Single-cell and tissue transcriptomes unveil factors regulating vein initiation and development in grass leaf primordia

Compared to the C3 plant rice (Oryza sativa), veins in the leaves of the C4 plant maize (Zea mays) are more densely arranged, but the mechanisms controlling vein initiation and differentiation remain unclear. This study systematically investigated the developmental patterning of vein formation in leaf primordia of maize and rice. Single-nucleus transcriptomic atlas of maize primordia revealed distinct middle ground tissue and procambium cell populations and a role for auxin in vein initiation inferred. Pseudo-time trajectory analysis further facilitated the identification of marker genes in ground tissue and procambial cell types including ETHYLENE-RESPONSIVE ELEMENT BINDING 114 (ZmEREB114), AUXIN IMPORT CARRIER 3 (ZmAIC3), ZmEREB161, and AUXIN AMIDO SYNTHETASE 2 (ZmAAS2). An experimental system was established in which the interplay between SHORT-ROOT1 (ZmSHR1) and auxin was used to suppress or restore vein formation in rice leaf primordia. Notably, expression of the rice genes GRETCHEN HAGEN 3.8 (OsGH3.8, homologous to ZmAAS2) and AUXIN RESISTANT 1 (OsAUX1, homologous to ZmAIC3) was suppressed by ZmSHR1 but promoted by auxin. Collectively this study provides single-cell resolved resources for early stages of grass leaf development, an experimental system for manipulating vein initiation in rice, and a model about how the interplay between SHR function and auxin response regulates vein patterning in maize and rice leaves.