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. 1999 Sep;153(1):453–473. doi: 10.1093/genetics/153.1.453

Inferences on the genome structure of progenitor maize through comparative analysis of rice, maize and the domesticated panicoids.

W A Wilson 1, S E Harrington 1, W L Woodman 1, M Lee 1, M E Sorrells 1, S R McCouch 1
PMCID: PMC1460744  PMID: 10471726

Abstract

Corn and rice genetic linkage map alignments were extended and refined by the addition of 262 new, reciprocally mapped maize cDNA loci. Twenty chromosomal rearrangements were identified in maize relative to rice and these included telomeric fusions between rice linkage groups, nested insertion of rice linkage groups, intrachromosomal inversions, and a nonreciprocal translocation. Maize genome evolution was inferred relative to other species within the Panicoideae and a progenitor maize genome with eight linkage groups was proposed. Conservation of composite linkage groups indicates that the tetrasomic state arose during maize evolution either from duplication of one progenitor corn genome (autoploidy) or from a cross between species that shared the composite linkages observed in modern maize (alloploidy). New evidence of a quadruplicated homeologous segment on maize chromosomes 2 and 10, and 3 and 4, corresponded to the internally duplicated region on rice chromosomes 11 and 12 and suggested that this duplication in the rice genome predated the divergence of the Panicoideae and Oryzoideae subfamilies. Charting of the macroevolutionary steps leading to the modern maize genome clarifies the interpretation of intercladal comparative maps and facilitates alignments and genomic cross-referencing of genes and phenotypes among grass family members.

