Genetics, Vol. 168, 1575-1584, November 2004, Copyright © 2004
doi:10.1534/genetics.103.022343

Comparing the Linkage Maps of the Close Relatives Arabidopsis lyrata and A. thaliana

Helmi Kuittinen^*,1, Anita A. de Haan^*,2, Claus Vogl, Sami Oikarinen^*,3, Johanna Leppälä^*, Marcus Koch^,4, Tom Mitchell-Olds, Charles H. Langley and Outi Savolainen^*

^* Department of Biology, University of Oulu, 90401 Oulu, Finland
Institute of Animal Husbandry and Genetics, Veterinary Medicine, University of Wien, A-1210 Wien, Austria
Department of Genetics and Evolution, Max-Planck Institute of Chemical Ecology, 07745 Jena, Germany
Center for Population Biology, University of California, Davis, California 95616

¹ Corresponding author: Department of Biology, P.O. Box 3000, University of Oulu, 90401 Oulu, Finland.
E-mail: helmi.kuittinen{at}oulu.fi

We have constructed a genetic map of Arabidopsis lyrata, a self-incompatible relative of the plant model species A. thaliana. A. lyrata is a diploid (n = 8) species that diverged from A. thaliana (n = 5) 5 MYA. Mapping was conducted in a full-sib progeny of two unrelated F₁ hybrids between two European populations of A. lyrata ssp. petraea. We used the least-squares method of the Joinmap program for map construction. The gross chromosomal differences between the two species were most parsimoniously explained with three fusions, two reciprocal translocations, and one inversion. The total map length was 515 cM, and the distances were 12% larger than those between corresponding markers in the linkage map of A. thaliana. The 72 markers, consisting of microsatellites and gene-based markers, were spaced on average every 8 cM. Transmission ratio distortion was extensive, and most distortions were specific to each reciprocal cross, suggesting cytoplasmic interactions. We estimate locations and most probable genotype frequencies of transmission ratio distorting loci (TRDL) with a Bayesian method and discuss the possible reasons for the observed distortions.

This article has been cited by other articles:

				P. A. Ziolkowski, G. Koczyk, L. Galganski, and J. Sadowski Genome sequence comparison of Col and Ler lines reveals the dynamic nature of Arabidopsis chromosomes Nucleic Acids Res., June 1, 2009; 37(10): 3189 - 3201. [Abstract] [Full Text] [PDF]

				B.-H. Song, A. J. Windsor, K. J. Schmid, S. Ramos-Onsins, M. E. Schranz, A. J. Heidel, and T. Mitchell-Olds Multilocus Patterns of Nucleotide Diversity, Population Structure and Linkage Disequilibrium in Boechera stricta, a Wild Relative of Arabidopsis Genetics, March 1, 2009; 181(3): 1021 - 1033. [Abstract] [Full Text] [PDF]

				D. E. Soltis, V. A. Albert, J. Leebens-Mack, C. D. Bell, A. H. Paterson, C. Zheng, D. Sankoff, C. W. dePamphilis, P. K. Wall, and P. S. Soltis Polyploidy and angiosperm diversification Am. J. Botany, January 1, 2009; 96(1): 336 - 348. [Abstract] [Full Text] [PDF]

				H. Tang, X. Wang, J. E. Bowers, R. Ming, M. Alam, and A. H. Paterson Unraveling ancient hexaploidy through multiply-aligned angiosperm gene maps Genome Res., December 1, 2008; 18(12): 1944 - 1954. [Abstract] [Full Text] [PDF]

				T. Mandakova and M. A. Lysak Chromosomal Phylogeny and Karyotype Evolution in x=7 Crucifer Species (Brassicaceae) PLANT CELL, October 1, 2008; 20(10): 2559 - 2570. [Abstract] [Full Text] [PDF]

				A. Kawabe, A. Forrest, S. I. Wright, and D. Charlesworth High DNA Sequence Diversity in Pericentromeric Genes of the Plant Arabidopsis lyrata Genetics, June 1, 2008; 179(2): 985 - 995. [Abstract] [Full Text] [PDF]

				K. M. Hazzouri, A. Mohajer, S. I. Dejak, S. P. Otto, and S. I. Wright Contrasting Patterns of Transposable-Element Insertion Polymorphism and Nucleotide Diversity in Autotetraploid and Allotetraploid Arabidopsis Species Genetics, May 1, 2008; 179(1): 581 - 592. [Abstract] [Full Text] [PDF]

