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

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Jul 31, 2023 version files 27.69 MB

Abstract

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.