Synteny in the Solanaceae.

<p>Eggplant chromosomes are represented by white bars, and the site of QTL detected by GWA analysis is indicated. Tomato chromosomes are represented by yellow bars, along with the position of candidate genes (shown in red). Asterisks indicate orthologous QTL detected in tomato (* Grandillo et al. [<a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0135200#pone.0135200.ref030" target="_blank">30</a>], ** Frary et al. [<a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0135200#pone.0135200.ref033" target="_blank">33</a>], *** Lippman and Tanksley [<a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0135200#pone.0135200.ref031" target="_blank">31</a>]) shown in red, and in pepper (**** Barchi et al. [<a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0135200#pone.0135200.ref039" target="_blank">39</a>], Zygier et al. [<a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0135200#pone.0135200.ref038" target="_blank">38</a>], Chaim et al. [<a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0135200#pone.0135200.ref037" target="_blank">37</a>]) shown in green.</p

Asparagus genus 454 reads

This tar.bz2 file contains 454 sequencing fasta files for A. aphyllus, A. asparagoides, A. densiflorus, A. falcatus, A. maritimus, A. officinalis, A. pyrimidalis, A. stipularis, and A. virgatus. There is an additional A. officinalis 454 dataset that is significantly higher coverage, named "A_officinalis_WGS_in.454.AdditionalHighCoverage.fasta"

Association Mapping for Fruit, Plant and Leaf Morphology Traits in Eggplant

<div><p>An eggplant (<i>Solanum melongena</i>) association panel of 191 accessions, comprising a mixture of breeding lines, old varieties and landrace selections was SNP genotyped and phenotyped for key breeding fruit and plant traits at two locations over two seasons. A genome-wide association (GWA) analysis was performed using the mixed linear model, which takes into account both a kinship matrix and the sub-population membership of the accessions. Overall, 194 phenotype/genotype associations were uncovered, relating to 30 of the 33 measured traits. These associations involved 79 SNP loci mapping to 39 distinct chromosomal regions distributed over all 12 eggplant chromosomes. A comparison of the map positions of these SNPs with those of loci derived from conventional linkage mapping showed that GWA analysis both validated many of the known controlling loci and detected a large number of new marker/trait associations. Exploiting established syntenic relationships between eggplant chromosomes and those of tomato and pepper recognized orthologous regions in ten eggplant chromosomes harbouring genes influencing breeders’ traits.</p></div

The set of germplasm used for genotypic and phenotypic characterization.

<p>Those shown in <i>italics</i> refer to entries retaining a level of heterozygosity >10%, and those shown <u>underlined</u> produced off-types with respect to plant and/or fruit type. Retained entries are shown in <b>bold</b>.</p

Regions identified by GWA in eggplant LG E01-E06 in comparison to QTL locations described by Portis et al. [2].

<p>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 regions are marked in red. The QTL locations are shown to the right of each chromosome.</p

Fruits of accessions belonging to the three main morphological groups.

<p>Group 1∶1a = AM 269-Talindo; 1b = AM 026-Dr2; Group 2∶2a = AM 168-Angio 5; 2b = AM 031-FantE63D; 2c = AM 160-Dourga; Group 3∶3a = AM 037-Violetta di Toscana; 3b = AM 291∶17CAAS; 3c = AM 210-67/3.</p

PCA based on geographical origin showing the clustering of the “Oriental” entries with their country of origin.

<p>The accessions from Myanmar and Thailand were classified as Indochinese region.</p

Asparagus officinalis RepeatMasker database

This fasta file contains a custom garden asparagus RepeatMasker database. A total of 893,623 454 FLX Titanium reads were generated from leaf tissue of a doubled haploid (YY) garden asparagus individual. Reads were stringently filtered to a 150nt minimum length. RepeatExplorer was then run, and the resulting cap3 consensus assemblies for each cluster were annotated using RepeatClassifier, part of the RepeatModeler (v1.0.8) suite, with default settings. A total of 22,361 sequences greater than 150nt in length and with annotations

HCPC analysis, based on the leading six PC’s (eigenvalues >1).

<p>a) Scree plot showing the proportion of variance explained by each PC. b) PCA based on the leading two PC’s. Entries belonging to each morphological group marked by a different color (red: group 1, blue: group 2, green: group 3).</p

Phenotype/genotype associations uncovered by GWA analysis.

<p>The associated SNPs’ ID, genomic location, chromosomal region, PVE (phenotypic variability explained) and MAF (minimum allele frequency) are given.</p><p>* Markers with unknown map position were positioned on the eggplant chromosomes using synteny with the tomato genome</p><p>Phenotype/genotype associations uncovered by GWA analysis.</p