Tissue-Dependent Variation Profiles of Tea Quality-Related Metabolites in New Shoots of Tea Accessions

Several metabolites define tea quality in new tea shoots composed of leaf and stem. To improve tea quality for breeding, it is important to understand the tissue-dependent genetic mechanisms and metabolic network responsible for the profile of tea quality-related metabolites. We analyzed the volatiles and specialized metabolites as the tea quality-related metabolites in leaves and stems of new shoots in 30 tea accessions to understand the tissue variation and network between tea quality-related metabolites. Our results provided the tissue-dependent variation network in the tea quality-related metabolites, including volatiles in new leaves and stems in tea accessions. Each volatile content in tea accessions showed the coefficient of variation ranging from 58.7 to 221.9% and 54.2 to 318.3% in new leaves and new stems, respectively. The accumulation pattern of tea quality-related metabolites in new leaves and stems varied depending on the accession. When comparing tea genetic populations, the profile of tea quality-related metabolites of new leaves, but not new stems, was the key to distinguishing tea genetic populations by chemical indicators. We described the network between tea quality-related metabolites, especially the dense network in new leaves. These results also will provide the key information for metabolic engineering and the selection of breeding materials in tea plants based on the tea quality-related metabolites and aid in understanding their molecular mechanisms and network of metabolic variation.

Download Full-text

Tea plant genomics: achievements, challenges and perspectives

Horticulture Research ◽

10.1038/s41438-019-0225-4 ◽

2020 ◽

Vol 7 (1) ◽

Cited By ~ 10

Author(s):

En-Hua Xia ◽

Wei Tong ◽

Qiong Wu ◽

Shu Wei ◽

Jian Zhao ◽

...

Keyword(s):

Cultural Values ◽

Molecular Mechanisms ◽

Tea Plant ◽

Plant Genome ◽

Alcoholic Beverages ◽

Plant Genomics ◽

Breeding Programs ◽

Tea Quality ◽

Genomic Studies ◽

Tea Plants

AbstractTea is among the world’s most widely consumed non-alcoholic beverages and possesses enormous economic, health, and cultural values. It is produced from the cured leaves of tea plants, which are important evergreen crops globally cultivated in over 50 countries. Along with recent innovations and advances in biotechnologies, great progress in tea plant genomics and genetics has been achieved, which has facilitated our understanding of the molecular mechanisms of tea quality and the evolution of the tea plant genome. In this review, we briefly summarize the achievements of the past two decades, which primarily include diverse genome and transcriptome sequencing projects, gene discovery and regulation studies, investigation of the epigenetics and noncoding RNAs, origin and domestication, phylogenetics and germplasm utilization of tea plant as well as newly developed tools/platforms. We also present perspectives and possible challenges for future functional genomic studies that will contribute to the acceleration of breeding programs in tea plants.

Download Full-text

Transcriptomic Analysis Reveals the Molecular Adaptation of Three Major Secondary Metabolic Pathways to Multiple Macronutrient Starvation in Tea (Camellia sinensis)

Genes ◽

10.3390/genes11030241 ◽

2020 ◽

Vol 11 (3) ◽

pp. 241 ◽

Cited By ~ 1

Author(s):

Hui Su ◽

Xueying Zhang ◽

Yuqing He ◽

Linying Li ◽

Yuefei Wang ◽

...

Keyword(s):

Camellia Sinensis ◽

Molecular Mechanisms ◽

Enrichment Analysis ◽

Element Analysis ◽

Cis Element ◽

Yield And Quality ◽

Tea Quality ◽

Function Enrichment Analysis ◽

Tea Plants ◽

Function Enrichment

Tea (Camellia sinensis (L.) O. Kuntze) is a widely consumed beverage. Lack of macronutrients is a major cause of tea yield and quality losses. Though the effects of macronutrient starvation on tea metabolism have been studied, little is known about their molecular mechanisms. Hence, we investigated changes in the gene expression of tea plants under nitrogen (N), phosphate (P), and potassium (K) deficient conditions by RNA-sequencing. A total of 9103 differentially expressed genes (DEG) were identified. Function enrichment analysis showed that many biological processes and pathways were common to N, P, and K starvation. In particular, cis-element analysis of promoter of genes uncovered that members of the WRKY, MYB, bHLH, NF-Y, NAC, Trihelix, and GATA families were more likely to regulate genes involved in catechins, l-theanine, and caffeine biosynthetic pathways. Our results provide a comprehensive insight into the mechanisms of responses to N, P, and K starvation, and a global basis for the improvement of tea quality and molecular breeding.

