rhizome development
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BMC Genomics ◽  
2022 ◽  
Vol 23 (1) ◽  
Author(s):  
Haitao Xing ◽  
Yuan Li ◽  
Yun Ren ◽  
Ying Zhao ◽  
Xiaoli Wu ◽  
...  

Abstract Background MicroRNAs (miRNAs) are endogenous, non-coding small functional RNAs that govern the post-transcriptional regulatory system of gene expression and control the growth and development of plants. Ginger is an herb that is well-known for its flavor and medicinal properties. The genes involved in ginger rhizome development and secondary metabolism have been discovered, but the genome-wide identification of miRNAs and their overall expression profiles and targets during ginger rhizome development are largely unknown. In this study, we used BGISEQ-500 technology to perform genome-wide identification of miRNAs from the leaf, stem, root, flower, and rhizome of ginger during three development stages. Results In total, 104 novel miRNAs and 160 conserved miRNAs in 28 miRNA families were identified. A total of 181 putative target genes for novel miRNAs and 2772 putative target genes for conserved miRNAs were predicted. Transcriptional factors were the most abundant target genes of miRNAs, and 17, 9, 8, 4, 13, 8, 3 conserved miRNAs and 5, 7, 4, 5, 5, 15, 9 novel miRNAs showed significant tissue-specific expression patterns in leaf, stem, root, flower, and rhizome. Additionally, 53 miRNAs were regarded as rhizome development-associated miRNAs, which mostly participate in metabolism, signal transduction, transport, and catabolism, suggesting that these miRNAs and their target genes play important roles in the rhizome development of ginger. Twelve candidate miRNA target genes were selected, and then, their credibility was confirmed using qRT-PCR. As the result of qRT-PCR analysis, the expression of 12 candidate target genes showed an opposite pattern after comparison with their miRNAs. The rhizome development system of ginger was observed to be governed by miR156, miR319, miR171a_2, miR164, and miR529, which modulated the expression of the SPL, MYB, GRF, SCL, and NAC genes, respectively. Conclusion This is a deep genome-wide investigation of miRNA and identification of miRNAs involved in rhizome development in ginger. We identified 52 rhizome-related miRNAs and 392 target genes, and this provides an important basis for understanding the molecular mechanisms of the miRNA target genes that mediate rhizome development in ginger.


PLoS ONE ◽  
2021 ◽  
Vol 16 (7) ◽  
pp. e0254669
Author(s):  
Lingdong Meng ◽  
Xiaomeng Zhang ◽  
Lina Wang ◽  
Haoyue Liu ◽  
Yihang Zhao ◽  
...  

Caucasian clover is the only perennial herb of the genus Leguminous clover with underground rhizomes. However, we know very little about its development process and mechanism. Transcriptome studies were conducted on the roots of Caucasian clover without a rhizome (NR) at the young seedling stage and the fully developed rhizome, including the root neck (R1), main root (R2), horizontal root (R3), and rhizome bud (R4), of the tissues in the mature phase. Compared with the rhizome in the mature phase, NR had 893 upregulated differentially expressed genes (DEGs), most of which were enriched in ‘phenylpropanoid biosynthesis’, ‘phenylalanine metabolism’, ‘DNA replication’ and ‘biosynthesis of amino acids’. A higher number of transcription factors (AP2/ERF, C2H2 and FAR1) were found in NR. There were highly expressed genes for R4, such as auxin response factor SAUR, galacturonosyltransferase (GAUT), and sucrose synthase (SUS). Phenylpropanoids are very important for the entire process of rhizome development. We drew a cluster heat map of genes related to the phenylpropanoid biosynthesis pathway, in which the largest number of genes belonged to COMT, and most of them were upregulated in R4.


2020 ◽  
Vol 11 ◽  
Author(s):  
Zhiquan Fan ◽  
Kai Wang ◽  
Jianglei Rao ◽  
Zhongquan Cai ◽  
Li-Zhen Tao ◽  
...  

2020 ◽  
Vol 11 (1) ◽  
Author(s):  
Therese Mitros ◽  
Adam M. Session ◽  
Brandon T. James ◽  
Guohong Albert Wu ◽  
Mohammad B. Belaffif ◽  
...  

Abstract Miscanthus is a perennial wild grass that is of global importance for paper production, roofing, horticultural plantings, and an emerging highly productive temperate biomass crop. We report a chromosome-scale assembly of the paleotetraploid M. sinensis genome, providing a resource for Miscanthus that links its chromosomes to the related diploid Sorghum and complex polyploid sugarcanes. The asymmetric distribution of transposons across the two homoeologous subgenomes proves Miscanthus paleo-allotetraploidy and identifies several balanced reciprocal homoeologous exchanges. Analysis of M. sinensis and M. sacchariflorus populations demonstrates extensive interspecific admixture and hybridization, and documents the origin of the highly productive triploid bioenergy crop M. × giganteus. Transcriptional profiling of leaves, stem, and rhizomes over growing seasons provides insight into rhizome development and nutrient recycling, processes critical for sustainable biomass accumulation in a perennial temperate grass. The Miscanthus genome expands the power of comparative genomics to understand traits of importance to Andropogoneae grasses.


