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Traditional and Modern Plant Breeding Methods With Examples in Rice (Oryza sativa L.).

Breseghello F, Coelho AS
Journal of Agricultural and Food Chemistry
January 1, 2013

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Task Force #12

Journal of Agricultural and Food Chemistry. 2013;61(35):8277-8286

Abstract: Plant breeding can be broadly defined as alterations caused in plants as a result of their use by humans, ranging from unintentional changes resulting from the advent of agriculture to the application of molecular tools for precision breeding. The vast diversity of breeding methods can be simplified into three categories: (i) plant breeding based on observed variation by selection of plants based on natural variants appearing in nature or within traditional varieties; (ii) plant breeding based on controlled mating by selection of plants presenting recombination of desirable genes from different parents; and (iii) plant breeding based on monitored recombination by selection of specific genes or marker profiles, using molecular tools for tracking within-genome variation. The continuous application of traditional breeding methods in a given species could lead to the narrowing of the gene pool from which cultivars are drawn, rendering crops vulnerable to biotic and abiotic stresses and hampering future progress. Several methods have been devised for introducing exotic variation into elite germplasm without undesirable effects. Cases in rice are given to illustrate the potential and limitations of different breeding approaches.

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References

  1. Harlan, J. R. Crops and Men, 2nd ed.; American Society of Agronomy, Crop Science Society: Madison, WI, 1992; 284 pp.
  2. Hartl, D. L.; Clark, A. G. Principles of Population Genetics, 3rd ed.; Sinauer: Sunderland, MA, 1997; 542 pp.
  3. Falconer, D. S.; Mackay, T. F. C. Introduction to Quantitative Genetics, 4th ed.; Pearson: London, UK, 1996; 464 pp. LINK
  4. Kok, E. J.; Keijer, J.; Kleter, G. A.; Kuiper, H. A. Comparative safety assessment of plant-derived foods Regul. Toxicol. Pharmacol. 2008, 50, 98– 113 LINK
  5. Doebley, J.; Stec, A.; Wendel, J.; Edwards, M. Genetic and morphological analysis of a maize-teosinte F2 population: implications for the origin of maize Proc. Natl. Acad. Sci. U.S.A. 1990, 87, 9888– 9892 LINK
  6. Roberts, H. F. Plant Hybridization Before Mendel; Princeton University Press: Princeton, NJ, 1929; 374 pp. LINK
  7. Wilks, W. Hybrid Conference Report. J. R. Hortic. Soc. 1900, 24.
  8. Xu, Y. Molecular Plant Breeding; CAB International, 2010; 734 pp. LINK
  9. Hartl, D. L.; Clark, A. G. Principles of Population Genetics; Sinauer Associates: Sunderland, MA, 2007; 565 pp.
  10. Tang, H.; Sezen, U.; Paterson, A. H. Domestication and plant genomes Curr. Opin. Plant Biol. 2010, 13, 160– 166 LINK
  11. Zamir, D. Improving plant breeding with exotic genetic libraries Nat. Rev. Genet. 2001, 2, 983– 989 LINK
  12. Zeven, A. C. Landraces: a review of definitions and classifications Euphytica 1998, 104, 127– 139 LINK
  13. Allard, R. W. Principles of Plant Breeding, 2nd ed.; Wiley: New York, 1999; 264 pp. LINK
  14. Rasmusson, D. C.; Phillips, R. L. Plant breeding progress and genetic diversity from de novo variation and elevated epistasis Crop Sci. 1997, 37, 303– 310 LINK
  15. Breseghello, F.; Morais, O. P.; Pinheiro, P. V.; Silva, A. C. S.; Castro, E. M.; Guimarães, E. P.; Castro, A. P.; Pereira, J. A.; Lopes, A. M.; Utumi, M. M.; Oliveira, J. P. Results of 25 years of upland rice breeding in Brazil Crop Sci. 2011, 51, 914– 923 LINK
  16. Donald, C. M. The breeding of crop ideotypes Euphytica 1968, 17, 385– 403 LINK
  17. Yuan, W.; Peng, S.; Cao, C.; Virk, P.; Xing, D.; Zhang, Y.; Visperas, R. M.; Laza, R. C. Agronomic performance of rice breeding lines selected based on plant traits or grain yield Field Crops Res. 2011, 121, 168– 174 LINK
  18. Ali, A. J.; Xu, J. L.; Ismail, A. M.; Fu, B. Y.; Vijaykumar, C. H. M; Gao, Y. M.; Domingo, J.; Maghirang, R.; Yu, S. B.; Gregorio, G.; Yanaghihara, S. Hidden diversity for abiotic and biotic stress tolerances in the primary gene pool of rice revealed by a large backcross breeding program Field Crops Res. 2006, 97, 66– 76 LINK
  19. Falk, D. E. Generating and maintaining diversity at the elite level in crop breeding Genome 2010, 53, 982– 991 LINK
  20. Souza, C. L., Jr.; Geraldi, I. O.; Vencovsky, R. Response to recurrent selection under small effective population size Genet. Mol. Biol. 2000, 23, 841– 846 LINK
  21. Morais, O. P. Tamaño efectivo de la población. In Selección Recurrente en Arroz; Guimarães, E. P., Ed.; Centro Internacional de Agricultura Tropical: Cali, Colombia, 1997; pp 25– 44.
