Abstract
Understanding the distribution of genetic diversity within and among individuals, populations, species and gene pools is crucial for the efficient management of germplasm collections. Molecular markers are playing an increasing role in germplasm characterization, yet their broad application is limited by the availability of markers, the costs and the low throughput of existing technologies. This is particularly true for crops of resource-poor farmers such as cassava, Manihot esculenta. Here we report on the development of Diversity Arrays Technology (DArT) for cassava. DArT uses microarrays to detect DNA polymorphism at several hundred genomic loci in a single assay without relying on DNA sequence information. We tested three complexity reduction methods and selected the two that generated genomic representations with the largest frequency of polymorphic clones (PstI/TaqI: 14.6%, PstI/BstNI: 17.2%) to produce large genotyping arrays. Nearly 1,000 candidate polymorphic clones were detected on the two arrays. The performance of the PstI/TaqI array was validated by typing a group of 38 accessions, 24 of them in duplicate. The average call rate was 98.1%, and the scoring reproducibility was 99.8%. DArT markers displayed fairly high polymorphism information content (PIC) values and revealed genetic relationships among the samples consistent with the information available on these samples. Our study suggests that DArT offers advantages over current technologies in terms of cost and speed of marker discovery and analysis. It can therefore be used to genotype large germplasm collections.
This is a preview of subscription content, log in via an institution to check access.
Similar content being viewed by others
References
Anderson JA, Churchill GA, Autrique JE, Tanksley SD, Sorrells ME (1993) Optimizing parental selection for genetic linkage maps. Genome 36:181–186
Awoleye F, van Duren M, Dolezel J, Novak FJ (1994) Nuclear DNA content and in vitro induced somatic polyploidization cassava (Manihot esculenta Crantz) breeding. Euphytica 76:195–20
Bellotti AC, Arias B (2001) Host plant resistance to whiteflies with emphasis on cassava as a case study. Crop Prot 20:813–823
Bezdek JC (1981) Pattern recognition with fuzzy objective function algorithms. Plenum Press, New York
Bonierbale MW, Maya MM, Claros JL, Iglesias C (1995) Application of molecular markers to describing the genetic structure of cassava gene pools. In: The cassava biotechnology network: Proc 2nd Int Sci Meet. Working document no. 50, Centro International de Agricultura Tropical, 2v, Cali, Colombia
Chavarriaga-Aguirre P, Maya MM, Bonierbale MW, Kresovich S, Fregene MA, Tohme J, Kochert G (1998) Microsatellites in cassava (Manihot esculenta Crantz): discovery, inheritance and variability. Theor Appl Genet 97:493–501
Chavarriaga-Aguirre P, Maya MM, Tohme J, Duque MC, Iglesias C, Bonierbale MW, Kresovich S, Kochert G (1999) Using microsatellites, isozymes and AFLPs to evaluate genetic diversity and redundancy in the cassava core collection and to assess the usefulness of DNA-based markers to maintain germplasm collections. Mol Breed 5:263–273
CIAT (2002) Assessing and utilizing agrobiodiversity through biotechnology: Annual Report: Project SB-02. Centro Internacional de Agricultura Tropical, Cali, Colombia
CIAT (2003) Assessing and utilizing agrobiodiversity through biotechnology: Annual Report: Project SB-02. Centro Internacional de Agricultura Tropical, Cali, Colombia
Dellaporta SL, Woods J, Hicks JR (1983) A plant DNA minipreparation: version II. Plant Mol Biol Rep 1:19–21
FAOSTAT (2001) FAO statistical databases. Rome, Italy
Felsenstein, J (1989) phylip—phylogeny inference package. Cladistics 5:164–166
Fregene MA, Bernal A, Dixon A, Roca W, Tohme J (2000) AFLP analysis of African cassava (Manihot esculenta Crantz) germplasm resistant to the cassava mosaic disease (CMD). Theor Appl Genet 100:678–685
Fregene M, Suarez M, Mkumbira J, Kulembeka H, Ndedya E, Kulaya A, Mitchel S, Gullberg U, Rosling H, Dixon A, Kresovich S (2003) Simple sequence repeat (SSR) diversity of cassava (Manihot esculenta Crantz) landraces: genetic diversity and differentiation in a predominantly asexually propagated crop. Theor Appl Genet 107:1083–1093
Jaccoud D, Peng K, Feinstein D, Kilian A (2001) Diversity arrays: a solid state technology for sequence information independent genotyping. Nucleic Acids Res 29:e25
Nei M, Li WH (1979) Mathematical model for studying genetic variation in terms of restriction endonucleases. Proc Natl Acad Sci USA 76:5269–5273
Ocampo C, Hershey C, Iglesias C, Iwanaga M (1992) Esterase isozyme fingerprinting of the cassava germplasm collection held at CIAT. In: Roca W, Thro AM (eds) Proc 1st Int Sci Meet Cassava Biotechnol Network CIAT. Cali, Colombia, pp 81–89
Second G, Allem A, Emperaire L, Ingram C, Colombo C, Mendes R, Carvalho L (1997) AFLP based Manihot and cassava numerical taxonomy and genetic structure analysis in progress: implications for dynamic conservation and genetic mapping. Afr J Root Tuber Crops 2:140–147
Wenzl P, Carling J, Kudrna D, Jaccoud D, Huttner E, Kleinhofs A, Kilian A (2004) diversity arrays technology (DArT) for whole-genome profiling of barley. Proc Natl Acad Sci USA 101:9915–9920
Acknowledgements
We thank our colleagues at DArT P/L and CAMBIA for helpful discussions and colleagues in CIAT for DNA extraction. Special thanks are extended to Cyril Cayla and Grzegorz Uszynski for help with data analysis and to Eric Huttner for his help with drafting the manuscript. Ling Xia and Kaiman Peng contributed equally to the manuscript.
Author information
Authors and Affiliations
Corresponding author
Additional information
Communicated by H.C. Becker
Electronic Supplementary Material
Rights and permissions
About this article
Cite this article
Xia, L., Peng, K., Yang, S. et al. DArT for high-throughput genotyping of Cassava (Manihot esculenta) and its wild relatives. Theor Appl Genet 110, 1092–1098 (2005). https://doi.org/10.1007/s00122-005-1937-4
Received:
Accepted:
Published:
Issue Date:
DOI: https://doi.org/10.1007/s00122-005-1937-4