Dissecting quantitative trait variation in the resequencing era: complementarity of bi-parental, multi-parental and association panels

• Published in: Plant science (Limerick) Vol. 242; pp. 120 - 130
• Main Authors: Pascual, Laura, Albert, Elise, Sauvage, Christopher, Duangjit, Janejira, Bouchet, Jean-Paul, Bitton, Frédérique, Desplat, Nelly, Brunel, Dominique, Le Paslier, Marie-Christine, Ranc, Nicolas, Bruguier, Laure, Chauchard, Betty, Verschave, Philippe, Causse, Mathilde
• Format: Journal Article
• Language: English
• Published: Ireland Elsevier B.V 01.01.2016; Elsevier
• Subjects: Chromosome Mapping - methods; Chromosomes, Plant - genetics; Crosses, Genetic; Founder Effect; Fruit - genetics; Fruit quality; Genetic Variation; Genetics, Population - methods; Genome, Plant - genetics; Genome-wide association; Genotype; Inbreeding; Life Sciences; Lycopersicon esculentum - genetics; Polymorphism, Single Nucleotide; QTL mapping; Quantitative Trait Loci - genetics; Resequencing; Sequence Analysis, DNA - methods; Tomato; Vegetal Biology; Resequencing; Genome-wide association; Tomato; Fruit quality; QTL mapping; tomato; genome wide association; resequencing; fruit quality
• ISSN: 0168-9452; 1873-2259
• DOI: 10.1016/j.plantsci.2015.06.017

•114 QTL for fruit quality and plant traits were identified in 3 populations.•The identification of 18 common QTL reduced the QTL support intervals.•MAGIC design increases map size and identifies allelic effects in each founder line.•Parental genome sequence allowed identification of candidate polymorphisms.•Genome information encourages new approaches for QTL mapping. 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.