Fig. 4

Differentially expressed genes in ears of the gif1 mutant and wild type. A Number and percentage of up-regulated and down-regulated genes. B Representative terms of differentially expressed genes enriched in ears of the gif1 mutant and wild type. Each box represents the median and interquartile range. Whiskers extend to maximum and minimum values. Numbers show the number of differentially expressed genes in terms. C Differentially expressed WUS-related homeobox (wox) genes and CLV3/ENDOSPERM SURROUNDING REGION (ESR)-related (cle) genes in ears of the gif1 and the wild type. The 999 and -999 represent genes expressed specifically in the gif1 and wild-type ear, respectively. D and E Relative expression levels of known inflorescence and floret-related genes. Inflorescence and floret-related genes with up-regulated expression (D) and down-regulated expression (E) in gif1 ears. Relative expression level is detected using RNA-seq and reverse transcription quantitative PCR (RT-qPCR), respectively. RT-qPCR is performed with three biological replicates, each with three technical replicates. Fold changes in RNA transcripts are calculated by the 2^−ΔCt method with maize Actin gene (Zm00001d010159) as an internal control. All bars represent means ± s.d.; s.d.: standard deviation. FC: fold change = FPKM of a given gene detected in the gif1/FPKM of the gene detected in the wild-type sibling. FPKM: fragments per kilobase of transcript per million fragments mapped