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Selected References

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  1. Ahn S., Anderson J. A., Sorrells M. E., Tanksley S. D. Homoeologous relationships of rice, wheat and maize chromosomes. Mol Gen Genet. 1993 Dec;241(5-6):483–490. doi: 10.1007/BF00279889. [DOI] [PubMed] [Google Scholar]
  2. Ahn S., Tanksley S. D. Comparative linkage maps of the rice and maize genomes. Proc Natl Acad Sci U S A. 1993 Sep 1;90(17):7980–7984. doi: 10.1073/pnas.90.17.7980. [DOI] [PMC free article] [PubMed] [Google Scholar]
  3. Burr B., Burr F. A., Thompson K. H., Albertson M. C., Stuber C. W. Gene mapping with recombinant inbreds in maize. Genetics. 1988 Mar;118(3):519–526. doi: 10.1093/genetics/118.3.519. [DOI] [PMC free article] [PubMed] [Google Scholar]
  4. Causse M. A., Fulton T. M., Cho Y. G., Ahn S. N., Chunwongse J., Wu K., Xiao J., Yu Z., Ronald P. C., Harrington S. E. Saturated molecular map of the rice genome based on an interspecific backcross population. Genetics. 1994 Dec;138(4):1251–1274. doi: 10.1093/genetics/138.4.1251. [DOI] [PMC free article] [PubMed] [Google Scholar]
  5. Chen M., SanMiguel P., de Oliveira A. C., Woo S. S., Zhang H., Wing R. A., Bennetzen J. L. Microcolinearity in sh2-homologous regions of the maize, rice, and sorghum genomes. Proc Natl Acad Sci U S A. 1997 Apr 1;94(7):3431–3435. doi: 10.1073/pnas.94.7.3431. [DOI] [PMC free article] [PubMed] [Google Scholar]
  6. D'Hont A., Grivet L., Feldmann P., Rao S., Berding N., Glaszmann J. C. Characterisation of the double genome structure of modern sugarcane cultivars (Saccharum spp.) by molecular cytogenetics. Mol Gen Genet. 1996 Mar 7;250(4):405–413. doi: 10.1007/BF02174028. [DOI] [PubMed] [Google Scholar]
  7. Devos K. M., Gale M. D. Comparative genetics in the grasses. Plant Mol Biol. 1997 Sep;35(1-2):3–15. [PubMed] [Google Scholar]
  8. Deynze A. E., Nelson J. C., Sorrells M. E., McCouch S. R., Dubcovsky J., Dvorák J., Gill K. S., Gill B. S., Lagudah E. S., Appels R. Molecular-genetic maps for group 1 chromosomes of Triticeae species and their relation to chromosomes in rice and oat. Genome. 1995 Feb;38(1):45–59. doi: 10.1139/g95-006. [DOI] [PubMed] [Google Scholar]
  9. Doyle J. J., Davis J. I., Soreng R. J., Garvin D., Anderson M. J. Chloroplast DNA inversions and the origin of the grass family (Poaceae). Proc Natl Acad Sci U S A. 1992 Aug 15;89(16):7722–7726. doi: 10.1073/pnas.89.16.7722. [DOI] [PMC free article] [PubMed] [Google Scholar]
  10. Flavell R. B., Bennett M. D., Smith J. B., Smith D. B. Genome size and the proportion of repeated nucleotide sequence DNA in plants. Biochem Genet. 1974 Oct;12(4):257–269. doi: 10.1007/BF00485947. [DOI] [PubMed] [Google Scholar]
  11. Gaut B. S., Doebley J. F. DNA sequence evidence for the segmental allotetraploid origin of maize. Proc Natl Acad Sci U S A. 1997 Jun 24;94(13):6809–6814. doi: 10.1073/pnas.94.13.6809. [DOI] [PMC free article] [PubMed] [Google Scholar]
  12. Gottlieb L. D. Conservation and duplication of isozymes in plants. Science. 1982 Apr 23;216(4544):373–380. doi: 10.1126/science.216.4544.373. [DOI] [PubMed] [Google Scholar]
  13. Harushima Y., Yano M., Shomura A., Sato M., Shimano T., Kuboki Y., Yamamoto T., Lin S. Y., Antonio B. A., Parco A. A high-density rice genetic linkage map with 2275 markers using a single F2 population. Genetics. 1998 Jan;148(1):479–494. doi: 10.1093/genetics/148.1.479. [DOI] [PMC free article] [PubMed] [Google Scholar]
  14. 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. doi: 10.1093/genetics/118.2.353. [DOI] [PMC free article] [PubMed] [Google Scholar]
  15. Kurata N., Nagamura Y., Yamamoto K., Harushima Y., Sue N., Wu J., Antonio B. A., Shomura A., Shimizu T., Lin S. Y. A 300 kilobase interval genetic map of rice including 883 expressed sequences. Nat Genet. 1994 Dec;8(4):365–372. doi: 10.1038/ng1294-365. [DOI] [PubMed] [Google Scholar]
  16. Kurata N., Umehara Y., Tanoue H., Sasaki T. Physical mapping of the rice genome with YAC clones. Plant Mol Biol. 1997 Sep;35(1-2):101–113. [PubMed] [Google Scholar]
  17. Lander E. S., Green P., Abrahamson J., Barlow A., Daly M. J., Lincoln S. E., Newberg L. A., Newburg L. MAPMAKER: an interactive computer package for constructing primary genetic linkage maps of experimental and natural populations. Genomics. 1987 Oct;1(2):174–181. doi: 10.1016/0888-7543(87)90010-3. [DOI] [PubMed] [Google Scholar]
