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Novel Insights into the Genetics of Root Development (2019)
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Novel Insights into the Genetics of Root Development (2019)

A special issue of Genes (ISSN 2073-4425). This special issue belongs to the section "Plant Genetics and Genomics".

Deadline for manuscript submissions: closed (20 September 2019) | Viewed by 30862

Special Issue Editor

Dr. Marc Libault

E-Mail Website
Guest Editor
Department of Agronomy and Horticulture, Center for Plant Science Innovation, University of Nebraska-Lincoln, Beadle Center, Lincoln, NE 68503, USA
Interests: regulation of gene expression; single cell; genomic and epigenomic regulation

Special Issue Information

Dear Colleagues,

Due to its basal function (i.e., uptake of water and nutrient from the soil), the root system is playing a critical role in plant growth and yield. Its constant adaptation to various environmental stresses including abiotic and biotic stresses (e.g., interaction between the plant root system and the soil microbiome), its simple cellular organization, and its well-described architecture are clear advantage when applying molecular genetic approaches to better understand its development and its response to environmental stresses.

In this Special Issue, we are inviting reviews, perspectives, and original research articles to advance our knowledge related to plant root development. Topics will include, but not limited to the development of new methods and technologies to analyze root architecture, genome-wide association studies focusing on root phenotypic traits, the characterization of the regulatory mechanisms controlling gene activity during root development notably in response to biotic and abiotic stresses (e.g., role of miRNA, DNA methylation and other epigenomic changes, functional genomic studies revealing the role of genes and proteins during root development).  This Special Issue will also consider manuscripts describing the development of unique plant organs such as legume nodules.

Dr. Marc Libault
Guest Editor

Manuscript Submission Information

Manuscripts should be submitted online at www.mdpi.com by registering and logging in to this website. Once you are registered, click here to go to the submission form. Manuscripts can be submitted until the deadline. All submissions that pass pre-check are peer-reviewed. Accepted papers will be published continuously in the journal (as soon as accepted) and will be listed together on the special issue website. Research articles, review articles as well as short communications are invited. For planned papers, a title and short abstract (about 100 words) can be sent to the Editorial Office for announcement on this website.

Submitted manuscripts should not have been published previously, nor be under consideration for publication elsewhere (except conference proceedings papers). All manuscripts are thoroughly refereed through a single-blind peer-review process. A guide for authors and other relevant information for submission of manuscripts is available on the Instructions for Authors page. Genes is an international peer-reviewed open access monthly journal published by MDPI.

Please visit the Instructions for Authors page before submitting a manuscript. The Article Processing Charge (APC) for publication in this open access journal is 2600 CHF (Swiss Francs). Submitted papers should be well formatted and use good English. Authors may use MDPI's English editing service prior to publication or during author revisions.

Keywords

  • root
  • development
  • biotic stress
  • abiotic stress
  • genomics.

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Published Papers (6 papers)

