Identification of genes involved in fruit development/ripening in Capsicum and development of functional markers

Dubey, Muchkund; Jaiswal, Vandana; Rawoof, Abdul; Kumar, Ajay; Nitin, Mukesh; Chhapekar, Sushil Satish; Kumar, Nitin; Ahmad, Ilyas; Islam, Khushbu; Brahma, Vijaya; Ramchiary, Nirala

doi:10.1016/j.ygeno.2019.01.002

Cited by 33 publications

(19 citation statements)

References 63 publications

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“…In an earlier study, gene-specific SSRs related to Capsicum fruit ripening showed high polymorphism among Capsicum spp (Dubey et al, 2019). In this study, the SSRs predicted in the genic and non-genic regions of Capsicum MYBs have rendered them useful in Capsicum breeding and improvement programs.…”

Section: Myb-specific Ssr Repeats Can Serve As Potential Molecular Markersmentioning

confidence: 59%

“…Full length gene sequences and 1.5-kb upstream of promoter sequences from the Transcription Start Site (TSS) of 251 C. chinense MYBs were used to identify simple sequence repeats (SSRs) using the online WebSat tool (Martins et al, 2009) as described previously (Dubey et al, 2019;Jaiswal et al, 2020). The maximum size of an SSR motif was kept at 6 nucleotides, while the minimum number of repeats of the motif was kept at 6.…”

Section: Simple Sequence Repeat (Ssr) Prediction In Capsicum Mybsmentioning

confidence: 99%

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Capsicum chinense MYB Transcription Factor Genes: Identification, Expression Analysis, and Their Conservation and Diversification With Other Solanaceae Genomes

et al. 2021

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Myeloblastosis (MYB) genes are important transcriptional regulators of plant growth, development, and secondary metabolic biosynthesis pathways, such as capsaicinoid biosynthesis in Capsicum. Although MYB genes have been identified in Capsicum annuum, no comprehensive study has been conducted on other Capsicum species. We identified a total of 251 and 240 MYB encoding genes in Capsicum chinense MYBs (CcMYBs) and Capsicum baccatum MYBs (CbMYBs). The observation of twenty tandem and 41 segmental duplication events indicated expansion of the MYB gene family in the C. chinense genome. Five CcMYB genes, i.e., CcMYB101, CcMYB46, CcMYB6, CcPHR8, and CcRVE5, and two CaMYBs, i.e., CaMYB3 and CaHHO1, were found within the previously reported capsaicinoid biosynthesis quantitative trait loci. Based on phylogenetic analysis with tomato MYB proteins, the Capsicum MYBs were classified into 24 subgroups supported by conserved amino acid motifs and gene structures. Also, a total of 241 CcMYBs were homologous with 225 C. annuum, 213 C. baccatum, 125 potato, 79 tomato, and 23 Arabidopsis MYBs. Synteny analysis showed that all 251 CcMYBs were collinear with C. annuum, C. baccatum, tomato, potato, and Arabidopsis MYBs spanning over 717 conserved syntenic segments. Using transcriptome data from three fruit developmental stages, a total of 54 CcMYBs and 81 CaMYBs showed significant differential expression patterns. Furthermore, the expression of 24 CcMYBs from the transcriptome data was validated by quantitative real-time (qRT) PCR analysis. Eight out of the 24 CcMYBs validated by the qRT-PCR were highly expressed in fiery hot C. chinense than in the lowly pungent C. annuum. Furthermore, the co-expression analysis revealed several MYB genes clustered with genes from the capsaicinoid, anthocyanin, phenylpropanoid, carotenoid, and flavonoids biosynthesis pathways, and related to determining fruit shape and size. The homology modeling of 126 R2R3 CcMYBs showed high similarity with that of the Arabidopsis R2R3 MYB domain template, suggesting their potential functional similarity at the proteome level. Furthermore, we have identified simple sequence repeat (SSR) motifs in the CcMYB genes, which could be used in Capsicum breeding programs. The functional roles of the identified CcMYBs could be studied further so that they can be manipulated for Capsicum trait improvement.

