Advertisement

Diversity Arrays Technology (DArT) Markers for Genetic Diversity

  • Dariusz GrzebelusEmail author
Chapter
Part of the Sustainable Development and Biodiversity book series (SDEB, volume 7)

Abstract

Diversity Arrays Technology (DArT) is a hybridization-based high-throughput genotyping technology that was proposed in the beginning of the twenty-first century as an efficient and cost-effective alternative to existing genotyping systems, and since then it has been used extensively to explore genetic diversity in many plant species. In this chapter, we describe the principles behind DArT genotyping, summarize the research on plant genetic diversity utilizing the DArT system, discuss advantages, limitations, and perspectives of the technology.

Keywords

Genetic diversity Genotyping High-throughput Cost-effective DArT system Genetic erosion Crop domestication 

Notes

Acknowledgments

This study was supported by the Polish Ministry of Science and Higher Education fund for statutory activities for the University of Agriculture in Krakow.

References

  1. Akbari M, Wenzl P, Caig V et al (2006) Diversity Arrays Technology (DArT) for high-throughput profiling of the hexaploid wheat genome. Theor Appl Genet 113:1409–1420CrossRefPubMedGoogle Scholar
  2. Amorim EP, Vilarinhos AD, Cohen KO et al (2009) Genetic diversity of carotenoid-rich bananas evaluated by Diversity Arrays Technology (DArT). Genet Mol Biol 32:96–103CrossRefPubMedPubMedCentralGoogle Scholar
  3. Atienza SG, de la Rosa R, Domínguez-Garcia MC et al (2013) Use of DArT markers as a means of better management of the diversity of olive cultivars. Food Res Int 54:2045–2053CrossRefGoogle Scholar
  4. Badea A, Eudes F, Graf RJ et al (2008) Phenotypic and marker-assisted evaluation of spring and winter wheat germplasm for resistance to fusarium head blight. Euphytica 164:803–819CrossRefGoogle Scholar
  5. Baird JH, Kopecký D, Lukaszewski AJ et al (2012) Genetic diversity of turf-type tall fescue using Diversity Arrays Technology. Crop Sci 52:408–412CrossRefGoogle Scholar
  6. Bolibok-Brągoszewska H, Heller-Uszyńska K, Wenzl P et al (2009) DArT markers for the rye genome—genetic diversity and mapping. BMC Genom 10:578CrossRefGoogle Scholar
  7. Botstein D, White RL, Skolnick M, Davis RW (1980) Construction of a genetic linkage map in man using restriction fragment length polymorphisms. Am J Hum Genet 32:314–331PubMedPubMedCentralGoogle Scholar
  8. Briñez B, Blair M, Kilian A et al (2012) A whole genome DArT assay to access germplasm collection diversity in common beans. Mol Breed 30:181–193CrossRefGoogle Scholar
  9. Courtois B, Audebert A, Dardou A et al (2013) Genome-wide association mapping of root traits in a Japonica rice panel. PLoS ONE 8:e78037CrossRefPubMedPubMedCentralGoogle Scholar
  10. Crossa J, Burgueño J, Dreisigacker S et al (2007) Association analysis of historical bread wheat germplasm using additive genetic covariance of relatives and population structure. Genetics 177:1889–1913CrossRefPubMedPubMedCentralGoogle Scholar
  11. Cruz VMV, Kilian A, Dierig DA (2013) Development of DArT marker platforms and genetic diversity assessment of the U.S. collection of the new oilseed crop Lesquerella and related species. PLoS ONE 8:e64062CrossRefPubMedPubMedCentralGoogle Scholar
  12. Davey JW, Hohenlohe PA, Etter PD et al (2011) Genome-wide genetic marker discovery and genotyping using next-generation sequencing. Nature Rev Genet 12:499–510CrossRefPubMedGoogle Scholar
