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Abstract
Primary root (PR) development is a crucial developmental process that is essential for plant survival. The elucidation of the PR transcriptome provides insight into the genetic mechanism controlling PR development in crops. In this study, we performed a comparative transcriptome analysis to investigate the genome-wide gene expression profiles of the seedling PRs of four Brassica napus genotypes that were divided into two groups, short group (D43 and D61), and long group (D69 and D72), according to their extremely different primary root lengths (PRLs). The results generated 55,341,366–64,631,336 clean reads aligned to 62,562 genes (61.9% of the current annotated genes) in the B. napus genome. We provide evidence that at least 44,986 genes are actively expressed in the B. napus PR. The majority of the genes that were expressed during seedling PR development were associated with metabolism, cellular processes, response to stimulus, biological regulation, and signaling. Using a pairwise comparison approach, 509 differentially expressed genes (DEGs; absolute value of log2 fold-change ≥1 and p ≤ 0.05) between the long and short groups were revealed, including phytohormone-related genes, protein kinases and phosphatases, oxygenase, cytochrome P450 proteins, etc. Combining GO functional category, KEGG, and MapMan pathway analyses indicated that the DEGs involved in cell wall metabolism, carbohydrate metabolism, lipid metabolism, secondary metabolism, protein modification and degradation, hormone pathways and signaling pathways were the main causes of the observed PRL differences. We also identified 16 differentially expressed transcription factors (TFs) involved in PR development. Taken together, these transcriptomic datasets may serve as a foundation for the identification of candidate genes and may provide valuable information for understanding the molecular and cellular events related to PR development.
Highlights
Root system architecture (RSA), which is defined as the threedimensional distribution of a root system within the soil, consists of root morphology, topology, and distribution and determines root plasticity to capture nutrients and water in a constantly changing environment (Lynch, 1995; Rogers and Benfey, 2015)
To select representative genotypes of B. napus for the comprehensive characterization of genes associated with Primary root (PR) development, the primary root lengths (PRLs) of 40 natural B. napus accessions were investigated after growth for 5, 10, and 18 days by a hydroponic test
For the upregulated differentially expressed genes (DEGs), the representative terms were “protein phosphorylation” “translation” “response to oxidative stress” and “metal ion transport” (Figure S4B). These analyses demonstrated that DEGs encoding diverse metabolic, regulatory, signaling and structural proteins related to metabolic activity and cell expansion and/or proliferation were responsible for the PRL differences between the short and long groups
Summary
Root system architecture (RSA), which is defined as the threedimensional distribution of a root system within the soil, consists of root morphology, topology, and distribution and determines root plasticity to capture nutrients and water in a constantly changing environment (Lynch, 1995; Rogers and Benfey, 2015). The PR develops from the division and differentiation of stem cell niche (SCN) cells that reside in the RAM (Giehl et al, 2014). The SCN is formed by the quiescent center (QC) and the surrounding stem cells (De Smet et al, 2015). The QC functions in the maintenance of adjacent meristematic stem cells (Drisch and Stahl, 2015). When new cells progress further away from the SCN, they stop dividing and undergo differentiation and elongation to form three distinct regions, the meristematic zone (MZ), the elongation zone (EZ), and the differentiation zone (DZ), which in turn determine the basis for the growth, development, and regeneration of the roots (De Smet et al, 2015). One notable feature of the DZ is the emergence of root hairs (Drisch and Stahl, 2015)
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