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Genetics. May 2003; 164(1): 359–372.
PMCID: PMC1462567

Comparison of a Brassica oleracea genetic map with the genome of Arabidopsis thaliana.

Abstract

Brassica oleracea is closely related to the model plant, Arabidopsis thaliana. Despite this relationship, it has been difficult to both identify the most closely related segments between the genomes and determine the degree of genome replication within B. oleracea relative to A. thaliana. These difficulties have arisen in part because both species have replicated genomes, and the criteria used to identify orthologous regions between the genomes are often ambiguous. In this report, we compare the positions of sequenced Brassica loci with a known position on a B. oleracea genetic map to the positions of their putative orthologs within the A. thaliana genome. We use explicit criteria to distinguish orthologous from paralogous loci. In addition, we develop a conservative algorithm to identify collinear loci between the genomes and a permutation test to evaluate the significance of these regions. The algorithm identified 34 significant A. thaliana regions that are collinear with >28% of the B. oleracea genetic map. These regions have a mean of 3.3 markers spanning 2.1 Mbp of the A. thaliana genome and 2.5 cM of the B. oleracea genetic map. Our findings are consistent with the hypothesis that the B. oleracea genome has been highly rearranged since divergence from A. thaliana, likely as a result of polyploidization.

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Selected References

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  • Helentjaris T, Weber D, Wright S. Identification of the genomic locations of duplicate nucleotide sequences in maize by analysis of restriction fragment length polymorphisms. Genetics. 1988 Feb;118(2):353–363. [PMC free article] [PubMed]
  • Koch MA, Haubold B, Mitchell-Olds T. Comparative evolutionary analysis of chalcone synthase and alcohol dehydrogenase loci in Arabidopsis, Arabis, and related genera (Brassicaceae). Mol Biol Evol. 2000 Oct;17(10):1483–1498. [PubMed]
  • Koch M, Haubold B, Mitchell-Olds T. Molecular systematics of the Brassicaceae: evidence from coding plastidic matK and nuclear Chs sequences. Am J Bot. 2001 Mar;88(3):534–544. [PubMed]
  • Kowalski SP, Lan TH, Feldmann KA, Paterson AH. Comparative mapping of Arabidopsis thaliana and Brassica oleracea chromosomes reveals islands of conserved organization. Genetics. 1994 Oct;138(2):499–510. [PMC free article] [PubMed]
  • Lagercrantz U. Comparative mapping between Arabidopsis thaliana and Brassica nigra indicates that Brassica genomes have evolved through extensive genome replication accompanied by chromosome fusions and frequent rearrangements. Genetics. 1998 Nov;150(3):1217–1228. [PMC free article] [PubMed]
  • Acarkan A, Rossberg M, Koch M, Schmidt R. Comparative genome analysis reveals extensive conservation of genome organisation for Arabidopsis thaliana and Capsella rubella. Plant J. 2000 Jul;23(1):55–62. [PubMed]
  • Lan TH, Paterson AH. Comparative mapping of quantitative trait loci sculpting the curd of Brassica oleracea. Genetics. 2000 Aug;155(4):1927–1954. [PMC free article] [PubMed]
  • Altschul SF, Madden TL, Schäffer AA, Zhang J, Zhang Z, Miller W, Lipman DJ. Gapped BLAST and PSI-BLAST: a new generation of protein database search programs. Nucleic Acids Res. 1997 Sep 1;25(17):3389–3402. [PMC free article] [PubMed]
  • Lan TH, DelMonte TA, Reischmann KP, Hyman J, Kowalski SP, McFerson J, Kresovich S, Paterson AH. An EST-enriched comparative map of Brassica oleracea and Arabidopsis thaliana. Genome Res. 2000 Jun;10(6):776–788. [PMC free article] [PubMed]
  • Analysis of the genome sequence of the flowering plant Arabidopsis thaliana. Nature. 2000 Dec 14;408(6814):796–815. [PubMed]