  13. Diatchenko L, Lau YF, Cambpbell AP et al (1996) Suppression subtractive hybridization: a method for generating differentially regulated or tissue-specific cDNA probes and libraries. Proc Natl Acad Sci USA 93:6025–6030CrossRefPubMedPubMedCentralGoogle Scholar
  14. Domínguez-Garcia MC, Belaj A, de la Rosa R et al (2012) Development of DArT markers in olive (Oleaeuropaea L.) and usefulness in variability studies and genome mapping. Sci Hortic 136:50–60CrossRefGoogle Scholar
  15. Grzebelus D, Iorizzo M, Senalik D et al (2014) Diversity, genetic mapping, and signatures of domestication in the carrot (Daucuscarota L.) genome, as revealed by Diversity Arrays Technology (DArT) markers. Mol Breed 33:625–637CrossRefPubMedGoogle Scholar
  16. Gupta PK, Rustgi S, Mir RR (2008) Array-based high-throughput DNA markers for crop improvement. Heredity 101:5–18CrossRefPubMedGoogle Scholar
  17. Hang Vu TT, Lawn RJ, Bielig LM et al (2012) Development and initial evaluation of diversity array technology for soybean and mungbean. Euphytica 186:741–754CrossRefGoogle Scholar
  18. Heller-Uszynska K, Uszynski G, Huttner E et al (2011) Diversity Arrays Technology effectively reveals DNA polymorphism in a large and complex genome of sugarcane. Mol Breed 28:37–55CrossRefGoogle Scholar
  19. Howard EL, Whittock SP, Jakše J et al (2011) High-throughput genotyping of hop (Humulus lupulus L.) utilising Diversity Arrays Technology (DArT). Theor Appl Genet 122:1265–1280CrossRefPubMedGoogle Scholar
  20. Hurtado P, Olsen KM, Buitrago C et al (2008) Comparison of simple sequence repeat (SSR) and diversity array technology (DArT) markers for assessing genetic diversity in cassava (Manihot esculenta Crantz). Plant Genet Resour Charact Utilization 6:208–214CrossRefGoogle Scholar
  21. Jaccoud D, Peng K, Feinstein D et al (2001) Diversity arrays: a solid state technology for sequence information independent genotyping. Nucleic Acids Res 29:e25CrossRefPubMedPubMedCentralGoogle Scholar
  22. James KE, Schneider H, Ansell SW et al (2008) Diversity Arrays Technology (DArT) for pan-genomic evolutionary studies of non-model organisms. PLoS ONE 3:e1682CrossRefPubMedPubMedCentralGoogle Scholar
  23. Jing H-C, Bayon C, Kanyuka K et al (2009) DArT markers: diversity analyses, genomes comparison, mapping and integration with SSR markers in Triticum monococcum. BMC Genom 10:458CrossRefGoogle Scholar
  24. Kilian A, Huttner E, Wenzl P et al (2005) The fast and the cheap: SNP and DArT-based whole genome profiling for crop improvement. In: Tuberosa R, Philips RL, Gale M (eds), Proceedings of the international congress “in the wake of the double helix: from the green revolution to the gene revolution”, Bologna, May 2003, Avenue Media, pp 443–461Google Scholar
  25. Lezar S, Myburg AA, Berger DK et al (2004) Development and assessment of microarray-based DNA fingerprinting in Eucalyptus grandis. Theor Appl Genet 109:1329–1336CrossRefPubMedGoogle Scholar
  26. Mace ES, Xia L, Jordan DR et al (2008) DArT markers: diversity analyses and mapping in Sorghum bicolor. BMC Genom 9:26CrossRefGoogle Scholar
  27. Macko-Podgórni A, Iorizzo M, Smółka K et al (2014) Conversion of a Diversity Arrays Technology marker differentiating wild and cultivated carrots to a co-dominant cleaved amplified polymorphic site marker. Acta Biochim Pol 61:19–22PubMedGoogle Scholar
  28. Ovesná J, Kučera L, Vaculová K et al (2013) Analysis of the genetic structure of a barley collection using DNA diversity array technology (DArT). Plant Mol Biol Rep 31:280–288CrossRefGoogle Scholar
