Deciphering phenotyping, DNA barcoding, and RNA secondary structure predictions in eggplant wild relatives provide insights for their future breeding strategies
Abstract Eggplant or aubergine (Solanum melongena L.) and its wild cousins, comprising 13 clades with 1500 species, have an unprecedented demand across the globe. Cultivated eggplant has a narrow molecular diversity that hinders eggplant breeding advancements. Wild eggplants need resurgent attention...
| Main Authors: | , , , , , , , , , |
|---|---|
| Format: | Article |
| Language: | English |
| Published: |
Nature Portfolio
2023-08-01
|
| Series: | Scientific Reports |
| Online Access: | https://doi.org/10.1038/s41598-023-40797-z |
| _version_ | 1797559666794823680 |
|---|---|
| author | Sansuta Mohanty Bandana Kumari Mishra Madhumita Dasgupta Gobinda Chandra Acharya Satyapriya Singh Ponnam Naresh Shyamlal Bhue Anshuman Dixit Arup Sarkar Manas Ranjan Sahoo |
| author_facet | Sansuta Mohanty Bandana Kumari Mishra Madhumita Dasgupta Gobinda Chandra Acharya Satyapriya Singh Ponnam Naresh Shyamlal Bhue Anshuman Dixit Arup Sarkar Manas Ranjan Sahoo |
| author_sort | Sansuta Mohanty |
| collection | DOAJ |
| description | Abstract Eggplant or aubergine (Solanum melongena L.) and its wild cousins, comprising 13 clades with 1500 species, have an unprecedented demand across the globe. Cultivated eggplant has a narrow molecular diversity that hinders eggplant breeding advancements. Wild eggplants need resurgent attention to broaden eggplant breeding resources. In this study, we emphasized phenotypic and genotypic discriminations among 13 eggplant species deploying chloroplast–plastid (Kim matK) and nuclear (ITS2) short gene sequences (400–800 bp) at DNA barcode region followed by ITS2 secondary structure predictions. The identification efficiency at the Kim matK region was higher (99–100%) than in the ITS2 region (80–90%). The eggplant species showed 13 unique secondary structures with a central ring with various helical orientations. Principal component analysis (PCoA) provides the descriptor–wise phenotypic clustering, which is essential for trait–specific breeding. Groups I and IV are categorized under scarlet complexes S. aethiopicum, S. trilobatum, and S. melongena (wild and cultivated). Group II represented the gboma clade (S. macrocarpon, S. wrightii, S. sisymbriifolium, and S. aculeatissimum), and group III includes S. mammosum, and S. torvum with unique fruit shape and size. The present study would be helpful in genetic discrimination, biodiversity conservation, and the safe utilization of wild eggplants. |
| first_indexed | 2024-03-10T17:48:34Z |
| format | Article |
| id | doaj.art-1245620f2d2c4b7086e25c6a069d86a8 |
| institution | Directory Open Access Journal |
| issn | 2045-2322 |
| language | English |
| last_indexed | 2024-03-10T17:48:34Z |
| publishDate | 2023-08-01 |
| publisher | Nature Portfolio |
| record_format | Article |
| series | Scientific Reports |
| spelling | doaj.art-1245620f2d2c4b7086e25c6a069d86a82023-11-20T09:26:25ZengNature PortfolioScientific Reports2045-23222023-08-0113111210.1038/s41598-023-40797-zDeciphering phenotyping, DNA barcoding, and RNA secondary structure predictions in eggplant wild relatives provide insights for their future breeding strategiesSansuta Mohanty0Bandana Kumari Mishra1Madhumita Dasgupta2Gobinda Chandra Acharya3Satyapriya Singh4Ponnam Naresh5Shyamlal Bhue6Anshuman Dixit7Arup Sarkar8Manas Ranjan Sahoo9Central Horticultural Experiment Station, ICAR–Indian Institute of Horticultural ResearchCentral Horticultural Experiment Station, ICAR–Indian Institute of Horticultural ResearchICAR Research Complex for Northeastern Hill Region, Manipur CentreCentral Horticultural Experiment Station, ICAR–Indian Institute of Horticultural ResearchCentral Horticultural Experiment Station, ICAR–Indian Institute of Horticultural ResearchICAR–Indian Institute of Horticultural ResearchInstitute of Life SciencesInstitute of Life SciencesTrident Academy of Creative TechnologyCentral Horticultural Experiment Station, ICAR–Indian Institute of Horticultural ResearchAbstract Eggplant or aubergine (Solanum melongena L.) and its wild cousins, comprising 13 clades with 1500 species, have an unprecedented demand across the globe. Cultivated eggplant has a narrow molecular diversity that hinders