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Comparative DNA sequence analysis of mapped wheat ESTs reveals the complexity of genome relationships between rice and wheat

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Abstract

The use of DNA sequence-based comparative genomics for evolutionary studies and for transferring information from model species to related large-genome species has revolutionized molecular genetics and breeding strategies for improving those crops. Comparative sequence analysis methods can be used to cross-reference genes between species maps, enhance the resolution of comparative maps, study patterns of gene evolution, identify conserved regions of the genomes, and facilitate interspecies gene cloning. In this study, 5,780 Triticeae ESTs that have been physically mapped using wheat (Triticum aestivum L.) deletion lines and segregating populations were compared using NCBI BLASTN to the first draft of the public rice (Oryza sativa L.) genome sequence data from 3,280 ordered BAC/PAC clones. A rice genome view of the homoeologous wheat genome locations based on sequence analysis shows general similarity to the previously published comparative maps based on Southern analysis of RFLP. For most rice chromosomes there is a preponderance of wheat genes from one or two wheat chromosomes. The physical locations of non-conserved regions were not consistent across rice chromosomes. Some wheat ESTs with multiple wheat genome locations are associated with the non-conserved regions of similarity between rice and wheat. The inverse view, showing the relationship between the wheat deletion map and rice genomic sequence, revealed the breakdown of gene content and order at the resolution conferred by the physical chromosome deletions in the wheat genome. An average of 35% of the putative single copy genes that were mapped to the most conserved bins matched rice chromosomes other than the one that was most similar. This suggests that there has been an abundance of rearrangements, insertions, deletions, and duplications eroding the wheat-rice genome relationship that may complicate the use of rice as a model for cross-species transfer of information in non-conserved regions.

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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

    CAS  PubMed  Google Scholar 

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

    PubMed  Google Scholar 

  • Anderson JA, Ogihara Y, Sorrells ME, Tanksley SD (1992) Development of a chromosomal arm map for wheat based on RFLP markers. Theor Appl Genet 83:1035–1043

    Google Scholar 

  • Appels R, Francki M, Chibbar R (2003) Advances in cereal functional genomics. Funct Integr Genomics 3:1–24

    CAS  PubMed  Google Scholar 

  • Barnes S (2002) Comparing Arabidopsis to other flowering plants. Curr Opin Plant Biol 5:128–134

    Article  CAS  PubMed  Google Scholar 

  • Bennetzen JL (2002) Mechanisms and rates of genome expansion and contraction in flowering plants. Genetica 115:29–36

    Article  CAS  PubMed  Google Scholar 

  • Bennetzen JL, Ma J (2003) The genetic colinearity of rice and other cereals on the basis of genomic sequence analysis. Curr Opin Plant Biol 6:128–133

    Article  CAS  PubMed  Google Scholar 

  • Bennetzen JL, Ramakrishna W (2002) Numerous small rearrangements of gene content, order and orientation differentiate grass genomes. Plant Mol Biol 48:821–827

    Article  CAS  PubMed  Google Scholar 

  • Benson DA, Karsch-Mizrachi I, Lipman DJ, Ostell J, Wheeler DL (2003) GenBank. Nucleic Acids Res 31:23–27

    Article  CAS  PubMed  Google Scholar 

  • Chen J, Gustafson JP (1997) Chromosomal rearrangement of wheat (T. aestivum) chromosome 4A by in situ hybridization. Chin J Genet 24:39–47

    Google Scholar 

  • Coe E, Cone K, McMullen M, Chen SS, Davis G, Gardiner J, Liscum E, Polacco M, Paterson A, Sanchez-Villeda H, Soderlund C, Wing R (2002) Access to the maize genome: an integrated physical and genetic map. Plant Physiol 128:9–12

    Article  CAS  PubMed  Google Scholar 

  • Delaney DE, Nasuda S, Endo TR, Gill BS, Hulbert SH (1995a) Cytologically based physical maps of the group 3 chromosomes of wheat. Theor Appl Genet 91:780–782

    CAS  Google Scholar 

  • Delaney DE, Nasuda S, Endo TR, Gill BS, Hulbert SH (1995b) Cytologically based physical maps of the group-2 chromosomes of wheat. Theor Appl Genet 91:568–573

