Advertisement

Indian Journal of Plant Physiology

, Volume 23, Issue 4, pp 622–629 | Cite as

Forward genetics using radiation hybrids (deletion mutants) in plants

  • Ajay KumarEmail author
  • Shalu Jain
Review Article
  • 28 Downloads

Abstract

Identification of the QTL/genes associated with traits of interest determines the successful application of those genes for crop improvement. After identification of QTL, fine mapping and cloning of important QTL can also enhance our understanding of the genetic structure of the underlying genes responsible for the phenotypic variation. Genetic or recombination mapping is the most common approach used to identify, map and clone QTL or genes in plants. However, genetic mapping approach for fine mapping or map-based cloning is associated with many drawbacks including the need of developing a homogenous and large population, the availability of polymorphic markers, and the poor recombination in certain chromosomal regions. In this article, we describe an alternative approach, called radiation hybrid (RH) mapping, for forward genetic studies in plants. This approach has been extensively used in animal system and offer greater prospects for forward genetic studies in plants as well. The RH mapping uses radiation induced chromosomal breaks to map markers, and thus offers many advantages compared to traditionally used genetic mapping approach, particularly for loci located in recombination cold spots and for the traits which lack genetic diversity. Here, we reviewed the progress made in application of RH approach for forward genetics in plants.

Keywords

Forward genetics Gene cloning High resolution map Physical mapping Quantitative trait loci mapping Radiation hybrid Recombination 