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Research

15 pages, 2947 KiB  
Article
Plant Hormones Differentially Control the Sub-Cellular Localization of Plasma Membrane Microdomains during the Early Stage of Soybean Nodulation
by Zhenzhen Qiao, Prince Zogli and Marc Libault
Genes 2019, 10(12), 1012; https://doi.org/10.3390/genes10121012 - 5 Dec 2019
Cited by 3 | Viewed by 3150
Abstract
Phytohormones regulate the mutualistic symbiotic interaction between legumes and rhizobia, nitrogen-fixing soil bacteria, notably by controlling the formation of the infection thread in the root hair (RH). At the cellular level, the formation of the infection thread is promoted by the translocation of [...] Read more.
Phytohormones regulate the mutualistic symbiotic interaction between legumes and rhizobia, nitrogen-fixing soil bacteria, notably by controlling the formation of the infection thread in the root hair (RH). At the cellular level, the formation of the infection thread is promoted by the translocation of plasma membrane microdomains at the tip of the RH. We hypothesize that phytohormones regulate the translocation of plasma membrane microdomains to regulate infection thread formation. Accordingly, we treated with hormone and hormone inhibitors transgenic soybean roots expressing fusions between the Green Fluorescent Protein (GFP) and GmFWL1 or GmFLOT2/4, two microdomain-associated proteins translocated at the tip of the soybean RH in response to rhizobia. Auxin and cytokinin treatments are sufficient to trigger or inhibit the translocation of GmFWL1 and GmFLOT2/4 to the RH tip independently of the presence of rhizobia, respectively. Unexpectedly, the application of salicylic acid, a phytohormone regulating the plant defense system, also promotes the translocation of GmFWL1 and GmFLOT2/4 to the RH tip regardless of the presence of rhizobia. These results suggest that phytohormones are playing a central role in controlling the early stages of rhizobia infection by regulating the translocation of plasma membrane microdomains. They also support the concept of crosstalk of phytohormones to control nodulation. Full article
(This article belongs to the Special Issue Novel Insights into the Genetics of Root Development (2019))
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23 pages, 4651 KiB  
Article
Natural Root Cellular Variation in Responses to Osmotic Stress in Arabidopsis thaliana Accessions
by Wendy Cajero-Sanchez, Pamela Aceves-Garcia, María Fernández-Marcos, Crisanto Gutiérrez, Ulises Rosas, Berenice García-Ponce, Elena R. Álvarez-Buylla, Maria de la Paz Sánchez and Adriana Garay-Arroyo
Genes 2019, 10(12), 983; https://doi.org/10.3390/genes10120983 - 29 Nov 2019
Cited by 18 | Viewed by 4933
Abstract
Arabidopsis naturally occurring populations have allowed for the identification of considerable genetic variation remodeled by adaptation to different environments and stress conditions. Water is a key resource that limits plant growth, and its availability is initially sensed by root tissues. The root’s ability [...] Read more.
Arabidopsis naturally occurring populations have allowed for the identification of considerable genetic variation remodeled by adaptation to different environments and stress conditions. Water is a key resource that limits plant growth, and its availability is initially sensed by root tissues. The root’s ability to adjust its physiology and morphology under water deficit makes this organ a useful model to understand how plants respond to water stress. Here, we used hyperosmotic shock stress treatments in different Arabidopsis accessions to analyze the root cell morphological responses. We found that osmotic stress conditions reduced root growth and root apical meristem (RAM) size, promoting premature cell differentiation without affecting the stem cell niche morphology. This phenotype was accompanied by a cluster of small epidermal and cortex cells with radial expansion and root hairs at the transition to the elongation zone. We also found this radial expansion with root hairs when plants are grown under hypoosmotic conditions. Finally, root growth was less affected by osmotic stress in the Sg-2 accession followed by Ws, Cvi-0, and Col-0; however, after a strong osmotic stress, Sg-2 and Cvi-0 were the most resilience accessions. The sensitivity differences among these accessions were not explained by stress-related gene expression. This work provides new cellular insights on the Arabidopsis root phenotypic variability and plasticity to osmotic stress. Full article
(This article belongs to the Special Issue Novel Insights into the Genetics of Root Development (2019))
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15 pages, 1562 KiB  