    CAS  Google Scholar 

  • Devos KM, Gale MD (1997) Comparative genetics in the grasses. Plant Mol Biol 35:3–15

    CAS  PubMed  Google Scholar 

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

    CAS  PubMed  Google Scholar 

  • Dubcovsky J, Luo M-C, Zhong G-Y, Bransteiter R, Desai A, Kilian A, Kleinhofs A, Dvorak J (1996) Genetic map of diploid wheat, Triticum monococcum L., and its comparison with maps of Hordeum vulgare L. Genetics 143:983–999

    CAS  PubMed  Google Scholar 

  • Endo TR, Gill BS (1996) The deletion stocks of common wheat. J Hered 87:295–307

    CAS  Google Scholar 

  • Feng Q, Zhang Y, Hao P, Wang S, Fu G, Huang Y, Li Y, Zhu J, Liu Y, Hu X, Jia P, Zhao Q, Ying K, Yu S, Tang Y, Weng Q, Zhang L, Lu Y, Mu J, Zhang LS, Yu Z, Fan D, Liu X, Lu T, Li C, Wu Y, Sun T, Lei H, Li T, Hu H, Guan J, Wu M, Zhang R, Zhou B, Chen Z, Chen L, Jin Z, Wang R, Yin H, Cai Z, Ren S, Lv G, Gu W, Zhu G, Tu Y, Jia J, Chen J, Kang H, Chen X, Shao C, Sun Y, Hu Q, Zhang X, Zhang W, Wang L, Ding C, Sheng H, Gu J, Chen S, Ni L, Zhu F, Chen W, Lan L, Lai Y, Cheng Z, Gu M, Jiang J, Li J, Hong G, Xue Y, Han B (2002) Sequence and analysis of rice chromosome 4. Nature 420:316–320

    Article  CAS  PubMed  Google Scholar 

  • Foote T, Roberts M, Kurata N, Sasaki T, Moore G (1997) Detailed comparative mapping of cereal chromosome regions corresponding to the Ph1 locus in wheat. Genetics 147:801–807

    CAS  PubMed  Google Scholar 

  • Fu H, Dooner HK (2002) Intraspecific violation of genetic colinearity and its implications in maize. Proc Natl Acad Sci USA 99:9573–9578

    CAS  PubMed  Google Scholar 

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

    CAS  PubMed  Google Scholar 

  • Gill KS, Gill BS, Endo TR, Boyko EV (1996a) Identification and high-density mapping of gene-rich regions in chromosome Group 5 of wheat. Genetics 143:1001–1012

    CAS  PubMed  Google Scholar 

  • Gill KS, Gill BS, Endo TR, Taylor T (1996b) Identification and high-density mapping of gene-rich regions in chromosome group 1 of wheat. Genetics 144:1883–1891

    CAS  PubMed  Google Scholar 

  • Goff SA, Ricke D, Lan T-H, Presting G, Wang R, Dunn M, Glazebrook J, Sessions A, Oeller P, Varma H, Hadley D, Hutchison D, Martin C, Katagiri F, Lange BM, Moughamer T, Xia Y, Budworth P, Zhong J, Miguel T, Paszkowski U, Zhang S, Colbert M, Sun W-l, Chen L, Cooper B, Park S, Wood TC, Mao L, Quail P, Wing R, Dean R, Yu Y, Zharkikh A, Shen R, Sahasrabudhe S, Thomas A, Cannings R, Gutin A, Pruss D, Reid J, Tavtigian S, Mitchell J, Eldredge G, Scholl T, Miller RM, Bhatnagar S, Adey N, Rubano T, Tusneem N, Robinson R, Feldhaus J, Macalma T, Oliphant A, Briggs S (2002) A draft sequence of the rice genome (Oryza sativa L. ssp. japonica). Science 296:92–100

    CAS  PubMed  Google Scholar 

  • Hohmann U, Endo TR, Gill KS, Gill BS (1994) Comparison of genetic and physical maps of group 7 chromosomes from Triticum aestivum L. Mol Gen Genet 245:644–653

    CAS  PubMed  Google Scholar 

  • Kellogg EA (2001) Evolutionary history of the grasses. Plant Physiol 125:1198–1205

