Change search
ReferencesLink to record
Permanent link

Direct link
Gene-based single nucleotide polymorphism markers for genetic and association mapping in common bean
Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Plant Ecology and Evolution.
Show others and affiliations
2012 (English)In: BMC Genetics, ISSN 1471-2156, Vol. 12, 48Article in journal (Refereed) Published
Abstract [en]

Background: In 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. 

Results: In 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 x G19833 recombinant inbred line (RIL) population. The new linkage map was used to build a consensus map, merging the linkage maps of the BAT93 x JALO EEP558 and DOR364 x 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. 

Conclusions: In 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.

Place, publisher, year, edition, pages
2012. Vol. 12, 48
National Category
Evolutionary Biology
URN: urn:nbn:se:uu:diva-190119DOI: 10.1186/1471-2156-13-48ISI: 000308829300001PubMedID: 22734675OAI: diva2:583048
Available from: 2013-01-07 Created: 2013-01-07 Last updated: 2015-08-11Bibliographically approved

Open Access in DiVA

fulltext(989 kB)33 downloads
File information
File name FULLTEXT01.pdfFile size 989 kBChecksum SHA-512
Type fulltextMimetype application/pdf

Other links

Publisher's full textPubMed

Search in DiVA

By author/editor
Cortés, Andres J.
By organisation
Plant Ecology and Evolution
In the same journal
BMC Genetics
Evolutionary Biology

Search outside of DiVA

GoogleGoogle Scholar
Total: 33 downloads
The number of downloads is the sum of all downloads of full texts. It may include eg previous versions that are now no longer available

Altmetric score

Total: 183 hits
ReferencesLink to record
Permanent link

Direct link