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Updated: Mar 30, 2026

Following the Dynamics of Structural Variants in Experimentally Evolved Populations
Published on: February 3, 2023
Dissecting quantitative trait variation in the resequencing era: complementarity of bi-parental, multi-parental and
Laura Pascual1, Elise Albert1, Christopher Sauvage1
1INRA, UR1052, Centre de Recherche PACA, 67 Allée des Chênes CS60094, 84143 Montfavet Cedex, France.
Abstract:
Quantitative trait loci (QTL) have been identified using traditional linkage mapping and positional cloning identified several QTLs. However linkage mapping is limited to the analysis of traits differing between two lines and the impact of the genetic background on QTL effect has been underlined. Genome-wide association studies (GWAs) were proposed to circumvent these limitations. In tomato, we have shown that GWAs is possible, using the admixed nature of cherry tomato genomes that reduces the impact of population structure. Nevertheless, GWAs success might be limited due to the low decay of linkage disequilibrium, which varies along the genome in this species. Multi-parent advanced generation intercross (MAGIC) populations offer an alternative to traditional linkage and GWAs by increasing the precision of QTL mapping. We have developed a MAGIC population by crossing eight tomato lines whose genomes were resequenced. We showed the potential of the MAGIC population when coupled with whole genome sequencing to detect candidate single nucleotide polymorphisms (SNPs) 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, are discussed.
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