The Pedunculate oak (Quercus robur) root database consolidates information currently available on RNA-seq research conducted on both coding and non-coding RNA.
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The Pedunculate oak (Quercus robur) root database (OakRootRNADB) consolidates information currently available on RNA-seq research conducted on both coding and non-coding RNA. The database contains the sequences of genes, transcripts, proteins, and microRNA (based on identified pre-miRNA) obtained from the meristematic and elongation zones of both taproot and lateral roots of Q. robur. The database contains two datasets:
Dataset 1 contains DNA sequences obtained from the meristematic zone of Q. robur taproots and all classes of lateral roots of trees grown in a container or rhizotron system. The sampled taproots are categorized into three length classes; short (5-9cm), medium (9,5-15cm) and long (15,5-35cm). The taproots in each length class were further classified into standard thickness (normal), those that had a thicker than normal diameter and were still actively growing, and dying roots (usually container taproots that grown to the bottom of the container). Samples were collected from three replicate experiments in 2019 when the oak seedlings were approximately 8-weeks-old.
Dataset 2 contains DNA sequences obtained from the meristematic and elongation zones of taproots and lateral roots of Q. robur growing in either a container or a rhizotron system, and oak seedlings that had been initially grown in a container in 2019 and then transferred to a rhizotron. The collected roots in both 2019 and 2020 were categorized as described in the section on dataset 1. The only exception was that 2-year-old acorns were used in the initial planting.
The presence of taproots enhances the ability of oak trees to forage for water in deep soil layers and represents a strategy that has evolved in oak trees growing in areas with strong water shortages. Unfortunately, “air-pruning”, the cultural management approach used in the container production of oak seedlings, damages developing taproots. This results in changes in the architecture of oak roots and may induce the development of oak seedlings with a shallow root distributions and render them more susceptible to injury in response to periodic episodes of drought (Zadworny et al., 2014; Zadworny et al., 2019; Zadworny et al., 2021). Thus, the practice of cutting taproots during the nursery production of oak seedlings could be a key factor inducing subsequent tree weakening and drought-induced decline. Chronic drought conditions and the continuing evidence of weak and dying oak stands indicate that the problem is severe and ongoing and that drought is having a major impact on the vigor and longevity of oak trees.
The aim of the proposed project is to better understand the impact of cultural management techniques, such as “air pruning”, on the growth and development of oak taproots and lateral roots in seedlings grown in containers and then planted in forest stands by identifying and analyzing the factors regulating root system development. Identifying root-related coding and non-coding RNA and their function is crucial for understanding the regulation of deep taproot growth, as well as overall root system architecture and how it functions, which determines root water absorption ability and root developmental response following root injury (Kościelniak et., 2021). Determining the factors that regulate taproot growth, are responsible for maintaining taproot growth, and enable regrowth of a taproot in container seedlings after they are planted in the field, will provide a mechanistic understanding of the effect of nursery management practices on seedling growth and its potential impact on subsequent managed forest stands.
Zadworny, M., Jagodziński, A.M., Łakomy, P., Ufnalski, K., and Oleksyn, J. (2014). The silent shareholder in deterioration of oak growth: common planting practices affect the long-term response of oaks to periodic drought. Forest Ecology and Management 318, 133-141. doi:10.1016/j.foreco.2014.01.017.
Zadworny, M., Jagodziński, A.M., Łakomy, P., Mucha, J., Oleksyn, J., Rodríguez-Calcerrada, J., et al. (2019). Regeneration origin affects radial growth patterns preceding oak decline and death - insights from tree-ring delta C-13 and delta O-18. Agricultural and Forest Meteorology 278, 12. doi:10.1016/j.agrformet.2019.107685.
Zadworny, M., Mucha, J., Jagodziński, A.M., Kościelniak, P., Łakomy, P., Modrzejewski, M., et al. (2021). Seedling regeneration techniques affect root systems and the response of Quercus robur seedlings to water shortages. Forest Ecology and Management 479, 11. doi:10.1016/j.foreco.2020.118552.
Kościelniak, P., Glazińska, P., Kęsy, J., Zadworny, M. (2021). Formation and Development of Taproots in Deciduous Tree Species Frontiers in Plant Science 12:772567. doi:10.3389/fpls.2021.772567.
If you make use of the data presented here, please cite the following article:
Kościelniak, P., Glazińska, P., Zadworny, M. (2022). OakRootRNADB—a consolidated RNA-seq database for coding and noncoding RNA in roots of pedunculate oak (Quercus robur) Database: The Journal of Biological Databases and Curation, Volume 2022, baac097 doi:10.1093/database/baac09.
Kościelniak Paulina (PhD)1
Glazińska Paulina (PhD)2
Zadworny Marcin (PhD)1
1 - Institute of Dendrology, Polish Academy of Sciences, Kórnik, Poland
2 - Department of Plant Physiology and Biotechnology, Faculty of Biological and Veterinary Sciences, Nicolaus Copernicus University, Toruń, Poland