Potential of a tomato MAGIC population to decipher the genetic control of quantitative traits and detect causal variants in the resequencing era - Archive ouverte HAL Accéder directement au contenu
Article Dans Une Revue Plant Biotechnology Journal Année : 2014

Potential of a tomato MAGIC population to decipher the genetic control of quantitative traits and detect causal variants in the resequencing era

Résumé

Identification of the polymorphisms controlling quantitative traits remains a challenge for plant geneticists. Multiparent advanced generation intercross (MAGIC) populations offer an alternative to traditional linkage or association mapping populations by increasing the precision of quantitative trait loci (QTL) mapping. Here, we present the first tomato MAGIC population and highlight its potential for the valorization of intraspecific variation, QTL mapping and causal polymorphism identification. The population was developed by crossing eight founder lines, selected to include a wide range of genetic diversity, whose genomes have been previously resequenced. We selected 1536 SNPs among the 4 million available to enhance haplotype prediction and recombination detection in the population. The linkage map obtained showed an 87% increase in recombination frequencies compared to biparental populations. The prediction of the haplotype origin was possible for 89% of the MAGIC line genomes, allowing QTL detection at the haplotype level. We grew the population in two greenhouse trials and detected QTLs for fruit weight. We mapped three stable QTLs and six specific of a location. Finally, we showed the potential of the MAGIC population when coupled with whole genome sequencing of founder lines to detect candidate SNPs underlying the QTLs. For a previously cloned QTL on chromosome 3, we used the predicted allelic effect of each founder and their genome sequences to select putative causal polymorphisms in the supporting interval. The number of candidate polymorphisms was reduced from 12 284 (in 800 genes) to 96 (in 54 genes), including the actual causal polymorphism. This population represents a new permanent resource for the tomato genetics community
Fichier principal
Vignette du fichier
OK Pascual_Causse 2014 Plant Biotechnology Journal 1-13_1.pdf (536.28 Ko) Télécharger le fichier
Origine : Fichiers produits par l'(les) auteur(s)
Loading...

Dates et versions

hal-01208731 , version 1 (27-05-2020)

Identifiants

Citer

Laura Pascual-Banuls, Nelly Desplat, Bevan E. Huang, Aurore Desgroux, Laure Bruguier, et al.. Potential of a tomato MAGIC population to decipher the genetic control of quantitative traits and detect causal variants in the resequencing era. Plant Biotechnology Journal, 2014, 13 (4), pp.565-77. ⟨10.1111/pbi.12282⟩. ⟨hal-01208731⟩
145 Consultations
63 Téléchargements

Altmetric

Partager

Gmail Facebook X LinkedIn More