Wednesday, April 13, 2011

Research History and Current Status

International collaborative research on quinoa genetics began at BYU in 1988. Throughout this 21-year period, BYU’s focus has been devoted to improving basic scientific understanding of quinoa, and applying discoveries in plant breeding programs, education, and extension in South America. Research on quinoa genomics began in 2001 with a collaborative research grant awarded to the Foundation for Promotion and Research of Andean Products (PROINPA) in Bolivia, and Brigham Young University (BYU) in the USA from the McKnight Foundation Collaborative Crops Research Program (CCRP). This grant was renewed for a second phase that will continue through February 2010. A portion of the McKnight CCRP grant is devoted to research on quinoa genomics, the results of which have provided a foundation for the research proposed here. PROINPA is a developing-country partner with BYU in this proposal. Practically no quinoa genomics has been done by other research groups. A brief summary of our research efforts to date includes the following:
- Salt-tolerance physiology: In a greenhouse experiment, saline solutions were applied to the quinoa varieties, Chipaya and KU-2, and to the model halophyte Thellungiella halophila to assess their relative responses to salt stress. Height and weight data from a seven-week time course demonstrated that both cultivars exhibited greater tolerance to salt than T. halophila. In a growth chamber experiment, three quinoa cultivars, Chipaya, Ollague, and CICA 17 were hydroponically grown and physiological responses were measured with four salt treatments. Tissues collected from the growth chamber treatments were used to obtain leaf succulence data, tissue ion concentrations, compatible solute concentrations, stomatal conductance, and RNA for real-time PCR. The expression profiles of SOS1, NHX1, TIP2 genes involved in salt stress showed constitutive expression in root tissue and up-regulation in leaf tissue in response to salt stress. These data suggest that quinoa tolerates salt through a combination of exclusion and accumulation mechanisms 1.
- Genetic markers, genetic mapping, and germplasm characterization: We have sequenced-characterized and genetically mapped numerous DNA markers in quinoa, including 403 characterized microsatellites2,3, of which 221 have been placed on the first genetic linkage map of the quinoa genome 3. These DNA markers have been used by BYU, PROINPA, and the Universidad de Arturo Prat, (Iquique, Chile) to evaluate genetic diversity within the USDA 4, Bolivian and Chilean 5 germplasm collections.
- Quinoa BAC library construction: We have completed a high-quality BAC library of the quinoa genome with approximately 70,000 clones and 9X genomic coverage 6. The library has been arrayed and deposited at the Arizona Genomics Institute (AGI) and is publicly available from AGI on a cost-recovery basis.
- Initial cDNA libraries and ESTs: A total of 424 ESTs from the floral and developing seed libraries have been characterized and annotated (GenBank accessions CN781906-CN782329. Forty-five ESTs were highly abundant and 27 of these had putative plant-defense functions (based on homologies with known genes)7. A more exhaustive maturing seed EST library is being developed in our laboratory from pooled RNA samples from 8-, 16-, 24-, 32-, and 40-day maturing seeds. To date we have Sanger sequenced 20,000 clones from a normalized cDNA library.
- Specific gene analysis: Using the BAC library resources, we have cloned and analyzed the expression patterns of the 11S seed storage gene 8 during seed development and most recently, we published cloning and characterization of the Salt Overly Sensitive (SOS1) gene homoeolog in quinoa 9.
- Germplasm: The haploid genome of quinoa (n = 18) is approximately 967 million nucleotide pairs, as determined by flow cytometry, and is thus relatively small compared to the genomes of most plant species 10. Using intergenic-spacer (IGS) sequence, we identified two subclasses of 5S rDNA sequences that likely originated from the two allopolypoid subgenomes of C. quinoa11. Quinoa has numerous wild relatives with chromosome numbers of 2 n = 18, 36, and 54, and one of our research goals has been to identify diploid ancestors of quinoa. Plant collections (2004- present) from in deserts, mountains, and coastal salt marshes of the Southwestern United States as well as Mexico, Bolivia and Chile have resulted in the collection of seed and herbarium specimens representing 14 additional diploid or tetraploid species not previously represented in the USDA-NPGS Chenopodium collection.
- Advanced germplasm: Six improved varieties of quinoa have been released as a result of our McKnight-CCRP research and several others are in the latter stages of development 12.

References Cited
1. Morales, J.A. in Plant and Wildlife Sciences 71 (Brigham Young University, Provo, Utah, 2009).
2. Mason, S.L. et al. Development and use of microsatellite markers for germplasm characterization in quinoa (Chenopodium quinoa Willd.). Crop Science45, 1618-1630 (2005).
3. Jarvis, D.E. et al. Simple sequence repeat marker development and genetic mapping in quinoa (Chenopodium quinoa Willd.). Journal of Genetics87, 39-51 (2008).
4. Christensen, S.A. et al. Assessment of genetic diversity in the USDA and CIP-FAO international nursery collections of quinoa (Chenopodium quinoa Willd.) using microsatellite markers. Plant Genetic Resources 5, 82-95 (2007).
5. Fuentes, F.F., Martinez, E.A., Hinrichsen, P.V., Jellen, E.N. & Maughan, P.J. Assessment of genetic diversity patterns in Chilean quinoa (Chenopodium quinoa Willd.) germplasm using multiplex fluorescent microsatellite markers. Conservation Genetics(2008).
6. Stevens, M.R. et al. Construction of a quinoa (Chenopodium quinoa Willd.) BAC library and its use in identifying genes encoding seed storage proteins. Theoretical and Applied Genetics112, 1593-1600 (2006).
7. Coles, N.D. et al. Development and use of an expressed sequenced tag library in quinoa (Chenopodium quinoa Willd.) for the discovery of single nucleotide polymorphisms. Plant Science168, 439-447 (2005).
8. Balzotti, M.B. et al. Expression and Evolutionary Relationships of the Chenopodium quinoa 11S Seed Storage Protein Gene. International Journal of Plant Sciences169, 281-291 (2008).
9. Maughan, P.J. et al. Characterization of Salt Overly Sensitive (SOS1) gene homoeologs in quinoa (Chenopodium quinoa Willd). Genome (2009).
10. Maughan, P.J. et al. A genetic linkage map of quinoa (Chenopodium quinoa) based on AFLP, RAPD, and SSR markers. Theor. Appl. Genet.109, 1188-1195 (2004).
11. Maughan, P.J. et al. Molecular and cytological characterization of ribosomal RNA genes in Chenopodium quinoa and Chenopodium berlandieri. Genome49, 825-839 (2006).
12. Bonifacio, A., Vargas, A. & Aroni, G. (Fundacion PROINPA, Cochabamba, Bolivia., 2003).

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