Anthocyanin accumulation and expression analysis of biosynthesis-related genes during chili pepper fruit development

2013 ◽  
Vol 57 (1) ◽  
pp. 49-55 ◽  
Author(s):  
C. Aza-Gonzalez ◽  
L. Herrera-Isidron ◽  
H. G. Nunez-Palenius ◽  
O. Martinez De La Vega ◽  
N. Ochoa-Alejo
Keyword(s):  
Expression Analysis ◽  
Fruit Development ◽  
Chili Pepper ◽  
Anthocyanin Accumulation ◽  
Pepper Fruit

scholarly journals An R Package for Data Mining Chili Pepper Fruit Transcriptomes

2020 ◽  
Author(s):  
Christian Escoto-Sandoval ◽  
Alan Flores-Díaz ◽  
M. Humberto Reyes-Valdés ◽  
Neftalí Ochoa-Alejo ◽  
Octavio Martinez
Keyword(s):  
Gene Expression ◽  
Data Mining ◽  
Fruit Development ◽  
Expression Profiles ◽  
Open Data ◽  
Enrichment Analysis ◽  
R Package ◽  
Chili Pepper ◽  
Rna Seq ◽  
Pepper Fruit

Abstract Background: Open data sharing is instrumental for the advance of biological sciences. Gene expression is the primary molecular phenotype, usually estimated through RNA-Seq experiments. Large scope interpretation of RNA-Seq results is complicated by the extensive gene expression range, as well as by the diversity of biological sources and experimental treatments. Here we present “Salsa”, an auto-contained R package for extracting useful knowledge about gene expression during the development of chili pepper fruit. Methods and Results: Data from 168 RNA-Seq libraries, comprising more than 3.4 billion reads, were analyzed and curated to represent standardized expression profiles (SEPs) for all genes expressed during fruit development in 12 chili pepper accessions. Accessions have representatives of domesticated varieties, wild ancestors and crosses, covering a broad spectrum of genotypes. Data are organized in a relational way, and functions allow data mining from the level of single genes up to whole genomes, grouping profiles by different criteria. Those include any combination of expression model, accession, protein description and gene ontology (GO) term, among others. Also, GO enrichment analysis can be performed over any set of genes. Conclusions: “Salsa” opens endless possibilities for mining the transcriptome of chili pepper during fruit development.

scholarly journals A method to analyze time expression profiles demonstrated in a database of chili pepper fruit development

2021 ◽  
Vol 11 (1) ◽  
Author(s):  
Christian Escoto-Sandoval ◽  
Alan Flores-Díaz ◽  
M. Humberto Reyes-Valdés ◽  
Neftalí Ochoa-Alejo ◽  
Octavio Martínez
Keyword(s):  
Gene Expression ◽  
Fruit Development ◽  
Time Course ◽  
Expression Profiles ◽  
R Package ◽  
Chili Pepper ◽  
Rna Seq ◽  
Genome Wide ◽  
Pepper Fruit ◽  
Relative Gene

AbstractRNA-Seq experiments allow genome-wide estimation of relative gene expression. Estimation of gene expression at different time points generates time expression profiles of phenomena of interest, as for example fruit development. However, such profiles can be complex to analyze and interpret. We developed a methodology that transforms original RNA-Seq data from time course experiments into standardized expression profiles, which can be easily interpreted and analyzed. To exemplify this methodology we used RNA-Seq data obtained from 12 accessions of chili pepper (Capsicum annuum L.) during fruit development. All relevant data, as well as functions to perform analyses and interpretations from this experiment, were gathered into a publicly available R package: “Salsa”. Here we explain the rational of the methodology and exemplify the use of the package to obtain valuable insights into the multidimensional time expression changes that occur during chili pepper fruit development. We hope that this tool will be of interest for researchers studying fruit development in chili pepper as well as in other angiosperms.

scholarly journals Isolation of UDP:flavonoid 3-O-glycosyltransferase (UFGT)-like Genes and Expression Analysis of Genes Associated with Anthocyanin Accumulation in Mango ‘Irwin’ skin

2019 ◽  
Vol 88 (4) ◽  
pp. 435-443 ◽  
Author(s):  
Shinya Kanzaki ◽  
Shiori Kamikawa ◽  
Asuka Ichihi ◽  
Yuta Tanaka ◽  
Kosuke Shimizu ◽  
...  
Keyword(s):  
Expression Analysis ◽  
Anthocyanin Accumulation

scholarly journals Identification of Optimal Reference Genes for Normalization of qPCR Analysis during Pepper Fruit Development

2017 ◽  
Vol 8 ◽  
Author(s):  
Yuan Cheng ◽  
Xin Pang ◽  
Hongjian Wan ◽  
Golam J. Ahammed ◽  
Jiahong Yu ◽  
...  
Keyword(s):  
Fruit Development ◽  
Reference Genes ◽  
Qpcr Analysis ◽  
Pepper Fruit

scholarly journals Genome-Wide Identification, Evolutionary Patterns, and Expression Analysis of bZIP Gene Family in Olive (Olea europaea L.)

