Bridging Comparative Genomics and DNA Marker-aided Molecular Breeding

  • Choi, Hong-Kyu (Department of Genetic Engineering, Dong-A University) ;
  • Cook, Douglas R. (Department of Plant Pathology, University of California)
  • 발행 : 2011.06.30

초록

In recent years, genomic resources and information have accumulated at an ever increasing pace, in many plant species, through whole genome sequencing, large scale analysis of transcriptomes, DNA markers and functional studies of individual genes. Well-characterized species within key plant taxa, co-called "model systems", have played a pivotal role in nucleating the accumulation of genomic information and databases, thereby providing the basis for comparative genomic studies. In addition, recent advances to "Next Generation" sequencing technologies have propelled a new wave of genomics, enabling rapid, low cost analysis of numerous genomes, and the accumulation of genetic diversity data for large numbers of accessions within individual species. The resulting wealth of genomic information provides an opportunity to discern evolutionary processes that have impacted genome structure and the function of genes, using the tools of comparative analysis. Comparative genomics provides a platform to translate information from model species to crops, and to relate knowledge of genome function among crop species. Ultimately, the resulting knowledge will accelerate the development of more efficient breeding strategies through the identification of trait-associated orthologous genes and next generation functional gene-based markers.

키워드

과제정보

연구 과제 주관 기관 : National Research Foundation of Korea (NRF)

