Maize Genomics and Genetics 2024, Vol.15, No.4, 204-217 http://cropscipublisher.com/index.php/mgg 210 Figure 3 Analysis of Biased Allelic Expression Patterns and Regulatory Variation Classification across Tissues (Adopted from Zhou et al., 2019) (A and B) A scatterplot shows the parental B73 allele ratio (x axis, CPMB/(CPMB/CPMM)) and hybrid B73 allele ratio (y axis) for DE genes (A) and non-DE genes (B) in maize root tissue. The colors represent different regulatory variation classifications determined for each gene (see Methods) (C) The pie chart (left) shows the proportion of all DE genes (between the two parents) that were assigned to different regulatory mechanisms across all 20 non-endosperm tissues. The plots on the right show the enrichment or depletion (as fold change relative to background proportion from the left pie chart) for subsets of genes for each regulatory variation classification. The subsets of genes include different levels of fold change in expression (DE2–4, DE4–8, DE8+, and SPE), different additivity patterns (BLP, LP, MP, HP, and AHP), and genes that were characterized by a previous eQTL study (in shoot apex meristem, Li et al., 2013) to be regulated by only cis-eQTL, only trans-eQTL, or both cis-eQTL and trans-eQTL. For each subset of genes the proportion of each regulatory classification was compared with background proportion (left pie chart) with the ratio plotted as bars along the x axis. P values were determined using a hypergeometric test (lower.tail = FALSE for enrichment and lower.tail=TRUE for depletion) and labeled with asterisks (*P<0.01 or **P<0.001); (D and E) For genes that are DE and have allele-specific expression data in at least five tissues, we assessed the consistency of regulation variation classifications. In (D) the subset of genes that are classified into each pattern in at least one tissue was used to assess the proportion of tissues that show this pattern. In (E) all genes classified into a specific pattern in at least one tissue were used to assess whether that classification was tissue specific (showing that pattern in less than 20% of DE tissues), intermediate frequency (20%–80% DE tissues), or constitutive (more than 80% of DE tissues) (Adopted from Zhou et al., 2019) 5.2 Functional genomics and gene expression studies Functional genomics studies have been instrumental in identifying key regulatory genes and understanding their roles in maize development and agronomic traits. Gene expression and eQTL analyses have uncovered natural
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