorophyll synthase (At4) and a yeast Sac1 homologue (A5). The Arabidopsis gene array was found to be conserved on a single linkage group in each of the Brassica genomes. However, partial complexes were found to be duplicated in other chromosome segments on the same or other linkage groups. Some of the At genes, which could not be genetically mapped because of lack of polymorphism, were assigned to their respective linkage groups by physical mapping. The presence of multiple copies of the A. thaliana gene cluster in the three Brassica genomes further establishes their complex nature, which results from extensive duplication and chromosomal rearrangement. In general, genetic distances between the At genes agreed with values expected for the physical distances determined in Brassica.

Comparative Mapping of the Brassica S Locus Region and Its Homeolog in Arabidopsis: Implications for the Evolution of Mating Systems in the Brassicaceae

“…However, a significant proportion (11 of 16 or 68%) of markers that were single-copy in Arabidopsis were also single-copy in Brassica. This result differs from previous Brassica and Arabidopsis comparative mapping studies in which single-copy Arabidopsis markers were found to be duplicated in the Brassica genome (Lagercrantz et al, 1996;Sadowski et al, 1996). …”

“…All three markers also hybridized consistently with a 780-kb SfiI fragment that is, in all likelihood, a partially digested fragment (incomplete digestion is often observed upon treatment of Brassica DNA with SfiI; Sadowski et al, 1996). Marker y14 hybridized with the same 510-and 780-kb SfiI fragments as did the HV8 probe and with the same 97-kb BssHII and 115-kb SmaI fragments as did sp400.…”

“…This comparative approach was spurred by the fact that extensive homeologies and microcolinearity (microsynteny) of markers are often found between the genomes of related species in animal systems (Dietrich et al, 1995) as well as in plants (Tanksley et al, 1992;Ahn et al, 1993;Dunford et al, 1995;Kilian et al, 1995;Chen et al, 1997) and by recent successes in the use of comparative mapping to facilitate the isolation and analysis of loci of interest (e.g., see Darling and Abbott, 1992). In the case of Arabidopsis and Brassica spp, it has been shown that the two genomes do contain islands of conserved organization, despite the fact that the Brassica genome is highly duplicated and rearranged relative to Arabidopsis (Kowalski et al, 1994;Lagercrantz et al, 1996;Sadowski et al, 1996). The results of our comparative study revealed a high degree of microsynteny between the Brassica S locus region and its homeolog in Arabidopsis, with the notable exception that sequences related to the Brassica SI genes were missing from this interval of the Arabidopsis genome.…”

Positional Cloning in Brassica napus: Strategies for Circumventing Genome Complexity in a Polyploid Plant

“…Initial efforts at determining the relationships between the Brassica and Arabidopsis genomes involved using molecular probes for co-linear sets derived from the developing Arabidopsis genomic resources to map RFLP polymorphisms in Brassica species (Kowalski et al, 1994). These studies indicated that there is extensive co-linearity between the Brassica and Arabidopsis genomes, but that most single copy Arabidopsis regions exist as multiple, on average 3 copies in modern Brassica genomes (Lagercrantz et al, 1995;Sadowski et al, 1996;Cavell et al, 1998). This in turn, gave rise to the hypothesis that the modern diploid Brassica species are derived from a hexaploid ancestor whose genome was generated from a diploid, Arabidopsis-like genome through polyploidization events.…”

Whole genome shotgun sequencing ofBrassica oleraceaand its application to gene discovery and annotation inArabidopsis

“…oleracea and A. thaliana diverged 15-20 million years ago (Yang et al 1999). Earlier comparative mapping studies of Brassica and Arabidopsis using molecular markers revealed extensive synteny between these two species, suggesting that knowledge gained in one species can be productively applied to the other (Lan et al 2000;Babula et al 2003) although deviation from colinearity was also noted (Kowalski et al 1994;Sadowski et al 1996;Ryder et al 2001). Nucleotide sequence conservation between these two species has been reported to be in the range of 75%-90% in exons, whereas in introns and intergenic regions, it is Յ70% .…”