Rationale

The future of crop improvement depends on the availability of genetic variation. Most modern crop varieties have undergone a genetic bottleneck associated with the process of domestication resulting in a restriction of the genetic options that are available to plant breeders. There is a larger pool of genetic variation available in landraces and wild relatives of crops. These resources are known to contain many interesting traits for breeding, including good to strong tolerance to abiotic and biotic stresses and various nutritional traits of interest (Sun et al 2001). However, it is often difficult to utilize these natural sources of genetic diversity because of fertility barriers, linkage drag, the time and resources required to recover useful recombinants. This project is designed to take advantage of the unexploited reservoir that exists in the wild relatives of cultivated rice (Oryza sativa L.) through the development of introgression lines that will be of immediate use to breeders and will simultaneously serve to enhance our understanding of the “wild alleles” that contribute favorably to plant performance under drought stress.
The cereal crops, rice, maize and wheat, are together the most important human food crops in the world. The demand for cereals is expected to increase dramatically, particularly in the developing world where population is increasing the fastest. Cereal production faces the difficult challenge of obtaining reliable yields under variable conditions, notably due to the prevalence of biotic and abiotic stresses. Among the abiotic stresses, water deficit is among the most prevalent and the most severe in terms of restricting yields in cereal crops. Fresh water is the most limiting resource on the planet and as it becomes more scarce, breeders will devote increasing energy to developing crops that are better able to withstand water deficits or to use water more efficiently.
Rice evolved as an aquatic plant and traditional rice cultivation makes use of standing irrigation water to control weeds. Upland rice represents an adaptation to dry land. There is enough genetic variation within the genus to enable rice to adapt to drought-prone conditions. Upland genotypes are widely grown throughout West Africa and large parts of Brazil. These areas represent important targets for our work to identify Chromosome Segment Substitution Lines (CSSLs) that perform well under drought. To improve current levels of drought tolerance in new varieties, we propose to search for “new” alleles associated with drought and acid soil tolerance in the reservoir of natural genetic diversity available in wild relatives.
It is well established that (1) a great deal of genetic diversity was left behind during rice domestication in Asia and (2) rice relatives belonging to the O. AA genome complex contain a high level of diversity that is sexually compatible with O. sativa and can be accessed via crossing and selection.
Plant geneticists have long recognized the value of exotic libraries. Interspecific crosses between O. sativa and two African species, O. glaberrima and O. barthii, an American species, O. glumaepatula and an Asian species, O. rufipogon, have demonstrated the utility of targeted introgressions as the basis for gene identification and plant improvement. These relatives are known to be a good source of genes for tolerance to biotic or abiotic stress and the transgressive behavior of progeny derived from interspecific crosses has been demonstrated in several studies.
The evaluation of complex phenotypes relevant to agriculture remains a laborious activity that requires direct and sustained attention. To make the exploration of the phenotype-genotype relationship more efficient, a series of tools is required that will leverage the availability of genomic information and link it directly to field evaluation of germplasm resources.
We propose to develop a comprehensive toolkit of genetic and genomic resources that will allow breeders and geneticists to explore and more efficiently utilize wild relatives in crop improvement. Our approach involves the systematic introduction of foreign alleles from four different AA genome O. species into one elite, highly productive O. sativa varieties and to provide introgression lines (ILs) or sets of overlapping CSSLs as the basis for genetic analysis and applied plant breeding.
CSSLs are particularly valuable when complex, quantitatively inherited phenotypes are the breeding target. Because they represent permanent (inbred) genetic resources that can be easily replicated by seed and distributed to collaborators working in different environments. Each set of CSSLs consists of a relatively small number of lines that can be evaluated in replicated trials. They are constructed to provide maximum power of statistical analysis because each line can be compared to all others or may simply be compared to the recurrent parent, making it possible to extract a great deal of valuable information from a relatively small number of lines. For phenotypes that are difficult to measure, or require repeated evaluation over years and environments, the ability to focus quickly on a small number of lines is a critical component of success.
Complex phenotypes can be dissected genetically by evaluating and comparing CSSLs as a first pass. By linking the information about gene identity back to the Gramene database, we will be able to provide a dictionary of genes with known function that are contained in each of the CSSLs. This dictionary is also a key ingredient in enabling comparative approaches to the study of phenotype-genotype relationships. Once an association is established between a phenotype and a specific introgression line, it is possible to use advanced forward and reverse approaches to genetic analysis to mine down and identify the gene(s) that are directly involved (Yano, 2001; Jander et al., 2002), but it is also feasible to use the introgression line directly in a breeding program without knowing the identity of the gene(s) that are involved (Gur and Zamir, 2004). Genes known to be associated with a plant’s response to water stress or adaptation to acid soils will be targeted for Single Nucleotide Polymorphisms (SNPs) development.
In addition to the targeted introgression of traits that can be identified phenotypically in the wild material, such as biotic or abiotic stress tolerance, it has been demonstrated that alleles hidden in low yielding, agronomically undesirable ancestors can enhance the productivity of many of the world’s most important crop varieties. These yield-enhancing alleles are the basis of ‘transgressive variation’ and may confer an advantage in both favorable (irrigated) and unfavorable conditions (drought and weed competition) (Moncada et al., 2000; Gur and Zamir, 2004). Thus, the use of wild and exotic germplasm for CSSLs construction carries with it the possibility that favorable transgressive segregants will be identified, providing the basis for studies aimed at understanding the genetic basis of transgressive variation associated with resistance or tolerance to drought and acid soils.