eggplant breeding advancements. Wild eggplants need resurgent attention to broaden eggplant breeding resources. In this study, we emphasized phenotypic and genotypic discriminations among 13 eggplant species deploying chloroplast–plastid (Kim matK) and nuclear (ITS2) short gene sequences (400–800 bp) at DNA barcode region followed by ITS2 secondary structure predictions. The identification efficiency at the Kim matK region was higher (99–100%) than in the ITS2 region (80–90%). The eggplant species showed 13 unique secondary structures with a central ring with various helical orientations. Principal component analysis (PCoA) provides the descriptor–wise phenotypic clustering, which is essential for trait–specific breeding. Groups I and IV are categorized under scarlet complexes S. aethiopicum, S. trilobatum, and S. melongena (wild and cultivated). Group II represented the gboma clade (S. macrocarpon, S. wrightii, S. sisymbriifolium, and S. aculeatissimum), and group III includes S. mammosum, and S. torvum with unique fruit shape and size. The present study would be helpful in genetic discrimination, biodiversity conservation, and the safe utilization of wild eggplants.https://doi.org/10.1038/s41598-023-40797-z |
| spellingShingle | Sansuta Mohanty Bandana Kumari Mishra Madhumita Dasgupta Gobinda Chandra Acharya Satyapriya Singh Ponnam Naresh Shyamlal Bhue Anshuman Dixit Arup Sarkar Manas Ranjan Sahoo Deciphering phenotyping, DNA barcoding, and RNA secondary structure predictions in eggplant wild relatives provide insights for their future breeding strategies Scientific Reports |
| title | Deciphering phenotyping, DNA barcoding, and RNA secondary structure predictions in eggplant wild relatives provide insights for their future breeding strategies |
| title_full | Deciphering phenotyping, DNA barcoding, and RNA secondary structure predictions in eggplant wild relatives provide insights for their future breeding strategies |
| title_fullStr | Deciphering phenotyping, DNA barcoding, and RNA secondary structure predictions in eggplant wild relatives provide insights for their future breeding strategies |
| title_full_unstemmed | Deciphering phenotyping, DNA barcoding, and RNA secondary structure predictions in eggplant wild relatives provide insights for their future breeding strategies |
| title_short | Deciphering phenotyping, DNA barcoding, and RNA secondary structure predictions in eggplant wild relatives provide insights for their future breeding strategies |
| title_sort | deciphering phenotyping dna barcoding and rna secondary structure predictions in eggplant wild relatives provide insights for their future breeding strategies |
| url | https://doi.org/10.1038/s41598-023-40797-z |
| work_keys_str_mv | AT sansutamohanty decipheringphenotypingdnabarcodingandrnasecondarystructurepredictionsineggplantwildrelativesprovideinsightsfortheirfuturebreedingstrategies AT bandanakumarimishra decipheringphenotypingdnabarcodingandrnasecondarystructurepredictionsineggplantwildrelativesprovideinsightsfortheirfuturebreedingstrategies AT madhumitadasgupta decipheringphenotypingdnabarcodingandrnasecondarystructurepredictionsineggplantwildrelativesprovideinsightsfortheirfuturebreedingstrategies AT gobindachandraacharya decipheringphenotypingdnabarcodingandrnasecondarystructurepredictionsineggplantwildrelativesprovideinsightsfortheirfuturebreedingstrategies AT satyapriyasingh decipheringphenotypingdnabarcodingandrnasecondarystructurepredictionsineggplantwildrelativesprovideinsightsfortheirfuturebreedingstrategies AT ponnamnaresh decipheringphenotypingdnabarcodingandrnasecondarystructurepredictionsineggplantwildrelativesprovideinsightsfortheirfuturebreedingstrategies AT shyamlalbhue decipheringphenotypingdnabarcodingandrnasecondarystructurepredictionsineggplantwildrelativesprovideinsightsfortheirfuturebreedingstrategies AT anshumandixit decipheringphenotypingdnabarcodingandrnasecondarystructurepredictionsineggplantwildrelativesprovideinsightsfortheirfuturebreedingstrategies AT arupsarkar decipheringphenotypingdnabarcodingandrnasecondarystructurepredictionsineggplantwildrelativesprovideinsightsfortheirfuturebreedingstrategies AT manasranjansahoo decipheringphenotypingdnabarcodingandrnasecondarystructurepredictionsineggplantwildrelativesprovideinsightsfortheirfuturebreedingstrategies |