Gene expression profiles in early leaf of rice (Oryza sativa) and foxtail millet (Setaria italica)

Plant anatomy is patterned early during leaf development which suggests studying the spatial–temporal transcriptomes of primordia will help identify critical regulative and functional genes. We successfully isolated the leaf primordia tissues from the C₃ grass rice and the C₄ grass foxtail millet by laser capture microdissection (LCM) and studied the gene expression throughout leaf developmental stages. Our data analysis uncovered the conserved expression patterns of certain gene clusters both in rice and foxtail millet during leaf development. We revealed genes and transcription factors involved in vein formation, stomatal development, and suberin accumulation. We identified 79 candidate genes associated with functional regulation of C₄ anatomy formation. Screening phenotype of the candidate genes revealed that knock-out of a putative polar auxin transport related gene NAL1 resulted significantly reduced veinal space in rice leaf. Our present work provides a foundation for future analyses of genes with novel functions in grasses and their role in leaf development, in particular the role in leaves with a contrasting C₃ vs. C₄ biosynthetic pathway.