Transcriptome profiling, simple sequence repeat markers development and genetic diversity analysis of potential industrial crops Capsicum chinense and C. frutescens of Northeast India

Chhapekar, Sushil Satish; Brahma, Vijaya; Rawoof, Abdul; Kumar, Nitin; Gaur, Rashmi; Jaiswal, Vandana; Kumar, Ajay; Yadava, Satish Kumar; Kumar, R. Kiran; Sharma, Vineet K.; Babu, Salga S.; Ramchiary, Nirala

doi:10.1016/j.indcrop.2020.112687

Cited by 15 publications

(5 citation statements)

References 109 publications

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“…Compared with the 1.5-kb upstream regions, more SSRs were present in the genic regions, 67.45% (Supplementary Table 9). However, previous studies have suggested higher conservation and less variation in the genic regions of different species (Kim et al, 2008;Zhang et al, 2014;Chhapekar et al, 2020). This may be due to the less coverage of the upstream region of MYB genes for SSR prediction, which is 1.5 Kb from the TSS in our study.…”

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

confidence: 63%

“…The RNA samples from three biological replicates of each fruit stage, with RNA integrity number (RIN) > 8, were used for library preparation using TruSeq RNA Sample Prep Kits (Illumina, San Diego, CA, United States) and sequenced using a HiSeq XTen (Illumina, San Diego, CA, United States) paired-end platform with an average read length of 150 bp. The quality of raw reads was evaluated with FastQC (v0.11.5), and adapter sequences along with low quality reads (phred score < 20) were removed using TrimGalore (v0.4.4) as descrbied earlier (Chhapekar et al, 2020;Rawoof et al, 2020). The filtered good quality reads from C. chinense and C. annuum were mapped to their respective genomes (Qin et al, 2014;Kim et al, 2017) using the Hisat2 (Kim et al, 2019) program.…”

Section: Rna Sequencing and Differential Gene Expression Analysismentioning

confidence: 99%

“…The Capsicum fruit is known for its unique attribute of pungency owing to alkaloids, known as capsaicinoids complex, mainly capsaicin and dihydrocapsaicin (Antonious and Jarret, 2006), which have pharmaceutical applications (Fattori et al, 2016). There exists a wide variation in capsaicin content in Capsicum genotypes, with the highest being reported in Bhut jolokia (C. chinense; Sarpras et al, 2016;Chhapekar et al, 2020). R2R3-MYB31 was reported as a transcriptional regulator of capsaicinoid biosynthetic genes (CBGs; Arce-Rodríguez and Ochoa-Alejo, 2017).…”

Section: Introductionmentioning

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 Markerscontrasting

confidence: 63%

Section: Rna Sequencing and Differential Gene Expression Analysismentioning

confidence: 99%

Section: Introductionmentioning

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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“…Alkaloids are a kind of basic organic compound containing N. Alkaloids, homologous metabolites of terpenoids, are compounds unique to Zanthoxylum fruits, and have high economic value in the food and pharmaceutical industries [ 38 , 39 , 40 ]. Meanwhile, some alkaloids have antibacterial properties.…”

Section: Discussionmentioning

confidence: 99%

Transcriptome and Metabolome Studies on Pre-Harvest Nitrogen Impact on Fruit Yield and Quality of Peach (Prunus persica L.)

et al. 2022

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Pre-harvest nitrogen (N) application has been proven effective for improving fruit yield and quality. However, a full understanding of how differences in N availability/plant N status influence the transcriptome and metabolism underlying yield formation and quality remains elusive. Here, a combined analysis of the morpho-physiological qualities, transcriptome, and metabolite of peach plants was performed under different nitrogen levels at fruit pit hardening (PH) and fruit expansion (FE). Nitrogen fertilizer directly affected the yield, fruit quality, and metabolites of peach at different growth stages. RNA-Seq was used to analyze the influence of N levels at PH and FE in peach. Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway analysis showed that the differentially expressed genes (DEGs) focused on flavonoid biosynthesis and secondary metabolite biosynthetic processes. The differential metabolites among the different treatments were mainly involved in flavonoid metabolism. Transcriptome analysis showed that applying different nitrogen fertilizers at different growth stages of peach mainly affected the synthesis of flavonoids in fruit. Overall, these results suggest that the impacts of pre-harvest N application on fruit yield and quality differ between developmental stages. This research provides a full understanding of the metabolic processes underlying fruit growth and development in peach, providing a theoretical basis for the improvement of nitrogen use efficiency in peach trees.

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“…in increasing food shelf-life, improving the sensory properties, seasoning, and coloring of foods, in cosmetic and pharma industry ( Baenas et al., 2019 ). Several studies reported the presence of intra and interspecific diversity of fruit traits, metabolites content, and other agronomic traits in Capsicum species ( Ahmad et al., 2021a , 2021b ; Araceli et al., 2009 ; Chhapekar et al., 2020 ; Liu et al., 2020 ; Sarpras et al, 2016 ; Sarpras et al., 2019 ). Furthermore, many studies on marker development, QTL/gene(s) mapping of economically important traits, whole transcriptome, and genome sequencing have been reported on Capsicum species ( Ahn et al., 2014 ; Chhapekar et al., 2021 ; Dubey et al., 2019 ; Jaiswal et al., 2020 ; Kim et al., 2020 ; Liu et al., 2019 ; Martínez et al., 2021 ; Razo-Mendivil et al., 2021 ).…”

Section: Introductionmentioning

confidence: 99%

Integrated analysis of DNA methylation, transcriptome, and global metabolites in interspecific heterotic Capsicum F1 hybrid

et al. 2022

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Transcriptome profiling, simple sequence repeat markers development and genetic diversity analysis of potential industrial crops Capsicum chinense and C. frutescens of Northeast India

Cited by 15 publications

References 109 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

Transcriptome and Metabolome Studies on Pre-Harvest Nitrogen Impact on Fruit Yield and Quality of Peach (Prunus persica L.)

Integrated analysis of DNA methylation, transcriptome, and global metabolites in interspecific heterotic Capsicum F1 hybrid

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