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

2014; Wiley; Volume: 13; Issue: 4 Linguagem: Inglês

10.1111/pbi.12282

1467-7652

Laura Pascual, Nelly Desplat, Bevan E. Huang, Aurore Desgroux, Laure Bruguier, Jean‐Paul Bouchet, Quang Hien Le, Betty Chauchard, Philippe Verschave, Mathilde Causse,

Plant Reproductive Biology

Summary 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 SNP s 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 QTL s for fruit weight. We mapped three stable QTL s 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 SNP s underlying the QTL s. 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.