Supplemental Figure 24: Bin mapping results for CotPaveCnt.

Supplemental Figure 24: Bin mapping results for CotPaveCnt. See Supplemental Dataset 7 online for trait details and Supplemental Figure 15 online for legend

Supplemental Figure 44: Bin mapping results for TermPC1.

Supplemental Figure 44: Bin mapping results for TermPC1. See Supplemental Dataset 7 online for trait details and Supplemental Figure 15 online for legend

Supplemental Figure 2: RNAseq-based genotyping of all chromosomes.

Supplemental Figure 2: RNAseq-based genotyping of all chromosomes. Shown are the S. pennellii introgression regions for ILs covering chromosomes 1 to 12 (A-L) as determined by RNA-Seq. The depth of coverage (distance from midpoint on y-axis) and genotype (color and direction on y-axis) of each SNP/indel is plotted against chromosomal position (x-axis). Polymorphisms that match S. pennellii are colored green and plotted on the top half of each IL panel, while polymorphisms matching cv. M82 are plotted in magenta in the bottom halves. The coloring is on a continuum such that the color approaches black as a position’s genotype approaches heterozygosity. The y-axis tick marks indicate depths of coverage ranging from 0 to 100. Subsequent to genotyping, introgression boundaries consistent between the RNA-Seq and RESCAN analyses were delineated. Using these breakpoints, S. pennellii and cv. M82 regions are summarized by horizontal lines at the top and bottom of each IL panel, respectively

Supplemental Figure 12: IL10-3 exhibits QTL affecting pavement cell size and stomatal density.

Supplemental Figure 12: IL10-3 exhibits QTL affecting pavement cell size and stomatal density. A) Images of epidermal peels from the adaxial side of mature leaves and cotyledons are shown. S. pennellii has larger pavement cells and decreased stomatal density relative to cv. M82, perhaps an adaptive feature to its native arid environment. IL10-3 exhibits decreased stomatal density on the adaxial side of mature leaves relative to cv. M82, and increased pavement cell size and decreased stomatal density on the adaxial side of cotyledons. B) IL10-3 is consistently one of the most extreme ILs for a suite of related traits, including adaxial leaf stomatal density, adaxial cotyledon stomatal density, and adaxial cotyledon pavement cell size. One perspective is that, because stomatal patterning in IL10-3 relative cv. M82 is not significantly changed, increases in pavement cell size decrease stomatal density

Supplemental Dataset 5: Modeled trait values and significance values.

Supplemental Dataset 5: Modeled trait values and significance values. For each trait studied, the model-fitted deviation for each IL from the estimated cv. M82 value is given (under the column “Estimate”). Additionally, standard error (“SE”), t-values (“t.value), and p-values (“p.value”) for the estimates are provided

Supplemental Figure 28: Bin mapping results for CotStomInd.

Supplemental Figure 28: Bin mapping results for CotStomInd. See Supplemental Dataset 7 online for trait details and Supplemental Figure 15 online for legend

Supplemental Figure 25: Bin mapping results for CotPaveRound.

Supplemental Figure 25: Bin mapping results for CotPaveRound. See Supplemental Dataset 7 online for trait details and Supplemental Figure 15 online for legend

Supplemental Figure 13: Developmentally insightful correlations between leaf development traits.

Supplemental Figure 13: Developmentally insightful correlations between leaf development traits. A) Pairwise correlations between leaf size (“TermLfSize” and “LatLfSize”) and leaf complexity (“CompPri,” “CompInt,” “CompSec,” “CompRachis,” and “CompAll”). Besides the high correlations within leaf size and leaf complexity traits, there is significant negative correlation between size and complexity. The least significant negative correlation (LatLfSize x CompPri, r = -0.33) is significant at a level of p = 0.0046 (two-tailed, n = 72). The correlation suggests that overall blade area in a leaf is not modulated through complexity, as any additional leaflets are on average smaller. This has implications for resource allocation at the level of the leaf, but also between different parts of the plant, as complexity only modulates the dissection of the leaf rather than its overall blade area. B) Pairwise correlations between absolute stomatal density on the adaxial side of the cotyledon (“CotStom”) and epidermal pavement cell size (“CotPaveArea”) and count (“CotPaveCnt”). The negative correlation between CotStom and CotPaveArea, and the positive correlation between CotStom and CotPaveCnt, suggests that as pavement cell size increases, stomatal density decreases. The least significant correlation between two traits of each class (CotPaveArea x CotStom, r = -0.44) is significant at a level of p = 0.00011 (two-tailed, n = 72). This has implications for mechanisms by which stomatal spacing is modulated in this population, which may not be directly through stomatal patterning, but rather changes in epidermal pavement cell size

Supplemental Figure 40: Bin mapping results for LftCirc.

Supplemental Figure 40: Bin mapping results for LftCirc. See Supplemental Dataset 7 online for trait details and Supplemental Figure 15 online for legend

Supplemental Figure 16: Bin mapping results for CompAll.

Supplemental Figure 16: Bin mapping results for CompAll. See Supplemental Dataset 7 online for trait details and Supplemental Figure 15 online for legend