    CAS  Google Scholar 

  • Kimber G, Sears ER (1979) Uses of wheat aneuploids. Basic Life Sci 13:427–443

    CAS  PubMed  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

    CAS  PubMed  Google Scholar 

  • Matthews DE, Carollo VL, Lazo GR, Anderson OD (2003) GrainGenes, the genome database for small-grain crops. Nucleic Acids Res 31:183–186

    Article  CAS  PubMed  Google Scholar 

  • McPherson JD, Marra M, Hillier L, Waterston RH, Chinwalla A, Wallis J, Sekhon M, Wylie K, Mardis ER, Wilson RK, Fulton R, Kucaba TA, Wagner-McPherson C, Barbazuk WB, Gregory SG, Humphray SJ, French L, Evans RS, Bethel G, Whittaker A, Holden JL, McCann OT, Dunham A, Soderlund C, Scott CE, Bentley DR, Schuler G, Chen HC, Jang W, Green ED, Idol JR, Maduro VV, Montgomery KT, Lee E, Miller A, Emerling S, Kucherlapati, Gibbs R, Scherer S, Gorrell JH, Sodergren E, Clerc-Blankenburg K, Tabor P, Naylor S, Garcia D, de Jong PJ, Catanese JJ, Nowak N, Osoegawa K, Qin S, Rowen L, Madan A, Dors M, Hood L, Trask B, Friedman C, Massa H, Cheung VG, Kirsch IR, Reid T, Yonescu R, Weissenbach J, Bruls T, Heilig R, Branscomb E, Olsen A, Doggett N, Cheng JF, Hawkins T, Myers RM, Shang J, Ramirez L, Schmutz J, Velasquez O, Dixon K, Stone NE, Cox DR, Haussler D, Kent WJ, Furey T, Rogic S, Kennedy S, Jones S, Rosenthal A, Wen G, Schilhabel M, Gloeckner G, Nyakatura G, Siebert R, Schlegelberger B, Korenberg J, Chen XN, Fujiyama A, Hattori M, Toyoda A, Yada T, Park HS, Sakaki Y, Shimizu N, Asakawa S, et al (2001) A physical map of the human genome. Nature 409:934–941

    PubMed  Google Scholar 

  • Mickelson-Young L, Endo TR, Gill BS (1995) A cytogenetic ladder-map of the wheat homoeologous group-4 chromosomes. Theor Appl Genet 90:1007–1011

    CAS  Google Scholar 

  • Moore G, Roberts M, Aragon-Alcaide L, Foote T (1997) Centromeric sites and cereal chromosome evolution. Chromosoma 35:17–23

    Article  CAS  Google Scholar 

  • Naranjo T, Roca P, Goicoechea PG, Giraldez R (1987) Arm homoeology of wheat and rye chromosomes. Genome 29:873–882

    Google Scholar 

  • Osborn TC, Pires JC, Birchler JA, Auger DL, Chen ZJ, Lee HS, Comai L, Madlung A, Doerge RW, Colot V, Martienssen RA (2003) Understanding mechanisms of novel gene expression in polyploids. Trends Genet 19:141–147

    Article  CAS  PubMed  Google Scholar 

  • Ramakrishna W, Dubcovsky J, Park YJ, Busso C, Emberton J, SanMiguel P, Bennetzen JL (2002) Different types and rates of genome evolution detected by comparative sequence analysis of orthologous segments from four cereal genomes. Genetics 162:1389–1400

    CAS  PubMed  Google Scholar 

  • Rice Chromosome 10 Sequencing Consortium (2003) In-depth view of structure, activity, and evolution of rice chromosome 10. Science 300:1566–1569

    Article  PubMed  Google Scholar 

  • Sarma RN, Fish L, Gill BS, Snape JW (2000) Physical characterization of the homoeologous Group 5 chromosomes of wheat in terms of rice linkage blocks, and physical mapping of some important genes. Genome 43:191–198

    Article  CAS  PubMed  Google Scholar 

  • Sears ER (1952) Misdivision of univalents in common wheat. Chromosoma 4:535–550

