Table of Contents Author Guidelines Submit a Manuscript
Journal of Biomedicine and Biotechnology
Volume 2012, Article ID 405940, 7 pages
http://dx.doi.org/10.1155/2012/405940
Methodology Report

Utilization of Super BAC Pools and Fluidigm Access Array Platform for High-Throughput BAC Clone Identification: Proof of Concept

Department of Plant & Wildlife Sciences, Brigham Young University, Provo, UT 84602, USA

Received 9 March 2012; Accepted 20 May 2012

Academic Editor: M. Ilyas Kamboh

Copyright © 2012 Peter J. Maughan et al. This is an open access article distributed under the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.

Linked References

  1. Y. S. Yim, P. Moak, H. Sanchez-Villeda et al., “A BAC pooling strategy combined with PCR-based screenings in a large, highly repetitive genome enables integration of the maize genetic and physical maps,” BMC Genomics, vol. 8, p. 47, 2007. View at Publisher · View at Google Scholar · View at Scopus
  2. P. J. Maughan, T. B. Turner, C. E. Coleman et al., “Characterization of salt overly sensitive 1 (SOS1) gene homoeologs in quinoa (Chenopodium quinoa Willd.),” Genome, vol. 52, no. 7, pp. 647–657, 2009. View at Publisher · View at Google Scholar · View at Scopus
  3. A. P. Monaco and Z. Larin, “YACs, BACs, PACs and MACs: artificial chromosomes as research tools,” Trends in Biotechnology, vol. 12, no. 7, pp. 280–286, 1994. View at Publisher · View at Google Scholar · View at Scopus
  4. S. S. Woo, J. Jiang, B. S. Gill, A. H. Paterson, and R. A. Wing, “Construction and characterization of a bacterial artificial chromosome library of Sorghum bicolor,” Nucleic Acids Research, vol. 22, no. 23, pp. 4922–4931, 1994. View at Google Scholar · View at Scopus
  5. J. Tomkins, M. Fregene, D. Main, H. Kim, R. Wing, and J. Tohme, “Bacterial artificial chromosome (BAC) library resource for positional cloning of pest and disease resistance genes in cassava (Manihot esculenta Crantz),” Plant Molecular Biology, vol. 56, no. 4, pp. 555–561, 2004. View at Publisher · View at Google Scholar · View at Scopus
  6. M. R. Stevens, C. E. Coleman, S. E. Parkinson et al., “Construction of a quinoa (Chenopodium quinoa Willd.) BAC library and its use in identifying genes encoding seed storage proteins,” Theoretical and Applied Genetics, vol. 112, no. 8, pp. 1593–1600, 2006. View at Publisher · View at Google Scholar · View at Scopus
  7. M. Luo, Y. H. Wang, D. Frisch, T. Joobeur, R. A. Wing, and R. A. Dean, “Melon bacterial artificial chromosome (BAC) library construction using improved methods and identification of clones linked to the locus conferring resistance to melon Fusarium wilt (Fom-2),” Genome, vol. 44, no. 2, pp. 154–162, 2001. View at Publisher · View at Google Scholar · View at Scopus
  8. C. Wu, S. Sun, P. Nimmakayala et al., “A BAC- and BIBAC-based physical map of the soybean genome,” Genome Research, vol. 14, no. 2, pp. 319–326, 2004. View at Publisher · View at Google Scholar · View at Scopus
  9. Y. S. Yim, G. L. Davis, N. A. Duru et al., “Characterization of three maize bacterial artificial chromosome libraries toward anchoring of the physical map to the genetic map using high-density bacterial artificial chromosome filter hybridization,” Plant Physiology, vol. 130, no. 4, pp. 1686–1696, 2002. View at Publisher · View at Google Scholar · View at Scopus
  10. W. J. Bruno, E. Knill, D. J. Balding et al., “Efficient pooling designs for library screening,” Genomics, vol. 26, no. 1, pp. 21–30, 1995. View at Publisher · View at Google Scholar · View at Scopus
  11. J. D. Sauer, “Grain amaranths,” in Evolution of Crop Plants, N. W. Simmonds, Ed., pp. 4–7, Longman Group, London, UK, 1976. View at Google Scholar
  12. R. Bressani, A. Sanchez-Marroquin, and E. Morales, “Chemical composition of grain amaranth cultivars and effects of processing on their nutritional quality,” Food Reviews International, vol. 8, no. 1, pp. 23–49, 1992. View at Publisher · View at Google Scholar