Download Full-text

Comparative Transcriptome Analysis Reveals Genetic Mechanisms of Sugarcane Aphid Resistance in Grain Sorghum

International Journal of Molecular Sciences ◽

10.3390/ijms22137129 ◽

2021 ◽

Vol 22 (13) ◽

pp. 7129

Author(s):

Desalegn D. Serba ◽

Xiaoxi Meng ◽

James Schnable ◽

Elfadil Bashir ◽

J. P. Michaud ◽

...

Keyword(s):

Differential Expression ◽

Molecular Mechanisms ◽

Grain Sorghum ◽

Lipid Binding ◽

Multiple Time ◽

Melanaphis Sacchari ◽

Resistant Genotype ◽

Sugarcane Aphid ◽

Genetic Mechanisms ◽

Moderately Resistant

The sugarcane aphid, Melanaphis sacchari (Zehntner) (Hemiptera: Aphididae) (SCA), has become a major pest of grain sorghum since its appearance in the USA. Several grain sorghum parental lines are moderately resistant to the SCA. However, the molecular and genetic mechanisms underlying this resistance are poorly understood, which has constrained breeding for improved resistance. RNA-Seq was used to conduct transcriptomics analysis on a moderately resistant genotype (TAM428) and a susceptible genotype (Tx2737) to elucidate the molecular mechanisms underlying resistance. Differential expression analysis revealed differences in transcriptomic profile between the two genotypes at multiple time points after infestation by SCA. Six gene clusters had differential expression during SCA infestation. Gene ontology enrichment and cluster analysis of genes differentially expressed after SCA infestation revealed consistent upregulation of genes controlling protein and lipid binding, cellular catabolic processes, transcription initiation, and autophagy in the resistant genotype. Genes regulating responses to external stimuli and stress, cell communication, and transferase activities, were all upregulated in later stages of infestation. On the other hand, expression of genes controlling cell cycle and nuclear division were reduced after SCA infestation in the resistant genotype. These results indicate that different classes of genes, including stress response genes and transcription factors, are responsible for countering the physiological effects of SCA infestation in resistant sorghum plants.

Download Full-text

Combining QTL Mapping and Gene Expression Analysis to Elucidate the Genetic Control of ‘Crumbly’ Fruit in Red Raspberry (Rubus idaeus L.)

Agronomy ◽

10.3390/agronomy11040794 ◽

2021 ◽

Vol 11 (4) ◽

pp. 794

Author(s):

Luca M. Scolari ◽

Robert D. Hancock ◽

Pete E. Hedley ◽

Jenny Morris ◽

Kay Smith ◽

...

Keyword(s):

Genetic Control ◽

Developmental Disorder ◽

Molecular Mechanisms ◽

Developmental Stages ◽

Microarray Experiment ◽

Rubus Idaeus ◽

Red Raspberry ◽

Genotype By Sequencing ◽

First Time ◽

Selection Of

‘Crumbly’ fruit is a developmental disorder in raspberry that results in malformed and unsaleable fruits. For the first time, we define two distinct crumbly phenotypes as part of this work. A consistent crumbly fruit phenotype affecting the majority of fruits every season, which we refer to as crumbly fruit disorder (CFD) and a second phenotype where symptoms vary across seasons as malformed fruit disorder (MFD). Here, segregation of crumbly fruit of the MFD phenotype was examined in a full-sib family and three QTL (Quantitative Trait Loci) were identified on a high density GbS (Genotype by Sequencing) linkage map. This included a new QTL and more accurate location of two previously identified QTLs. A microarray experiment using normal and crumbly fruit at three different developmental stages identified several genes that were differentially expressed between the crumbly and non-crumbly phenotypes within the three QTL. Analysis of gene function highlighted the importance of processes that compromise ovule fertilization as triggers of crumbly fruit. These candidate genes provided insights regarding the molecular mechanisms involved in the genetic control of crumbly fruit in red raspberry. This study will contribute to new breeding strategies and diagnostics through the selection of molecular markers associated with the crumbly trait.

Download Full-text

Evolution of stickleback spines through independent cis-regulatory changes at HOXDB

10.1101/2021.12.14.472698 ◽

2021 ◽

Author(s):

Julia I Wucherpfennig ◽

Timothy R Howes ◽

Jessica N Au ◽

Eric H Au ◽

Garrett A Roberts Kingman ◽

...

