Screening of wild species and transcriptome profiling to identify differentially regulated genes in response to late blight resistance in potato
Late blight (Phytophthora infestans) is a serious disease of potatoes. The aim of this study was to screen wild potato species and identify differentially expressed genes (DEGs) associated with late blight resistance. Wild potato species such as PIN45 (Solanum pinnatisectum), CPH62 (Solanum cardioph...
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| Format: | Article |
| Language: | English |
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Frontiers Media S.A.
2023-07-01
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| Series: | Frontiers in Plant Science |
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| Online Access: | https://www.frontiersin.org/articles/10.3389/fpls.2023.1212135/full |
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| author | Nisha Bhatia Nisha Bhatia Jagesh Kumar Tiwari Jagesh Kumar Tiwari Chandresh Kumari Rasna Zinta Rasna Zinta Sanjeev Sharma Ajay Kumar Thakur Tanuja Buckseth Dalamu Dalamu Rajesh Kumar Singh Rajesh Kumar Singh Vinod Kumar |
| author_facet | Nisha Bhatia Nisha Bhatia Jagesh Kumar Tiwari Jagesh Kumar Tiwari Chandresh Kumari Rasna Zinta Rasna Zinta Sanjeev Sharma Ajay Kumar Thakur Tanuja Buckseth Dalamu Dalamu Rajesh Kumar Singh Rajesh Kumar Singh Vinod Kumar |
| author_sort | Nisha Bhatia |
| collection | DOAJ |
| description | Late blight (Phytophthora infestans) is a serious disease of potatoes. The aim of this study was to screen wild potato species and identify differentially expressed genes (DEGs) associated with late blight resistance. Wild potato species such as PIN45 (Solanum pinnatisectum), CPH62 (Solanum cardiophyllum), JAM07 (Solanum jamesii), MCD24 (Solanum microdontum), PLD47 (Solanum polyadenium), and cv. Kufri Bahar (control) were tested by artificial inoculation of P. infestans under controlled conditions. Transcriptomes of the leaf tissues (96 h post-inoculation) were sequenced using the Illumina platform. Statistically significant (p < 0.05) DEGs were analyzed in wild species by comparison with the control, and upregulated (>2 log2 fold change, FC) and downregulated (<−2 log2 FC) genes were identified. DEGs were functionally characterized with Gene Ontology (GO) terms and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathways. Selected genes were validated by real-time PCR analysis to confirm RNA-seq results. We identified some upregulated genes associated with late blight resistance in wild species such as cytochrome P450, proline-rich protein, MYB transcription factor MYB139, ankyrin repeat-containing protein, and LRR receptor-like serine/threonine-protein kinase in PIN45; glucosyltransferase, fructose-bisphosphate aldolase, and phytophthora-inhibited protease 1 in CPH62; steroid binding protein and cysteine proteinase 3 in JAM07; glycine-rich cell wall structural protein 1 and RING finger protein in MCD24; and cysteine proteinase 3 and major latex protein in PLD47. On the other hand, downregulated genes in these species were snakin-2 and WRKY transcription factor 3 in PIN45; lichenase and phenylalanine ammonia-lyase 1 in CPH62; metallothionein and LRR receptor-like serine/threonine-protein kinase in JAM07; UDP-glucoronosyl/UDP-glucosyl transferase family protein and steroid binding protein in MCD24; and cytoplasmic small heat shock protein class I and phosphatase PLD47. Our study identified highly resistant wild potato species and underlying genes such as disease resistance, stress response, phytohormones, and transcription factors (e.g., MYB, WRKY, AP2/ERF, and AN1) associated with late blight resistance in wild potato species. |
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| institution | Directory Open Access Journal |
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| last_indexed | 2024-03-13T00:06:48Z |
| publishDate | 2023-07-01 |
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| spelling | doaj.art-728c9e030b2d4f7f8202cfb774efc6e62023-07-12T23:23:22ZengFrontiers Media S.A.Frontiers in Plant Science1664-462X2023-07-011410.3389/fpls.2023.12121351212135Screening of wild species and transcriptome profiling to identify differentially regulated genes in response to late blight resistance in potatoNisha Bhatia0Nisha Bhatia1Jagesh Kumar Tiwari2Jagesh Kumar Tiwari3Chandresh Kumari4Rasna Zinta5Rasna Zinta6Sanjeev Sharma7Ajay Kumar Thakur8Tanuja Buckseth9Dalamu Dalamu10Rajesh Kumar Singh11Rajesh Kumar Singh12Vinod Kumar13Division of Crop Improvement, Indian Council of Agricultural Research—Central Potato Research Institute, Shimla, Himachal Pradesh, IndiaSchool of Biotechnology, Shoolini University, Solan, Himachal Pradesh, IndiaDivision of Crop Improvement, Indian Council of Agricultural Research—Central Potato Research Institute, Shimla, Himachal Pradesh, IndiaDivision of Vegetable Improvement, Indian Council of Agricultural Research—Indian Institute of Vegetable Research, Varanasi, Uttar Pradesh, IndiaSchool of Biotechnology, Shoolini University, Solan, Himachal Pradesh, IndiaDivision of Crop Improvement, Indian Council of Agricultural Research—Central Potato Research