Research Activities

Creation of O. glaberrima CSSL populations

Creation of Wild CSSL populations

Universal Core Genetic Map

Development of a kit of SNP (Single Nucleotide Polymorphism) markers

References

• Ahn SN, JP Suh, CS Oh, SJ Lee, and HS Suh (2002) Development of introgression lines of weedy rice in the background of Tongil-type rice. Rice Genetics Newsletter 19:14
  • Albar, L., M.-N. Ndjiondjop, Z. Essibak, A. Berger, A. Pinel, M. Jones, D. Fargette and A. Ghesquière, 2003. Fine genetic mapping of a gene required for rice yellow mottle virus cell to-cell movement. Theo. Appl. Genet 107: 371–378.
  • Aluko G., C. Martinez, J. Tohme, C. Castano, C. Bergman, J.H. Oard 2004. QTL Mapping of Grain Quality Traits From the Interspecific Cross Oryza sativa x O. glaberrima .Theor.Appl. Genet.109:630-639
  • Brondani, C, N. Rangel, V. Brondani, and E. Ferreira, 2002. QTL mapping and introgression of yield-related traits from Oryza glumaepatula to cultivated rice (Oryza sativa) using microsatellite markers. Theo. Appl. Genet 104: 1192–1203
  • Doi K, Sobrizal, K Ikeda PL Sanchez, T Kurakazu, Y Nagai and A Yoshimura (2003) Developing and evaluating rice chromosome segment substitution lines. Proc. IRRI Conference, Sept. 16-19, 2002. Beijing, China. p. 275-287
  • Enriquez, EC, DS Brar, TL Rosario, M Jones, GS Khush (2000) Production and characterization of doubled haploids from anther culture of the F1s of Oryza sativa L. x O. glaberrima Steud. Rice Genet News 17:26-27
  • Eshed, Y. and D. Zamir (1995). "An introgression line population of Lycopersicon pennellii in the cultivated tomato enables the identification and fine mapping of yield-associated QTL." Genetics 141: 1147-1162.
  • Frey KJ, EG Hammond and PK Lawrence (1975) Inheritance of oil percentage in interspecific crosses of hexaploid oats. Crop Sci 15:94-95
  • Ghesquière, A., J. Séquier, et al. (1997). "First steps towards a rational use of African rice, Oryza glaberrima, in rice breeding through a 'contig line' concept." Euphytica 96: 31-39.
  • Gur A and D Zamir (2004) Unused natural variation can lift yield barriers in plant breeding. Public Library of Science (in press)
  • Hash CT (1999) Contiguous segment substitution lines: New tool for elite pearl millet hybrid parental lines enhancement http://www.dfid-psp.org/projects/7382.htm
  • Jander G, SR Norris, SD Rounsley, DF Bush, IM Levin and RL Last (2002) Arabidopsis map-based cloning in the post-genomic era. Plant Phys 129:440-450
  • Koumproglou R, TM Wilkes, P Townson, XY Wang, J Beynon, HS Pooni, HJ Newbury (2002) STAIRS: A new genetic resource for functional genomic studies of Arabidopsis. The Pl. J. 31:355-364
  • M. Lorieux, G. Reversat, S. X. Garcia Diaz, C. Denance, N. Jouvenet, Y. Orieux, N. Bourger, A. Pando-Bahuon, A. Ghesquière. 2003. Linkage mapping of Hsa-1Og, a resistance gene of African rice to the cyst nematode, Heterodera sacchari. Theo. Appl. Genet 107:691-696
  • Moncada, M.P., C.P. Martínez, J. Tohme, E. Guimaraes, M. Chatel, J. Borrero, H. Gauch, Jr. and S.R. McCouch, 2001. Quantitative trait loci for yield and yield components in an Oryza sativa x Oryza rufipogon BC2F2 population evaluated in an upland environment. Theor Appl Genet 102:41–52