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Section: Myb-specific Ssr Repeats Can Serve As Potential Molecular Markersmentioning

confidence: 59%

Section: Simple Sequence Repeat (Ssr) Prediction In Capsicum Mybsmentioning

confidence: 99%

Capsicum chinense MYB Transcription Factor Genes: Identification, Expression Analysis, and Their Conservation and Diversification With Other Solanaceae Genomes

et al. 2021

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“…Tomato and chili pepper are close relatives; however, the size of the pepper genome is three times larger than the tomato genome. We expected to find multiple ortholog copies in the pepper genome, as it has been shown in previous studies [46]. For this, we used Inparanoid, a software capable of finding ortholog groups, where we identified 18,797 tomato orthologs.…”

Section: Functional Annotation and Enrichment Analysismentioning

confidence: 99%

Transcriptomic analysis of a wild and a cultivated varieties of Capsicum annuum over fruit development and ripening

et al. 2021

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Chili pepper (Capsicum annuum) is one of the most important crops worldwide. Its fruits contain metabolites produced over the maturation process like capsaicinoids and carotenoids. This metabolic process produces internal changes in flavor, color, texture, and aroma in fruits to make them more attractive for seed dispersal organisms. The chiltepin (C. annuum L. var. glabriusculum) is a wild variety of the C. annuum L. species that is considered a source of genetic resources that could be used to improve the current chili crops. In this study, we performed a transcriptomic analysis on two fruit maturation stages: immature stage (green fruit) and mature stage (red fruit) of a wild and a cultivated pepper variety. We found 19,811 genes expressed, and 1,008 genes differentially expressed (DEGs) in at least one of the five contrast used; 730 DEGs were found only in one contrast, and most DEGs in all contrasts were downregulated. GO enrichment analysis showed that the majority of DEGs are related to stress responses. KEGG enrichment analysis detected differences in expression patterns in metabolic pathways related to phenylpropanoid biosynthesis, secondary metabolites, plant hormone signal transduction, carotenoid biosynthesis and sesquiterpenoid and triterpenoid biosynthesis. We selected 105 tomato fruit ripening-related genes, and found 53 pepper homologs differentially expressed related to shape, size, and secondary metabolite biosynthesis. According to the transcriptome analysis, the two peppers showed very similar gene expression patterns; differences in expression patterns of genes related to shape, size, ethylene and secondary metabolites biosynthesis suggest that changes produced by domestication of chilli pepper could be very specific to the expression of genes related to traits desired in commercial fruits.

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“…Considering the importance of pepper as a vegetable crop, it is highly desirable to identify and evaluate valuable traits to improve the productivity, disease and environmental resistance, and commercial value of pepper. The whole genome of pepper has been sequenced (Kim et al, 2014;Qin et al, 2014), and highthroughput transcriptome studies have identified a large number of genes associated with various biological processes (Liu et al, 2013;Dubey et al, 2019). However, most of the identified pepper genes remain to be elucidated because of the lack of efficient methods for gain-and loss-of-function studies in pepper.…”

Section: Optimization Of the Bbwv2-based Vigs In Peppermentioning

confidence: 99%

“…Pepper (Capsicum annuum), a member of the family Solanaceae, is an important crop grown worldwide. Recently, intensive high-throughput genomic sequencing studies have provided extensive data on transcriptomic regulation in pepper and increased the need for rapid and simple gene function analysis systems (Liu et al, 2013;Kim et al, 2014;Qin et al, 2014;Dubey et al, 2019). However, limited progress has been made in terms of functional studies of pepper genes owing to the lack of efficient genetic transformation methods for pepper (Lee et al, 2004;Bulle et al, 2016).…”

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confidence: 99%

A Plant Virus-Based Vector System for Gene Function Studies in Pepper

et al. 2019

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While pepper (Capsicum annuum) is a highly recalcitrant species for genetic transformation studies, plant virus-based vectors can provide alternative and powerful tools for transient regulation and functional analysis of genes of interest in pepper. In this study, we established an effective virus-based vector system applicable for transient gain-and loss-of-function studies in pepper using Broad bean wilt virus2 (BBWV2). We engineered BBWV2 as a dual gene expression vector for simultaneous expression of two recombinant proteins in pepper cells. In addition, we established enhanced and stable expression of recombinant proteins from the BBWV2-based dual vector via coexpression of a heterologous viral suppressor of RNA silencing. We also developed a BBWV2-based virus-induced gene silencing (VIGS) vector, and we successfully silenced the phytoene desaturase gene (PDS) using the BBWV2-based VIGS vector in various pepper cultivars. Additionally, we optimized the BBWV2-based VIGS system in pepper by testing the efficiency of PDS gene silencing under different conditions. This BBWV2-based vector system represents a convenient approach for rapid and simple analysis of gene functions in pepper.

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Identification of genes involved in fruit development/ripening in Capsicum and development of functional markers

Cited by 33 publications

References 63 publications

Capsicum chinense MYB Transcription Factor Genes: Identification, Expression Analysis, and Their Conservation and Diversification With Other Solanaceae Genomes

Capsicum chinense MYB Transcription Factor Genes: Identification, Expression Analysis, and Their Conservation and Diversification With Other Solanaceae Genomes

Transcriptomic analysis of a wild and a cultivated varieties of Capsicum annuum over fruit development and ripening

A Plant Virus-Based Vector System for Gene Function Studies in Pepper

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