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Molecular Markers and Their Application to Cassava Breeding: Past, Present and Future

Abstract

The advent of relatively low-cost, massively parallel, high-throughput genome sequencing and the resultant availability of high density markers are revolutionizing the ways in which molecular markers can be applied to plant breeding. With the availability of the draft cassava genome sequence, the cassava community is poised to take advantage of these new tools. Here we review the development of molecular markers applied to cassava breeding and describe the achievements that have been made using predominantly simple sequence repeat (SSR) markers. At this time of change, we report on the curation of 3,367 published and unpublished SSR primer pairs and provide a non-redundant database. We also describe ways in which new tools, particularly single nucleotide polymorphism (SNP) markers, can be applied to the development of high density maps and to fine mapping, association mapping, gene discovery, transcript profiling, inbred line development and the prediction of heterosis, gene mining in wild species and introgressions, and genome-wide approaches, including marker-assisted recurrent selection (MARS) and genomic selection (GS). Where applicable we describe how these tools are already being applied for amassing genetic gain in cassava.

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Fig. 1

Abbreviations

ABC-QTL:

Advanced backcross QTL mapping scheme

AFLPs:

Amplified fragment length polymorphism

BAC:

Bacterial artificial chromosome

CBSD:

Cassava brown streak disease

cDNA:

Complimentary DNA

CGM:

Cassava green mite

CIAT:

Centro Internacional de Agricultura Tropical

CMD:

Cassava mosaic disease

DArT:

Diversity Array Technology

EMBRAPA:

Empresa Brasileira de Pesquisa Agropecuária

ESTs:

Expressed sequence tags

GCP:

Generation Challenge Program

GEBV:

Genomic estimate of breeding value

GS:

Genomic selection

IITA:

International Institute of Tropical Agriculture

LD:

Linkage disequilibrium

MARS:

Marker-assisted recurrent selection

MAS:

Marker-assisted selection

NGS:

Next-generation sequencing

PCR:

Polymerase chain reaction

PPD:

Post-harvest physiological determination

QTL:

Quantitative trait loci

RAPD:

Random amplified polymorphic DNA

RE:

Restriction enzyme

RFLP:

Restriction fragment length polymorphism

RGCs:

Resistance gene candidates

SEC:

Southern, eastern and central

SNP:

Single nucleotide polymorphism

SSR:

Simple sequence repeat

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Correspondence to Morag Ferguson.

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Communicated by: Nigel Taylor

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Ferguson, M., Rabbi, I., Kim, DJ. et al. Molecular Markers and Their Application to Cassava Breeding: Past, Present and Future. Tropical Plant Biol. 5, 95–109 (2012). https://doi.org/10.1007/s12042-011-9087-0

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Keywords

  • Single nucleotide polymorphism (SNP) markers
  • Marker-assisted breeding
  • Simple sequence repeat (SSR) markers
  • Manihot esculenta