Keyword(s):

Gene Expression ◽

Evolutionary Biology ◽

Gasterosteus Aculeatus ◽

Molecular Mechanisms ◽

Wild Populations ◽

Gene Variation ◽

Regulatory Changes ◽

Fundamental Goal ◽

Apeltes Quadracus ◽

Genetic Mechanisms

Understanding the genetic mechanisms leading to new traits is a fundamental goal of evolutionary biology. We show that HOXDB regulatory changes have been used repeatedly in different stickleback fish species to alter the length and number of bony dorsal spines. In Gasterosteus aculeatus, a variant HOXDB allele is genetically linked to shortening an existing spine and adding a spine. In Apeltes quadracus, a variant allele is associated with lengthening an existing spine and adding a spine. The alleles alter the same conserved non-coding HOXDB enhancer by diverse molecular mechanisms, including SNPs, deletions, and transposable element insertions. The independent cis-acting regulatory changes are linked to anterior expansion or contraction of HOXDB expression. Our findings support the long-standing hypothesis that natural Hox gene variation underlies key morphological patterning changes in wild populations and illustrate how different mutational mechanisms affecting the same region may produce opposite gene expression changes with similar phenotypic outcomes.

Download Full-text

First person – Fanny Jaudon and Martina Albini

Journal of Cell Science ◽

10.1242/jcs.259251 ◽

2021 ◽

Vol 134 (16) ◽

Keyword(s):

Neurotrophic Factor ◽

Neurological Disorders ◽

Molecular Mechanisms ◽

Neurological Diseases ◽

Early Career ◽

First Person ◽

Early Career Researchers ◽

And Function ◽

The University ◽

Selection Of

ABSTRACT First Person is a series of interviews with the first authors of a selection of papers published in Journal of Cell Science, helping early-career researchers promote themselves alongside their papers. Fanny Jaudon and Martina Albini are co-first authors on ‘ A developmental stage- and Kidins220-dependent switch in astrocyte responsiveness to brain-derived neurotrophic factor’, published in JCS. Fanny is a postdoc at the University of Trieste in the lab of Lorenzo A. Cingolani at Center for Synaptic Neuroscience and Technology, Istituto Italiano di Tecnologia, Genova, Italy, investigating the molecular mechanisms controlling development and function of neuronal circuits and implementing genome-editing approaches for the treatment of neurological disorders. Martina is a PhD student at the Istituto Italiano di Tecnologia in the lab of Fabio Benfenati and Fabrizia Cesca investigating neurotrophin biology and its involvement in neurological diseases.

Download Full-text

Microglia in cerebral ischemia: molecular actions and interactionsThis paper is one of a selection of papers published in this Special Issue, entitled Young Investigator's Forum.

Canadian Journal of Physiology and Pharmacology ◽

10.1139/y05-143 ◽

2006 ◽

Vol 84 (1) ◽

pp. 49-59 ◽

Cited By ~ 121

Author(s):

Aaron Y. Lai ◽

Kathryn G. Todd

Keyword(s):

Cerebral Ischemia ◽

Intracellular Signaling ◽

Molecular Mechanisms ◽

Extracellular Signals ◽

Messenger Molecules ◽

Membrane Bound ◽

The Subject ◽

Survey Review ◽

Selection Of

The precise role of microglia in stroke and cerebral ischemia has been the subject of debate for a number of years. Microglia are capable of synthesizing numerous soluble and membrane-bound biomolecules, some known to be neuroprotective, some neurotoxic, whereas others have less definitive bioactivities. The molecular mechanisms through which microglia activate these molecules have thus become an important area of ischemia research. Here we provide a survey review that summarizes the key actions of microglial factors in cerebral ischemia including complement proteins, chemokines, pro-inflammatory cytokines, neurotrophic factors, hormones, and proteinases, as well several important messenger molecules that play a part in how these factors respond to extracellular signals during ischemic injuries. We also provide some new perspectives on how microglial intracellular signaling may contribute to the seemingly contradictory roles of several microglial effector molecules.

Download Full-text

Transcriptome changes reveal the genetic mechanisms of the reproductive plasticity of workers in lower termites

BMC Genomics ◽

10.1186/s12864-019-6037-y ◽

2019 ◽

Vol 20 (1) ◽

Author(s):

Chenxu Ye ◽

Humaira Rasheed ◽

Yuehua Ran ◽

Xiaojuan Yang ◽

Lianxi Xing ◽

...