참고문헌

  1. Abrouk M, Murat F, Pont C, Messing J, Jackson S, Faraut T, Tannier E, Plomion C, Cooke R, Feuillet C, Salse J. 2010. Paleogenomics of plants: synteny-based modeling of extinct ancestors. Trends in Plant Sci. 15:479-487. https://doi.org/10.1016/j.tplants.2010.06.001
  2. Alm V, Busso CS, Ergon A, Rudi H, Larsen A, Humphreys MW, Rognli OA. QTL analyses and comparative genetic mapping of frost tolerance, winter survival and drought tolerance in meadow fescue (Fescuta pratensis Huds.). Theor. Appl. Genet. DOI 10.1007/s00122-011-1590-z.
  3. Andersen JR, Lubberstedt T. 2005. Functional markers in plants. Trends Plant Sci. 8:554-560.
  4. Barnes S. 2002 Comparing Arabidopsis to other flowering plants. Curr. Opin. Plant Biol. 5:128-133. https://doi.org/10.1016/S1369-5266(02)00239-X
  5. Beilstein MA, Al-Shehbaz IA, Kellog EA. 2006. Brassicaceae phylogeny and trichome evolution. Am. J. Bot. 93: 607-619. https://doi.org/10.3732/ajb.93.4.607
  6. Bennetzen JL, Freeling M. 1997. The unified grass genome: synergy in synteny. Genome Res. 7:301-306. https://doi.org/10.1101/gr.7.4.301
  7. Boivin K, Akarkan A, Mbulu R, Clarenz O, Schmidt R. 2004. The Arabidopsis genome sequence as a tool for genome analysis in Brassicaceae. A comparison of the Arabidopsis and Capsella genomes. Plant Physiol. 135: 735-744. https://doi.org/10.1104/pp.104.040030
  8. Boutin SR, Young ND, Olson TC, Yu ZH, Shoemaker RC, Vallejos CE. 1995. Genome conservation among three legume genera detected with DNA markers. Genome 38:928-937. https://doi.org/10.1139/g95-122
  9. Choi H, Kim D, Uhm T, Limpens E, Lim H, Mun J, Kalo P, Penmetsa RV, Kulikova O, Roe BA, Bisseling T, Kiss GB, Cook DR. 2004a. A sequence-based genetic map of Medicago truncatula and comparison of marker colinearity with M. sativa. Genetics 166:1463-1502. https://doi.org/10.1534/genetics.166.3.1463
  10. Choi H, Mun J, Kim D, Zhu H, Baek J, Mudge J, Roe B, Ellis N, Doyle J, Kiss GB, Young ND, Cook DR. 2004b. Estimating genome conservarion between crop and model legume species. Proc. Natl. Acad. Sci. USA 101: 15289-15294. https://doi.org/10.1073/pnas.0402251101
  11. Choi H, Luckow M, Doyle J, Cook DR. 2006. Development of nuclear gene-derived molecular markers linked to legume genetic maps. Mol. Gen. Genomics 276:56-70. https://doi.org/10.1007/s00438-006-0118-8
  12. Devos KM, Gale MD. 2000. Genome relationships: the grass model in current research. The Plant Cell 12:637- 646. https://doi.org/10.1105/tpc.12.5.637
  13. Devos KM. 2005. Updating the 'Crop Circl'. Curr. Opin. Plant Biol. 8:155-162. https://doi.org/10.1016/j.pbi.2005.01.005
  14. Ellwood SR, Phan HTT, Jordan M, Hane J, Torres AM, Avila CM, Cruz-Izquierdo S, Oliver RP. 2008. Constuction of a comparative genetic map in faba bean (Vicia fava L.); conservation of genome structure with Lens culinaris. BMC Genomics DOI: 10.1186/1471-2164-9-380.
  15. Gale MD, Devos KM. 1998a. Plant comparative genetics after 10 years. Science. 282:656-659. https://doi.org/10.1126/science.282.5389.656
  16. Gale MD, Devos KM. 1998b. Comparative genetics in grass. Proc. Natl. Acad. Sci. USA 95:1971-1974. https://doi.org/10.1073/pnas.95.5.1971
  17. Graham PH, Vance CP. 2003. Legumes: importance and constraints to greater use. Plant Physiol. 131:872-877. https://doi.org/10.1104/pp.017004
  18. Kaga A, Ishii T. Tsukimoto K, Kokoro E, Kamijima O. 2000. Comparative molecular mapping in Ceratotropis species using an interspecific cross between azuki bean (Vigna angularis) and rice bean (V. umbellata). Theor. Appl. Genet. 100:207-213. https://doi.org/10.1007/s001220050028
  19. Keller B, Feuillet C. 2000. Colinearity and gene density in grass genomes. Trends Plant Sci. 5:246-251. https://doi.org/10.1016/S1360-1385(00)01629-0
  20. Kellog EA. 1998. Relationships of cereal crops and other grasses. Proc. Natl. Acad. SCI. USA 95:2005-2010. https://doi.org/10.1073/pnas.95.5.2005
  21. Kennard WC, Phillips RL, Porter RA, Grombacher AW. 2000. A comparative map of wild rice (Zizania palustris L. 2n=2x=30). Theor. Appl. Genet. 101:677-684. https://doi.org/10.1007/s001220051530
  22. Kim M, Lee S, Van K, Kim T, Jeong S, Choi I, Kim D, Lee Y, Park D, Ma J, Kim W, Kim B, Park S, Lee K, Kim D, Kim K, Shin J, Jang Y, Kim K, Liu WX, Chaisan T, Kang Y, Lee Y, Kim K, Moon J, Schmutz J, Jackson SA, Bhak J, Lee S. 2011. Whole-genome sequencing and intensive analysis of the undomesticated soybean (Glycine soja Sieb. and Zucc.) genome. Proc. Natl. Acad. SCI. USA DOI:10.1073/pnas.1009526107.
  23. Koch MA, Kiefer M. 2005. Genome evolution among cruciferous plants: a lecture from the comparison of the genetic map of three diploid species-Capsella rubella, Arabidopsis lyrata subsp. petraea, and A. thaliana. Am. J. Bot. 92:761-767. https://doi.org/10.3732/ajb.92.4.761
  24. Kuittinen H, de Haan AA, Vogl C, Oikarinen S, Leppala J, Koch M, Mitchell-Olds T, Langley CH, Savolainen O. 2004. Comparing the linkage maps of the close relatives Arabidopsis lyrata and A. thaliana. Genetics 168:1575- 1584. https://doi.org/10.1534/genetics.103.022343
