scholarly journals Transcriptome profiling of laser-captured crown root primordia reveals new pathways activated during early stages of crown root formation in rice

PLoS ONE ◽  
2020 ◽  
Vol 15 (11) ◽  
pp. e0238736
Author(s):  
Jérémy Lavarenne ◽  
Mathieu Gonin ◽  
Antony Champion ◽  
Marie Javelle ◽  
Hélène Adam ◽  
...  
Keyword(s):  
Root Formation ◽  
Developmental Stages ◽  
Transcriptome Profiling ◽  
Rice Root ◽  
Primary Data ◽  
Root Initiation ◽  
Root Primordia ◽  
Data Resource ◽  
Crown Root ◽  
Crown Roots

Crown roots constitute the main part of the rice root system. Several key genes involved in crown root initiation and development have been identified by functional genomics approaches. Nevertheless, these approaches are impaired by functional redundancy and mutant lethality. To overcome these limitations, organ targeted transcriptome analysis can help to identify genes involved in crown root formation and early development. In this study, we generated an atlas of genes expressed in developing crown root primordia in comparison with adjacent stem cortical tissue at three different developmental stages before emergence, using laser capture microdissection. We identified 3975 genes differentially expressed in crown root primordia. About 30% of them were expressed at the three developmental stages, whereas 10.5%, 19.5% and 12.8% were specifically expressed at the early, intermediate and late stages, respectively. Sorting them by functional ontology highlighted an active transcriptional switch during the process of crown root primordia formation. Cross-analysis with other rice root development-related datasets revealed genes encoding transcription factors, chromatin remodeling factors, peptide growth factors, and cell wall remodeling enzymes that are likely to play a key role during crown root primordia formation. This atlas constitutes an open primary data resource for further studies on the regulation of crown root initiation and development.

scholarly journals Transcriptomic Analysis of the Anthocyanin Biosynthetic Pathway Reveals the Molecular Mechanism Associated with Purple Color Formation in Dendrobium Nestor

Life ◽  
2021 ◽  
Vol 11 (2) ◽  
pp. 113
Author(s):  
Xueqiang Cui ◽  
Jieling Deng ◽  
Changyan Huang ◽  
Xuan Tang ◽  
Xianmin Li ◽  
...  
Keyword(s):  
Molecular Mechanism ◽  
Developmental Stages ◽  
Anthocyanin Biosynthesis ◽  
Transcriptome Profiling ◽  
Flower Color ◽  
Flower Bud ◽  
Color Formation ◽  
Color Development ◽  
Purple Coloration ◽  
Purple Color

Dendrobium nestor is a famous orchid species in the Orchidaceae family. There is a diversity of flower colorations in the Dendrobium species, but knowledge of the genes involved and molecular mechanism underlying the flower color formation in D. nestor is less studied. Therefore, we performed transcriptome profiling using Illumina sequencing to facilitate thorough studies of the purple color formation in petal samples collected at three developmental stages, namely—flower bud stage (F), half bloom stage (H), and full bloom stage (B) in D. nestor. In addition, we identified key genes and their biosynthetic pathways as well as the transcription factors (TFs) associated with purple flower color formation. We found that the phenylpropanoid–flavonoid–anthocyanin biosynthesis genes such as phenylalanine ammonia lyase, chalcone synthase, anthocyanidin synthase, and UDP-flavonoid glucosyl transferase, were largely up-regulated in the H and B samples as compared to the F samples. This upregulation might partly account for the accumulation of anthocyanins, which confer the purple coloration in these samples. We further identified several differentially expressed genes related to phytohormones such as auxin, ethylene, cytokinins, salicylic acid, brassinosteroid, and abscisic acid, as well as TFs such as MYB and bHLH, which might play important roles in color formation in D. nestor flower. Sturdy upregulation of anthocyanin biosynthetic structural genes might be a potential regulatory mechanism in purple color formation in D. nestor flowers. Several TFs were predicted to regulate the anthocyanin genes through a K-mean clustering analysis. Our study provides valuable resource for future studies to expand our understanding of flower color development mechanisms in D. nestor.

Cadmium decreases crown root number by decreasing endogenous nitric oxide, which is indispensable for crown root primordia initiation in rice seedlings

Planta ◽  
2009 ◽  
Vol 230 (4) ◽  
pp. 599-610 ◽  
Author(s):  
Jie Xiong ◽  
Han Lu ◽  
Kaixing Lu ◽  
Yuxing Duan ◽  
Lingyao An ◽  
...  
Keyword(s):  
Nitric Oxide ◽  
Root Number ◽  
Rice Seedlings ◽  
Root Primordia ◽  
Crown Root ◽  
Endogenous Nitric Oxide

scholarly journals Growth and yield of wheat (Triticum aestivum) under deficit irrigation

2014 ◽  
Vol 38 (4) ◽  
pp. 719-732 ◽  
Author(s):  
PK Sarkar ◽  
MSU Talukder ◽  
SK Biswas ◽  
A Khatun
Keyword(s):  
Water Stress ◽  
Grain Yield ◽  
Water Deficit ◽  
Deficit Irrigation ◽  
Water Productivity ◽  
Root Initiation ◽  
Moisture Condition ◽  
Soil Moisture Condition ◽  
Crown Root ◽  
Initiation Stage