Keyword(s):

Gene Expression ◽

Signal Transduction ◽

Molecular Mechanisms ◽

Environmental Changes ◽

Mapk Pathway ◽

Specific Expression ◽

Expression Of Genes ◽

Genetic Mechanisms ◽

Ecological Success ◽

Reproductive Plasticity

Abstract Background The reproductive plasticity of termite workers provides colonies with tremendous flexibility to respond to environmental changes, which is the basis for evolutionary and ecological success. Although it is known that all colony members share the same genetic background and that differences in castes are caused by differences in gene expression, the pattern of the specific expression of genes involved in the differentiation of workers into reproductives remains unclear. In this study, the isolated workers of Reticulitermes labralis developed into reproductives, and then comparative transcriptomes were used for the first time to reveal the molecular mechanisms underlying the reproductive plasticity of workers. Results We identified 38,070 differentially expressed genes and found a pattern of gene expression involved in the differentiation of the workers into reproductives. 12, 543 genes were specifically upregulated in the isolated workers. Twenty-five signal transduction pathways classified into environmental information processing were related to the differentiation of workers into reproductives. Ras functions as a signalling switch regulates the reproductive plasticity of workers. The catalase gene which is related to longevity was up-regulated in reproductives. Conclusion We demonstrate that workers leaving the natal colony can induce the expression of stage-specific genes in the workers, which leads to the differentiation of workers into reproductives and suggests that the signal transduction along the Ras-MAPK pathway crucially controls the reproductive plasticity of the workers. This study also provides an important model for revealing the molecular mechanism of longevity changes.

Download Full-text

New gene discoveries in skeletal diseases with short stature

Endocrine Connections ◽

10.1530/ec-21-0083 ◽

2021 ◽

Author(s):

Alice Costantini ◽

Mari H Muurinen ◽

Outi Mäkitie

Keyword(s):

Short Stature ◽

Molecular Mechanisms ◽

Bone Growth ◽

Massively Parallel Sequencing ◽

Matrix Composition ◽

Biological Processes ◽

Novel Gene ◽

Genetic Mechanisms ◽

New Gene ◽

And Function

In the last decade, the widespread use of massively-parallel sequencing has considerably boosted the number of novel gene discoveries in monogenic skeletal diseases with short stature. Defects in genes playing a role in the maintenance and function of the growth plate, the site of longitudinal bone growth, are a well-known cause of skeletal diseases with short stature. However, several genes involved in extracellular matrix composition or maintenance as well as genes partaking in various biological processes have also been characterized. This review aims to describe the latest genetic findings in spondyloepiphyseal and spondyloepimetaphyseal dysplasias and in some monogenic forms of isolated short stature. Strategies on how to successfully characterize novel skeletal phenotypes with short stature and genetic approaches to detect and validate novel gene-disease correlations will be discussed in detail. Finally, novel genetic mechanisms in the field of skeletal diseases, including variants affecting miRNAs and disrupting the chromatin structure, will be described. In summary, we discuss the latest gene discoveries underlying skeletal diseases with short stature and emphasize the importance of characterizing novel molecular mechanisms for genetic counseling, optimal management of the disease and for therapeutic innovations.

Download Full-text

First person – Elin Schoultz and Ellen Johansson

Disease Models & Mechanisms ◽

10.1242/dmm.049155 ◽

2021 ◽

Vol 15 (2) ◽

Keyword(s):

Thyroid Gland ◽

Cell Biology ◽

Molecular Mechanisms ◽

Tumor Development ◽

Neck Region ◽

Early Career ◽

Field Cancerization ◽

First Person ◽

Head And Neck Region ◽

Selection Of

ABSTRACT First Person is a series of interviews with the first authors of a selection of papers published in Disease Models & Mechanisms, helping early-career researchers promote themselves alongside their papers. Elin Schoultz and Ellen Johansson are co-first authors on ‘ Tissue architecture delineates field cancerization in BrafV600E-induced tumor development’, published in DMM. Elin is an MD, PhD student in the lab of Mikael Nilsson at Sahlgrenska Centre for Cancer Research, Gothenburg University, Gothenburg. She has a great interest in the thyroid gland in particular, and the mechanisms of tumor development, progression and treatment associated with epithelial carcinomas in general. Ellen is an MD, resident physician in oto-rhino-laryngology and postdoctoral researcher in the lab of Karin Roberg at Department of Biomedical and Clinical Sciences, Division of Cell Biology, Linköping University, Linköping, with broad interest the thyroid gland, tumors of the head and neck region, and the molecular mechanisms that are important for tumor initiation, development, and treatment.

Download Full-text