References

  1. Akbari, M., Wenzl, P., Caig, V., Carling, J., Xia, L., Yang, S., et al. (2006). Diversity arrays technology (DArT) for high-throughput profiling of the hexaploid wheat genome. Theoretical and Applied Genetics, 113, 1409–1420.CrossRefGoogle Scholar
  2. Balcárková, B., Frenkel, Z., Škopová, M., Abrouk, M., Kumar, A., Chao, S., et al. (2017). A high resolution radiation hybrid map of wheat chromosome 4A. Frontiers in Plant Science, 7, 2063.  https://doi.org/10.3389/fpls.2016.02063.CrossRefPubMedPubMedCentralGoogle Scholar
  3. Bassi, F. M., Ghavami, F., Hayden, M. J., Wang, Y., Forrest, K. L., Kong, S., et al. (2016). Fast-forward genetics by radiation hybrids to saturate the locus regulating nuclear-cytoplasmic compatibility in Triticum. Plant Biotechnology Journal, 14, 1716–1726.CrossRefGoogle Scholar
  4. Bassi, F. M., Kumar, A., Zhang, Q., Paux, E., Huttner, E., Kilian, A., et al. (2013). Radiation hybrid QTL mapping of Tdes2 involved in the first meiotic division of wheat. Theoretical and Applied Genetics, 126(8), 1977–1990.CrossRefGoogle Scholar
  5. Buerstmayr, H., Lemmens, M., Hartl, L., Doldi, L., Steiner, B., Stierschneider, M., et al. (2002). Molecular mapping of QTLs for Fusarium head blight resistance in spring wheat. I. Resistance to fungal spread (type II resistance). Theoretical and Applied Genetics, 104, 84–91.CrossRefGoogle Scholar
  6. Buerstmayr, H., Steiner, B., Hartl, L., Griesser, M., Angerer, N., Lengauer, D., et al. (2003). Molecular mapping of QTLs for Fusarium head blight resistance in spring wheat. II. Resistance to fungal penetration and spread. Theoretical and Applied Genetics, 107, 503–508.CrossRefGoogle Scholar
  7. Buerstmayr, M., Steiner, B., Wagner, C., Schwarz, P., Brugger, K., Barabaschi, D., et al. (2018). High-resolution mapping of the pericentromeric region on wheat chromosome arm 5AS harbouring the Fusarium head blight resistance QTL Qfhs.ifa-5A. Plant Biotechnology Journal, 16, 1046–1056.CrossRefGoogle Scholar
  8. Chapman, J. A., Mascher, M., Bulucc, A., Barry, K., Georganas, E., Session, A., et al. (2015). A whole-genome shotgun approach for assembling and anchoring the hexaploid bread wheat genome. Genome Biology, 16, 26.CrossRefGoogle Scholar
  9. Devos, K. M., Sorrells, M. E., Anderson, J. A., Miller, T. E., Reader, S. M., Lukaszewski, A. J., et al. (1999). Chromosome aberrations in wheat nullisomic-tetrasomic and ditelosomic lines. Cereal Research Communication, 27, 231–239.Google Scholar
  10. Erayman, M., Sanduh, D., Sidhu, D., Dilbirligi, M., Baenziger, P. S., & Gill, K. S. (2004). Demarcating the gene-rich regions of the wheat genome. Nucleic Acids Research, 32, 3546–3565.CrossRefGoogle Scholar
  11. Gadaleta, A., Giancaspro, A., Nigro, D., Giove, S. L., Incerti, O., Simeone, R., et al. (2014). A new genetic and deletion map of wheat chromosome 5A to detect candidate genes for quantitative traits. Molecular Breeding, 34, 1599–1611.CrossRefGoogle Scholar
  12. Gao, W., Chen, Z. J., Yu, J. Z., Kohel, R. J., Womack, J. E., & Stelly, D. M. (2006). Wide-cross whole-genome radiation hybrid mapping of the cotton (Gossypium barbadense L.) genome. Molecular Genetics and Genomics, 275, 105–113.CrossRefGoogle Scholar
  13. Gao, W., Chen, Z. J., Yu, J. Z., Raska, D., Kohel, R. J., Womack, J. E., et al. (2004). Wide-cross whole-genome radiation hybrid mapping of cotton (Gossypium hirsutum L.). Genetics, 167, 1317–1329.CrossRefGoogle Scholar
  14. Goss, S. J., & Harris, H. (1975). New method for mapping genes in human chromosomes. Nature, 255, 680–684.CrossRefGoogle Scholar
  15. Haenel, Q., Laurentino, T. G., Roesti, M., & Berner, D. (2018). Meta-analysis of chromosome-scale crossover rate variation in eukaryotes and its significance to evolutionary genomics. Molecular Ecology, 27, 2477–2497.CrossRefGoogle Scholar
  16. Haider, N. (2012). Evidence for the origin of the B genome of bread wheat based on chloroplast DNA. Turkish Journal of Agriculture and Forestry, 36, 13–25.Google Scholar