Institute, Shimla, Himachal Pradesh, IndiaSchool of Bioengineering and Biosciences, Lovely Professional University, Phagwara, Punjab, IndiaDivision of Crop Improvement, Indian Council of Agricultural Research—Central Potato Research Institute, Shimla, Himachal Pradesh, IndiaDivision of Crop Improvement, Indian Council of Agricultural Research—Central Potato Research Institute, Shimla, Himachal Pradesh, IndiaDivision of Crop Improvement, Indian Council of Agricultural Research—Central Potato Research Institute, Shimla, Himachal Pradesh, IndiaDivision of Crop Improvement, Indian Council of Agricultural Research—Central Potato Research Institute, Shimla, Himachal Pradesh, IndiaDivision of Crop Improvement, Indian Council of Agricultural Research—Central Potato Research Institute, Shimla, Himachal Pradesh, IndiaDivision of Vegetable Improvement, Indian Council of Agricultural Research—Indian Institute of Vegetable Research, Varanasi, Uttar Pradesh, IndiaDivision of Crop Improvement, Indian Council of Agricultural Research—Central Potato Research Institute, Shimla, Himachal Pradesh, IndiaLate blight (Phytophthora infestans) is a serious disease of potatoes. The aim of this study was to screen wild potato species and identify differentially expressed genes (DEGs) associated with late blight resistance. Wild potato species such as PIN45 (Solanum pinnatisectum), CPH62 (Solanum cardiophyllum), JAM07 (Solanum jamesii), MCD24 (Solanum microdontum), PLD47 (Solanum polyadenium), and cv. Kufri Bahar (control) were tested by artificial inoculation of P. infestans under controlled conditions. Transcriptomes of the leaf tissues (96 h post-inoculation) were sequenced using the Illumina platform. Statistically significant (p < 0.05) DEGs were analyzed in wild species by comparison with the control, and upregulated (>2 log2 fold change, FC) and downregulated (<−2 log2 FC) genes were identified. DEGs were functionally characterized with Gene Ontology (GO) terms and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathways. Selected genes were validated by real-time PCR analysis to confirm RNA-seq results. We identified some upregulated genes associated with late blight resistance in wild species such as cytochrome P450, proline-rich protein, MYB transcription factor MYB139, ankyrin repeat-containing protein, and LRR receptor-like serine/threonine-protein kinase in PIN45; glucosyltransferase, fructose-bisphosphate aldolase, and phytophthora-inhibited protease 1 in CPH62; steroid binding protein and cysteine proteinase 3 in JAM07; glycine-rich cell wall structural protein 1 and RING finger protein in MCD24; and cysteine proteinase 3 and major latex protein in PLD47. On the other hand, downregulated genes in these species were snakin-2 and WRKY transcription factor 3 in PIN45; lichenase and phenylalanine ammonia-lyase 1 in CPH62; metallothionein and LRR receptor-like serine/threonine-protein kinase in JAM07; UDP-glucoronosyl/UDP-glucosyl transferase family protein and steroid binding protein in MCD24; and cytoplasmic small heat shock protein class I and phosphatase PLD47. Our study identified highly resistant wild potato species and underlying genes such as disease resistance, stress response, phytohormones, and transcription factors (e.g., MYB, WRKY, AP2/ERF, and AN1) associated with late blight resistance in wild potato species.https://www.frontiersin.org/articles/10.3389/fpls.2023.1212135/fullgeneslate blight resistancepotatoscreeningSolanum speciestranscriptome sequencing |
| spellingShingle | Nisha Bhatia Nisha Bhatia Jagesh Kumar Tiwari Jagesh Kumar Tiwari Chandresh Kumari Rasna Zinta Rasna Zinta Sanjeev Sharma Ajay Kumar Thakur Tanuja Buckseth Dalamu Dalamu Rajesh Kumar Singh Rajesh Kumar Singh Vinod Kumar Screening of wild species and transcriptome profiling to identify differentially regulated genes in response to late blight resistance in potato Frontiers in Plant Science genes late blight resistance potato screening Solanum species transcriptome sequencing |
| title | Screening of wild species and transcriptome profiling to identify differentially regulated genes in response to late blight resistance in potato |
| title_full | Screening of wild species and transcriptome profiling to identify differentially regulated genes in response to late blight resistance in potato |
| title_fullStr | Screening of wild species and transcriptome profiling to identify differentially regulated genes in response to late blight resistance in potato |
| title_full_unstemmed | Screening of wild species and transcriptome profiling to identify differentially regulated genes in response to late blight resistance in potato |
| title_short | Screening of wild species and transcriptome profiling to identify differentially regulated genes in response to late blight resistance in potato |
| title_sort | screening of wild species and transcriptome profiling to identify differentially regulated genes in response to late blight resistance in potato |
| topic | genes late blight resistance potato screening Solanum species transcriptome sequencing |
| url | https://www.frontiersin.org/articles/10.3389/fpls.2023.1212135/full |
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