Data from: Sorghum bicolor TX08001 nodal root tissue development gene expression profiling

Bioenergy sorghum’s large nodal root system enables deposition of soil
organic carbon deep in soil profiles aiding production of low carbon
intensity biofuels from this crop. During bioenergy sorghum’s long growing
season, plants produce ~175 nodal roots In review bearing lateral roots
that take up water and nutrients from >2 m deep in soil profiles,
and aerial roots that support a complex phyllosphere. In the current
study, nodal root bud development, a slow process spanning ~40 days, was
characterized using microscopy and transcriptome analysis. A first ring of
10-15 nodal root buds was initiated in the stem pulvinus of phytomer 7
near sub-epidermal vascular bundles. A second ring of buds formed above
the first ring much later in phytomer development. Nascent nodal root buds
from phytomer 7 exhibited relatively high expression of pericycle marker
genes (PFA) and genes involved in auxin transport (ABCB19, PIN4, LAX2),
cytokinin signaling (TSO, MYB3R1), and cell proliferation (CYCB2;4,
CDKB2;1, REM1). Following initiation, expression of genes involved in cell
proliferation and cytokinin-signaling decreased while expression of genes
involved in proliferative arrest, ABA-signaling, dormancy and stress
tolerance increased. Further bud development was correlated with increased
expression of WOX11 and PLT5 followed by PLT2, PLT4 and genes encoding RGF
peptides that regulate PLT-expression and bud development. Expression of
the ARF7-regulated LBD29, a gene required for nodal root formation,
increased in parallel with increasing bud size to a maximum late in NRB
development. Appearance of the nodal root bud cap late in development
coincided with expression of SMB and FEZ, whereas genes such as WOX5 and
two MYB36 family members were expressed at higher levels in outgrowing
aerial roots. Genes involved in gibberellin, brassinosteroid,
strigolactone, ethylene, jasmonate, salicyclic acid, and eATP signaling
showed complex patterns of expression during nodal root bud formation.
Overall, this study provides a detailed description of bioenergy sorghum
nodal root bud development and transcriptome information useful for
molecular analysis of networks that regulate nodal root development.