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Micro-colinearity between rice, Brachypodium, and Triticum monococcum at the wheat domestication locus Q

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Abstract

Brachypodium, a wild temperate grass with a small genome, was recently proposed as a new model organism for the large-genome grasses. In this study, we evaluated gene content and microcolinearity between diploid wheat (Triticum monococcum), Brachypodium sylvaticum, and rice at a local genomic region harboring the major wheat domestication gene Q. Gene density was much lower in T. monococcum (one per 41 kb) because of gene duplication and an abundance of transposable elements within intergenic regions as compared to B. sylvaticum (one per 14 kb) and rice (one per 10 kb). For the Q gene region, microcolinearity was more conserved between wheat and rice than between wheat and Brachypodium because B. sylvaticum contained two genes apparently not present within the orthologous regions of T. monococcum and rice. However, phylogenetic analysis of Q and leukotriene A-4 hydrolase-like gene orthologs, which were colinear among the three species, showed that Brachypodium is more closely related to wheat than rice, which agrees with previous studies. We conclude that Brachypodium will be a useful tool for gene discovery, comparative genomics, and the study of evolutionary relationships among the grasses but will not preclude the need to conduct large-scale genomics experiments in the Triticeae.

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References

  • Ahn S, Anderson JA, Sorrells ME, Tanksley SD (1993) Homoeologous relationships of rice, wheat and maize chromosomes. Mol Gen Genet 241:483–490

    Article  PubMed  CAS  Google Scholar 

  • Altschul SF, Madden TL, Schaffer AA, Zhang J, Zhang Z, Miller W, Lipman DJ (1997) A new generation of protein database search programs. Nucleic Acids Res 25:3389–3402

    Article  PubMed  CAS  Google Scholar 

  • Bennett MD, Leitch IJ (2005) Nuclear DNA amounts in Angiosperms: progress, problems and prospects. Ann Bot 95:45–90

    Article  PubMed  CAS  Google Scholar 

  • Bennetzen JL (2000) Comparative sequence analysis of plant nuclear genomes: microcolinearity and its many exceptions. Plant Cell 12:1021–1029

    Article  PubMed  CAS  Google Scholar 

  • Bossolini E, Wicker T, Knobel PA, Keller B (2007) Comparison of orthologous loci from small grass genomes Brachypodium and rice: implications for wheat genomics and grass genome annotation. Plant J 49:704–717

    Article  PubMed  CAS  Google Scholar 

  • Catalan P, Olmstead RG (2000) Phylogenetic reconstruction of the genus Brachypodium P. Beauv. (Poaceae) from combined sequences of chloroplast ndhF gene and nuclear ITS. Plant Syst Evol 220:1–19

    Article  CAS  Google Scholar 

  • Catalan P, Ying S, Armstrong L, Draper J, Stace CA (1995) Molecular phylogeny of the grass genus Brachypodium P. Beauv. based on RFLP and RAPD analysis. Bot J Linn Soc 117:263–280

    Article  Google Scholar 

  • Chantret N, Cenci A, Sabot F, Anderson O, Dubcovsky J (2004) Sequencing of the Triticum monococcum hardness locus reveals good microcolinearity with rice. Mol Gen Genomics 271:377–386

    Article  CAS  Google Scholar 

  • Chuck G, Meeley RB, Hake S (1998) The control of maize spikelet meristem fate by the APETALA2-like gene indeterminate spikelet1. Genes Dev 12:1145–1154

    Article  PubMed  CAS  Google Scholar 

  • Devos KM, Gale MD (2000) Genome relationships: the grass model in current research. Plant Cell 12:637–646

    Article  PubMed  CAS  Google Scholar 

  • Distelfeld A, Uauy C, Olmos S, Schlatter AR, Dubcovsky J, Fahima T (2004) Microcolinearity between a 2-cM region encompassing the grain protein content locus Gpc-6B1 on wheat chromosome 6B and a 350-kb region on rice chromosome 2. Funct Integr Genomics 4:59–66