Article
Integrating GWAS and Gene Expression Analysis Identifies Candidate Genes for Root Morphology Traits in Maize at the Seedling Stage
by Houmiao Wang, Jie Wei, Pengcheng Li, Yunyun Wang, Zhenzhen Ge, Jiayi Qian, Yingying Fan, Jinran Ni, Yang Xu, Zefeng Yang and Chenwu Xu
Genes 2019, 10(10), 773; https://doi.org/10.3390/genes10100773 - 2 Oct 2019
Cited by 34 | Viewed by 5269
Abstract
Root system plays an essential role in water and nutrient acquisition in plants. Understanding the genetic basis of root development will be beneficial for breeding new cultivars with efficient root system to enhance resource use efficiency in maize. Here, the natural variation of [...] Read more.
Root system plays an essential role in water and nutrient acquisition in plants. Understanding the genetic basis of root development will be beneficial for breeding new cultivars with efficient root system to enhance resource use efficiency in maize. Here, the natural variation of 13 root and 3 shoot traits was evaluated in 297 maize inbred lines and genome-wide association mapping was conducted to identify SNPs associated with target traits. All measured traits exhibited 2.02- to 21.36-fold variations. A total of 34 quantitative trait loci (QTLs) were detected for 13 traits, and each individual QTL explained 5.7% to 15.9% of the phenotypic variance. Three pleiotropic QTLs involving five root traits were identified; SNP_2_104416607 was associated with lateral root length (LRL), root surface area (RA), root length between 0 and 0.5mm in diameter (RL005), and total root length (TRL); SNP_2_184016997 was associated with RV and RA, and SNP_4_168917747 was associated with LRL, RA and TRL. The expression levels of candidate genes in root QTLs were evaluated by RNA-seq among three long-root lines and three short-root lines. A total of five genes that showed differential expression between the long- and short-root lines were identified as promising candidate genes for the target traits. These QTLs and the potential candidate genes are important source data to understand root development and genetic improvement of root traits in maize. Full article
(This article belongs to the Special Issue Novel Insights into the Genetics of Root Development (2019))
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16 pages, 3744 KiB  
Article
Heterologous Expression of GbTCP4, a Class II TCP Transcription Factor, Regulates Trichome Formation and Root Hair Development in Arabidopsis
by Yi Wang, Yuehua Yu, Quanjia Chen, Guanghong Bai, Wenwei Gao, Yanying Qu and Zhiyong Ni
Genes 2019, 10(9), 726; https://doi.org/10.3390/genes10090726 - 19 Sep 2019
Cited by 11 | Viewed by 3987
Abstract
Two class I family teosinte branched1/cycloidea/proliferating cell factor1 (TCP) proteins from allotetraploid cotton are involved in cotton fiber cell differentiation and elongation and root hair development. However, the biological function of most class II TCP proteins is unclear. This study sought to reveal [...] Read more.
Two class I family teosinte branched1/cycloidea/proliferating cell factor1 (TCP) proteins from allotetraploid cotton are involved in cotton fiber cell differentiation and elongation and root hair development. However, the biological function of most class II TCP proteins is unclear. This study sought to reveal the characteristics and functions of the sea-island cotton class II TCP gene GbTCP4 by biochemical, genetic, and molecular biology methods. GbTCP4 protein localizes to nuclei, binding two types of TCP-binding cis-acting elements, including the one in its promoter. Expression pattern analysis revealed that GbTCP4 is widely expressed in tissues, with the highest level in flowers. GbTCP4 is expressed at different fiber development stages and has high transcription in fibers beginning at 5 days post anthesis (DPA). GbTCP4 overexpression increases primary root hair length and density and leaf and stem trichomes in transgenic Arabidopsis relative to wild-type plants (WT). GbTCP4 binds directly to the CAPRICE (CPC) promoter, increasing CPC transcript levels in roots and reducing them in leaves. Compared with WT plants, lignin content in the stems of transgenic Arabidopsis overexpressing GbTCP4 increased, and AtCAD5 gene transcript levels increased. These results suggest that GbTCP4 regulates trichome formation and root hair development in Arabidopsis and may be a candidate gene for regulating cotton fiber elongation. Full article
(This article belongs to the Special Issue Novel Insights into the Genetics of Root Development (2019))
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18 pages, 3656 KiB  
Article
Overexpression of Nitrate Transporter OsNRT2.1 Enhances Nitrate-Dependent Root Elongation