  18. Ming R., Liu S. C., Lin Y. R., da Silva J., Wilson W., Braga D., van Deynze A., Wenslaff T. F., Wu K. K., Moore P. H. Detailed alignment of saccharum and sorghum chromosomes: comparative organization of closely related diploid and polyploid genomes. Genetics. 1998 Dec;150(4):1663–1682. doi: 10.1093/genetics/150.4.1663. [DOI] [PMC free article] [PubMed] [Google Scholar]
  19. Moore G., Devos K. M., Wang Z., Gale M. D. Cereal genome evolution. Grasses, line up and form a circle. Curr Biol. 1995 Jul 1;5(7):737–739. doi: 10.1016/s0960-9822(95)00148-5. [DOI] [PubMed] [Google Scholar]
  20. Nagamura Y., Antonio B. A., Sasaki T. Rice molecular genetic map using RFLPs and its applications. Plant Mol Biol. 1997 Sep;35(1-2):79–87. [PubMed] [Google Scholar]
  21. Panaud O., Chen X., McCouch S. R. Development of microsatellite markers and characterization of simple sequence length polymorphism (SSLP) in rice (Oryza sativa L.). Mol Gen Genet. 1996 Oct 16;252(5):597–607. doi: 10.1007/BF02172406. [DOI] [PubMed] [Google Scholar]
  22. Paterson A. H., Lin Y. R., Li Z., Schertz K. F., Doebley J. F., Pinson S. R., Liu S. C., Stansel J. W., Irvine J. E. Convergent domestication of cereal crops by independent mutations at corresponding genetic Loci. Science. 1995 Sep 22;269(5231):1714–1718. doi: 10.1126/science.269.5231.1714. [DOI] [PubMed] [Google Scholar]
  23. Pereira M. G., Lee M., Bramel-Cox P., Woodman W., Doebley J., Whitkus R. Construction of an RFLP map in sorghum and comparative mapping in maize. Genome. 1994 Apr;37(2):236–243. doi: 10.1139/g94-033. [DOI] [PubMed] [Google Scholar]
  24. SanMiguel P., Tikhonov A., Jin Y. K., Motchoulskaia N., Zakharov D., Melake-Berhan A., Springer P. S., Edwards K. J., Lee M., Avramova Z. Nested retrotransposons in the intergenic regions of the maize genome. Science. 1996 Nov 1;274(5288):765–768. doi: 10.1126/science.274.5288.765. [DOI] [PubMed] [Google Scholar]
  25. Shen B., Carneiro N., Torres-Jerez I., Stevenson B., McCreery T., Helentjaris T., Baysdorfer C., Almira E., Ferl R. J., Habben J. E. Partial sequencing and mapping of clones from two maize cDNA libraries. Plant Mol Biol. 1994 Nov;26(4):1085–1101. doi: 10.1007/BF00040691. [DOI] [PubMed] [Google Scholar]
  26. Silva J. A., Sorrells M. E., Burnquist W. L., Tanksley S. D. RFLP linkage map and genome analysis of Saccharum spontaneum. Genome. 1993 Aug;36(4):782–791. doi: 10.1139/g93-103. [DOI] [PubMed] [Google Scholar]
  27. Singh K., Ishii T., Parco A., Huang N., Brar D. S., Khush G. S. Centromere mapping and orientation of the molecular linkage map of rice (Oryza sativa L.). Proc Natl Acad Sci U S A. 1996 Jun 11;93(12):6163–6168. doi: 10.1073/pnas.93.12.6163. [DOI] [PMC free article] [PubMed] [Google Scholar]
  28. Song W. Y., Wang G. L., Chen L. L., Kim H. S., Pi L. Y., Holsten T., Gardner J., Wang B., Zhai W. X., Zhu L. H. A receptor kinase-like protein encoded by the rice disease resistance gene, Xa21. Science. 1995 Dec 15;270(5243):1804–1806. doi: 10.1126/science.270.5243.1804. [DOI] [PubMed] [Google Scholar]
  29. Van Deynze A. E., Nelson J. C., Yglesias E. S., Harrington S. E., Braga D. P., McCouch S. R., Sorrells M. E. Comparative mapping in grasses. Wheat relationships. Mol Gen Genet. 1995 Oct 25;248(6):744–754. doi: 10.1007/BF02191715. [DOI] [PubMed] [Google Scholar]
  30. Wang Z. X., Yano M., Yamanouchi U., Iwamoto M., Monna L., Hayasaka H., Katayose Y., Sasaki T. The Pib gene for rice blast resistance belongs to the nucleotide binding and leucine-rich repeat class of plant disease resistance genes. Plant J. 1999 Jul;19(1):55–64. doi: 10.1046/j.1365-313x.1999.00498.x. [DOI] [PubMed] [Google Scholar]
  31. Yamamoto K., Sasaki T. Large-scale EST sequencing in rice. Plant Mol Biol. 1997 Sep;35(1-2):135–144. [PubMed] [Google Scholar]
  32. Yoshimura S., Yamanouchi U., Katayose Y., Toki S., Wang Z. X., Kono I., Kurata N., Yano M., Iwata N., Sasaki T. Expression of Xa1, a bacterial blight-resistance gene in rice, is induced by bacterial inoculation. Proc Natl Acad Sci U S A. 1998 Feb 17;95(4):1663–1668. doi: 10.1073/pnas.95.4.1663. [DOI] [PMC free article] [PubMed] [Google Scholar]
  33. Zhang H. B., Wing R. A. Physical mapping of the rice genome with BACs. Plant Mol Biol. 1997 Sep;35(1-2):115–127. [PubMed] [Google Scholar]

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