    Article  PubMed  CAS  Google Scholar 

  • Draper J, Mur LAJ, Jenkins G, Ghosh-Biswas GC, Bablak P, Hasterok R, Routledge APM (2001) Brachypodium dystachyon: a new model system for functional genomics in grasses. Plant Phys 127:1539–1555

    Article  CAS  Google Scholar 

  • Faris JD, Gill BS (2002) Genomic targeting and high-resolution mapping of the domestication gene Q in wheat. Genome 45:706–718

    Article  PubMed  CAS  Google Scholar 

  • Faris JD, Haen KM, Gill BS (2000) Saturation mapping of a gene-rich recombination hot spot in wheat. Genetics 154:823–835

    PubMed  CAS  Google Scholar 

  • Faris JD, Fellers JP, Brooks SA, Gill BS (2003) A bacterial artificial chromosome contig spanning the major domestication gene Q in wheat and identification of a candidate gene. Genetics 164:311–321

    PubMed  CAS  Google Scholar 

  • Feuillet C, Keller B (1999) High gene density is conserved at syntenic loci of small and large grass genomes. Proc Natl Acad Sci USA 96:8265–8270

    Article  PubMed  CAS  Google Scholar 

  • Feuillet C, Keller B (2002) Comparative genomics in the grass family: molecular characterization of grass genome structure and evolution. Ann Bot 89:3–10

    Article  PubMed  CAS  Google Scholar 

  • Feuillet C, Penger A, Gellner K, Mast A, Keller B (2001) Molecular evolution of receptor-like kinase genes in hexaploid wheat. Independent evolution of orthologs after polyploidization and mechanisms of local rearrangements at paralogous loci. Plant Physiol 125:1304–1313

    Article  PubMed  CAS  Google Scholar 

  • Foote TN, Griffiths S, Allouis S, Moore G (2004) Construction and analysis of a BAC library in the grass Brachypodium sylvaticum: its use as a tool to bridge the gap between rice and wheat in elucidating gene content. Funct Integr Genomics 4:26–33

    Article  PubMed  CAS  Google Scholar 

  • Francki M, Carter M, Byan K, Hunter A, Bellgard M, Appels R (2004) Comparative organization of wheat homoeologous group 3S and 7L using wheat-rice synteny and identification of potential markers for genes controlling xanthophyll content in wheat. Funct Integr Genomics 4:118–130

    Article  PubMed  CAS  Google Scholar 

  • Gale MD, Devos KM (1998) Comparative genetics in the grasses. Proc Natl Acad Sci USA 95:1971–1974

    Article  PubMed  CAS  Google Scholar 

  • Griffiths S, Sharp R, Foote TN, Bertin I, Wanous M, Reader S, Colas I, Moore M (2006) Molecular characterization of Ph1 as a major chromosome pairing locus in polyploid wheat. Nature 439:749–752

    Article  PubMed  CAS  Google Scholar 

  • Hasterok R, Marasek A, Donnison IS, Armstead I, Thomas A, King IP, Wolny E, Idziak D, Draper J, Jenkins G (2006) Alignment of the genomes of Brachypodium distachyon and temperate cereals and grasses using bacterial artificial chromosome landing with fluorescence in situ hybridization. Genetics 173:349–362

    Article  PubMed  CAS  Google Scholar 

  • International Rice Genome Sequencing Project (2005) The map-based sequence of the rice genome. Nature 436:793–800

    Article  Google Scholar 

  • Kato K, Miura H, Sawada S (1999) QTL mapping of genes controlling ear emergence time and plant height on chromosome 5A of wheat. Theor Appl Genet 98:472–477

    Article  CAS  Google Scholar 

  • Lagudah ES, McFadden H, Singh RP, Huerta-Espino J, Bariana HS, Spielmeyer W (2006) Molecular genetic characterization of the Lr34/Yr18 slow rusting resistance gene region in wheat. Theor Appl Genet 114:21–30

