Discovery of cold-resistance genes in Vitis amurensis using bud-based quantitative trait locus mapping and RNA-seq
Abstract Background In cold regions, low temperature is the main limiting factor affecting grape production. As an important breeding resource, V. amurensis Rupr. has played a crucial role in the discovery of genes which confer cold resistance in grapes. Thus far, many cold-resistance genes have bee...
| Main Authors: | , , , , |
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| Format: | Article |
| Language: | English |
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BMC
2022-08-01
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| Series: | BMC Genomics |
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| Online Access: | https://doi.org/10.1186/s12864-022-08788-y |
| _version_ | 1817968063338774528 |
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| author | Xiaolele Ma Fangyuan Zhao Kai Su Hong Lin Yinshan Guo |
| author_facet | Xiaolele Ma Fangyuan Zhao Kai Su Hong Lin Yinshan Guo |
| author_sort | Xiaolele Ma |
| collection | DOAJ |
| description | Abstract Background In cold regions, low temperature is the main limiting factor affecting grape production. As an important breeding resource, V. amurensis Rupr. has played a crucial role in the discovery of genes which confer cold resistance in grapes. Thus far, many cold-resistance genes have been reported based on the study of V. amurensis. In order to identify more candidate genes related to cold resistance in V. amurensis, QTL mapping and RNA-seq was conducted based on the hybrid population and different cold-resistance cultivars in this study. Results In this study, highly cold-resistant grape cultivar ‘Shuangyou’ (SY) which belongs to V. amurensis, and cold-sensitive cultivar ‘Red Globe’ (RG) which belongs to Vitis vinifera L. were used to identify cold resistance genes. Cold-resistance quantitative trait locus (QTL) mapping was performed based on genetic population construction through interspecific crossing of ‘Shuangyou’ and ‘Red Globe’. Additionally, transcriptome analysis was conducted for the dormant buds of these two cultivars at different periods. Based on transcriptome analysis and QTL mapping, many new structural genes and transcription factors which relate to V. amurensis cold resistance were discovered, including CORs (VaCOR413IM), GSTs (VaGST-APIC, VaGST-PARB, VaGSTF9 and VaGSTF13), ARFs (VaIAA27 and VaSAUR71), ERFs (VaAIL1), MYBs (VaMYBR2, VaMYBLL and VaMYB3R-1) and bHLHs (VaICE1 and VabHLH30). Conclusions This discovery of candidate cold-resistance genes will provide an important theoretical reference for grape cold-resistance mechanisms, research, and cold-resistant grape cultivar breeding in the future. |
| first_indexed | 2024-04-13T20:03:00Z |
| format | Article |
| id | doaj.art-706b31552f6042b2a587c10f9d602074 |
| institution | Directory Open Access Journal |
| issn | 1471-2164 |
| language | English |
| last_indexed | 2024-04-13T20:03:00Z |
| publishDate | 2022-08-01 |
| publisher | BMC |
| record_format | Article |
| series | BMC Genomics |
| spelling | doaj.art-706b31552f6042b2a587c10f9d6020742022-12-22T02:32:07ZengBMCBMC Genomics1471-21642022-08-0123111410.1186/s12864-022-08788-yDiscovery of cold-resistance genes in Vitis amurensis using bud-based quantitative trait locus mapping and RNA-seqXiaolele Ma0Fangyuan Zhao1Kai Su2Hong Lin3Yinshan Guo4College of Horticulture, Shenyang Agricultural UniversityCollege of Horticulture, Shenyang Agricultural UniversityCollege of Horticulture, Shenyang Agricultural UniversityCollege of Horticulture, Shenyang Agricultural UniversityCollege of Horticulture, Shenyang Agricultural UniversityAbstract Background In cold regions, low temperature is the main limiting factor affecting grape production. As an important breeding resource, V. amurensis Rupr. has played a crucial role in the discovery of genes which confer cold resistance in grapes. Thus far, many cold-resistance genes have been reported based on the study of V. amurensis. In order to identify more candidate genes related to cold resistance in V. amurensis, QTL mapping and RNA-seq was conducted based on the hybrid population and different cold-resistance cultivars in this study. Results In this study, highly cold-resistant grape cultivar ‘Shuangyou’ (SY) which belongs to V. amurensis, and cold-sensitive cultivar ‘Red Globe’ (RG) which belongs to Vitis vinifera L. were used to identify cold resistance genes. Cold-resistance quantitative trait locus (QTL) mapping was performed based on genetic population construction through interspecific crossing of ‘Shuangyou’ and ‘Red Globe’. Additionally, transcriptome analysis was conducted for the dormant buds of these two cultivars at different periods. Based on transcriptome analysis and QTL mapping, many new structural genes and transcription factors which relate to V. amurensis cold resistance were discovered, including CORs (VaCOR413IM), GSTs (VaGST-APIC, VaGST-PARB, VaGSTF9 and VaGSTF13), ARFs (VaIAA27 and VaSAUR71), ERFs (VaAIL1), MYBs (VaMYBR2, VaMYBLL and VaMYB3R-1) and bHLHs (VaICE1 and VabHLH30). Conclusions This discovery of candidate cold-resistance genes will provide an important theoretical reference for grape cold-resistance mechanisms, research, and cold-resistant grape cultivar breeding in the future.https://doi.org/10.1186/s12864-022-08788-yVitus amurensisGrape budCold resistance breedingTranscriptome analysisQTL mapping |
| spellingShingle | Xiaolele Ma Fangyuan Zhao Kai Su Hong Lin Yinshan Guo Discovery of cold-resistance genes in Vitis amurensis using bud-based quantitative trait locus mapping and RNA-seq BMC Genomics Vitus amurensis Grape bud Cold resistance breeding Transcriptome analysis QTL mapping |
| title | Discovery of cold-resistance genes in Vitis amurensis using bud-based quantitative trait locus mapping and RNA-seq |
| title_full | Discovery of cold-resistance genes in Vitis amurensis using bud-based quantitative trait locus mapping and RNA-seq |
| title_fullStr | Discovery of cold-resistance genes in Vitis amurensis using bud-based quantitative trait locus mapping and RNA-seq |
| title_full_unstemmed | Discovery of cold-resistance genes in Vitis amurensis using bud-based quantitative trait locus mapping and RNA-seq |
| title_short | Discovery of cold-resistance genes in Vitis amurensis using bud-based quantitative trait locus mapping and RNA-seq |
| title_sort | discovery of cold resistance genes in vitis amurensis using bud based quantitative trait locus mapping and rna seq |
| topic | Vitus amurensis Grape bud Cold resistance breeding Transcriptome analysis QTL mapping |
| url | https://doi.org/10.1186/s12864-022-08788-y |
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