  29. Powell W, Machray G, Provan J (1996) Polymorphism revealed by simple sequence repeats. Trends Plant Sci 1:215–222CrossRefGoogle Scholar
  30. Rafalski A (2002) Applications of single nucleotide polymorphismsin crop genetics. Curr Opin Plant Biol 5:94–100CrossRefPubMedGoogle Scholar
  31. Raman H, Raman R, Nelson MN et al (2012) Diversity Arrays Technology markers: genetic diversity analyses and linkage map construction in rapeseed (Brassica napus L.). DNA Res 19:51–65CrossRefPubMedGoogle Scholar
  32. Risterucci A-M, Hippolyte I, Perrier X et al (2009) Development ad assessment of Diversity Arrays Technology for high-throughput DNA analyses in Musa. Theor Appl Genet 119:1093–1103CrossRefPubMedGoogle Scholar
  33. Soahil Q, Shehzad T, Kilian A et al (2012) Development of diversity array technology (DArT) markers for assessment of population structure and diversity in Aegilops tauschii. Breed Sci 62:38–45CrossRefGoogle Scholar
  34. Tinker NA, Kilian A, Wight CP et al (2009) New DArT markers for oat provide enhanced map coverage and global germplasm characterization. BMC Genom 10:39CrossRefGoogle Scholar
  35. Traini A, Iorizzo M, Mann H et al (2013) Genome microscale heterogeneity among wild potatoes revealed by Diversity Arrays Technology marker sequences. Int J Genom. doi: 10.1155/2013/257218
  36. Varshney RK, Glaszmann J-C, Leung H et al (2010) More genomic resources for less-studied crops. Trends Biotechnol 28:452–460CrossRefPubMedGoogle Scholar
  37. Vos P, Hogers R, Bleeker M et al (1995) AFLP: a new technique for DNA fingerprinting. Nucleic Acids Res 23:4407–4414CrossRefPubMedPubMedCentralGoogle Scholar
  38. Wenzl P, Carling J, Kudrna D et al (2004) Diversity Arrays Technology (DArT) for whole-genome profiling of barley. Proc Natl Acad Sci USA 101:9915–9920CrossRefPubMedPubMedCentralGoogle Scholar
  39. White J, Law JR, MacKay KJ et al (2008) The genetic diversity of UK, US and Australian cultivars of Triticum aestivum measured by DArT markers and considered by genome. Theor Appl Genet 116:439–453CrossRefPubMedGoogle Scholar
  40. Williams JGK, Kubelik AR, Livak KJ et al (1990) DNA polymorphisms amplified by arbitrary primers are useful as genetic markers. Nucleic Acids Res 18:6531–6535CrossRefPubMedPubMedCentralGoogle Scholar
  41. Wittenberg AHJ, van der Lee T, Cayla C et al (2005) Validation of the high-throughput marker technology DArT using the model plant Arabidopsis thaliana. Mol Genet Genom 274:30–39CrossRefGoogle Scholar
  42. Xia L, Peng K, Yang S et al (2005) DArT for high-throughput genotyping of cassava (Manihot esculenta) and its wild relatives. Theor Appl Genet 110:1092–1098CrossRefPubMedGoogle Scholar
  43. Xie Y, McNally K, Li C-Y et al (2006) A high-throughput genomic tool: diversity array technology complementary for rice genotyping. J Integr Plant Biol 48:1069–1076CrossRefGoogle Scholar
  44. Yang S, Pang W, Ash G et al (2006) Low level of genetic diversity in cultivated Pigeonpea compared to its wild relatives is revealed by Diversity Arrays Technology. Theor Appl Genet 113:585–595CrossRefPubMedGoogle Scholar
  45. Zalapa JE, Cuevas H, Zhu H et al (2012) Using next-generation sequencing approaches to isolate simple sequence repeats (SSR) loci in the plant sciences. Am J Bot 99:193–208CrossRefPubMedGoogle Scholar

Copyright information

© Springer International Publishing Switzerland 2015

Authors and Affiliations

  1. 1.Institute of Plant Biology and BiotechnologyUniversity of Agriculture in KrakowKrakowPoland

Personalised recommendations