    Article  PubMed  CAS  Google Scholar 

  • Lander ES, Green P, Abranhamson J, Barlow A, Daly MJ, Lincoln SE, Newburg L (1987) Mapmaker: an interactive computer package for constructing primary genetic linkage maps of experimental and natural populations. Genomics 1:174–181

    Article  PubMed  CAS  Google Scholar 

  • Leighty CE, Boshnakian S (1921) Genetic behaviour of the spelt form in crosses between Triticum spelta and Triticum aestivum. J Agric Res 7:335–364

    Google Scholar 

  • Li W, Gill BS (2002) The colinearity of the Sh2/A1 orthologous region in rice, sorghum and maize is interrupted and accompanied by genome expansion in the Triticeae. Genetics 160:1153–1162

    PubMed  CAS  Google Scholar 

  • Lu HJ, Faris JD (2006) Macro- and micro-colinearity between the genomic region of wheat chromosome 5B containing the Tsn1 gene and the rice genome. Funct Integr Genomics 6:90–103

    Article  PubMed  CAS  Google Scholar 

  • MacKey J (1954) Neutron and X-ray experiments in wheat and a revision of the speltoid problem. Hereditas 40:65–180

    Google Scholar 

  • Muramatsu M (1963) Dosage effect of the spelta gene q of hexaploid wheat. Genetics 48:469–482

    PubMed  CAS  Google Scholar 

  • Muramatsu M (1986) The vulgare super gene, Q: its universality in durum wheat and its phenotypic effects in tetraploid and hexaploid wheats. Can J Genet Cytol 28:30–41

    Google Scholar 

  • Paterson AH, Bowers JE, Chapman BA (2004) Ancient polyploidization predating divergence of the cereals and consequences for comparative genomics. Proc Natl Acad Sci USA 101:9903–9908

    Article  PubMed  CAS  Google Scholar 

  • SanMiguel PJ, Ramakrishna W, Bennetzen JL, Busso C, Dubcovsky J (2002) Transposable elements, genes and recombination in a 215-kb contig from wheat chromosome 5Am. Funct Integr Genomics 2:70–80

    Article  PubMed  CAS  Google Scholar 

  • Schnurbusch T, Collins NC, Eastwood RF, Sutton T, Jefferies SP, Langridge P (2007) Fine mapping and targeted SNP survey using rice-wheat gene colinearity in the region of the Bo1 boron toxicity tolerance locus of bread wheat. Theor Appl Genet 115:451–461

    Article  PubMed  CAS  Google Scholar 

  • Sears ER (1954) The aneuploids of common wheat. MO Agr Exp Sta Res Bull 572:1–59

    Google Scholar 

  • Simons KJ, Fellers JP, Trick HN, Zhang Z, Tai Y-S, Gill BS, Faris JD (2006) Molecular characterization of the major wheat domestication gene Q. Genetics 172:547–555

    Article  PubMed  CAS  Google Scholar 

  • Sorrells ME, La Rota M, Bermudez-Kandianis CE, Greene RA, Kantety R, Munkvold JD, Miftahudin, Mahmoud A, Ma X, Gustafson PJ, Qi LL, Echalier B, Gill BS, Matthews DE, Lazo GR, Chao S, Anderson OD, Edwards H, Linkiewicz AM, Dubcovsky J, Akhunov ED, Dvorak J, Zhang D, Nguyen HT, Peng J, Lapitan NLV, Gonzalez-Hernandez JL, Anderson JA, Hossain K, Kalavacharla V, Kianian SK, Choi DW, Close TJ, Dilbirligi M, Gill KS, Steber C, Walker-Simmons MK, McGuire PE, Qualset CO (2003) Comparative DNA sequence analysis of wheat and rice genomes. Genome Res 13:1818–1827