  17. Hossain, K. G., Riera-lizarazu, O., Kalavacharla, V., Vales, M. I., Maan, S. S., & Kianian, S. F. (2004). Radiation hybrid mapping of the species cytoplasm-specific (scs ae) gene in wheat. Genetics, 168, 415–423.CrossRefGoogle Scholar
  18. Huang, B. E., George, A. W., Forrest, K. L., Kilian, A., Hayden, M. J., Morell, M. K., et al. (2012). A multiparent advanced generation inter-cross population for genetic analysis in wheat. Plant Biotechnol Journal, 10, 826–839.CrossRefGoogle Scholar
  19. Kalavacharla, V., Hossain, K., Gu, Y., Riera-Lizarazu, O., Vales, M. I., Bhamidimarri, S., et al. (2006). High-resolution radiation hybrid map of wheat chromosome 1D. Genetics, 173, 1089–1099.CrossRefGoogle Scholar
  20. Kilian, B., Ozkan, H., Deusch, O., Effgen, S., Brandolini, A., Kohl, J., et al. (2007). Independent wheat B and G genome origins in outcrossing Aegilops progenitor haplotypes. Molecular Biology and Evolution, 24, 217–227.CrossRefGoogle Scholar
  21. Kobayashi, F., Wu, J., Kanamori, H., Tanaka, T., Katagiri, S., Karasawa, W., et al. (2015). A high-resolution physical map integrating an anchored chromosome with the BAC physical maps of wheat chromosome 6B. BMC Genomics, 16, 595.CrossRefGoogle Scholar
  22. Kumar, A., Bassi, F. M., Michalack de Jimenez, M., Ghavami, F., Mazaheri, M., et al. (2014). Radiation hybrids: A valuable tool for genetic, genomic and functional analysis of plant genomes. In R. Tuberosa, A. Graner, & E. Frison (Eds.), Genomics of plant genetic resources (pp. 285–318). Dordrecht: Springer.CrossRefGoogle Scholar
  23. Kumar, A., Bassi, F. M., Paux, E., Al-Azzam, O., Michalak de Jimenez, M., Denton, A. M., et al. (2012a). DNA repair and crossing over favor similar chromosome regions as discovered in radiation hybrid of Triticum. BMC Genomics, 13, 339.CrossRefGoogle Scholar
  24. Kumar, A., Seetan, R., Mergoum, M., Tiwari, V. K., Iqbal, M. J., Wang, Y., et al. (2015). Radiation hybrid maps of the D-genome of Aegilops tauschii and their application in sequence assembly of large and complex plant genomes. BMC Genomics, 16, 800.CrossRefGoogle Scholar
  25. Kumar, A., Simons, K., Iqbal, M. J., de Jiménez, M., Bassi, F. M., Ghavami, F., et al. (2012b). Physical mapping resources for large plant genomes: radiation hybrids for wheat D-genome progenitor Aegilops tauschii accession AL8/78. BMC Genomics, 13, 597.CrossRefGoogle Scholar
  26. Kynast, R. G., Okagaki, R. J., Galatowitsch, M. W., Granath, S. R., Jacobs, M. S., Stecet, A. O., et al. (2004). Dissecting the maize genome by using chromosome addition and radiation hybrid lines. Proceedings of The National Academy of Sciences of the USA, 101, 9921–9926.CrossRefGoogle Scholar
  27. Kynast, R. G., Okagaki, R. J., Rines, H. W., & Phillips, R. L. (2002). Maize individualized chromosome and derived radiation hybrid lines and their use in functional genomics. Functional & Integrative Genomics, 2, 60–69.CrossRefGoogle Scholar
  28. Lukowitz, W., Gillmor, C. S., & Scheible, W. R. (2000). Positional cloning in arabidopsis. Why it feels good to have a genome initiative working for you. Plant Physiology, 123, 795–805.CrossRefGoogle Scholar
  29. Luo, M. C., Gu, Y. Q., You, F. M., Deal, K. R., Ma, Y., Hu, Y., et al. (2013). A 4-gigabase physical map unlocks the structure and evolution of the complex genome of Aegilops tauschii, the wheat D-genome progenitor. Proceedings of The National Academy of Sciences of the USA, 110, 7940–7945.CrossRefGoogle Scholar
  30. Maan, S. S. (1992). Transfer of a species specific cytoplasm (scs) from Triticum timopheevii to T. turgidum. Genome, 35, 238–243.CrossRefGoogle Scholar
  31. Maan, S. S., Joppa, L. R., & Kianian, S. F. (1999). Linkage between the centromere and a gene producing nucleocytoplasmic compatibility in durum wheat. Crop Science, 39, 1044–1048.CrossRefGoogle Scholar
  32. Mazaheri, M., Kianian, P. M. A., Kumar, A., Mergoum, M., Seetan, R., Soltani, A., et al. (2015). Radiation hybrid map of barley 1 chromosome 3H. The Plant Genome, 8.  https://doi.org/10.3835/plantgenome2015.02.0005.