    Google Scholar 

  • Sears ER (1954) The aneuploids of common wheat. Univ Mo Agric Exp Stn Res Bull 572:1–58

    Google Scholar 

  • Sears ER (1966) Nullisomic-tetrasomic combinations in hexaploid wheat. In: Riley R, Lewis KR (eds) Chromosome manipulations and plant genetics: the contributions to a symposium held during the Tenth International Botanical Congress, Edinburgh, 1964. Plenum Press, New York, p vii

  • Sears ER (1976) Genetic control of chromosome pairing in wheat. Annu Rev Genet 10:31–51

    CAS  PubMed  Google Scholar 

  • Sears ER, Miller TE (1985) The history of Chinese Spring wheat. Cereal Res Comm 13:261–263

    Google Scholar 

  • Sears ER, Sears MS (1978) The telocentric chromosomes of common wheat. In: Ramanujam S (ed) Proceedings of the 5th international wheat genetics symposium of the Indian society of genetics and plant breeding, New Delhi, India, pp 389–407

  • Sorrells ME, La Rota M, Bermudez-Kandianis CE, Greene RA, Kantety RV, 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 SF, 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

    CAS  PubMed  Google Scholar 

  • Tarchini R, Biddle P, Wineland R, Tingey S, Rafalski A (2000) The complete sequence of 340 kb of DNA around the rice Adh1-Adh2 region reveals interrupted colinearity with maize chromosome 4. Plant Cell 12:381–391

    CAS  PubMed  Google Scholar 

  • Tikhonov AP, SanMiguel PJ, Nakajima Y, Gorenstein NM, Bennetzen JL, Avramova Z (1999) Colinearity and its exceptions in orthologous adh regions of maize and sorghum. Proc Natl Acad Sci USA 96:7409–7414

    CAS  PubMed  Google Scholar 

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

    PubMed  Google Scholar 

  • Weng Y, Tuleen NA, Hart GE (2000) Extended physical maps and a consensus physical map of the homoeologous group-6 chromosomes of wheat (Triticum aestivum L. em Thell.). Theor Appl Genet 100:519–527

    CAS  Google Scholar 

  • Werner JE, Endo TR, Gill BS (1992) Toward a cytogenetically based physical map of the wheat genome. Proc Natl Acad Sci USA 89:11307–11311

    CAS  PubMed  Google Scholar 

  • Wilson WA, Harrington SE, Woodman WL, Lee M, Sorrells ME, McCouch SR (1999) Inferences on the genome structure of progenitor maize through comparative analysis of rice, maize and the domesticated panicoids. Genetics 153:453–473

    CAS  PubMed  Google Scholar 

  • Wu J, Kurata N, Tanoue H, Shimokawa T, Umehara Y, Yano M, Sasaki T (1998) Physical mapping of duplicated genomic regions of two chromosome ends in rice. Genetics 150:1595–1603

    CAS  PubMed  Google Scholar 

  • Wu J, Maehara T, Shimokawa T, Yamamoto S, Harada C, Takazaki Y, Ono N, Mukai Y, Koike K, Yazaki J, Fujii F, Shomura A, Ando T, Kono I, Waki K, Yamamoto K, Yano M, Matsumoto T, Sasaki T (2002) A comprehensive rice transcript map containing 6591 expressed sequence tag sites. Plant Cell 14:525–535

    CAS  PubMed  Google Scholar 

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

    Article  CAS  PubMed  Google Scholar 

  • Zhang Z, Schwartz S, Wagner L, Miller W (2000) A greedy algorithm for aligning DNA sequences. J Comput Biol 7:203–214

    Article  CAS  PubMed  Google Scholar 

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Acknowledgements

This publication is based upon work supported by the National Science Foundation under cooperative agreement no. DBI-9975989, USDA/NRI project no. 2001-35301-10612, Hatch Project 419149, and Syngenta.

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Correspondence to Mark E. Sorrells.

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La Rota, M., Sorrells, M.E. Comparative DNA sequence analysis of mapped wheat ESTs reveals the complexity of genome relationships between rice and wheat. Funct Integr Genomics 4, 34–46 (2004). https://doi.org/10.1007/s10142-003-0098-2

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  • DOI: https://doi.org/10.1007/s10142-003-0098-2

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