				H. Kuittinen, A. Niittyvuopio, P. Rinne, and O. Savolainen Natural Variation in Arabidopsis lyrata Vernalization Requirement Conferred by a FRIGIDA Indel Polymorphism Mol. Biol. Evol., February 1, 2008; 25(2): 319 - 329. [Abstract] [Full Text] [PDF]

				M. A. Lysak, K. Cheung, M. Kitschke, and P. Bures Ancestral Chromosomal Blocks Are Triplicated in Brassiceae Species with Varying Chromosome Number and Genome Size Plant Physiology, October 1, 2007; 145(2): 402 - 410. [Abstract] [Full Text] [PDF]

				E. Kamau, B. Charlesworth, and D. Charlesworth Linkage Disequilibrium and Recombination Rate Estimates in the Self-Incompatibility Region of Arabidopsis lyrata Genetics, August 1, 2007; 176(4): 2357 - 2369. [Abstract] [Full Text] [PDF]

				S. F. McDaniel, J. H. Willis, and A. J. Shaw A Linkage Map Reveals a Complex Basis for Segregation Distortion in an Interpopulation Cross in the Moss Ceratodon purpureus Genetics, August 1, 2007; 176(4): 2489 - 2500. [Abstract] [Full Text] [PDF]

				M. Courbot, G. Willems, P. Motte, S. Arvidsson, N. Roosens, P. Saumitou-Laprade, and N. Verbruggen A Major Quantitative Trait Locus for Cadmium Tolerance in Arabidopsis halleri Colocalizes with HMA4, a Gene Encoding a Heavy Metal ATPase Plant Physiology, June 1, 2007; 144(2): 1052 - 1065. [Abstract] [Full Text] [PDF]

				G. Willems, D. B. Drager, M. Courbot, C. Gode, N. Verbruggen, and P. Saumitou-Laprade The Genetic Basis of Zinc Tolerance in the Metallophyte Arabidopsis halleri ssp. halleri (Brassicaceae): An Analysis of Quantitative Trait Loci Genetics, May 1, 2007; 176(1): 659 - 674. [Abstract] [Full Text] [PDF]

				M. E. Schranz, A. J. Windsor, B.-h. Song, A. Lawton-Rauh, and T. Mitchell-Olds Comparative Genetic Mapping in Boechera stricta, a Close Relative of Arabidopsis Plant Physiology, May 1, 2007; 144(1): 286 - 298. [Abstract] [Full Text] [PDF]

				M. A. Koch and M. Matschinger Evolution and genetic differentiation among relatives of Arabidopsis thaliana PNAS, April 10, 2007; 104(15): 6272 - 6277. [Abstract] [Full Text] [PDF]

				J. B. Nasrallah, P. Liu, S. Sherman-Broyles, R. Schmidt, and M. E. Nasrallah Epigenetic Mechanisms for Breakdown of Self-Incompatibility in Interspecific Hybrids Genetics, April 1, 2007; 175(4): 1965 - 1973. [Abstract] [Full Text] [PDF]

				S. M. Rogers, N. Isabel, and L. Bernatchez Linkage Maps of the dwarf and Normal Lake Whitefish (Coregonus clupeaformis) Species Complex and Their Hybrids Reveal the Genetic Architecture of Population Divergence Genetics, January 1, 2007; 175(1): 375 - 398. [Abstract] [Full Text] [PDF]

				A. Kawabe, S. Nasuda, and D. Charlesworth Duplication of Centromeric Histone H3 (HTR12) Gene in Arabidopsis halleri and A. lyrata, Plant Species With Multiple Centromeric Satellite Sequences Genetics, December 1, 2006; 174(4): 2021 - 2032. [Abstract] [Full Text] [PDF]

				S. I. Wright, J. P. Foxe, L. DeRose-Wilson, A. Kawabe, M. Looseley, B. S. Gaut, and D. Charlesworth Testing for Effects of Recombination Rate on Nucleotide Diversity in Natural Populations of Arabidopsis lyrata Genetics, November 1, 2006; 174(3): 1421 - 1430. [Abstract] [Full Text] [PDF]

				L. Timms, R. Jimenez, M. Chase, D. Lavelle, L. McHale, A. Kozik, Z. Lai, A. Heesacker, S. Knapp, L. Rieseberg, et al. Analyses of Synteny Between Arabidopsis thaliana and Species in the Asteraceae Reveal a Complex Network of Small Syntenic Segments and Major Chromosomal Rearrangements Genetics, August 1, 2006; 173(4): 2227 - 2235. [Abstract] [Full Text] [PDF]

				E. G. Bakker, C. Toomajian, M. Kreitman, and J. Bergelson A Genome-Wide Survey of R Gene Polymorphisms in Arabidopsis PLANT CELL, August 1, 2006; 18(8): 1803 - 1818. [Abstract] [Full Text] [PDF]

