Gene-Based Single Nucleotide Polymorphism Markers for Genetic and Association Mapping in Common BeanReportar como inadecuado

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BMC Genetics

, 13:48

First Online: 26 June 2012Received: 06 March 2012Accepted: 21 June 2012DOI: 10.1186-1471-2156-13-48

Cite this article as: Galeano, C.H., Cortés, A.J., Fernández, A.C. et al. BMC Genet 2012 13: 48. doi:10.1186-1471-2156-13-48


BackgroundIn common bean, expressed sequence tags ESTs are an underestimated source of gene-based markers such as insertion-deletions Indels or single-nucleotide polymorphisms SNPs. However, due to the nature of these conserved sequences, detection of markers is difficult and portrays low levels of polymorphism. Therefore, development of intron-spanning EST-SNP markers can be a valuable resource for genetic experiments such as genetic mapping and association studies.

ResultsIn this study, a total of 313 new gene-based markers were developed at target genes. Intronic variation was deeply explored in order to capture more polymorphism. Introns were putatively identified after comparing the common bean ESTs with the soybean genome, and the primers were designed over intron-flanking regions. The intronic regions were evaluated for parental polymorphisms using the single strand conformational polymorphism SSCP technique and Sequenom MassARRAY system. A total of 53 new marker loci were placed on an integrated molecular map in the DOR364 × G19833 recombinant inbred line RIL population. The new linkage map was used to build a consensus map, merging the linkage maps of the BAT93 × JALO EEP558 and DOR364 × BAT477 populations. A total of 1,060 markers were mapped, with a total map length of 2,041 cM across 11 linkage groups. As a second application of the generated resource, a diversity panel with 93 genotypes was evaluated with 173 SNP markers using the MassARRAY-platform and KASPar technology. These results were coupled with previous SSR evaluations and drought tolerance assays carried out on the same individuals. This agglomerative dataset was examined, in order to discover marker-trait associations, using general linear model GLM and mixed linear model MLM. Some significant associations with yield components were identified, and were consistent with previous findings.

ConclusionsIn short, this study illustrates the power of intron-based markers for linkage and association mapping in common bean. The utility of these markers is discussed in relation with the usefulness of microsatellites, the molecular markers by excellence in this crop.

Electronic supplementary materialThe online version of this article doi:10.1186-1471-2156-13-48 contains supplementary material, which is available to authorized users.

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Autor: Carlos H Galeano - Andrés J Cortés - Andrea C Fernández - Álvaro Soler - Natalia Franco-Herrera - Godwill Makunde - J


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