A Multiplex Microsatellite Marker Kit for Diversity Assessment of Large Cassava (Manihot esculenta Crantz) Germplasm Collections

• Published in: Plant molecular biology reporter Vol. 29; no. 3; pp. 655 - 662
• Main Authors: de Bang, Thomas C., Raji, Adebola A., Ingelbrecht, Ivan L.
• Format: Journal Article
• Language: English
• Published: New York Springer-Verlag 01-09-2011; Springer Nature B.V
• Subjects: Agricultural management; Agricultural research; Alleles; Amplified fragment length polymorphism; Bioinformatics; Biomedical and Life Sciences; Cassava; Chemical fingerprinting; Cost analysis; Cultivars; Fingerprinting; Fluorescence; Gene polymorphism; Genetic diversity; Genetic markers; Genotypes; Germplasm; Life Sciences; Manihot esculenta; Metabolomics; Microsatellites; Multiplexing; Plant Breeding/Biotechnology; Plant Sciences; Polymorphism; Proteomics; R&D; Reproduction (copying); Research & development; Research facilities; Research institutions; Diversity analysis; Multiplex PCR; Crantz; Microsatellite primers; Cassava
• ISSN: 0735-9640; 1572-9818
• DOI: 10.1007/s11105-010-0273-2

Current methods for molecular fingerprinting of cassava (
Manihot esculenta
Crantz) have limited throughput or are costly, thus preventing the characterization of large germplasm collections such as those held by the International Agricultural Research Centers or National Research Institutions, which comprise hundreds to thousands of accessions. Here, we report the development of a fluorescence-based multiplex simple sequence repeat (SSR) marker kit that enables accurate and cost-effective cassava fingerprinting. The kit comprises 16 SSR markers assembled into five multiplex panels and was tested on 21 cassava cultivars alongside one accession of
Manihot epruinosa
, a wild relative. A total of 68 alleles were detected with, on average, 4.25 alleles per locus and a polymorphism information content of 0.53. The marker kit reported here is comparable to previously published amplified fragment length polymorphism and SSR marker systems in terms of discriminating power and informativeness while offering significant advantages in speed and cost of marker analysis. Previous molecular genetic diversity studies have suggested that cassava germplasm collections contain duplicate entries based on the occurrence of identical genetic profiles. Using the newly developed microsatellite kit, three out of six putative duplicate accessions could be readily differentiated, showing that these are distinct genotypes. The relevance of these findings with respect to the characterization and management of large cassava germplasm collections is discussed.