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Open Access item Gene and QTL detection in a three-way barley cross under selection by a mixed model with kinship information using SNPs

Authors:Malosetti, Marcos
van Eeuwijk, Fred A.
Boer, Martin P.
Casas Cendoya, Ana María
Elía, Mónica
Moralejo, María Ángeles
Bhat, Prasanna R.
Ramsay, Luke D.
Molina-Cano, José Luis
Keywords:mixed model, kinship, SNP, QTL, barley
Issue Date:May-2011
Publisher:Springer
Citation:Malosetti M, van Eeuwijk FA, Boer MP, Casas AM, Elía M, Moralejo M, Bhat PR, Ramsay L, Molina-Cano JL. Gene and QTL detection in a three-way barley cross under selection by a mixed model with kinship information using SNPs. Theoretical and applied genetics 122 (8): 1605-1616 (2011)
Abstract:Quantitative trait locus (QTL) detection is commonly performed by analysis of designed segregating populations derived from two inbred parental lines, where absence of selection, mutation and genetic drift is assumed. Even for designed populations, selection cannot always be avoided, with as consequence varying correlation between genotypes instead of uniform correlation. Akin to linkage disequilibrium mapping, ignoring this type of genetic relatedness will increase the rate of false-positives. In this paper, we advocate using mixed models including genetic relatedness, or ‘kinship’ information for QTL detection in populations where selection forces operated. We demonstrate our case with a three-way barley cross, designed to segregate for dwarfing, vernalization and spike morphology genes, in which selection occurred. The population of 161 inbred lines was screened with 1,536 single nucleotide polymorphisms (SNPs), and used for gene and QTL detection. The coefficient of coancestry matrix was estimated based on the SNPs and imposed to structure the distribution of random genotypic effects. The model incorporating kinship, coancestry, information was consistently superior to the one without kinship (according to the Akaike information criterion). We show, for three traits, that ignoring the coancestry information results in an unrealistically high number of marker–trait associations, without providing clear conclusions about QTL locations. We used a number of widely recognized dwarfing and vernalization genes known to segregate in the studied population as landmarks or references to assess the agreement of the mapping results with a priori candidate gene expectations. Additional QTLs to the major genes were detected for all traits as well.
Description:25 Pag., 5 Tabl., 6 Fig. The definitive version is available at: www.springerlink.com
Publisher version (URL):http://dx.doi.org/10.1007/s00122-011-1558-z
URI:http://hdl.handle.net/10261/37408
ISSN:0040-5752
E-ISSNmetadata.dc.identifier.doi = DOI:1432-2242
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Appears in Collections:(EEAD) Artículos

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