  22. Dudley, J. W.; Lambert, R. J. 100 generations of selection for oil and protein in corn. Plant Breed. Rev. 2004, 24 (Part 1), 79– 110.
  23. Shull, G. H. What is “heterosis”? Genetics 1948, 33, 439– 446 LINK
  24. Moll, R. H.; Lonnquist, J. H.; Vélez-Fortuno, J.; Johnson, E. C. The relationship of heterosis and genetic divergence in maize Genetics 1965, 52, 139– 144 LINK
  25. Reif, J. C.; Hallauer, A. R.; Melchinger, A. E. Heterosis and heterotic patterns in maize Maydica 2005, 50, 215– 223
  26. Melchinger, A. E.; Gumber, R. K. Overview of heterosis and heterotic groups in agronomic crops. In Concepts and Breeding of Heterosis in Crop Plants; Larnkey, K. R.; Staub, J. E., Eds.; Crop Science Society of America: Madison, WI, 1998; pp 29– 44.
  27. McNally, K. L.; Childs, K. L.; Bohnert, R.; Davidson, R. M.; Zhao, K.; Ulat, V. J.; Zeller, G.; Clark, R. M.; Hoen, D. R.; Bureau, T. E.; Stokowski, R.; Ballinger, D. G.; Frazer, K. A.; Cox, D. R.; Padhukasahasram, B.; Bustamante, C. D.; Weigel, D.; Mackill, D. J.; Bruskiewich, R. M.; Ratsch, G.; Buell, C. R.; Leung, H.; Leach, J. E. Genomewide SNP variation reveals relationships among landraces and modern varieties of rice. Proc. Natl. Acad. Sci. U.S.A. 2009, 106 ( 30), 1– 6. LINK
  28. Price, A. H. Believe it or not, QTLs are accurate! Trends Plant Sci. 2006, 11, 213– 216 LINK
  29. Breseghello, F.; Sorrells, M. E. Association analysis as a strategy for improvement of quantitative traits in plants Crop Sci. 2006, 46, 1323– 1330 LINK
  30. Breseghello, F.; Sorrells, M. E. Association mapping of kernel size and milling quality in wheat (Triticum aestivum L.) cultivars Genetics 2006, 172, 1165– 1177 LINK
  31. Pritchard, J. K.; Stephens, M.; Rosenberg, N. A.; Donnelly, P. Association mapping in structured populations Am. J. Hum. Genet. 2000, 67, 170– 181 LINK
  32. Huang, X.; Wei, X.; Sang, T.; Zhao, Q.; Feng, Q.; Zhao, Y.; Li, C.; Zhu, C.; Lu, T.; Zhang, Z.; Li, M.; Fan, D.; Guo, Y.; Wang, A.; Wang, L.; Deng, L.; Li, W.; Lu, Y.; Weng, Q.; Liu, K.; Huang, T.; Zhou, T.; Jing, Y.; Li, W.; Lin, Z.; Buckler, E. S.; Qian, Q.; Zhang, Q.; Li, J.; Han, B. Genome-wide association studies of 14 agronomic traits in rice landraces Nat. Genet. 2010, 42, 961– 967 LINK
  33. McCouch, S. Diversifying selection in plant breeding PLoS Biol. 2004, 2, e347 LINK
  34. Neeraja, C. N.; Maghirang-Rodriguez, R.; Pamplona, A.; Heuer, S.; Collard, B. C. Y.; Septiningsih, E. M.; Vergara, G.; Sanchez, D.; Xu, K.; Ismail, A. M.; Mackill, D. J. A marker-assisted backcross approach for developing submergence-tolerant rice cultivars Theor. Appl. Genet. 2007, 115, 767– 776 LINK
  35. Frisch, M.; Melchinger, A. E. Selection theory for marker-assisted backcrossing Genetics 2005, 170, 909– 917 LINK
  36. Ali, A. L.; Sanchez, P. L.; Yu, S.; Lorieux, M.; Eizenga, G. C. Chromosome segment substitution lines: a powerful tool for the introgression of valuable genes from Oryza wild species into cultivated rice (O. sativa) Rice 2010, 3, 218– 234 LINK
  37. Hittalmani, S.; Parco, A.; Mew, T. V.; Zeigler, R. S.; Huang, N. Fine mapping and DNA marker-assisted pyramiding of the three major genes for blast resistance in rice Theor. Appl. Genet. 2000, 100, 1121– 1128 LINK
  38. Thomson, M.; Zhao, K.; Wright, M.; McNally, K.; Rey, J.; Tung, C.-W.; Reynolds, A.; Scheffler, B.; Eizenga, G.; McClung, A.; Kim, H.; Ismail, A.; Ocampo, M.; Mojica, C.; Reveche, M.; Dilla-Ermita, C.; Mauleon, R.; Leung, H.; Bustamante, C.; McCouch, S. High-throughput single nucleotide polymorphism genotyping for breeding applications in rice using the BeadXpress platform Mol. Breed. 2012, 29, 875– 886 LINK