by Misbah Naz, Bingbing Luo, Xueya Guo, Bin Li, Jingguang Chen and Xiaorong Fan
Genes 2019, 10(4), 290; https://doi.org/10.3390/genes10040290 - 9 Apr 2019
Cited by 38 | Viewed by 5065
Abstract
Root morphology is essential for plant survival. NO3− is not only a nutrient, but also a signal substance affecting root growth in plants. However, the mechanism of NO3−-mediated root growth in rice remains unclear. In this study, we [...] Read more.
Root morphology is essential for plant survival. NO3− is not only a nutrient, but also a signal substance affecting root growth in plants. However, the mechanism of NO3−-mediated root growth in rice remains unclear. In this study, we investigated the effect of OsNRT2.1 on root elongation and nitrate signaling-mediated auxin transport using OsNRT2.1 overexpression lines. We observed that the overexpression of OsNRT2.1 increased the total root length in rice, including the seminal root length, total adventitious root length, and total lateral root length in seminal roots and adventitious roots under 0.5-mM NO3− conditions, but not under 0.5-mM NH4+ conditions. Compared with wild type (WT), the 15NO3− influx rate of OsNRT2.1 transgenic lines increased by 24.3%, and the expressions of auxin transporter genes (OsPIN1a/b/c and OsPIN2) also increased significantly under 0.5-mM NO3− conditions. There were no significant differences in root length, ß-glucuronidase (GUS) activity, and the expressions of OsPIN1a/b/c and OsPIN2 in the pDR5::GUS transgenic line between 0.5-mM NO3− and 0.5-mM NH4+ treatments together with N-1-naphthylphalamic acid (NPA) treatment. When exogenous NPA was added to 0.5-mM NO3− nutrient solution, there were no significant differences in the total root length and expressions of OsPIN1a/b/c and OsPIN2 between transgenic plants and WT, although the 15NO3− influx rate of OsNRT2.1 transgenic lines increased by 25.2%. These results indicated that OsNRT2.1 is involved in the pathway of nitrate-dependent root elongation by regulating auxin transport to roots; i.e., overexpressing OsNRT2.1 promotes an effect on root growth upon NO3− treatment that requires active polar auxin transport. Full article
(This article belongs to the Special Issue Novel Insights into the Genetics of Root Development (2019))
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16 pages, 4551 KiB  
Article
RNA-Seq Transcriptome Analysis of Rice Primary Roots Reveals the Role of Flavonoids in Regulating the Rice Primary Root Growth
by Yu Xu, Junjie Zou, Hongyan Zheng, Miaoyun Xu, Xuefeng Zong and Lei Wang
Genes 2019, 10(3), 213; https://doi.org/10.3390/genes10030213 - 13 Mar 2019
Cited by 18 | Viewed by 7734
Abstract
Flavonoids play important roles in root development and in its tropic responses, whereas the flavonoids-mediated changes of the global transcription levels during root growth remain unclear. Here, the global transcription changes in quercetin-treated rice primary roots were analyzed. Quercetin treatment significantly induced the [...] Read more.
Flavonoids play important roles in root development and in its tropic responses, whereas the flavonoids-mediated changes of the global transcription levels during root growth remain unclear. Here, the global transcription changes in quercetin-treated rice primary roots were analyzed. Quercetin treatment significantly induced the inhibition of root growth and the reduction of H2O2 and O2− levels. In addition, the RNA-seq analysis revealed that there are 1243 differentially expressed genes (DEGs) identified in quercetin-treated roots, including 1032 up-regulated and 211 down-regulated genes. A gene ontology (GO) enrichment analysis showed that the enriched GO terms are mainly associated with the cell wall organization, response to oxidative stress, and response to hormone stimulus. The Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment pathway analysis showed that the enriched DEGs are involved in phenylpropanoid biosynthesis, glutathione metabolism, and plant hormone signal transduction. Moreover, the quercetin treatment led to an increase of the antioxidant enzyme activities of catalase (CAT), peroxidase (POD), and superoxide dismutase (SOD) in rice roots. Also, the quercetin treatment altered the DR5:GUS expression pattern in the root tips. All of these data indicated that the flavonoids-mediated transcription changes of genes are related to the genes involved in cell wall remodeling, redox homeostasis, and auxin signaling, leading to a reduced cell division in the meristem zone and cell elongation in the elongation zone of roots. Full article
(This article belongs to the Special Issue Novel Insights into the Genetics of Root Development (2019))
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