Interaction LOD scores for phenotypes significant at the genome-wide level (P<0.05).

<p>Two-way epistatic interactions for <i>S. lycopersicum/S. pimpinellifolium</i> RIL population across all 12 chromosomes.</p>a<p>Lod.full is the LOD score of the full model with two loci and their interaction compared to the null model with no QTL.</p>b<p>Lod.fv1 is the LOD score of the full model compared to the best single QTL model with one locus on either chromosome A or B.</p>c<p>Lod.int is the LOD score of the interaction term which is found by comparing the full model with an interaction term, to the two QTL models with no interaction term.</p

Overview of significant QTLs associated with seed and seedling traits of <i>S. lycopersicum</i> and <i>S. pimpinellifolium</i> tomato RIL population.

1<p>FrRt = Fresh Root weight, DrRt = Dry root weight, FrSh = Fresh shoot weight, DrSh = Dry Shoot weight, HypL = Hypocotyl length, SW = Dry Seed weight. SS = Dry seed size, SL = Dry seed length, SC = Dry Seed circularity, ImbSS = Imbibed seed size, ImbSL = Imbibed seed length, FrShwn = Fresh Shoot weight under nutrientless condition, FrRtwn = Fresh Root weight under nutrientless condition, DrShwn = Dry shoot weight under nutrientless condition, DrRtwn = Dry root weight under nutrientless condition, MRL = Main Root Length, TRS = Total root size, LRn = Lateral root number per main root, LRD/Bz = Lateral roots density per branched zone.</p>2<p>Chromosome on which the QTLs were detected.</p>3<p>Nearest marker to the position of the identified QTLs.</p>4<p>A positive sign means that the allele of <i>S. pimpinellifolium</i> contributed to the increase of particular trait while the negative sign means that the allele of <i>S. lycopersicum</i> increased the trait at this particular locus.</p

Phenotypic analysis of seed and seedling related vigor traits of a <i>S. lycopersicum</i> and <i>S. pimpinellifolium</i> RIL population and its two parents.

1<p>FrRt = Fresh Root weight, FrSh = Fresh shoot weight, DrRt = Dry root weight. DrSh = Dry Shoot weight, HypL = Hypocotyl length, SW = Dry Seed weight. SS = Dry seed size, SL = Dry seed length, SC = Dry Seed circularity, ImbSS = imbibed seed size, ImbSL = Imbibed seed length, FrShwn = Fresh Shoot weight under nutrientless condition, DrShwn = Dry shoot weight in nutrientless condition, FrRtwn = Fresh root weight in nutrientless condition, DrRtwn = Dry root weight under nutreintless condition, MRL = Main Root path Length, TRS = Total root size, LRn = Lateral root number per main root, LRD/Bz = Lateral roots density per branched zone.</p>2<p>standard deviation.</p>3<p>F-value and P- value were calculated for the population mean.</p

Correlation among seed and seedling traits.

<p>SW = Seed weight, SS = Seed size SL = Seed length. FrRt = Fresh root weight, DrRt = Dry root weight, FrSh = Fresh shoot weight, DrSh = Dry shoot weight, FrShwn = Fresh shoot weight in nutrientless conditions, DrShwn = Dry shoot weight in nutrientless conditions, FrRtwn = Fresh root weight in nutrientless conditions, DrRtwn = Dry Root weight in nutrientless conditions, G_max = Maximum total germination in %, t₅₀ = time to complete 50% germination, U₇₅₂₅ = Uniformity of germination (time between 25 to 75% germination).</p

Heatmap of QTLs identified for seed and seedling quality traits.

<p>Tomato chromosomes are identified by numbers (1–12), with centimorgans ascending from the left to right; chromosomes are separated by yellow lines. SW = Seed Weight, SS = Seed Size SL = Seed Length. FrRt = Fresh Root weight, DrRt = Dry Root weight, FrSh = Fresh Shoot weight, DrSh Dry Shoot weight, FrShwn = Fresh Shoot weight in nutrientless conditions, DrShWn = Dry Shoot weight in nutrientless conditions, FrRtwn = Fresh Root weight in nutrientless conditions, DrRtwn = Dry Root weight in nutrientless conditions, MRL = Main Root Length, TRS = Total Root Size, LRn = Lateral Root number per main root, LRD/Bz = Lateral Root Density per Branched zone. Colors indicate QTLs significant at <i>P</i> = 0.002 in multiple QTL mapping models (1-LOD intervals). Blue and light blue colors indicate a larger effect of the trait in <i>S. pimpinellifolium</i>, and yellow and red in <i>S. lycopersicum</i>.</p

Frequency distributions of non-normalized data of all measured seed and seedling phenotypes in the <i>Solanum lycopersicum</i> x <i>Solanum pimpinellifolium</i> RIL population.

<p>wn: without nutrition. The parental values are indicated with a solid arrow. P = <i>S. pimpinellifolium</i> parent and M = <i>S. lycopersicum</i> parent.</p

Reduction in biomass of seedling grown under nutrient stress condition as compared to the biomass obtained under normal nutrient conditions.

1<p>Normal = Seedling grown under normal nutrients condition,</p>2<p>Wn = Seedling grown on Copenhagen table without nutrition,</p>3<p>Decr = Seedling grown on Copenhagen table without nutrition,</p>4<p>FrRt = Fresh Root weight, DrRt = Dry root weight, FrSh = Fresh shoot weight, DrSh = Dry Shoot weight,</p>5<p>FrRtwn = Fresh root weight in nutrientless condition, DrRtwn = Dry root weight under nutrientless condition, FrShwn = Fresh Shoot weight under nutrientless condition, DrShwn = Dry shoot weight in nutrientless condition.</p

Epistatic interaction network of QTLs identified for seed and seedling quality traits.

<p>Graphical visualization of the epistatic interactions observed among different loci controlling seed and seedling quality phenotypes. The 12 chromosomes are represented as different circle segments, and their sizes are proportional to the corresponding genetic sizes measured in cM. The colour of the lines indicates the trait for which the epistatic interaction was observed <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0043991#pone.0043991-Arends1" target="_blank">[86]</a>.</p