  39. Bhullar, N. K.; Zhang, Z.; Wicker, T.; Keller, B. Wheat gene bank accessions as a source of new alleles of the powdery mildew resistance gene Pm3: a large scale allele mining project BMC Plant Biol. 2010, 10, 88– 100 LINK
  40. Meuwissen, T. H. E.; Hayes, B. J.; Goddard, M. E. Prediction of total genetic value using genome-wide dense marker maps Genetics 2001, 157, 1819– 1829 LINK
  41. Bernardo, R.; Yu, J. Prospects for genomewide selection for quantitative traits in maize Crop Sci. 2007, 47, 1082– 1090 LINK
  42. Heffner, E. L.; Sorrells, M. E.; Jannink, J.-L. Genomic selection for crop improvement Crop Sci. 2009, 49, 1– 12 LINK
  43. Eathington, S. R.; Crosbie, T. M.; Edwards, M. D.; Reiter, R. S.; Bull, J. K. Molecular markers in a commercial breeding program Crop Sci. 2007, 47, S154– S163 LINK
  44. Sweeney, M.; McCouch, S. The complex history of the domestication of rice Ann. Bot. 2007, 100, 951– 957 LINK
  45. Futakuchi, K.; Sié, M. Better exploitation of Africa rice (Oryza glaberrima Steud.) in varietal development for resource-poor framers in West and Central Africa Agric. J. 2009, 4, 96– 102
  46. Li, C.; Zhou, A.; Sang, T. Genetic analysis of rice domestication syndrome with the wild annual species Oryza nivara New Phytol. 2006, 170, 185– 194 LINK
  47. Vaughan, D. A.; Lu, B.-R.; Tomooka, N. The evolving story of rice evolution Plant Sci. 2008, 174, 394– 408 LINK
  48. Kovach, M. J.; Sweeney, M. T.; McCouch, S. R. New insights into the history of rice domestication Trends Genet. 2007, 23, 578– 587 LINK
  49. Vitte, C.; Ishii, T.; Lamy, F.; Brar, D.; Panaud, O. Genomic paleontology provides evidence for two distinct origins of Asian rice (Oryza sativa L.) Mol. Gen. Genomics 2004, 272, 504– 511 LINK
  50. Londo, J. P.; Chiang, Y.-C.; Hung, K.-H.; Chiang, T.-Y.; Schaal, B. A. Phylogeography of Asian wild rice, Oryza rufipogon, reveals multiple independent domestications of cultivated rice, Oryza sativa Proc. Natl. Acad. Sci. U.S.A. 2006, 103, 9578– 9583 LINK
  51. Zhang, L.-B.; Zhu, Q.; Wu, Z.-Q.; Ross-Ibarra, J.; Gaut, B. S.; Ge, S.; Sang, T. Selection on grain shattering genes and rates of rice domestication New Phytol. 2009, 184, 707– 720 LINK
  52. Vaughan, D. A.; Lu, B.-R.; Tomooka, N.Was Asian rice (Oryza sativa) domesticated more than once? Rice 2008, 1, 16– 24 LINK
  53. Xiao, J.; Li, J.; Grandillo, S.; Ahn, S. N.; Yuan, L.; Tanksley, S. D.; McCouch, S. R. Identification of trait-improving quantitative trait loci alleles from a wild rice relative, Oryza rufipogon Genetics 1998, 150, 899– 909 LINK
  54. Thomson, M. J.; Tai, T. H.; McClung, A. M.; Lai, X. H.; Hinga, M. E.; Lobos, K. B.; Xu, Y.; Martinez, C. P.; McCouch, S. R. Mapping quantitative trait loci for yield, yield components and morphological traits in an advanced backcross population between Oryza rufipogon and the Oryza sativa cultivar Jefferson Theor. Appl. Genet. 2003, 107, 479– 493 LINK
  55. McCouch, S. R.; McNally, K. L.; Wang, W.; Hamilton, R. S. Genomics of gene banks: a case study in rice Am. J. Bot. 2012, 99, 407– 423 LINK
  56. Peng, S.; Khush, G. S. Four decades of breeding for varietal improvement of irrigated lowland rice in the International Rice Research Institute Plant Prod. Sci. 2003, 6, 157– 164 LINK
  57. Dingkhun, M.; Penning de Vries, F. W. T.; De Datta, S. D.; van Laar, H. H. Concepts for a new plant type for direct seeded flooded tropical rice. In Direct Seeded Flooded Rice in the Tropics; IRRI: Los Baños, Philippines, 1991; pp 17– 38.
