Transcriptional regulation of root development in cacao: a genome-wide comparative analysis between zygotic and...

The knowledge gaps on cacao root biology deeply hamper the possibility to efficiently develop tissue culture-based regeneration adapted to cacao physiology. Dissecting the regulatory mechanisms controlling cacao root development and identifying molecular disorders associated with root defects in somatic embryo-derived seedlings (SES) is critical to elucidate potential targets for optimizing somatic embryogenesis protocols as well as to develop resilient elite genotypes that can tolerate environmental alterations. The current study aimed to systematically identify the transcriptional patterns underlying cacao root development in zygotic embryo-derived seedlings (ZES) and SES, with a focus on the emergence of lateral roots.

The study examined roots from four cacao seedling types: 4-day-old ZES, 7-day-old ZES, a lateral-rootless SES variant, and SES with fully developed lateral roots. Root morphology was assessed through tissue microscopy, and whole-root transcriptomes were profiled using genome-wide RNA sequencing (RNA-seq).

Histological analysis revealed mispatterning of pericycle and vascular tissues in roots of lateral-rootless SES. Genome-wide transcriptomic profiling revealed 12,979 differentially expressed genes, encompassing pathways related to amino acid and carbohydrate metabolism, phytohormone signaling, mitogen-activated protein kinase (MAPK) cascades, motor-protein function, and homologous recombination-core regulatory modules that underpin cacao root patterning and adaptive plasticity. More than 900 transcription factors, including members of the AP2/ERF, MYB, NAC, LOB, GNAT, SET, and WRKY families, were also differentially regulated. Our work identified common and distinctive features of root growth and lateral branching in ZES and in normal and misshaped SES at the transcriptional level.

Collectively, our results show that early root morphogenesis in cacao is orchestrated by precise transcriptional reprogramming. Yet, the heightened stress associated with in vitro culture perturbs this developmental trajectory in SES, inducing pericycle and vascular tissue defects that ultimately constrain primary root growth and lateral root initiation.