ArticleTAG. Theoretical and applied genetics. Theoretische und angewandte Genetik2011
Gene and QTL detection in a three-way barley cross under selection by a mixed model with kinship information using SNPs.
Article in TAG. Theoretical and applied genetics. Theoretische und angewandte Genetik, 2011. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 31 papers.
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31 citing papers in PubMed, 59 citations in OpenAlex.
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- Tracking Changes in the Spring Barley Gene Pool in Poland during 120 Years of Breeding.International journal of molecular sciences · 2022Article
- An IBD-based mixed model approach for QTL mapping in multiparental populations.TAG. Theoretical and applied genetics. Theoretische und angewandte Genetik · 2021Article
- Major flowering time genes of barley: allelic diversity, effects, and comparison with wheat.TAG. Theoretical and applied genetics. Theoretische und angewandte Genetik · 2021Review
- Perennial Rye: Genetics of Perenniality and Limited Fertility.Plants (Basel, Switzerland) · 2021Article
- Lessons from a GWAS study of a wheat pre-breeding program: pyramiding resistance alleles to Fusarium crown rot.TAG. Theoretical and applied genetics. Theoretische und angewandte Genetik · 2021Article
- Genetic dissection of the interactions between semi-dwarfing genesMolecular breeding : new strategies in plant improvement · 2020Article
- Genotyping-by-sequencing and multilocation evaluation of two interspecific backcross populations identify QTLs for yield-related traits in pigeonpea.TAG. Theoretical and applied genetics. Theoretische und angewandte Genetik · 2020Article
- Genetic Architecture of Flowering Time and Sex Determination in Hemp (Frontiers in plant science · 2020Article
- Elucidating the Genetic Architecture of Fiber Quality in Hemp (Frontiers in genetics · 2020Article
- Mapping Stem Rust (Frontiers in plant science · 2020Article
- Genome-wide association of barley plant growth under drought stress using a nested association mapping population.BMC plant biology · 2019Article
- Efficient QTL detection of flowering date in a soybean RIL population using the novel restricted two-stage multi-locus GWAS procedure.TAG. Theoretical and applied genetics. Theoretische und angewandte Genetik · 2018Article
- Resistance to Rhynchosporium commune in a collection of European spring barley germplasm.TAG. Theoretical and applied genetics. Theoretische und angewandte Genetik · 2018Article
- Loci That Control Nonlinear, Interdependent Responses to Combinations of Drought and Nitrogen Limitation.G3 (Bethesda, Md.) · 2018Article
- GWAS analysis in spring barley (Hordeum vulgare L.) for morphological traits exposed to drought.PloS one · 2018Article
- QTLs for earliness and yield-forming traits in the Lubuski × CamB barley RIL population under various water regimes.Journal of applied genetics · 2017Article
- Quantitative trait loci for plant height in Maresi × CamB barley population and their associations with yield-related traits under different water regimes.Journal of applied genetics · 2017Article
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Corrections and comments
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Authors and funding
9 authors at 4 institutions in 3 countries.
Funding
No grant is acknowledged in the PubMed record.
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.
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