Using cDNA and genomic sequences as tools to develop SNP strategies in cassava (Manihot esculenta Crantz) View Full Text


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Article Info

DATE

2005-02

AUTHORS

C. Lopez, B. Piégu, R. Cooke, M. Delseny, J. Tohme, V. Verdier

ABSTRACT

Single nucleotide polymorphisms (SNP) are the most abundant type of DNA polymorphism found in animal and plant genomes. They provide an important new source of molecular markers that are useful in genetic mapping, map-based positional cloning, quantitative trait locus mapping and the assessment of genetic distances between individuals. Very little is known on the frequency of SNPs in cassava. We have exploited the recently-developed collection of cassava expressed sequence tags (ESTs) to detect SNPs in the five cultivars of cassava used to generate the sequences. The frequency of intra-cultivar and inter-cultivar SNPs after analysis of 111 contigs was one polymorphism per 905 and one per 1,032 bp, respectively; totaling 1 each 509 bp. We have obtained further information on the frequency of SNPs in six cassava cultivars by analysis of 33 amplicons obtained from 3' EST and BAC end sequences. Overall, about 11 kb of DNA sequence was obtained for each cultivar. A total of 186 SNPs (136 and 50 from ESTs and BAC ends, respectively) were identified. Among these, 146 were intra-cultivar polymorphisms, while 80 were inter-cultivar polymorphisms. Thus the total frequency of SNPs was one per 62 bp. This information will help to develop new strategies for EST mapping as well as their association with phenotypic characteristics. More... »

PAGES

425-431

References to SciGraph publications

  • 2001-01. Simple sequence repeat (SSR) markers survey of the cassava (Manihot esculenta Crantz) genome: towards an SSR-based molecular genetic map of cassava in THEORETICAL AND APPLIED GENETICS
  • 1999-12. A general approach to single-nucleotide polymorphism discovery in NATURE GENETICS
  • 1999-10. Genome-wide mapping with biallelic markers in Arabidopsis thaliana in NATURE GENETICS
  • 2003-09. Snipping polymorphisms from large EST collections in barley (Hordeum vulgare L.) in MOLECULAR GENETICS AND GENOMICS
  • 1997-08. A molecular genetic map of cassava (Manihot esculenta Crantz) in THEORETICAL AND APPLIED GENETICS
  • 2003-08. Isolation of Resistance Gene Candidates (RGCs) and characterization of an RGC cluster in cassava in MOLECULAR GENETICS AND GENOMICS
  • 2004-11. A unigene catalogue of 5700 expressed genes in cassava in PLANT MOLECULAR BIOLOGY
  • 1985-03. An estimate of unique DNA sequence heterozygosity in the human genome in HUMAN GENETICS
  • 2002-12. SNP frequency, haplotype structure and linkage disequilibrium in elite maize inbred lines in BMC GENETICS
  • 1997-04. Genome mapping, molecular markers and marker-assisted selection in crop plants in MOLECULAR BREEDING
  • 2000-10. Genetic mapping of resistance to bacterial blight disease in cassava (Manihot esculenta Crantz) in THEORETICAL AND APPLIED GENETICS
  • 2003-01. ESTs as a source for sequence polymorphism discovery in sugarcane: example of the Adh genes in THEORETICAL AND APPLIED GENETICS
  • 2001-03. QTL analysis of field resistance to Xanthomonas axonopodis pv. manihotis in cassava in THEORETICAL AND APPLIED GENETICS
  • 2003-11. Genetic mapping of QTLs affecting productivity and plant architecture in a full-sib cross from non-inbred parents in Cassava (Manihot esculenta Crantz) in THEORETICAL AND APPLIED GENETICS
  • 1983-09. A plant DNA minipreparation: Version II in PLANT MOLECULAR BIOLOGY REPORTER
  • Identifiers

    URI

    http://scigraph.springernature.com/pub.10.1007/s00122-004-1833-3

    DOI

    http://dx.doi.org/10.1007/s00122-004-1833-3

    DIMENSIONS

    https://app.dimensions.ai/details/publication/pub.1018151104

    PUBMED

    https://www.ncbi.nlm.nih.gov/pubmed/15650816


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