  25. Kurata N, Moore G, Nagamura Y, Foote T, Yano M, Minobe Y, Gale MD. 1994. Conservation of genome structure between rice and wheat, Biotechnology 12:276- 278. https://doi.org/10.1038/nbt0394-276
  26. Lam H, Xu X, Liu X, Chen W, Yang G, Wong F, Li M, He W, Qin N, Wang B, Li J, Jian M, Wang J, Shao G, Wang J, Sun SS, Zhang G. 2010. Resequencing of 31 wild and cultivated soybean genomes identifies patterns of genetic diversity and selection. Nature Genet. 42:1053- 1061. https://doi.org/10.1038/ng.715
  27. Lin J, Stupar RM, Hans C, Hyten D, Jackson S. 2010. Structural and functional divergence of a 1-Mb duplicated region in the soybean (Glycine max) genome and comparison to an orthologous region from Phaseolous vulgaris. Plant Cell 22:2545-2561. https://doi.org/10.1105/tpc.110.074229
  28. Lysak M, Berr A, Pecinka A, Schmidt R, McBreen K, Schubert I. 2006. Mechanisms of chromosome number reduction in Arabidopsis thaliana and related Brassicaceae species. Proc. Natl. Acad. Sci. U.S.A. 103:5224-5229. https://doi.org/10.1073/pnas.0510791103
  29. Mayer KFX, Martis M, Hedley PE, Simkova H, Liu H, Morris JA, Steuemagel B, Taudien S, Roessner S, Gundlach H, Kubalakova M, Suchankova P, Murat F, Felder M, Nussbaumer T, Graner A, Salse J, Endo T, Sakai H, Tanaka T, Itoh T, Sato K, Platzer M, Matsimoto T, Scholz U, Dolezel J, Waugh R, Stein N. 2011. Unlocking the barley genome by chromosomal and comparative genomics. doi/10.1105/tpc.110.082537
  30. Menancia-Hautea D, Fatokun CA, Kuma L, Danesh D, Young ND. 1993. Comparative genome analysis of mungbean (Vigna radiata L. Wilczek) and cowpea (V. unguiculata L. Walpers) using RFLP mapping data. Theor. Appl. Genet. 86:797-810. https://doi.org/10.1007/BF00212605
  31. Parkin IAP, Gulden SM, Sharpe AG, Lukens L, Trick M, Osborn TC, Lydiate DJ. 2005. Segmental structure of the Brassica napus genome based on comparative analysis with Arabidopsis thaliana. Genetics 171:765-781 https://doi.org/10.1534/genetics.105.042093
  32. Peleman JD, van der Voort JR. 2003. Breeding by design. Trends in Plant Sci. 8:330-334. https://doi.org/10.1016/S1360-1385(03)00134-1
  33. Sakai H, Ikawa H, Tanaka T, Numa H, Minami H, Fujisawa M, Shibata M, Kurita K, Kikuta A, Hamada M, Kanamori H, Namiki N, Wu J, Itoh T, Matsumoto T, Sasaki T. 2011. Distinct evolutionary patterns of Oryza glaberrima deciphered by genome sequencing and comparative analysis. Plant J. DOI: 10.1111/j.1365-313X.2011.04539.x
  34. Haun WJ, Hyten DL, Xu WW, Gerhardt DJ, Albert TJ, Richmond T, Jeddeloh JA, Jia G, Springer NM, Vance CP, Stupar RM. 2011. The composition and origins of genomic variation among individuals of the soybean reference cultivar Williams $82^{1[W][OA]}$. Plant Physiol. 155: 645-655. https://doi.org/10.1104/pp.110.166736
  35. Schmitz J, et al. 2010. Genome sequence of the paleopolyploid soybean. Nature 463:178-183. https://doi.org/10.1038/nature08670
  36. Schranz ME, Lysak MA, Mitchell-Olds T. 2006. The ABC's of comparative genomics in the Brassicaceae: building blocks of crucifer genomes. Tr. Plant Sci. 11:535 -542. https://doi.org/10.1016/j.tplants.2006.09.002
  37. Vos P, Hogers R, Bleeker M, Reijans M, Van Delee T, Hornes M, Frijters A, Pot J, Peleman J, Kuiper M, Zabeau M. 1995. AFLP: a new technique for DNA fingerprinting. Nucleic Acids Res. 23:4407-4414. https://doi.org/10.1093/nar/23.21.4407
  38. Warwick SI, Al-Shehbaz IA. 2006. Brassicaceae: chromosome number index and database on CD-Rom. Plant Systemat. Evol. 259:237-248. https://doi.org/10.1007/s00606-006-0421-1
  39. Weeden NF, Muehlbauer FJ, Ladizinsky G. 1992. Extensive conservation of linkage relationships between pea and lentil genetic maps. J. Heredity 83:123-129. https://doi.org/10.1093/oxfordjournals.jhered.a111171
  40. Williams JGK, Kubelik AR, Livak KJ, Rafalski JA, Tingey SV. 1990. DNA polymorphisms amplified by arbitrary primers are useful as genetic markers. Nucleic Acids Res. 18:6531-6535. https://doi.org/10.1093/nar/18.22.6531
  41. Xu P, Wu X, Wang B, Liu Y, Ehlers JD, Close TJ, Roberts PA, Diop N, Qin D, Hu T, Lu Z, Li G. 2011. A SNP and SSR based genetic map of asparagus bean (Vigna unguiculata ssp. sesquipedialis) and comparison with the broader species. PLoS ONE 6(1): e15952. Doi: 10.1371/journal.pone.0015952.
  42. Yogeeswaran K, Frary A, York TL, Amenta A, Lesser AH, Nasrallah JB, Tanksley SD, Nasrallah ME. 2005. Comparative genome analysis of Arabidopsis spp: inferring chromosomal rearrangement events in the evolutionary history of A. thaliana. Genome Res. 15:505-515. https://doi.org/10.1101/gr.3436305
  43. Young ND, Mudge J, Ellis THN. 2003. Legume genomes: more than peas in a pod. Cur. Op. Plant Biol. 6:199-204. https://doi.org/10.1016/S1369-5266(03)00006-2
  44. Zhu H, Choi H, Cook DR, Shoemaker RC. 2005. Bridging model and crop legumes through comparative genomics. Plant Physiol. 137:1189-1196. https://doi.org/10.1104/pp.104.058891
  45. Zhu H, Kim D, Baek J, Choi H, Ellis LC, Kűester H, McCombe R, Peng H, Cook DR. 2003. Syntenic relationships between Medicago truncatula and Arabidopsis reveal extensive divergence of genome organization. 131: 1018-1026. https://doi.org/10.1104/pp.102.016436