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Construction of a quinoa (Chenopodium quinoa Willd.) BAC library and its use in identifying genes encoding seed storage proteins

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Abstract

Quinoa (Chenopodium quinoa Willd.) is adapted to the harsh environments of the Andean Altiplano region. Its seeds have a well-balanced amino acid composition and exceptionally high protein content with respect to human nutrition. Quinoa grain is a staple in the diet of some of the most impoverished people in the world. The plant is an allotetraploid displaying disomic inheritance (2n=4x=36) with a di-haploid genome of 967 Mbp (megabase pair), or 2C=2.01 pg. We constructed two quinoa BAC libraries using BamHI (26,880 clones) and EcoRI (48,000 clones) restriction endonucleases. Cloned inserts in the BamHI library average 113 kb (kilobase) with approximately 2% of the clones lacking inserts, whereas cloned inserts in the EcoRI library average 130 kb and approximately 1% lack inserts. Three plastid genes used as probes of high-density arrayed blots of 73,728 BACs identified approximately 2.8% of the clones as containing plastid DNA inserts. We estimate that the combined quinoa libraries represent at least 9.0 di-haploid nuclear genome equivalents. An average of 12.2 positive clones per probe were identified with 13 quinoa single-copy ESTs as probes of the high-density arrayed blots, suggesting that the estimate of 9.0× coverage of the genome is conservative. Utility of the BAC libraries for gene identification was demonstrated by probing the library with a partial sequence of the 11S globulin seed storage protein gene and identifying multiple positive clones. The presence of the 11S globulin gene in four of the clones was verified by direct comparison with quinoa genomic DNA on a Southern blot. Besides serving as a useful tool for gene identification, the quinoa BAC libraries will be an important resource for physical mapping of the quinoa genome.

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Acknowledgements

We acknowledge the contribution to this work by Jared Tyler. This research was made possible by financial support from the McKnight Foundation-CCRP, Holmes Family Foundation, and the Ezra Taft Benson Agriculture and Food Institute and germplasm contributions by PROINPA (La Paz, Bolivia) and the National University of the Altiplano/FAO (Puno, Peru). The work reported here was carried out in compliance with laws governing genetic experimentation in the United States.

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  1. S. E. Parkinson

    Present address: Department of Plant and Microbial Biology, University of California Berkeley, 111 Koshland Hall, Berkeley, CA, 94720, USA

Authors and Affiliations

  1. Department of Plant and Animal Sciences, Brigham Young University, Provo, UT, 84602-5157, USA

    M. R. Stevens, C. E. Coleman, S. E. Parkinson, P. J. Maughan, M. R. Balzotti, D. J. Fairbanks, E. N. Jellen & J. J. Stevens

  2. Department of Soil and Crop Sciences and Institute for Plant Genomics and Biotechnology, 2123 TAMU, Texas A&M University, College Station, TX, 77843-2123, USA

    H.-B. Zhang

  3. Department of Physiology and Developmental Biology, Brigham Young University, Provo, UT, 84602, USA

    D. L. Kooyman

  4. Flow and Image Cytometry Core Laboratories, Benaroya Research Institute at Virginia Mason, 1201 Ninth Avenue, Seattle, WA, 98101, USA

    K. Arumuganathan

  5. The Foundation for the Promotion and Investigation of Andean Products (PROINPA), La Paz, Bolivia

    A. Bonifacio

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  1. M. R. Stevens
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Correspondence to M. R. Stevens.

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Communicated by E. Guiderdoni

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Stevens, M.R., Coleman, C.E., Parkinson, S.E. et al. Construction of a quinoa (Chenopodium quinoa Willd.) BAC library and its use in identifying genes encoding seed storage proteins. Theor Appl Genet 112, 1593–1600 (2006). https://doi.org/10.1007/s00122-006-0266-6

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