  58. Peng, S.; Khush, G. S.; Virk, P.; Tang, Q.; Zou, Y. Progress in ideotype breeding to increase rice yield potential Field Crops Res. 2008, 108, 32– 38 LINK
  59. Cheng, S.-H.; Cao, L.-Y.; Zhuang, J.-Y.; Chen, S.-G.; Zhan, X.-D.; Fan, Y.-Y.; Zhu, D.-F.; Min, S.-K. Super hybrid rice breeding in China: achievements and prospects J. Integrative Plant Biol. 2007, 49, 805– 810 LINK
  60. Wu, X. Prospects of developing hybrid rice with super high yield Agron. J. 2009, 101, 688– 695 LINK
  61. Goff, S. A.; Ricke, D.; Lan, T. H.; Presting, G.; Wang, R.; Dunn, M. A draft sequence of the rice genome (Oryza sativa L. ssp. japonica) Science 2002, 296, 92– 100 LINK
  62. Yu, J.; Hu, S.; Wang, J.; Wong, G. K. S.; Li, S.; Liu, B. A draft sequence of the rice genome (Oryza sativa L. ssp. indica) Science 2002, 296, 79– 92 LINK
  63. Tung, C.-W; Zhao, K.; Wright, M.; Ali, M..; Jung, J.; Kimball, J.; Tyagi, W.; Thomson, M.; McNally, K.; Leung, H.; Kim, H.; Ahn, S.-N.; Reynolds, A.; Scheffler, B.; Eizenga, G.; McClung, A.; Bustamante, C.; McCouch, S. Development of a research platform for dissecting phenotype–genotype associations in rice Rice 2010, 3, 205– 217 LINK
  64. Xue, W.; Xing, Y.; Weng, X.; Zhao, Y.; Tang, W.; Wang, L.; Zhou, H.; Yu, S.; Xu, C.; Li, X.; Zhang, Q. Natural variation in Ghd7 is an important regulator of heading date and yield potential in rice Nat. Genet. 2008, 40, 761– 767 LINK
  65. Xu, K.; Mackill, D. J. A major locus for submergence tolerance mapped on rice chromosome 9 Mol. Breed. 1996, 2, 219– 224 LINK
  66. Xu, K.; Xu, X.; Fukao, T.; Canlas, P.; Maghirang-Rodriguez, R.; Heuer, S.; Ismail, A. M.; Bailey-Serres, J.; Ronald, P. C.; Mackill, D. J. Sub1A is an ethylene-response-factor-like gene that confers submergence tolerance to rice Nature 2006, 442, 705– 708 LINK
  67. Xu, K.; Deb, R.; Mackill, D. J. A microsatellite marker and a codominant PCR-based marker for marker-assisted selection of submergence tolerance in rice Crop Sci. 2004, 44, 248– 253 LINK
  68. Wissuwa, M.; Yano, M.; Ae, N. Mapping of QTLs for phosphorus deficiency tolerance in rice (Oryza sativa L.) Theor. Appl. Genet. 1998, 97, 777– 783 LINK
  69. Gamuyao, R.; Chin, J. H.; Pariasca-Tanaka, J.; Pesaresi, P.; Catausan, S.; Dalid, C.; Slamet-Loedin, I.; Tecson-Mendoza, E. M.; Wissuwa, M.; Heuer, S. The protein kinase Pstol1 from traditional rice confers tolerance of phosphorus deficiency Nature 2012, 488, 535– 539 LINK
  70. Chin, J. H.; Gamuyao, R.; Dalid, C.; Bustamam, M.; Prasetiyono, J.; Moeljopawiro, S.; Wissuwa, M.; Heuer, S. Developing rice with high yield under phosphorus deficiency: Pup1 sequence to application Plant Physiol. 2011, 156, 1202– 1216 LINK