Genetic dissection of tomato fruit quality in the genome era: new tools for in depth QTL characterization
Résumé
Tomato fruit quality is characterized by a large number of components influenced by the genotypes and the
environment. To better understand t~e genetic control of these components, quantitative trait loci (QTL)
have been mapped for years. Today the genome sequence availability changes the paradigm of genetic
approaches. QTL have been first identified using linkage mapping populations and positional cloning
identified a few QTLs. However Iinkage mapping is Iimited to the analysis of traits differing between two
parentallines. Genome-wide association (GWA) has then been proposed to assess a large range ofvariability.
ln tomato, we have shown that GWAstudy is possible, using the admixed nature of cherry tomato genomes
that reduces the impact of population structure. Nevertheless, GWAsuccess is limited in sorne regions due to
the low decay of linkage disequilibrium, which varies along the genome. Rare alleles are also difficult to
detect with GWA studies. Multi-parent advanced generation intercross (MAGIC) populations offer an
alternative to traditionallinkage and GWAs by increasing the precision of QTLmapping but with equilibrated
allelic frequencies. We have developed a MAGICpopulation by crossing eight tomato lines whose genomes
were resequenced. We showed the potential of the MAGIC population when coupled with whole genome
sequèncing to detect candidate single nuc\eotide polymorphisms (SNP) underlying the QTLs. QTLs for fruit
quality traits were mapped and related to the variations detected at the genome sequence and expression
levels. The advantages and limitations of the three types of population, in the context of the available genome
sequence and resequencing facilities, will be discussed.
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