Utilization of super BAC pools and Fluidigm access array platform for high-throughput BAC clone identification: Proof of concept

Journal of Biomedicine and Biotechnology

Volumn 2012, Issue , 2012, Pages

  Maughan, Peter J ^a   Smith, Scott M ^a   Raney, Joshua A ^a  

^a BRIGHAM YOUNG UNIVERSITY   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

AMARANTHUS; AMARANTHUS HYPOCHONDRIACUS; ARTICLE; BACTERIAL ARTIFICIAL CHROMOSOME; CLONE; GENE AMPLIFICATION; GENE LOCUS; GENOMICS; GENOTYPE; INTEGRATED FLUIDIC CHIP; MICROCHIP ANALYSIS; NONHUMAN; POLYMERASE CHAIN REACTION; SINGLE NUCLEOTIDE POLYMORPHISM; DNA SEQUENCE; GENETIC LINKAGE; GENETIC MARKER; GENETIC SCREENING; GENETICS; GENOTYPING TECHNIQUE; HIGH THROUGHPUT SEQUENCING; METHODOLOGY; MOLECULAR CLONING; REPRODUCIBILITY;

AMARANTHUS; CHROMOSOMES, ARTIFICIAL, BACTERIAL; CLONING, MOLECULAR; GENETIC LINKAGE; GENETIC MARKERS; GENETIC TESTING; GENOTYPING TECHNIQUES; HIGH-THROUGHPUT NUCLEOTIDE SEQUENCING; POLYMERASE CHAIN REACTION; POLYMORPHISM, SINGLE NUCLEOTIDE; REPRODUCIBILITY OF RESULTS; SEQUENCE ANALYSIS, DNA;

EID: 84864935191     PISSN: 11107243     EISSN: 11107251     Source Type: Journal    
DOI: 10.1155/2012/405940     Document Type: Article

References (26)