  13. R. Bressani, L. G. Elias, and A. Garcia-Soto, “Limiting amino acids in raw and processed amaranth grain protein from biological tests,” Plant Foods for Human Nutrition, vol. 39, no. 3, pp. 223–234, 1989. View at Publisher · View at Google Scholar · View at Scopus
  14. W. M. Breene, “Food uses of grain Amaranth,” Cereal Foods World, vol. 36, no. 5, pp. 426–430, 1991. View at Google Scholar
  15. D. K. Transue, D. J. Fairbanks, L. R. Robison, and W. R. Andersen, “Species identification by RAPD analysis of grain amaranth genetic resources,” Crop Science, vol. 34, no. 5, pp. 1385–1389, 1994. View at Google Scholar · View at Scopus
  16. N. Mandal and P. K. Das, “Intra- and interspecific genetic diversity in grain amaranthus using ramdom amplified polymorphic DNA markers,” Plant Tissue Culture and Biotechnology, vol. 12, no. 1, pp. 49–56, 2002. View at Google Scholar · View at Scopus
  17. K. F. Chan and M. Sun, “Genetic diversity and relationships detected by isozyme and RAPD analysis of crop and wild species of Amaranthus,” Theoretical and Applied Genetics, vol. 95, no. 5-6, pp. 865–873, 1997. View at Publisher · View at Google Scholar · View at Scopus
  18. F. Xu and M. Sun, “Comparative analysis of phylogenetic relationships of grain amaranths and their wild relatives (Amaranthus; Amaranthaceae) using internal transcribed spacer, amplified fragment length polymorphism, and double-primer fluorescent intersimple sequence repeat markers,” Molecular Phylogenetics and Evolution, vol. 21, no. 3, pp. 372–387, 2001. View at Publisher · View at Google Scholar · View at Scopus
  19. M. A. Mallory, R. V. Hall, A. R. McNabb, D. B. Pratt, E. N. Jellen, and P. J. Maughan, “Development and characterization of microsatellite markers for the grain amaranths,” Crop Science, vol. 48, no. 3, pp. 1098–1106, 2008. View at Publisher · View at Google Scholar · View at Scopus
  20. P. J. Maughan, S. M. Yourstone, E. N. Jellen, and J. A. Udall, “SNP discovery via genomic reduction, barcoding and 454-pyrosequencing in amaranth,” Plant Genome, vol. 2, no. 2, pp. 260–270, 2009. View at Google Scholar
  21. P. J. Maughan, N. Sisneros, M. Luo, D. Kudrna, J. S. S. Ammiraju, and R. A. Wing, “Construction of an Amaranthus hypochondriacus bacterial artificial chromosome library and genomic sequencing of herbicide target genes,” Crop Science, vol. 48, no. 1, pp. S85–S94, 2008. View at Publisher · View at Google Scholar · View at Scopus
  22. P. Maughan, S. Smith, D. Fairbanks, and E. Jellen, “Development, characterization, and linkage mapping of single nucleotide polymorphisms in the grain amaranths (Amaranthus sp.),” Plant Genome, vol. 4, no. 1, pp. 92–101, 2011. View at Publisher · View at Google Scholar
  23. J. P. Delano-Frier, H. Aviles-Arnaut, K. Casarrubias-Castillo et al., “Transcriptomic analysis of grain amaranth (Amaranthus hypochondriacus) using 454 pyrosequencing: comparison with A. tuberculatus, expression profiling in stems and in response to biotic and abiotic stress,” BMC Genomics, vol. 12, p. 363, 2011. View at Publisher · View at Google Scholar
  24. M. F. Bouzidi, J. Franchel, Q. Tao et al., “A sunflower BAC library suitable for PCR screening and physical mapping of targeted genomic regions,” Theoretical and Applied Genetics, vol. 113, no. 1, pp. 81–89, 2006. View at Publisher · View at Google Scholar · View at Scopus
  25. J. Wang, M. Lin, A. Crenshaw et al., “High-throughput single nucleotide polymorphism genotyping using nanofluidic Dynamic Arrays,” BMC Genomics, vol. 10, p. 561, 2009. View at Publisher · View at Google Scholar · View at Scopus
  26. M. D. Bennett and J. B. Smith, “Nuclear dna amounts in angiosperms,” Philosophical transactions of the Royal Society of London B, vol. 274, no. 933, pp. 227–274, 1976. View at Google Scholar · View at Scopus