    PubMed  CAS  Google Scholar 

  • Stein N (2007) Triticeae genomics: advances in sequence analysis of large genome cereal crops. Chromosome Res 15:21–31

    Article  PubMed  CAS  Google Scholar 

  • Tatusova TA, Madden TL (1999) BLAST 2 Sequences: a new tool for comparing protein and nucleotide sequences. FEMS Microbiol Lett 174:247–250

    Article  PubMed  CAS  Google Scholar 

  • Valarik M, Linkiewicz AM, Dubcovsky J (2006) A microcolinearity study at the earliness per se gene Eps-A m 1 region reveals an ancient duplication that preceded the wheat-rice divergence. Theor Appl Genet 112:945–957

    Article  PubMed  CAS  Google Scholar 

  • Van Deynze AE, Dubcovsky J, Gill KS, Nelson JC, Sorrells ME, Dvorak J, Gill BS, Lagudah ES, McCouch SR, Appels R (1995a) Molecular-genetics maps for group 1 chromosomes of Triticeae species and their relation to chromosomes in rice and oat. Genome 38:45–59

    Google Scholar 

  • Van Deynze AE, Nelson JC, Yglesis ES, Harrington SE, Braga DP, McCouch SR, Sorrells ME (1995b) Comparative mapping in grasses. Wheat relationships. Mol Gen Genet 248:744–754

    Article  PubMed  Google Scholar 

  • Vogel JP, Garvin DF, Leong OM, Hayden DM (2006a) Agrobacterium-mediated transformation and inbred line development in the model grass Brachypodium distachyon. Plant Cell Tissue Organ Cult 85:199–211

    Google Scholar 

  • Vogel JP, Gu Y-Q, Twigg P, Lazo GR, Laudencia-Chingcuanco D, Hayden DM, Donze TJ, Vivian LA, Stamova B, Coleman-Derr D (2006b) EST sequencing and phylogenetic analysis of the model grass Brachypodium distachyon. Theor Appl Genet 113:186–195

    Article  PubMed  CAS  Google Scholar 

  • Ware DH, Jaiswal P, Ni J, Yap IV, Pan X, Clark KY, Teytelman L, Schmidt SC, Zhao W, Chang K, Cartinhour S, Stein LD, McCouch SR (2002) Gramene, a tool for grass genomics. Plant Physiol 130:1606–1613

    Article  PubMed  CAS  Google Scholar 

  • Yan L, Loukoianov A, Tranquilli G, Helguera M, Fahima T, Dubcovsky J (2003) Positional cloning of wheat vernalization gene VRN1. Proc Natl Acad Sci USA 100:6263–6268

    Article  PubMed  CAS  Google Scholar 

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Acknowledgments

This research was supported by USDA-ARS CRIS project 5442-22000-030.

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Authors and Affiliations

  1. USDA-ARS Cereal Crops Unit, Northern Crop Science Laboratory, 1307 18th Street North, Fargo, ND, 58105, USA

    Justin D. Faris

  2. Department of Plant Sciences, Lofsgard Hall, North Dakota State University, Fargo, ND, 58105, USA

    Zengcui Zhang

  3. USDA-ARS Plant Science and Entomology Research Unit, Throckmorton Plant Sciences Center, Kansas State University, Manhattan, KS, 66506, USA

    John P. Fellers

  4. Department of Plant Pathology, Throckmorton Plant Sciences Center, Kansas State University, Manhattan, KS, 66506, USA

    Bikram S. Gill

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  1. Justin D. Faris
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Correspondence to Justin D. Faris.

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Faris, J.D., Zhang, Z., Fellers, J.P. et al. Micro-colinearity between rice, Brachypodium, and Triticum monococcum at the wheat domestication locus Q . Funct Integr Genomics 8, 149–164 (2008). https://doi.org/10.1007/s10142-008-0073-z

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  • DOI: https://doi.org/10.1007/s10142-008-0073-z

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