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. 2002 Mar;160(3):1153–1162. doi: 10.1093/genetics/160.3.1153

The colinearity of the Sh2/A1 orthologous region in rice, sorghum and maize is interrupted and accompanied by genome expansion in the triticeae.

Wanlong Li 1, Bikram S Gill 1
PMCID: PMC1462018  PMID: 11901130

Abstract

The Sh2/A1 orthologous region of maize, rice, and sorghum contains five genes in the order Sh2, X1, X2, and two A1 homologs in tandem duplication. The Sh2 and A1 homologs are separated by approximately 20 kb in rice and sorghum and by approximately 140 kb in maize. We analyzed the fate of the Sh2/A1 region in large-genome species of the Triticeae (wheat, barley, and rye). In the Triticeae, synteny in the Sh2/A1 region was interrupted by a break between the X1 and X2 genes. The A1 and X2 genes remained colinear in homeologous chromosomes as in other grasses. The Sh2 and X1 orthologs also remained colinear but were translocated to a nonhomeologous chromosome. Gene X1 was duplicated on two nonhomeologous chromosomes, and surprisingly, a paralog shared homology much higher than that of the orthologous copy to the X1 gene of other grasses. No tandem duplication of A1 homologs was detected but duplication of A1 on a nonhomeologous barley chromosome 6H was observed. Intergenic distances expanded greatly in wheat compared to rice. Wheat and barley diverged from each other 12 million years ago and both show similar changes in the Sh2/A1 region, suggesting that the break in colinearity as well as X1 duplications and genome expansion occurred in a common ancestor of the Triticeae species.

