Isolation of putative pepper defense-related genes against the pathogen Phytophthora capsici using suppression subtractive hybridization/macroarray and RNA-sequencing analyses

Kim, Dong Hwan; Kang, Won-Hee; Yeom, Seon-In; Kim, Byung-Dong

doi:10.1007/s13580-019-00157-1

Cited by 8 publications

(3 citation statements)

References 67 publications

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“…These pathogenesis-related (PR) genes were jointly involved in resisting against the P. capsici infection in the leaf of pepper. Varieties of PR proteins were coordinated by cross-talk stress signals and endogenous plant hormones such as salicylic acid (SA), methyl jasmonate (MeJA), and ethylene (ET) (Kim et al, 2019). The effect of many PR genes (polygenes) associated with resistance response against P. capsici and the regulatory mechanisms of pepper against the P. capsici infection were complex (Shen et al, 2015).…”

Section: Discussionmentioning

confidence: 99%

Integrative RNA-Seq analysis ofCapsicum annuum L.-Phytophthora capsici L.pathosystem reveals molecular cross-talk and activation of host defence response

Rabuma

Gupta

Yadav

et al. 2021

Preprint

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Background: Chili pepper (Capsicum annuum L.) being one of an important member of the Solanaceae family, and its productivity is highly affected by the fungal pathogen Phytophthora capsici L. Other to CM-344, the unavailability of resistant landraces to all possible strains of P. capsici imposes a serious threat to its global production. This is because of our current understanding of the molecular mechanisms associated with the defence response in C. annuum-P. capsici pathosystem is limited. Therefore, the current study used RNA-seq technology to dissect the genes associated with defence response against P. capsici infection in two contrasting landraces, i.e. GojamMecha_9086 (Resistant) and Dabat_80045 (susceptible) exposed to P. capsici infection. Results: The transcriptomes from 4 leaf samples (RC, RI, SC and SI) of chili pepper resulted in a total of 1,18, 879 assembled transcripts (with a mean TL of 813.23bp and N50 of 1,277bp) along with 52,384 pooled unigenes with (mean UL of 1029.36 bp and N50 of 1,403bp). The enrichment analysis of the transcripts indicated 23 different KEGG pathways under five main categories. Further, 774 and 484 differentially expressed genes (DEGs) were obtained from RC vs. RI and SC vs. SI leaf samples, respectively. Of these, 57 DEGs were found to be associated with defence responses against P. capsici infection. The defence-related genes, such as LTPL, defensin J1-2-like, peroxidase 5-like, UGT, and GRP proteins-like, were more significantly upregulated in RC vs. RI. Furthermore, RT-qPCR analysis of six randomly selected genes validated the results of Illumina NextSeq500 sequencing results. Furthermore, a total of 58 TF families (bHLH most abundant) and 2,095 protein families (Protein kinase, PF00069, most abundant) were observed across all the samples with maximum hits in RI and SI samples. Conclusions: RNA-Seq analysis of chili peppers during P.capsici infection revealed differential regulation of genes associated with defence and signaling response with shared coordination of molecular function, cellular component and biological processing. The results presented here would enhance our present understanding of the defence response in chili pepper against P. capsici infection, which could be utilized by the molecular breeders to develop resistant chili genotypes. Keywords: Capsicum annuum, Phytophthora capsici, transcriptome sequence, differential gene expression

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Section: Discussionmentioning

confidence: 99%

Integrative RNA-Seq analysis ofCapsicum annuum L.-Phytophthora capsici L.pathosystem reveals molecular cross-talk and activation of host defence response

Rabuma

Gupta

Yadav

et al. 2021

Preprint

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“…Analyses of chile pepper transcriptome further demonstrated variation in the gene expression profiles during fruit development, particularly for genes related to cell cycle and division among wild and cultivated species ( Martínez et al, 2021 ). RNA-sequencing (RNA-seq) previously identified genes, namely, CA00g9220 and CA00g96010 , to be strongly expressed in the resistant landrace, CM-334, upon infection by the pathogen, providing valuable information on the defense mechanisms of chile pepper against infection by P. capsici ( Kim et al, 2019 ). In another study, at least 50 differentially expressed genes were identified through an RNA-seq approach, where the level of resistance and susceptibility to P. capsici was related to the differences in gene expression levels and molecular variations in the resistance mechanisms ( Rabuma et al, 2022 ).…”