Timing and the extent of water deficit were studied in a field experiment on wheat (cv. Shatabdi) for three consecutive years from 2003-04 through 2005-06 at Jamalpur area. The effects of number and timing of irrigation application on yields were investigated under variable soil moisture condition in the root zone of different treatments. Eight deficit irrigations, including one no stress and one rainfed treatments were selected to subject the crop to various degrees of soil water deficit at different stages of crop growth. Measured amount of irrigation water was applied as per schedule prescribed for a particular treatment. Grain yield (GY), biomass, harvest index (HI), and water productivity (WP) were reasonably affected by deficit irrigation. Other yield contributing parameters like 1000-grain weight, grains/spike and spike, length were also affected by different levels of deficit irrigation. During grain formation stage, water deficit did not affect the grain yield but saved water significantly. Such water deficit treatments also shortened the grain maturation period. Differences in grain and straw yield among the stressed and no stress treatments are comparatively small, and statistically insignificant in some cases. The highest water productivity (2.02 kg/m3) was observed in treatment which was irrigated only once at crown root initiation stage (T2) although the yield was comparatively low. The CRI (crown root initiation) stage was found the most sensitive to water stress. Water stress at vegetative stage also reduced the yield considerably. DOI: http://dx.doi.org/10.3329/bjar.v38i4.19663 Bangladesh J. Agril. Res. 38(4): 719-732, December 2013

scholarly journals Transcriptome Profiling Provides Insight into the Genes in Carotenoid Biosynthesis during the Mesocarp and Seed Developmental Stages of Avocado (Persea americana)

2019 ◽  
Vol 20 (17) ◽  
pp. 4117 ◽  
Author(s):  
Yu Ge ◽  
Zhihao Cheng ◽  
Xiongyuan Si ◽  
Weihong Ma ◽  
Lin Tan ◽  
...  
Keyword(s):  
Single Molecule ◽  
Developmental Stages ◽  
Gene Dosage ◽  
Average Length ◽  
Beta Carotene ◽  
Transcriptome Profiling ◽  
Carotenoid Biosynthesis ◽  
Persea Americana ◽  
Sequencing Data ◽  
Long Read

Avocado (Persea americana Mill.) is an economically important crop because of its high nutritional value. However, the absence of a sequenced avocado reference genome has hindered investigations of secondary metabolism. For next-generation high-throughput transcriptome sequencing, we obtained 365,615,152 and 348,623,402 clean reads as well as 109.13 and 104.10 Gb of sequencing data for avocado mesocarp and seed, respectively, during five developmental stages. High-quality reads were assembled into 100,837 unigenes with an average length of 847.40 bp (N50 = 1725 bp). Additionally, 16,903 differentially expressed genes (DEGs) were detected, 17 of which were related to carotenoid biosynthesis. The expression levels of most of these 17 DEGs were higher in the mesocarp than in the seed during five developmental stages. In this study, the avocado mesocarp and seed transcriptome were also sequenced using single-molecule long-read sequencing to acquired 25.79 and 17.67 Gb clean data, respectively. We identified 233,014 and 238,219 consensus isoforms in avocado mesocarp and seed, respectively. Furthermore, 104 and 59 isoforms were found to correspond to the putative 11 carotenoid biosynthetic-related genes in the avocado mesocarp and seed, respectively. The isoform numbers of 10 out of the putative 11 genes involved in the carotenoid biosynthetic pathway were higher in the mesocarp than those in the seed. Besides, alpha- and beta-carotene contents in the avocado mesocarp and seed during five developmental stages were also measured, and they were higher in the mesocarp than in the seed, which validated the results of transcriptome profiling. Gene expression changes and the associated variations in gene dosage could influence carotenoid biosynthesis. These results will help to further elucidate carotenoid biosynthesis in avocado.

Effect of naphthaleneacetic acid on the formation of lateral roots in the adventitious root of Allium cepa: number and arrangement of laterals along the parent root

1992 ◽  
Vol 70 (9) ◽  
pp. 1891-1896 ◽  
Author(s):  
Pedro G. Lloret ◽  
Antonio Pulgarín
Keyword(s):  
Allium Cepa ◽  
Adventitious Root ◽  
Lateral Root ◽  
Root Formation ◽  
Lateral Roots ◽  
Naphthaleneacetic Acid ◽  
Root Primordia ◽  
Sharp Rise ◽  
Allium Cepa L ◽  
Do So

The exogenous application of an auxin (α-naphthaleneacetic acid) to the adventitious root of Allium cepa L. promotes lateral root formation and inhibits main root elongation. If the adventitious roots are released from the influence of this auxin, they may resume elongation after 10−5 M but not after 10−4 treatment. Auxin leads to the appearance of late-forming root primordia intercalated between previously formed laterals. The arrangement of laterals along the adventitious root is another feature altered by treatment, i.e., control roots develop the same number of laterals throughout the length of the zone in which laterals appear, whereas in treated roots the number of laterals rises steadily as the distal end of this zone is approached. In 10−5 M auxin-treated roots, no increase in the number of laterals occurs in basal zones of the parent root, whereas treatment with 10−4 M naphthaleneacetic acid leads to a sharp rise in the number of laterals formed at these zones. Our results suggest that the basal part of onion roots is less sensitive than the apical portion of the effects of naphthaleneacetic acid. This chemical seems to have a rejuvenating effect on cells of the pericycle, enabling them to initiate lateral primordia when under normal conditions they would no do so. Key words: Allium cepa, auxin, lateral root, naphthaleneacetic acid, onion.

scholarly journals CYTOKININ OXIDASE/DEHYDROGENASE4 Integrates Cytokinin and Auxin Signaling to Control Rice Crown Root Formation

2014 ◽  
Vol 165 (3) ◽  
pp. 1035-1046 ◽  
Author(s):  
Shaopei Gao ◽  
Jun Fang ◽  
Fan Xu ◽  
Wei Wang ◽  
Xiaohong Sun ◽  
...  
Keyword(s):  
Root Formation ◽  
Auxin Signaling ◽  
Cytokinin Oxidase ◽  
Crown Root
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