				A. Kawabe, B. Hansson, J. Hagenblad, A. Forrest, and D. Charlesworth Centromere Locations and Associated Chromosome Rearrangements in Arabidopsis lyrata and A. thaliana Genetics, July 1, 2006; 173(3): 1613 - 1619. [Abstract] [Full Text] [PDF]

				A. J. Heidel, M. J. Clauss, J. Kroymann, O. Savolainen, and T. Mitchell-Olds Natural Variation in MAM Within and Between Populations of Arabidopsis lyrata Determines Glucosinolate Phenotype Genetics, July 1, 2006; 173(3): 1629 - 1636. [Abstract] [Full Text] [PDF]

				M. Benderoth, S. Textor, A. J. Windsor, T. Mitchell-Olds, J. Gershenzon, and J. Kroymann Positive selection driving diversification in plant secondary metabolism PNAS, June 13, 2006; 103(24): 9118 - 9123. [Abstract] [Full Text] [PDF]

				J. Hagenblad, J. Bechsgaard, and D. Charlesworth Linkage Disequilibrium Between Incompatibility Locus Region Genes in the Plant Arabidopsis lyrata Genetics, June 1, 2006; 173(2): 1057 - 1073. [Abstract] [Full Text] [PDF]

				A. J. Windsor, M. E. Schranz, N. Formanova, S. Gebauer-Jung, J. G. Bishop, D. Schnabelrauch, J. Kroymann, and T. Mitchell-Olds Partial Shotgun Sequencing of the Boechera stricta Genome Reveals Extensive Microsynteny and Promoter Conservation with Arabidopsis. Plant Physiology, April 1, 2006; 140(4): 1169 - 1182. [Abstract] [Full Text] [PDF]

				M. A. Lysak, A. Berr, A. Pecinka, R. Schmidt, K. McBreen, and I. Schubert Mechanisms of chromosome number reduction in Arabidopsis thaliana and related Brassicaceae species PNAS, March 28, 2006; 103(13): 5224 - 5229. [Abstract] [Full Text] [PDF]

				A. E. Hall, G. C. Kettler, and D. Preuss Dynamic evolution at pericentromeres Genome Res., March 1, 2006; 16(3): 355 - 364. [Abstract] [Full Text] [PDF]

				A. Bouck, R. Peeler, M. L. Arnold, and S. R. Wessler Genetic Mapping of Species Boundaries in Louisiana Irises Using IRRE Retrotransposon Display Markers Genetics, November 1, 2005; 171(3): 1289 - 1303. [Abstract] [Full Text] [PDF]

				I. A. P. Parkin, S. M. Gulden, A. G. Sharpe, L. Lukens, M. Trick, T. C. Osborn, and D. J. Lydiate Segmental Structure of the Brassica napus Genome Based on Comparative Analysis With Arabidopsis thaliana Genetics, October 1, 2005; 171(2): 765 - 781. [Abstract] [Full Text] [PDF]

				N. L. Prigoda, A. Nassuth, and B. K. Mable Phenotypic and Genotypic Expression of Self-incompatibility Haplotypes in Arabidopsis lyrata Suggests Unique Origin of Alleles in Different Dominance Classes Mol. Biol. Evol., July 1, 2005; 22(7): 1609 - 1620. [Abstract] [Full Text] [PDF]

				M. A. Koch and M. Kiefer Genome evolution among cruciferous plants: a lecture from the comparison of the genetic maps of three diploid species--Capsella rubella, Arabidopsis lyrata subsp. petraea, and A. thaliana Am. J. Botany, April 1, 2005; 92(4): 761 - 767. [Abstract] [Full Text] [PDF]

				K. Yogeeswaran, A. Frary, T. L. York, A. Amenta, A. H. Lesser, J. B. Nasrallah, S. D. Tanksley, and M. E. Nasrallah Comparative genome analyses of Arabidopsis spp.: Inferring chromosomal rearrangement events in the evolutionary history of A. thaliana Genome Res., April 1, 2005; 15(4): 505 - 515. [Abstract] [Full Text] [PDF]

				M. A. Lysak, M. A. Koch, A. Pecinka, and I. Schubert Chromosome triplication found across the tribe Brassiceae Genome Res., April 1, 2005; 15(4): 516 - 525. [Abstract] [Full Text] [PDF]

International Access Link

Online ISSN: 1943-2361  Print ISSN: 0016-6731
Copyright 2009 by the Genetics Society of America
phone: 412-268-1812   fax: 412-268-1813   email: genetics-gsa{at}andrew.cmu.edu