Purple corn is a rich source of anthocyanins. In the experiment, two anthocyanins-enriched purple corn lines Ha0414 and Ha6130 were identified. The anthocyanins were respectively accumulated in the pericarp of Ha0414 and the aleurone layer of Ha6130 with different composition and content. Transcriptome analysis of the two tissues in both lines identified 16 and 14 differentially expressed genes belonging to anthocyanin metabolism pathway in pericarp and the aleurone layer, individually. Of these genes, two genes encoding 2-oxoglutarate (2OG) and Fe (II)-dependent oxygenase superfamily proteins, and one gene annotated as UDP-glycosyltransferase superfamily protein exhibited increased transcript abundance in both the colored pericarp and aleurone layer. Otherwise, one gene annotated as flavonoid 3′, 5′-hydroxylase, and another gene encoding flavonoid 3′-monooxygenase displayed increased transcript abundance in the aleurone layer of Ha6130. Moreover, 36 transcription factors were identified with increased transcript abundance in the pericarp of Ha0414, such as bHLH transcription factors, WRKY transcription factors, and HB transcription factors. And 79 transcription factors were isolated with an increased expression level in the aleurone layer of Ha6130, including MYB transcription factors, MYB-related transcription factors, and bHLH transcription factors. These genes expression may result in the tissue-specific accumulation of anthocyanins in pericarp and aleurone layer.

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Chlorophylls, green pigments in chloroplasts, are essential for photosynthesis. Reduction in chlorophyll content may result in retarded growth, dwarfism, and sterility. In this study, a yellow-green leaf mutant of maize, indicative of abnormity in chlorophyll content, was identified. The physiological parameters of this mutant were measured. Next, global gene expression of this mutant was determined using transcriptome analysis and compared to that of wild-type maize plants. The yellow-green leaf mutant of maize was found to contain lower contents of chlorophyll a, chlorophyll b and carotenoid compounds. It contained fewer active PSII centers and displayed lower values of original chlorophyll fluorescence parameters than the wild-type plants. The real-time fluorescence yield, the electron transport rate, and the net photosynthetic rate of the mutant plants showed reduction as well. In contrast, the maximum photochemical quantum yield of PSII of the mutant plants was similar to that of the wild-type plants. Comparative transcriptome analysis of the mutant plants and wild-type plants led to the identification of differentially expressed 1,122 genes, of which 536 genes were up-regulated and 586 genes down-regulated in the mutant. Five genes in the chlorophyll metabolism pathway, nine genes in the tricarboxylic acid cycle and seven genes related to the conversion of sucrose to starch displayed down-regulated expression. In contrast, genes encoding a photosystem II reaction center PsbP family protein and the PGR5-like protein 1A (PGRL1A) exhibited increased transcript abundance.