Diversity arrays technology

Diversity Arrays Technology (DArT) is a high-throughput genetic marker technique that can detect allelic variations to provide comprehensive genome coverage without any DNA sequence information for genotyping and other genetic analysis.[1][2][3] The general steps involve reducing the complexity of the genomic DNA with specific restriction enzymes, choosing diverse fragments to serve as representations for the parent genomes, amplify via polymerase chain reaction (PCR), inserting fragments into a vector to be placed as probes within a microarray, and then fluorescent targets from a reference sequence will be allowed to hybridize with probes and put through an imaging system.[1][2] The objective is to identify and quantify various forms of DNA polymorphism within genomic DNA of sampled species.[1]

First reported in 2001 by Damian Jaccoud, Andrzej Kilian, David Feinstein, and Kaiman Peng, DArT prioritized significant advantages over other traditional primer-based methods like the ability to analyze large amounts of various samples from a low amount of initial DNA.[1][2][4][5] It also afforded low costs and faster results compared to related solid state DNA arrays that detected Single Nucleotide Polymorphisms (SNPs).[1][2] Since its inception, the technology has been a major instrument in the analysis of polyploid plants as well as in the construction of physical and genetic maps to understand relations between species based on similarities and allelic variances among their genomes.[1][2][6][7][8][3]

  1. ^ a b c d e f Jaccoud D, Peng K, Feinstein D, Kilian A (February 2001). "Diversity arrays: a solid state technology for sequence information independent genotyping". Nucleic Acids Research. 29 (4): 25e–25. doi:10.1093/nar/29.4.e25. PMC 29632. PMID 11160945.
  2. ^ a b c d e Kilian A, Wenzl P, Huttner E, Carling J, Xia L, Blois H, et al. (2012). "Diversity arrays technology: a generic genome profiling technology on open platforms". In Pompanon F, Bonin A (eds.). Data Production and Analysis in Population Genomics. Methods in Molecular Biology. Vol. 888. Totowa, NJ: Humana Press. pp. 67–89. doi:10.1007/978-1-61779-870-2_5. ISBN 978-1-61779-870-2. PMID 22665276. Data Production and Analysis in Population Genomics: Methods and Protocols
  3. ^ a b Risterucci AM, Hippolyte I, Perrier X, Xia L, Caig V, Evers M, et al. (October 2009). "Development and assessment of Diversity Arrays Technology for high-throughput DNA analyses in Musa". Theoretical and Applied Genetics. 119 (6): 1093–1103. doi:10.1007/s00122-009-1111-5. PMID 19693484. S2CID 23747800.
  4. ^ Vos P, Hogers R, Bleeker M, Reijans M, van de Lee T, Hornes M, et al. (November 1995). "AFLP: a new technique for DNA fingerprinting". Nucleic Acids Research. 23 (21): 4407–4414. doi:10.1093/nar/23.21.4407. PMC 307397. PMID 7501463.
  5. ^ Weber JL, May PE (March 1989). "Abundant class of human DNA polymorphisms which can be typed using the polymerase chain reaction". American Journal of Human Genetics. 44 (3): 388–396. PMC 1715443. PMID 2916582.
  6. ^ Rabinowicz PD, Schutz K, Dedhia N, Yordan C, Parnell LD, Stein L, et al. (November 1999). "Differential methylation of genes and retrotransposons facilitates shotgun sequencing of the maize genome". Nature Genetics. 23 (3): 305–308. doi:10.1038/15479. PMID 10545948. S2CID 19943394.
  7. ^ Wenzl P, Carling J, Kudrna D, Jaccoud D, Huttner E, Kleinhofs A, Kilian A (June 2004). "Diversity Arrays Technology (DArT) for whole-genome profiling of barley". Proceedings of the National Academy of Sciences of the United States of America. 101 (26): 9915–9920. Bibcode:2004PNAS..101.9915W. doi:10.1073/pnas.0401076101. PMC 470773. PMID 15192146.
  8. ^ Akbari M, Wenzl P, Caig V, Carling J, Xia L, Yang S, et al. (November 2006). "Diversity arrays technology (DArT) for high-throughput profiling of the hexaploid wheat genome". Theoretical and Applied Genetics. 113 (8): 1409–1420. doi:10.1007/s00122-006-0365-4. PMID 17033786. S2CID 12636193.