Hostname: page-component-cd9895bd7-dk4vv Total loading time: 0 Render date: 2024-12-24T12:34:02.976Z Has data issue: false hasContentIssue false
  • English
  • Français

Comparison of simple sequence repeat (SSR) and diversity array technology (DArT) markers for assessing genetic diversity in cassava (Manihot esculenta Crantz)

Published online by Cambridge University Press:  22 August 2008

P. Hurtado ,
K. M. Olsen ,
C. Buitrago ,
C. Ospina ,
J. Marin ,
M. Duque ,
C. de Vicente ,
P. Wongtiem ,
P. Wenzel  and
A. Killian
...Show all authors
P. Hurtado
Affiliation:
Centro Internacional de Agricultura Tropical (CIAT), Cali, Colombia
K. M. Olsen
Affiliation:
Biology Department, Washington University, St. Louis, MO, USA
C. Buitrago
Affiliation:
Centro Internacional de Agricultura Tropical (CIAT), Cali, Colombia
C. Ospina
Affiliation:
Centro Internacional de Agricultura Tropical (CIAT), Cali, Colombia
J. Marin
Affiliation:
Centro Internacional de Agricultura Tropical (CIAT), Cali, Colombia
M. Duque
Affiliation:
Centro Internacional de Agricultura Tropical (CIAT), Cali, Colombia
C. de Vicente
Affiliation:
Bioversity International, Cali, Colombia
P. Wongtiem
Affiliation:
Field Crop Research Station, Rayong, Thailand Center for the Application of Molecular Biology to Agriculture (CAMBIA), Canberra, Australia
P. Wenzel
Affiliation:
Center for the Application of Molecular Biology to Agriculture (CAMBIA), Canberra, Australia
A. Killian
Affiliation:
Center for the Application of Molecular Biology to Agriculture (CAMBIA), Canberra, Australia
M. Adeleke
Affiliation:
Department of Biology, Rivers State University of Science and Technology (RUST), Port Harcourt, Nigeria
M. Fregene*
Affiliation:
Centro Internacional de Agricultura Tropical (CIAT), Cali, Colombia
*
*Corresponding author. Email [email protected]
Get access Rights & Permissions [Opens in a new window]

Abstract

Several molecular marker systems have been developed for assessing genetic diversity in crop germplasm collections. A trade-off often exists between the number of loci that can feasibly be sampled by a marker system and the amount of information provided by each locus. We compared the usefulness of two marker systems for revealing genetic diversity and population structure in cassava (Manihot esculenta Crantz): simple sequence repeats (SSRs) and diversity array technology (DArT) markers. DArTs survey many more loci per reaction than do SSRs; however, as bi-allelic, dominant markers, DArTs provide less polymorphism information per locus. Genetic differentiation was assessed in a randomly selected set of 436 cassava accessions, consisting of 155 African and 281 Latin American accessions. A genome-wide set of 36 SSR markers and a DArT array of approximately 1000 polymorphic clones were used to assess genetic diversity and differentiation. Cluster analyses were performed using principal coordinate analysis (PCoA). Results were compared with a priori expectations of genetic differentiation based on previous genetic analyses. Analyses of the two datasets generated broadly similar clustering patterns. However, SSRs revealed greater differentiation than DArTs, and more effectively recovered patterns of genetic differentiation observed in previous analyses (differentiation between Latin American and African accessions, and some geographical differentiation within each of these groups). These results suggest that SSR markers, while low throughput in comparison with DArTs, are relatively better at detecting genetic differentiation in cassava germplasm collections. Nonetheless, DArTs will likely prove useful in ‘orphan crop’ species, where alternative molecular markers have not been developed.

Keywords

cassavaDArT markergenetic differentiationgenetic diversitySSR markers
Type
Research Article
Information
Plant Genetic Resources , Volume 6 , Issue 3 , December 2008 , pp. 208 - 214
Copyright
Copyright © NIAB 2008

Access options

Get access to the full version of this content by using one of the access options below. (Log in options will check for institutional or personal access. Content may require purchase if you do not have access.)