  • Monforte AJ, Tanksley SD (2000) Development of a set of near isogenic and backcross recombinant inbred lines containing most of the Lycopersicon hirsutum genome in a L. esculentum genetic background: A tool for gene mapping and gene discovery. Genome 43: 803–813
  • Pestsova EG, Borner A, Roder MS (2002) Development of wheat D-genome introgression lines assisted by microsatellite markers. In: Hernández P, Moreno MT, Cubero JI, Martin A, editors. Proceedings of the Fourth International Triticeae Symposium; 2001 September; Cordoba, Spain. Published in Cordoba by Junta de Andalucia. Consejera de Agricultura y Pesca, pp. 207–210.
  • Pestsova EG, Borner A, Roder MS (2003) Application of microsatellite markers to develop Triticum aestivum–Aegilops tauschii defined introgression lines. In: Borner A., Snape JW, Law CN, editors. Proceedings of the Twelfth International EWAC (European Wheat Aneuploid Co-operative) Workshop; 2002 July 1–6; Norwich, United Kingdom, John Innes Centre, publisher. pp 32-35
  • Ramsay LD, Jennings DE, Bohuon EJR, Arthur AE, Lydiate DJ, et al. (1996) The construction of a substitution library of recombinant backcross lines in Brassica oleracea for the precision mapping of quantitative trait loci (QTL). Genome 39: 558–567
  • Rick CM (1976) Natural variability in wild species of Lycopersicon and its bearing on tomato breeding. Agraria 30: 249–510
  • Rick CM (1983) Conservation and use of exotic tomato germplasm. Conservation and Utilization of exotic germplasm to improve varieties. The 1983 Plant Breeding Research Forum: Conservation and utilization of exotic germplasm to improve varieties. Brown WL, editor. August 9-11, 1983, Heber Springs, Arkansas: Des Moines, Iowa, Pioneer Hybrid Int’l Inc., publisher. pp. 147–167.
  • Sears E (1956) The transfer of leaf-rust resistance from Aegilops umbellulata to wheat. Brookhaven Symp Biol 9: 1–22
  • Sobrizal K, Ikeda K, Sanchez PL, Doi K, Angeles ER, et al. (1996) Development of Oryza glumaepatula introgression lines in rice, O. sativa L. Rice Genet Newsl 16: 107
  • Sun et al 2001 Theo. Appl. Genet 102:157-162
  • Tanksley SD, McCouch SR (1997) Seed banks and molecular maps: Unlocking genetic potential from the wild. Science 277: 1063–1066
  • Thomson M, Tai T, McClung A, Xai X-H, Hinga M, Lobos K, Xu Y, Martinez P, McCouch S (2003) 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 107:479–493
  • Xiao J, Li J, Grandillo S, Ahn SN, Yuan L, et al. (1998) Identification of trait-improving quantitative trait loci alleles from a wild rice relative, Oryza rufipogon. Genetics 150: 899–909.
  • Yano M (2001) Genetic and molecular dissection of naturally occurring variation. Curr Opin Plant Biol 4: 130–135
  • Zamir D (2001) Improving plant breeding with exotic genetic libraries. Nat Rev Genet 2:983-9
  • Zhu, Y.-L, Q.-J. Song, D.L. Hyten, C.P. Van Tassell, L.K. Matukumalli, D.R. Grimm, S.M. Hyatt, E.W. Fickus, N.D. Young, and P.B. Cregan. 2003. Single nucleotide polymorphisms (SNPs) in soybean. Genetics 163: 1123-1134.