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. 2014 Oct 14;15(1):896.
doi: 10.1186/1471-2164-15-896.

Linkage Disequilibrium and Genome-Wide Association Analysis for Anthocyanin Pigmentation and Fruit Color in Eggplant

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Free PMC article

Linkage Disequilibrium and Genome-Wide Association Analysis for Anthocyanin Pigmentation and Fruit Color in Eggplant

Fabio Cericola et al. BMC Genomics. .
Free PMC article

Abstract

Background: The genome-wide association (GWA) approach represents an alternative to biparental linkage mapping for determining the genetic basis of trait variation. Both approaches rely on recombination to re-arrange the genome, and seek to establish correlations between phenotype and genotype. The major advantages of GWA lie in being able to sample a much wider range of the phenotypic and genotypic variation present, in being able to exploit multiple rounds of historical recombination in many different lineages and to include multiple accessions of direct relevance to crop improvement.

Results: A 191 accessions eggplant (Solanum melongena L.) association panel, comprising a mixture of breeding lines, old varieties and landrace selections originating from Asia and the Mediterranean Basin, was SNP genotyped and scored for anthocyanin pigmentation and fruit color at two locations over two years. The panel formed two major clusters, reflecting geographical provenance and fruit type. The global level of linkage disequilibrium was 3.4 cM. A mixed linear model appeared to be the most appropriate for GWA. A set of 56 SNP locus/phenotype associations was identified and the genomic regions harboring these loci were distributed over nine of the 12 eggplant chromosomes. The associations were compared with the location of known QTL for the same traits.

Conclusion: The GWA mapping approach was effective in validating a number of established QTL and, thanks to the wide diversity captured by the panel, was able to detect a series of novel marker/trait associations.

Figures

Figure 1
Figure 1
The genetic architecture of the full germplasm panel. A) Ln(K) and DK plots derived from the SNP data. B) UPGMA dendrogram derived after taking account of the STRUCTURE analysis. C) PCoA visualization of the genetic relationships between members of the association panel. Cluster A is shown in orange, cluster B in blue and admixtures in grey.
Figure 2
Figure 2
LD decay. The curve was fitted using a locally weighted scatterplot smooth regression with the threshold set at 0.15. A) r2 model, B) r2 s model, C) r2 sv model.
Figure 3
Figure 3
Heat maps indicating genome-wide variation in LD across the genome. A) r2 model, B) r2 s model, C) r2 sv model.
Figure 4
Figure 4
Cumulative density function using three alternative association models: the GLM Naive (violet trace), GLM Q-model (green trace) and MLM (red trace). Traits showing significant associations are indicated. The latter provided the most consistent p-values.
Figure 5
Figure 5
Regions identified by GWA in comparison to QTL locations described by Barchi et al. [10]. The GWA outcome is given to the left of each chromosome (the vertical bars represent a ±3.4 cM interval around the position of the associated SNP loci) and the various association groups are indicated in panels and marked in red. The QTL locations are shown to the right of each chromosome.
Figure 6
Figure 6
Synteny between tomato and eggplant chromosomes. The latter are shown on the left with bars indicating the site of QTL for anthocyanin content and fruit color. Their tomato orthologs are shown on the right, along with the position of possible candidate genes.

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