References

Bonierbale, MW, Maya, MM, Claros, JL and Iglesias, C (1995) Application of molecular markers to describing the genetic structure of cassava gene pools. In: The Cassava Biotechnology Network: Proceedings of the Second International Scientific Meeting of the Cassava Biotechnology Network. Working document no 50. Cali, Colombia: Centro International de Agricultura Tropical, 2v..Google Scholar
Botstein, D, White, RL, Skolnick, M and Davis, RW (1980) Construction of a genetic linkage map in man using restriction fragment length polymorphisms. American Journal of Human Genetics 32: 314–331.Google ScholarPubMed
Chavarriaga-Aguirre, P, Maya, MM, Bonierbale, MW, Kresovich, S, Fregene, MA, Tohme, J and Kochert, G (1998) Microsatellites in cassava (Manihot esculenta Crantz): discovery, inheritance and variability. Theoretical and Applied Genetics 97: 493–501.CrossRefGoogle Scholar
Chavarriaga-Aguirre, P, Maya, MM, Tohme, J, Duque, MC, Iglesias, C, Bonierbale, MW, Kresovich, S and 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. Molecular Breeding 5: 263–273.CrossRefGoogle Scholar
Dellaporta, SL, Woods, J and Hicks, JR (1983) A plant DNA mini-preparation: version II. Plant Molecular Biology Reports 1: 19–21.CrossRefGoogle Scholar
FAO (2001) FAOSTAT Statistical Databases. Rome, Italy: Food and Agriculture Organization.Google Scholar
Fregene, M, Angel, F, Gómez, R, Rodríguez, F, Bonierbale, M, Iglesias, C, Tohme, J and Roca, W (1997) A molecular genetic map of cassava (Manihot esculenta Crantz). Theoretical and Applied Genetics 95: 431–441.CrossRefGoogle Scholar
Fregene, MA, Bernal, A, Duque, M, Dixon, A and Tohme, J (2000) AFLP analysis of African cassava (Manihot esculenta Crantz) germplasm resistant to the cassava mosaic disease (CMD). Theoretical and Applied Genetics 100: 678–685.CrossRefGoogle Scholar
Fregene, M, Suarez, M, Mkumbira, J, Kulembeka, H, Ndedya, E, Kulaya, A, Mitchel, S, Gullberg, U, Rosling, H, Dixon, A and Kresovich, S (2003) Simple sequence repeat (SSR) diversity of cassava (Manihot esculenta Crantz) landraces: genetic diversity and differentiation in a predominantly asexually propagated crop. Theoretical and Applied Genetics 107: 1083–1093.CrossRefGoogle Scholar
International Center for Tropical Agriculture (2002) Annual report, Cali, Colombia..Google Scholar
International Center for Tropical Agriculture (2003) Annual report, Cali, Colombia..Google Scholar
International Center for Tropical Agriculture (2004) Annual report, Cali, Colombia..Google Scholar
Jaccoud, D, Peng, K, Feinstein, D and Kilian, A (2001) Diversity arrays: a solid state technology for sequence information independent genotyping. Nucleic Acids Research 29: e25.CrossRefGoogle ScholarPubMed
Mba, REC, Stephenson, P, Edwards, K, Melzer, S, Mkumbira, J, Gullberg, U, Apel, K, Gale, M, Tohme, J and Fregene, M (2001) Simple sequence repeat (SSR) markers survey of the cassava (Manihot esculenta Crantz) genome: towards an SSR-based molecular genetic map of cassava. Theoretical and Applied Genetics 102: 21–31.CrossRefGoogle Scholar
Ocampo, C, Hershey, C, Iglesias, C and Iwanaga, M (1992) Esterase isozyme fingerprinting of the cassava germplasm collection held at CIAT. In: Roca, W and Thro, AM (eds) Proceedings of the First International Scientific Meeting of the Cassava Biotechnology Network. Cali, Colombia: CIAT, pp. 81–89.Google Scholar
Okogbenin, E, Marin, J and Fregene, M (2006) An SSR-based molecular genetic map of cassava. Euphytica 147: 433–440.CrossRefGoogle Scholar
Olsen, KM (2004) SNPs, SSRs and inferences on cassava's origin. Plant Molecular Biology 56: 517–526.CrossRefGoogle ScholarPubMed
Olsen, KM and Schaal, BA (1999) Evidence on the origin of cassava: phylogeography of Manihot esculenta. Proceedings of the National Academy of Sciences of the United States of America 96: 5586–5591.CrossRefGoogle ScholarPubMed
Roa, AC, Maya, MM, Duque, MC, Tohme, J, Allem, AC and Bonierbale, MW (1997) AFLP analysis of relationships among cassava and other Manihot species. Theoretical and Applied Genetics 95: 741–750.CrossRefGoogle Scholar
Rohlf, FJ (1998) NTSYS-pc Numerical Taxonomy and Multivariate Analysis System Ver21. New York: Exeter Software.Google Scholar
Second, G, Allem, A, Emperaire, L, Ingram, C, Colombo, C, Mendes, R and Carvalho, L (1997) AFLP based Manihot and cassava numerical taxonomy and genetic structure analysis in progress: implications for dynamic conservation and genetic mapping. African Journal of Root and Tuber Crops 2: 140–147.Google Scholar
Wenzl, P, Carling, J, Kudrna, D, Jaccoud, D, Huttner, E, Kleinhofs, A and Kilian, A (2004) Diversity array technology (DArT) for whole-genome profiling of barley. Proceedings of the National Academy of Sciences of the United States of America 101: 9915–9920.CrossRefGoogle ScholarPubMed
Xia, L, Peng, K, Yang, S, Wenzl, P, De Vicente, MC, Fregene, M and Killian, A (2005) DArT for high-throughput genotyping of cassava (Manihot esculenta) and its wild relatives. Theoretical and Applied Genetics 110: 1092–1098.CrossRefGoogle ScholarPubMed
Supplementary material: File

Hurtado Supplementary Material

Table1.doc

Download Hurtado Supplementary Material(File)
File 49.7 KB
Supplementary material: File

Hurtado Supplementary Material

Table2.doc

Download Hurtado Supplementary Material(File)
File 99.3 KB