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SSCP-SNP-based conserved ortholog set (COS) markers for comparative genomics in cassava (Manihot esculenta crantz)

Abstract

The ever increasing body of information on genomics and functional genomics from model plants, and new tools of comparative genomics, provide an opportunity to accelerate the development of molecular markers for increasing the efficiency of breeding of lesser studied crops, so-called “orphan crops.” Conserved ortholog set (COS) markers represent orthologous genes in widely divergent plant species, and are currently the principal tool of choice for comparative genomics. EST sequences of 3 drought tolerance related genes—chalcone synthase (CHS), dihydroflavonol-4-reductase (DHRF) and drought responsive element binding factor 1 (DREB-1) fromMusa sp—were used to identify cassava EST homologs that were then scanned against the Arabidopsis genome database to identify them as COS markers. The CHS and DHRF ESTs were demonstrated to be COS markers, while the DREB EST was shown to belong to a gene family. The three genes were evaluated as single strand conformation polymorphism—single nucleotide polymorphism (SSCP-SNP) markers in the parents of an F1 mapping population and subsequently in the progenies. The DHRF COS marker mapped to linkage group R of the female-derived map while the DREB-1 EST mapped at an end of the male-derived linkage group K. The CHS COS marker could not be mapped because it was not polymorphic in the parents of the mapping population. These new marker tools should accelerate the development of markers associated with genes controlling traits of agronomic interest via the candidate gene loci (CGL) QTL-mapping approach.

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Abbreviations

CGL:

candidate gene loci

CHS:

chalcone synthase

COS:

conserved ortholog set

DHRF:

dihydroflavonol-4-reductase

DREB:

drought responsive element binding factor

EST:

expressed sequence tag

QTL:

quantitative trait locus

RAPD:

random amplification of polymorphic DNA

RFLP:

restriction fragment length polymorphism

SDRF:

single-dose fragment restriction

SNP:

single nucleotide polymorphism

SSCP:

single strand conformation polymorphism

SSR:

simple sequence repeat

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Correspondence to M. Fregene.

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Castelblanco, W., Fregene, M. SSCP-SNP-based conserved ortholog set (COS) markers for comparative genomics in cassava (Manihot esculenta crantz). Plant Mol Biol Rep 24, 229–236 (2006). https://doi.org/10.1007/BF02914061

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Keywords

  • SSCP-SNPs
  • COS markers
  • Genetic Mapping of ESTs