Gene and QTL detection in a three-way barley cross under selection by a mixed model with kinship information using SNPs
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Author
Malosetti, Marcos
van Eeuwijk, Fred A.
Boer, Martin P.
Casas, Ana M.
Elía, Mónica
Moralejo, Marian
Bhat, Prasanna R.
Ramsay, Luke
Molina-Cano, José-Luis
Publication date
2011-03-04ISSN
0040-5752
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.
Document Type
Article
Document version
Published version
Language
English
Subject (CDU)
575 - General genetics. General cytogenetics
633 - Field crops and their production
Pages
12
Publisher
Springer
Is part of
Theoretical and Applied Genetics
Citation
Malosetti, Marcos, Fred A. Van Eeuwijk, Martin P. Boer, Ana M. Casas, Mónica Elía, Marian Moralejo, Prasanna R. Bhat, Luke Ramsay, and José-Luis Molina-Cano. 2011. “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. doi: 10.1007/s00122-011-1558-z
Grant agreement number
MEC/ /AGL2005-07195-C02-02/ES/DESARROLLO DE MATERIALES Y TECNICAS PARA EL ANALISIS INTEGRADO DE LA RESPUESTA DE LA CEBADA (HORDEUM VULGARE L.) AL ESTRES ABIOTICO/AGR
MEC/ /GEN2006-28560-E/ES/Acceso de grupos españoles a una plataforma genómica internacional en desarrollo para la cebada/
Program
Cultius Extensius Sostenibles
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Except where otherwise noted, this item's license is described as http://creativecommons.org/licenses/by-nc/4.0/