1. Volume 28, Issue 3, Pages 431-437.e4 (February 2018)
Single-Parent Expression Is a General Mechanism Driving Extensive Complementation of Non-syntenic Genes in Maize Hybrids 
Jutta A. Baldauf, Caroline Marcon, Andrew Lithio, Lucia Vedder, Lena Altrogge, Hans-Peter Piepho, Heiko Schoof, Dan Nettleton, Frank Hochholdinger 
Current Biology 
Volume 28, Issue 3, Pages e4 (February 2018)
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2. Figure 1
Phylogenetic and Transcriptomic Relationship of Maize Inbred Lines Used in This Study
(A) Selection of maize inbred lines based on their phylogenetic relationship (see also Figure S2). The selected inbred lines are highlighted by a thicker branch. Different clades of the phylogenetic tree are indicated by different colors.
(B) Multidimensional scaling (MDS) plot of all 180 RNA-seq samples. Each genotype is highlighted by a different color (see also Figure S1B). Inbred line clusters are labeled with the corresponding genotype tag. Hybrids are represented in lighter shade of the same color as the paternal inbred line. The three developmental stages are distinguished by the shapes of their features.
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3. Figure 2 SPE Complementation Is Universal in Maize Hybrids
(A) Number of SPE_B (B) and SPE_X (X) genes in the six parent-hybrid triplets. I–III indicate the three developmental stages of the analyzed primary roots: I, 2–4 cm; II, 6–8 cm; and III, 10–12 cm (see also Figure S1A).
(B) Number of expressed genes in hybrids and their parental inbred lines at each of the three developmental stages (I–III).
SPE, single-parent expression.
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4. Figure 3 Overrepresentation of Non-syntenic Genes among SPE Genes
Proportion of non-syntenic genes among SPE_B (B, darker color) and SPE_X (X, lighter color) patterns and among the total number of expressed genes that are not SPE (E, gray) per parent-hybrid triplet during the three developmental stages I–III. The proportion of non-syntenic genes among all protein-coding genes is represented by the dashed line. Significant differences (α = 0.05) are indicated by an asterisk.
See also Data S1 and Figure S4D.
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5. Figure 4
Overrepresentation of Non-syntenic bZIP and bHLH Transcription Factors TFs among All TFs Displaying SPE Patterns
(A and B) Proportion of non-syntenic genes among all expressed bZIP (A) and bHLH (B) TFs that do not display SPE (E, gray bars; sample size n = 106–113 bZIP, 135–145 bHLH) and of bZIP (A) and bHLH (B) TFs displaying SPE (S, colored bars; sample size n = 3–8 bZIP, 6–17 bHLH) for each of the six parent-hybrid triplets and developmental stages (I–III). The proportion of non-syntenic TFs displaying SPE refers to the sum of SPE_B and SPE_X genes per parent-hybrid triplet. Significant differences (α = 0.05) are indicated by an asterisk.
See also Figure S4, Table S4, and Data S1.
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