Section: The “Panomics” Platform: Integrating Multi-omics Tools For T...mentioning

confidence: 99%

Chile Pepper (Capsicum) Breeding and Improvement in the “Multi-Omics” Era

et al. 2022

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Chile pepper (Capsicum spp.) is a major culinary, medicinal, and economic crop in most areas of the world. For more than hundreds of years, chile peppers have “defined” the state of New Mexico, USA. The official state question, “Red or Green?” refers to the preference for either red or the green stage of chile pepper, respectively, reflects the value of these important commodities. The presence of major diseases, low yields, decreased acreages, and costs associated with manual labor limit production in all growing regions of the world. The New Mexico State University (NMSU) Chile Pepper Breeding Program continues to serve as a key player in the development of improved chile pepper varieties for growers and in discoveries that assist plant breeders worldwide. Among the traits of interest for genetic improvement include yield, disease resistance, flavor, and mechanical harvestability. While progress has been made, the use of conventional breeding approaches has yet to fully address producer and consumer demand for these traits in available cultivars. Recent developments in “multi-omics,” that is, the simultaneous application of multiple omics approaches to study biological systems, have allowed the genetic dissection of important phenotypes. Given the current needs and production constraints, and the availability of multi-omics tools, it would be relevant to examine the application of these approaches in chile pepper breeding and improvement. In this review, we summarize the major developments in chile pepper breeding and present novel tools that can be implemented to facilitate genetic improvement. In the future, chile pepper improvement is anticipated to be more data and multi-omics driven as more advanced genetics, breeding, and phenotyping tools are developed.

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“…It appears that foliar blight and root rot are different P. capsici disease symptoms that should be studied independently (Foster and Hausbeck, 2010). Furthermore, resistance to Phytophthora-induced diseases such as root rot and foliar blight showed different patterns of complex inheritance (Reifschneider et al, 1992;Oelke et al, 2003;Thabuis et al, 2004;Ogundiwin et al, 2005;Yeom et al, 2011;Kim et al, 2019aKim et al, , 2019b.…”

Section: Introductionmentioning

confidence: 99%

Differential Responses of Capsicum Accessions to Foliar Blight and Root Rot by Phytophthora capsici

Kang,

Nam,

Kwon

et al. 2022

HST

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The oomycete Phytophthora capsici is one of the most destructive pepper pathogens, reducing product quality and resulting in major yield losses in Capsicum spp. To date, little is known about the defense responses of the host pepper against different P. capsici isolates. Although foliar blight and root rot are caused by the same pathogen, the host resistance responses may differ among disease symptoms and must be studied independently. In this study, 30 Capsicum accessions were inoculated with two P. capsici isolates by root drenching, and the severity of root rot was evaluated. In addition, one P. capsici strain was injected into the leaves of the same 30 accessions to evaluate the difference in host defense responses to foliar blight and root rot caused by the same strain. Among 30 accessions, 6 showed different resistance levels to the two P. capsici isolates. When comparing the resistance levels to root rot and foliar blight, 14 pepper accessions showed different resistance responses based on the inoculation site. These results suggest that the resistance to foliar blight in peppers differs according to the isolate of P. capsici and the inoculation site, even within the same pepper cultivar. The results of this study will provide useful information for the breeding of Phytophthora root rot and foliar blight-resistant Capsicum peppers.

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Isolation of putative pepper defense-related genes against the pathogen Phytophthora capsici using suppression subtractive hybridization/macroarray and RNA-sequencing analyses

Cited by 8 publications

References 67 publications

Integrative RNA-Seq analysis ofCapsicum annuum L.-Phytophthora capsici L.pathosystem reveals molecular cross-talk and activation of host defence response

Integrative RNA-Seq analysis ofCapsicum annuum L.-Phytophthora capsici L.pathosystem reveals molecular cross-talk and activation of host defence response

Chile Pepper (Capsicum) Breeding and Improvement in the “Multi-Omics” Era

Differential Responses of Capsicum Accessions to Foliar Blight and Root Rot by Phytophthora capsici

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