  • Bennetzen JL. Comparative sequence analysis of plant nuclear genomes:m microcolinearity and its many exceptions. Plant Cell. 2000 Jul;12(7):1021–1029. [PMC free article] [PubMed]
  • Liu B, Vega JM, Feldman M. Rapid genomic changes in newly synthesized amphiploids of Triticum and Aegilops. II. Changes in low-copy coding DNA sequences. Genome. 1998 Aug;41(4):535–542. [PubMed]
  • Bohuon EJ, Ramsay LD, Craft JA, Arthur AE, Marshall DF, Lydiate DJ, Kearsey MJ. The association of flowering time quantitative trait loci with duplicated regions and candidate loci in Brassica oleracea. Genetics. 1998 Sep;150(1):393–401. [PMC free article] [PubMed]
  • Lynch M, Conery JS. The evolutionary fate and consequences of duplicate genes. Science. 2000 Nov 10;290(5494):1151–1155. [PubMed]
  • Nadeau JH, Taylor BA. Lengths of chromosomal segments conserved since divergence of man and mouse. Proc Natl Acad Sci U S A. 1984 Feb;81(3):814–818. [PMC free article] [PubMed]
  • Camargo LE, Savides L, Jung G, Nienhuis J, Osborn TC. Location of the self-incompatibility locus in an RFLP and RAPD map of Brassica oleracea. J Hered. 1997 Jan-Feb;88(1):57–60. [PubMed]
  • Cavell AC, Lydiate DJ, Parkin IA, Dean C, Trick M. Collinearity between a 30-centimorgan segment of Arabidopsis thaliana chromosome 4 and duplicated regions within the Brassica napus genome. Genome. 1998 Feb;41(1):62–69. [PubMed]
  • O'Neill CM, Bancroft I. 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. Plant J. 2000 Jul;23(2):233–243. [PubMed]
  • Copenhaver GP, Browne WE, Preuss D. Assaying genome-wide recombination and centromere functions with Arabidopsis tetrads. Proc Natl Acad Sci U S A. 1998 Jan 6;95(1):247–252. [PMC free article] [PubMed]
  • Parkin IAP, Lydiate DJ, Trick M. Assessing the level of collinearity between Arabidopsis thaliana and Brassica napus for A. thaliana chromosome 5. Genome. 2002 Apr;45(2):356–366. [PubMed]
  • Quiros CF, Grellet F, Sadowski J, Suzuki T, Li G, Wroblewski T. Arabidopsis and Brassica comparative genomics: sequence, structure and gene content in the ABI-Rps2-Ck1 chromosomal segment and related regions. Genetics. 2001 Mar;157(3):1321–1330. [PMC free article] [PubMed]
  • Gaut BS. Patterns of chromosomal duplication in maize and their implications for comparative maps of the grasses. Genome Res. 2001 Jan;11(1):55–66. [PMC free article] [PubMed]
  • Rossberg M, Theres K, Acarkan A, Herrero R, Schmitt T, Schumacher K, Schmitz G, Schmidt R. Comparative sequence analysis reveals extensive microcolinearity in the lateral suppressor regions of the tomato, Arabidopsis, and Capsella genomes. Plant Cell. 2001 Apr;13(4):979–988. [PMC free article] [PubMed]
  • Ryder CD, Smith LB, Teakle GR, King GJ. Contrasting genome organisation: two regions of the Brassica oleracea genome compared with collinear regions of the Arabidopsis thaliana genome. Genome. 2001 Oct;44(5):808–817. [PubMed]
  • Schranz M Eric, Quijada Pablo, Sung Si-Bum, Lukens Lewis, Amasino Richard, Osborn Thomas C. Characterization and effects of the replicated flowering time gene FLC in Brassica rapa. Genetics. 2002 Nov;162(3):1457–1468. [PMC free article] [PubMed]
  • Shaked H, Kashkush K, Ozkan H, Feldman M, Levy AA. Sequence elimination and cytosine methylation are rapid and reproducible responses of the genome to wide hybridization and allopolyploidy in wheat. Plant Cell. 2001 Aug;13(8):1749–1759. [PMC free article] [PubMed]
  • Wolfe KH, Shields DC. Molecular evidence for an ancient duplication of the entire yeast genome. Nature. 1997 Jun 12;387(6634):708–713. [PubMed]
  • Yuan YP, Eulenstein O, Vingron M, Bork P. Towards detection of orthologues in sequence databases. Bioinformatics. 1998;14(3):285–289. [PubMed]
  • Song K, Lu P, Tang K, Osborn TC. Rapid genome change in synthetic polyploids of Brassica and its implications for polyploid evolution. Proc Natl Acad Sci U S A. 1995 Aug 15;92(17):7719–7723. [PMC free article] [PubMed]

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