  33. Michalak de Jimenez, M. K., Bassi, F. M., Ghavami, F., Simons, K., Dizon, R., Seetan, R. I., et al. (2013). A radiation hybrid map of chromosome 1D reveals synteny conservation at a wheat speciation locus. Functional & Integrative Genomics, 13, 19–32.CrossRefGoogle Scholar
  34. Peters, J. L., Crude, F., & Gerats, T. (2003). Forward genetics and map-based cloning approaches. Trends in Plant Science, 8, 484–491.CrossRefGoogle Scholar
  35. Riera-Lizarazu, O., Leonard, J. M., Tiwari, V. K., & Kianian, S. F. (2010). A method to produce radiation hybrids for the D-genome chromosomes of wheat (Triticum aestivum L.). Cytogenetic and Genome Research, 129, 234–240.CrossRefGoogle Scholar
  36. Riera-Lizarazu, O., Vales, M. I., Ananiev, E. V., Rines, H. W., & Phillips, R. L. (2000). Production and characterization of maize chromosome 9 radiation hybrids derived from an oat-maize addition line. Genetics, 156, 327–339.PubMedPubMedCentralGoogle Scholar
  37. Saintenac, C., Falque, M., Martin, O. C., Paux, E., Feuillet, C., & Sourdille, P. (2009). Detailed recombination studies along chromosome 3B provide new insights on crossover distribution in wheat (Triticum aestivum L.). Genetics, 181, 393–403.CrossRefGoogle Scholar
  38. Salvi, S., & Tuberosa, R. (2005). To clone or not to clone plant QTLs: Present and future challenges. Trends in Plant Science, 10, 297–304.CrossRefGoogle Scholar
  39. Sears, E. R. (1954). The aneuploids of common wheat. Missouri Agricultural Experiment Station Research Bulletin, 572, 1–58.Google Scholar
  40. Singh, R., Matus-Cadiz, M., Baga, M., Hucl, P., & Chibbar, R. N. (2010). Identification of genomic regions associated with seed dormancy in white-grained wheat. Euphytica, 174, 391–408.CrossRefGoogle Scholar
  41. Sorrells, M. E., Gustafson, J. P., Somers, D., Chao, S., Benscher, D., Guedira-Brown, G., et al. (2011). Reconstruction of the synthetic W7984 × Opata M85 wheat reference population. Genome, 54, 875–882.CrossRefGoogle Scholar
  42. Tiwari, V. K., Heesacker, A., Riera-Lizarazu, O., Gunn, H., Wang, S., Wang, Y., et al. (2016). A whole-genome, radiation hybrid mapping resource of hexaploid wheat. The Plant Journal, 86, 195–207.CrossRefGoogle Scholar
  43. Tiwari, V. K., Riera-Lizarazu, O., Gunn, H. L., Lopez, K., Iqbal, M. J., Kianian, S. F., et al. (2012). Endosperm tolerance of paternal aneuploidy allows radiation-hybrid mapping of the wheat D-genome and a measure of γ-ray induced chromosome breaks. PLoS ONE, 7, e48815.CrossRefGoogle Scholar
  44. Tsunewaki, K. (1980). Genetic diversity of the cytoplasm in Triticum and Ae (pp. 49–100). Japan Society for the promotion of science 5-3-1 Kojimachi, Chiyodaku, Tokyo, Japan.Google Scholar
  45. Tsunewaki, K. (2009). Plasmon analysis in the TriticumAegilops complex. Breeding Science, 59, 455–470.CrossRefGoogle Scholar
  46. Walter, M. A., Spillet, D. J., Thomas, P., Weissenbach, J., & Goodfellow, P. N. (1994). A method for constructing radiation hybrid maps of whole genomes. Nature Genetics, 7, 22–28.CrossRefGoogle Scholar
  47. Wang, S., Wong, D., Forrest, K., Allen, A., Chao, S., Huang, B. E., et al. (2014). Characterization of polyploid wheat genomic diversity using a high-density 90,000 single nucleotide polymorphism array. Plant Biotechnology Journal, 12, 787–796.CrossRefGoogle Scholar
  48. Wang, Y. Y., Sun, X. Y., Zhao, Y., Kong, F. M., Guo, Y., Zhang, G. Z., et al. (2011). Enrichment of a common wheat genetic map and QTL mapping for fatty acid content in grain. Plant Science, 181, 65–75.CrossRefGoogle Scholar
  49. Zhirov, E. G., Bessarab, K. S., & Gubanova, M. A. (1974). Genetic studies on partial desynapsis in soft wheat. Soviet Genetics, 9, 10–18.PubMedGoogle Scholar

Copyright information

© Indian Society for Plant Physiology 2018

Authors and Affiliations

  1. 1.Department of Plant SciencesNorth Dakota State UniversityFargoUSA
  2. 2.Department of Plant PathologyNorth Dakota State UniversityFargoUSA

Personalised recommendations