Gene and QTL detection in a three-way barley cross under selection by a mixed model with kinship information using SNPs
Eeuwijk, Fred A. van
Boer, Martin P.
Casas Cendoya, Ana Maria
Bhat, Prasanna R.
Ramsay, Luke D.
Molina Cano, José Luis
MetadataShow full item record
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.
Is part ofTheoretical and Applied Genetics, 2011, vol. 122, núm. 8, p. 1605–1616
The following license files are associated with this item:
Except where otherwise noted, this item's license is described as cc-by-nc (c) Marcos Malosetti et al., 2011
Showing items related by title, author, creator and subject.
Selection footprints in barley breeding lines detected by combining genotyping-by-sequencing with reference genome information Igartua Arregui, Ernesto; Mansour, Elsayed; Cantalapiedra, Carlos P.; Contreras‐Moreira, Bruno; Gracia Gimeno, Ma. Pilar; Fuster, Prudencio; Escribano, J.; Molina Cano, José Luis; Moralejo Vidal, Mª Angeles; Ciudad, F. J.; Thomas, William T. B.; Karsai, Ildikó; Casas Cendoya, Ana Maria (Springer, 2015)This study is a retrospective analysis of an elite cross from the Spanish National Barley Breeding Program. This was the most successful cross produced in the breeding program in the past 20 years. The progeny from this ...
Quantitative trait loci for agronomic traits in an elite barley population for Mediterranean conditions Mansour Elsayed, Elsayed; Casas Cendoya, Ana Maria; Gracia Gimeno, Ma. Pilar; Molina Cano, José Luis; Moralejo Vidal, Mª Angeles; Cattivelli, Luigi; Thomas, William T. B.; Igartua Arregui, Ernesto (Springer, 2013-09-15)Advances in plant breeding through marker-assisted selection (MAS) are only possible when genes or quantitative trait loci (QTLs) can contribute to the improvement of elite germplasm. A population of recombinant inbred ...
Cuesta-Marcos, Alfonso; Igartua Arregui, Ernesto; Ciudad, F. J.; Codesal, P.; Russell, Joanne; Molina Cano, José Luis; Moralejo Vidal, Mª Angeles; Szűcs, Péter; Gracia Gimeno, Ma. Pilar; Lasa Dolhagaray, José Manuel; Casas Cendoya, Ana Maria (Springer Verlag, 2008)Heading date is a key trait for the adaptation of barley to Mediterranean environments. We studied the genetic control of flowering time under Northern Spanish (Mediterranean) conditions using a new population derived from ...