Combined linkage and linkage disequilibrium QTL mapping in multiple families of maize (Zea mays L.) line crosses highlights complementarities between models based on parental haplotype and single locus polymorphism

Autor: N. Bardol, Marjolaine Ventelon, L. Moreau, Philippe Blanchard, Brigitte Mangin, F. Couton, C. Derue, V. Loywick, Alain Charcosset, Sylvain Jasson
Přispěvatelé: Génétique Quantitative et Evolution - Le Moulon (Génétique Végétale) (GQE-Le Moulon), Centre National de la Recherche Scientifique (CNRS)-AgroParisTech-Université Paris-Sud - Paris 11 (UP11)-Institut National de la Recherche Agronomique (INRA), Euralis Semences, Unité de Mathématiques et Informatique Appliquées de Toulouse (MIAT INRA), Institut National de la Recherche Agronomique (INRA), Université Paris-Sud - Paris 11 (UP11), National Agency of French Research (ANR), platform of bioinformatics Toulouse Midi-Pyrenees
Jazyk: angličtina
Rok vydání: 2013
Předmět:
0106 biological sciences
Linkage disequilibrium
[SDV]Life Sciences [q-bio]
POWER
Inheritance Patterns
Biology
Quantitative trait locus
Zea mays
01 natural sciences
Linkage Disequilibrium
GENETIC ARCHITECTURE
03 medical and health sciences
Family-based QTL mapping
MARKERS
Genetic linkage
Inclusive composite interval mapping
Genetics
Cluster Analysis
[SDV.BV]Life Sciences [q-bio]/Vegetal Biology
[INFO]Computer Science [cs]
GENOME-WIDE ASSOCIATION
[MATH]Mathematics [math]
Association mapping
Alleles
Crosses
Genetic
POPULATION
030304 developmental biology
Linkage (software)
0303 health sciences
QUANTITATIVE TRAIT LOCI
Polymorphism
Genetic
Models
Genetic
COMPLEX TRAITS
Chromosome Mapping
food and beverages
General Medicine
ALLELIC NUMBER
Haplotypes
Genetic Loci
Linkage based QTL mapping
IDENTITY
DIALLEL CROSS
Agronomy and Crop Science
Genome
Plant
010606 plant biology & botany
Biotechnology
Zdroj: TAG Theoretical and Applied Genetics
TAG Theoretical and Applied Genetics, Springer Verlag, 2013, 126 (11), pp.2717-2736. ⟨10.1007/s00122-013-2167-9⟩
ISSN: 0040-5752
1432-2242
Popis: International audience; Advancements in genotyping are rapidly decreasing marker costs and increasing marker density. This opens new possibilities for mapping quantitative trait loci (QTL), in particular by combining linkage disequilibrium information and linkage analysis (LDLA). In this study, we compared different approaches to detect QTL for four traits of agronomical importance in two large multi-parental datasets of maize (Zea mays L.) of 895 and 928 testcross progenies composed of 7 and 21 biparental families, respectively, and genotyped with 491 markers. We compared to traditional linkage-based methods two LDLA models relying on the dense genotyping of parental lines with 17,728 SNP: one based on a clustering approach of parental line segments into ancestral alleles and one based on single marker information. The two LDLA models generally identified more QTL (60 and 52 QTL in total) than classical linkage models (49 and 44 QTL in total). However, they performed inconsistently over datasets and traits suggesting that a compromise must be found between the reduction of allele number for increasing statistical power and the adequacy of the model to potentially complex allelic variation. For some QTL, the model exclusively based on linkage analysis, which assumed that each parental line carried a different QTL allele, was able to capture remaining variation not explained by LDLA models. These complementarities between models clearly suggest that the different QTL mapping approaches must be considered to capture the different levels of allelic variation at QTL involved in complex traits.
Databáze: OpenAIRE
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