Genes ◽  
2020 ◽  
Vol 11 (5) ◽  
pp. 510
Author(s):  
Siyu Rong ◽  
Zhiyang Wu ◽  
Zizhang Cheng ◽  
Shan Zhang ◽  
Huan Liu ◽  
...  
Keyword(s):  
Gene Family ◽  
Expression Analysis ◽  
Fruit Development ◽  
Leucine Zipper ◽  
Expression Patterns ◽  
Lipid Synthesis ◽  
Structural Features ◽  
Oil Accumulation ◽  
Evolutionary Patterns ◽  
Bzip Family

Olive (Olea europaea.L) is an economically important oleaginous crop and its fruit cold-pressed oil is used for edible oil all over the world. The basic region-leucine zipper (bZIP) family is one of the largest transcription factors families among eukaryotic organisms; its members play vital roles in environmental signaling, stress response, plant growth, seed maturation, and fruit development. However, a comprehensive report on the bZIP gene family in olive is lacking. In this study, 103 OebZIP genes from the olive genome were identified and divided into 12 subfamilies according to their genetic relationship with 78 bZIPs of A. thaliana. Most OebZIP genes are clustered in the subgroup that has a similar gene structure and conserved motif distribution. According to the characteristics of the leucine zipper region, the dimerization characteristics of 103 OebZIP proteins were predicted. Gene duplication analyses revealed that 22 OebZIP genes were involved in the expansion of the bZIP family. To evaluate the expression patterns of OebZIP genes, RNA-seq data available in public databases were analyzed. The highly expressed OebZIP genes and several lipid synthesis genes (LPGs) in fruits of two varieties with different oil contents during the fast oil accumulation stage were examined via qRT-PCR. By comparing the dynamic changes of oil accumulation, OebZIP1, OebZIP7, OebZIP22, and OebZIP99 were shown to have a close relationship with fruit development and lipid synthesis. Additionally, some OebZIP had a significant positive correlation with various LPG genes. This study gives insights into the structural features, evolutionary patterns, and expression analysis, laying a foundation to further reveal the function of the 103 OebZIP genes in olive.

scholarly journals Analysis of Quantitative Traits in Pepper Using Molecular Markers

2000 ◽  
Author(s):  
Ilan Paran ◽  
Molly Jahn
Keyword(s):  
Ssr Markers ◽  
Fruit Quality ◽  
Fruit Development ◽  
Simple Sequence Repeat ◽  
Quantitative Traits ◽  
Fruit Shape ◽  
Sequence Repeat ◽  
Molecular Tools ◽  
Pepper Fruit ◽  
Simple Sequence

Original objectives: The overall goal of the proposal was to determine the genetic and molecular control of pathways leading to the production of secondary metabolites determining major fruit quality traits in pepper. The specific objectives were to: (1) Generate a molecular map of pepper based on simple sequence repeat (SSR) markers. (2) Map QTL for capsaicinoids content (3) Determine possible association between capsaicinoids and carotenoid content and structural genes for capsaicinoid and carotenoid biosynthesis. (4) Map QTL for quantitative traits controlling additional fruit traits. (5) Map fruit-specific ESTs and determine possible association with fruit QTL (6) Map the C locus that determines the presence and absence of capsaicinoids in pepper fruit and identify candidate genes for C. Background: Pungency, color, fruit shape and fruit size are among the most important fruit quality characteristics of pepper. Despite the importance of the pepper crop both in the USA and Israel, the genetic basis of these traits was only little known prior to the studies conducted in the present proposal. In addition, molecular tools for use in pepper improvement were lacking. Major conclusions and achievements: Our studies enabled the development of a saturated genetic map of pepper that includes numerous simple sequence repeat (SSR) markers and the integration of several independent maps into a single resource map that consists of over 2000 markers. Unlike previous maps that consisted mostly of tomato-originated RFLP markers, the SSR-based map consists of largely pepper markers. Therefore, the SSR and integrated maps provide ample of tools for use in marker-assisted selection for diverse targets throughout the Capsicum genome. We determined the genetic and molecular bases of qualitative and quantitative variation of pungency, the most unique characteristics of pepper fruit. We mapped and subsequently cloned the Pun1 gene that serves as a master key for capsaicinoids accumulation and showed that it is an acyltransferase. By sequencing the Pun1 gene in pungent and non-pungent cultivars we identified a deletion that abolishes the expression of the gene in the latter cultivars. We also identified QTLs that control capsaicinoids content and therefore pungency level. These genes will allow pepper breeders to manipulate the level of pungency for specific agricultural and industrial purposes. In addition to pungency we identified genes and QTLs that control other key developmental processes of fruit development such as color, texture and fruit shape. The A gene controlling anthocyanin accumulation in the immature fruit was found as the ortholog of the petunia transcription factor Anthocyanin2. The S gene required for the soft flesh and deciduous fruit nature typical of wild peppers was identified as the ortholog of tomato polygalacturonase. We identified two major QTLs controlling fruit shape, fs3.1 and fs10.1, that differentiate between elongated and blocky and round fruit shapes, respectively. Scientific and agricultural implications: Our studies allowed significant advancement of our understanding at the genetic and molecular levels of important processes of pepper fruit development. Concomitantly to gaining biological knowledge, we were able to develop molecular tools that can be implemented for pepper improvement. 

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