2020 ◽  
Vol 126 (3) ◽  
pp. 481-497
Author(s):  
Xiqing Ma ◽  
Jingjin Yu ◽  
Lili Zhuang ◽  
Yi Shi ◽  
William Meyer ◽  
...  

Abstract Background and Aims Rhizomes are key organs for the establishment of perennial grass stands and adaptation to environmental stress. However, mechanisms regulating rhizome initiation and elongation under drought stress and during post-drought recovery remain unclear. The objective of this study is to investigate molecular factors and metabolic processes involved in drought effects and post-drought recovery in rhizome growth in perennial grass species by comparative transcriptomic and proteomic profiling. Methods Tall fescue (Festuca arundinacea) (B-type rhizome genotype, ‘BR’) plants were exposed to drought stress and re-watering in growth chambers. The number and length of rhizomes were measured following drought stress and re-watering. Hormone and sugar contents were analysed, and transcriptomic and proteomic analyses were performed to identify metabolic factors, genes and proteins associated with rhizome development. Key Results Rhizome initiation and elongation were inhibited by drought stress, and were associated with increases in the contents of abscisic acid (ABA) and soluble sugars, but declines in the contents of indoleacetic acid (IAA), zeatin riboside (ZR) and gibberellin (GA4). Genes involved in multiple metabolic processes and stress defence systems related to rhizome initiation exhibited different responses to drought stress, including ABA signalling, energy metabolism and stress protection. Drought-inhibition of rhizome elongation could be mainly associated with the alteration of GA4 and antioxidants contents, energy metabolism and stress response proteins. Upon re-watering, new rhizomes were regenerated from rhizome nodes previously exposed to drought stress, which was accompanied by the decline in ABA content and increases in IAA, ZR and GA4, as well as genes and proteins for auxin, lipids, lignin and nitrogen metabolism. Conclusions Drought-inhibition of rhizome initiation and elongation in tall fescue was mainly associated with adjustments in hormone metabolism, carbohydrate metabolism and stress-defence systems. Rhizome regeneration in response to re-watering involved reactivation of hormone and lipid metabolism, secondary cell-wall development, and nitrogen remobilization and cycling.


2020 ◽  
Vol 50 ◽  
Author(s):  
Freddy Forero Longas ◽  
Adriana Pulido Diaz

ABSTRACT Canna edulis, also known as achira or sagu, is widely grown in South America because its rhizomes are a major source of starch for food and agroindustry. This study aimed to assess the accumulation rate and physicochemical changes of starch from four canna cultivars (Verde, Nativa, Maituna and Morada), grown under a traditional system, in the southwest region of Colombia. The rhizomes were harvested after planting (between five and nine months) to extract and characterize the starch. It was found that the starch yield (% wb) was related to the plant development age, reaching a maximum at eight months for all cultivars (12.78 ± 0.19 % - Verde; 12.46 ± 0.18 % - Maituna; 12.17 ± 0.19 % - Nativa; 11.10 ± 0.18 % - Morada). The average chemical composition (% wb) of the native starch throughout the rhizome development, for all cultivars, was: 86.68 % of starch, 1.12 % of protein, 0.43 % of dietary fiber, 0.14 % of ash and 11.57 % of moisture. At the optimum harvest age, the minimum and maximum amylose contents were 45.63 % (Maituna) and 54.47 % (Verde). The starch granule size among the cultivars showed a normal distribution, with a range of 40 µm to 80 µm and mean of 59.9 µm. The pasting curves per cultivar showed that the starch generated very high viscosity gels, unstable to the heating-cooling cycles, and high retrogradation.


2019 ◽  
Author(s):  
Taotao Wang ◽  
Yong Yang ◽  
Shuaitong Lou ◽  
Wei Wei ◽  
Zhixin Zhao ◽  
...  

ABSTRACTBackgroundMoso bamboo is well-known for its rapid-growth shoots and widespread rhizomes. However, the regulatory genes of these two processes are largely unexplored. GATA factors regulate many developmental processes, but its role in plant height control and rhizome development remains unclear.ResultsHere, we found that bamboo GATA factors (PeGATAs) are involved in the growth regulation of bamboo shoots and rhizomes. Bioinformatics and evolutionary analysis showed that there are 31 PeGATA factors in bamboo, which can be divided into three subfamilies. Light, hormone, and stress-related cis-elements were found in the promoter region of the PeGATA genes. Gene expression of 12 PeGATA genes was regulated by phytohormone-GA but there was no correlation between auxin and PeGATA gene expression. More than 27 PeGATA genes were differentially expressed in different tissues of rhizomes, and almost all PeGATAs have dynamic gene expression level during the rapid-growth of bamboo shoots. These results indicate that PeGATAs regulate rhizome development and bamboo shoot growth partially via GA signaling pathway. In addition, PeGATA26, a rapid-growth negative regulatory candidate gene modulated by GA treatment, was overexpressed in Arabidopsis, and over-expression of PeGATA26 significantly repressed Arabidopsis primary root length and plant height. The PeGATA26 overexpressing lines were also resistant to exogenous GA treatment, further emphasizing that PeGATA26 inhibits plant height from Arabidopsis to moso bamboo via GA signaling pathway.ConclusionsOur results provide an insight into the function of GATA transcription factors in regulating shoot rapid-growth and rhizome development, and provide genetic resources for engineering plant height.


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