1. Yim Y. S., Moak P., Sanchez-Villeda H., Musket T. A., Close P., Klein P. E., Mullet J. E., McMullen M. D., Fang Z., Schaeffer M. L., Gardiner J. M., Coe E. H., Davis G. L., 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 2007 8 47
2. Maughan P. J., Turner T. B., Coleman C. E., Elzinga D. B., Jellen E. N., Morales J. A., Udall J. A., Fairbanks D. J., Bonifacio A., Characterization of salt overly sensitive 1 (SOS1) gene homoeologs in quinoa (Chenopodium quinoa Willd.) Genome 2009 52 7 647 657
3. Monaco A. P., Larin Z., YACs, BACs, PACs and MACs: artificial chromosomes as research tools Trends in Biotechnology 1994 12 7 280 286 (Pubitemid 24221975)
4. Woo S. S., Jiang J., Gill B. S., Paterson A. H., Wing R. A., Construction and characterization of a bacterial artificial chromosome library of Sorghum bicolor Nucleic Acids Research 1994 22 23 4922 4931
5. Tomkins J., Fregene M., Main D., Kim H., Wing R., Tohme J., Bacterial artificial chromosome (BAC) library resource for positional cloning of pest and disease resistance genes in cassava (Manihot esculenta Crantz) Plant Molecular Biology 2004 56 4 555 561
6. Stevens M. R., Coleman C. E., Parkinson S. E., Maughan P. J., Zhang H. B., Balzotti M. R., Kooyman D. L., Arumuganathan K., Bonifacio A., Fairbanks D. J., Jellen E. N., Stevens J. J., Construction of a quinoa (Chenopodium quinoa Willd.) BAC library and its use in identifying genes encoding seed storage proteins Theoretical and Applied Genetics 2006 112 8 1593 1600
7. Luo M., Wang Y. H., Frisch D., Joobeur T., Wing R. A., Dean R. A., 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 2001 44 2 154 162 (Pubitemid 32333529)
8. Wu C., Sun S., Nimmakayala P., Santos F. A., Meksem K., Springman R., Ding K., Lightfoot D. A., Zhang H. B., A BAC- and BIBAC-based physical map of the soybean genome Genome Research 2004 14 2 319 326 (Pubitemid 38219846)
9. Yim Y. S., Davis G. L., Duru N. A., Musket T. A., Linton E. W., Messing J. W., McMullen M. D., Soderlund C. A., Polacco M. L., Gardiner J. M., Coe E. H., 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 2002 130 4 1686 1696 (Pubitemid 36035166)
10. Bruno W. J., Knill E., Balding D. J., Bruce D. C., Doggett N. A., Sawhill W. W., Stallings R. L., Whittaker C. C., Torney D. C., Efficient pooling designs for library screening Genomics 1995 26 1 21 30
11. Sauer J. D., Simmonds N. W., Grain amaranths Evolution of Crop Plants 1976 London, UK Longman Group 4 7
12. Bressani R., Sanchez-Marroquin A., Morales E., Chemical composition of grain amaranth cultivars and effects of processing on their nutritional quality Food Reviews International 1992 8 1 23 49
13. Bressani R., Elias L. G., Garcia-Soto A., Limiting amino acids in raw and processed amaranth grain protein from biological tests Plant Foods for Human Nutrition 1989 39 3 223 234
14. Breene W. M., Food uses of grain Amaranth Cereal Foods World 1991 36 5 426 430
15. Transue D. K., Fairbanks D. J., Robison L. R., Andersen W. R., Species identification by RAPD analysis of grain amaranth genetic resources Crop Science 1994 34 5 1385 1389 (Pubitemid 2144884)
16. Mandal N., Das P. K., Intra- and interspecific genetic diversity in grain amaranthus using ramdom amplified polymorphic DNA markers Plant Tissue Culture and Biotechnology 2002 12 1 49 56
17. Chan K. F., Sun M., Genetic diversity and relationships detected by isozyme and RAPD analysis of crop and wild species of Amaranthus Theoretical and Applied Genetics 1997 95 5-6 865 873 (Pubitemid 27493057)
18. Xu F., Sun M., 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 2001 21 3 372 387 (Pubitemid 34068018)
19. Mallory M. A., Hall R. V., McNabb A. R., Pratt D. B., Jellen E. N., Maughan P. J., Development and characterization of microsatellite markers for the grain amaranths Crop Science 2008 48 3 1098 1106 (Pubitemid 351955479)
20. Maughan P. J., Yourstone S. M., Jellen E. N., Udall J. A., SNP discovery via genomic reduction, barcoding and 454-pyrosequencing in amaranth Plant Genome 2009 2 2 260 270
21. Maughan P. J., Sisneros N., Luo M., Kudrna D., Ammiraju J. S. S., Wing R. A., Construction of an Amaranthus hypochondriacus bacterial artificial chromosome library and genomic sequencing of herbicide target genes Crop Science 2008 48 1 S85 S94
22. Maughan P., Smith S., Fairbanks D., Jellen E., Development, characterization, and linkage mapping of single nucleotide polymorphisms in the grain amaranths (Amaranthus sp.) Plant Genome 2011 4 1 92 101
23. Delano-Frier J. P., Aviles-Arnaut H., Casarrubias-Castillo K., Casique-Arroyo G., Castrillon-Arbelaez P. A., Herrera-Estrella L., Massange-Sanchez J., Martinez-Gallardo N. A., Parra-Cota F. I., Vargas-Ortiz E., 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 2011 12 363
24. Bouzidi M. F., Franchel J., Tao Q., Stormo K., Mraz A., Nicolas P., Mouzeyar S., A sunflower BAC library suitable for PCR screening and physical mapping of targeted genomic regions Theoretical and Applied Genetics 2006 113 1 81 89
25. Wang J., Lin M., Crenshaw A., Hutchinson A., Hicks B., Yeager M., Berndt S., Huang W. Y., Hayes R. B., Chanock S. J., Jones R. C., Ramakrishnan R., High-throughput single nucleotide polymorphism genotyping using nanofluidic Dynamic Arrays BMC Genomics 2009 10 561
26. Bennett M. D., Smith J. B., Nuclear dna amounts in angiosperms Philosophical transactions of the Royal Society of London B 1976 274 933 227 274