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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. Ainsworth C., Hosein F., Tarvis M., Weir F., Burrell M., Devos K. M., Gale M. D. Adenosine diphosphate glucose pyrophosphorylase genes in wheat: differential expression and gene mapping. Planta. 1995;197(1):1–10. doi: 10.1007/BF00239933. [DOI] [PubMed] [Google Scholar]
  4. Chen M., Bennetzen J. L. Sequence composition and organization in the Sh2/A1-homologous region of rice. Plant Mol Biol. 1996 Dec;32(6):999–1001. doi: 10.1007/BF00041383. [DOI] [PubMed] [Google Scholar]
  5. Chen M., SanMiguel P., Bennetzen J. L. Sequence organization and conservation in sh2/a1-homologous regions of sorghum and rice. Genetics. 1998 Jan;148(1):435–443. doi: 10.1093/genetics/148.1.435. [DOI] [PMC free article] [PubMed] [Google Scholar]
  6. 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]
  7. Davis G. L., McMullen M. D., Baysdorfer C., Musket T., Grant D., Staebell M., Xu G., Polacco M., Koster L., Melia-Hancock S. A maize map standard with sequenced core markers, grass genome reference points and 932 expressed sequence tagged sites (ESTs) in a 1736-locus map. Genetics. 1999 Jul;152(3):1137–1172. doi: 10.1093/genetics/152.3.1137. [DOI] [PMC free article] [PubMed] [Google Scholar]
  8. Dubcovsky J., Luo M. C., Zhong G. Y., Bransteitter R., Desai A., Kilian A., Kleinhofs A., Dvorák J. Genetic map of diploid wheat, Triticum monococcum L., and its comparison with maps of Hordeum vulgare L. Genetics. 1996 Jun;143(2):983–999. doi: 10.1093/genetics/143.2.983. [DOI] [PMC free article] [PubMed] [Google Scholar]
  9. Faris J. D., Haen K. M., Gill B. S. Saturation mapping of a gene-rich recombination hot spot region in wheat. Genetics. 2000 Feb;154(2):823–835. doi: 10.1093/genetics/154.2.823. [DOI] [PMC free article] [PubMed] [Google Scholar]
  10. Feuillet C., Keller B. High gene density is conserved at syntenic loci of small and large grass genomes. Proc Natl Acad Sci U S A. 1999 Jul 6;96(14):8265–8270. doi: 10.1073/pnas.96.14.8265. [DOI] [PMC free article] [PubMed] [Google Scholar]
  11. Foote T., Roberts M., Kurata N., Sasaki T., Moore G. Detailed comparative mapping of cereal chromosome regions corresponding to the Ph1 locus in wheat. Genetics. 1997 Oct;147(2):801–807. doi: 10.1093/genetics/147.2.801. [DOI] [PMC free article] [PubMed] [Google Scholar]
  12. Fransz P. F., Alonso-Blanco C., Liharska T. B., Peeters A. J., Zabel P., de Jong J. H. High-resolution physical mapping in Arabidopsis thaliana and tomato by fluorescence in situ hybridization to extended DNA fibres. Plant J. 1996 Mar;9(3):421–430. doi: 10.1046/j.1365-313x.1996.09030421.x. [DOI] [PubMed] [Google Scholar]
  13. Havukkala I. J. Cereal genome analysis using rice as a model. Curr Opin Genet Dev. 1996 Dec;6(6):711–714. doi: 10.1016/s0959-437x(96)80025-6. [DOI] [PubMed] [Google Scholar]
  14. Hulbert S. H., Richter T. E., Axtell J. D., Bennetzen J. L. Genetic mapping and characterization of sorghum and related crops by means of maize DNA probes. Proc Natl Acad Sci U S A. 1990 Jun;87(11):4251–4255. doi: 10.1073/pnas.87.11.4251. [DOI] [PMC free article] [PubMed] [Google Scholar]
  15. Kellogg E. A. Evolutionary history of the grasses. Plant Physiol. 2001 Mar;125(3):1198–1205. doi: 10.1104/pp.125.3.1198. [DOI] [PMC free article] [PubMed] [Google Scholar]
  16. Lijavetzky D., Muzzi G., Wicker T., Keller B., Wing R., Dubcovsky J. Construction and characterization of a bacterial artificial chromosome (BAC) library for the A genome of wheat. Genome. 1999 Dec;42(6):1176–1182. [PubMed] [Google Scholar]
  17. Messing J., Llaca V. Importance of anchor genomes for any plant genome project. Proc Natl Acad Sci U S A. 1998 Mar 3;95(5):2017–2020. doi: 10.1073/pnas.95.5.2017. [DOI] [PMC free article] [PubMed] [Google Scholar]
  18. 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]
  19. Nelson J. C., Deynze A. E., Sorrells M. E., Autrique E., Lu Y. H., Negre S., Bernard M., Leroy P. Molecular mapping of wheat. Homoeologous group 3. Genome. 1995 Jun;38(3):525–533. doi: 10.1139/g95-068. [DOI] [PubMed] [Google Scholar]
  20. Panstruga R., Büschges R., Piffanelli P., Schulze-Lefert P. A contiguous 60 kb genomic stretch from barley reveals molecular evidence for gene islands in a monocot genome. Nucleic Acids Res. 1998 Feb 15;26(4):1056–1062. doi: 10.1093/nar/26.4.1056. [DOI] [PMC free article] [PubMed] [Google Scholar]
  21. Paterson A. H., Bowers J. E., Burow M. D., Draye X., Elsik C. G., Jiang C. X., Katsar C. S., Lan T. H., Lin Y. R., Ming R. Comparative genomics of plant chromosomes. Plant Cell. 2000 Sep;12(9):1523–1540. doi: 10.1105/tpc.12.9.1523. [DOI] [PMC free article] [PubMed] [Google Scholar]
  22. 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]
  23. Shirasu K., Schulman A. H., Lahaye T., Schulze-Lefert P. A contiguous 66-kb barley DNA sequence provides evidence for reversible genome expansion. Genome Res. 2000 Jul;10(7):908–915. doi: 10.1101/gr.10.7.908. [DOI] [PMC free article] [PubMed] [Google Scholar]
  24. Spielmeyer W., Moullet O., Laroche A., Lagudah E. S. Highly recombinogenic regions at seed storage protein loci on chromosome 1DS of Aegilops tauschii, the D-genome donor of wheat. Genetics. 2000 May;155(1):361–367. doi: 10.1093/genetics/155.1.361. [DOI] [PMC free article] [PubMed] [Google Scholar]
  25. Tarchini R., Biddle P., Wineland R., Tingey S., Rafalski A. The complete sequence of 340 kb of DNA around the rice Adh1-adh2 region reveals interrupted colinearity with maize chromosome 4. Plant Cell. 2000 Mar;12(3):381–391. doi: 10.1105/tpc.12.3.381. [DOI] [PMC free article] [PubMed] [Google Scholar]
  26. Tikhonov A. P., SanMiguel P. J., Nakajima Y., Gorenstein N. M., Bennetzen J. L., Avramova Z. Colinearity and its exceptions in orthologous adh regions of maize and sorghum. Proc Natl Acad Sci U S A. 1999 Jun 22;96(13):7409–7414. doi: 10.1073/pnas.96.13.7409. [DOI] [PMC free article] [PubMed] [Google Scholar]
  27. Tranquilli G., Lijavetzky D., Muzzi G., Dubcovsky J. Genetic and physical characterization of grain texture-related loci in diploid wheat. Mol Gen Genet. 1999 Dec;262(4-5):846–850. doi: 10.1007/s004380051149. [DOI] [PubMed] [Google Scholar]
  28. Wicker T., Stein N., Albar L., Feuillet C., Schlagenhauf E., Keller B. Analysis of a contiguous 211 kb sequence in diploid wheat (Triticum monococcum L.) reveals multiple mechanisms of genome evolution. Plant J. 2001 May;26(3):307–316. doi: 10.1046/j.1365-313x.2001.01028.x. [DOI] [PubMed] [Google Scholar]

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