Development of EST-SSR primers and genetic diversity analysis of the southern blight pathogen Sclerotium rolfsii using transcriptome data
IntroductionSclerotium rolfsii Sacc. is a globally dispersed pathogenic fungus that causes southern blight disease in many crops and Chinese herbal medicine. The high degree of variation and diversity in the fungi altered population genetic structure. Therefore, the important factors of variation wi...
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Frontiers Media S.A.
2023-05-01
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| Series: | Frontiers in Microbiology |
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| Online Access: | https://www.frontiersin.org/articles/10.3389/fmicb.2023.1152865/full |
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| author | Fanfan Wang Fanfan Wang Fanfan Wang Tao Tang Tao Tang Ting Mao Yuanyuan Duan Yuanyuan Duan Xiaoliang Guo Xiaoliang Guo Jingmao You Jingmao You |
| author_facet | Fanfan Wang Fanfan Wang Fanfan Wang Tao Tang Tao Tang Ting Mao Yuanyuan Duan Yuanyuan Duan Xiaoliang Guo Xiaoliang Guo Jingmao You Jingmao You |
| author_sort | Fanfan Wang |
| collection | DOAJ |
| description | IntroductionSclerotium rolfsii Sacc. is a globally dispersed pathogenic fungus that causes southern blight disease in many crops and Chinese herbal medicine. The high degree of variation and diversity in the fungi altered population genetic structure. Therefore, the important factors of variation within the pathogen population should be considered during the development of management strategies for the disease.MethodsIn this study, S. rolfsii isolates from 13 hosts in 7 provinces of China were collected and analyzed to identify their morphological features and perform molecular characterization. To develop EST-SSR primers, transcriptome sequencing was performed on isolated CB1, and its SSR loci were comprehensively analyzed. In addition, we analyzed the polymorphisms among different populations based on screened EST-SSR primers.ResultsThe results showed that all of these clean reads with total 36,165,475 assembled bases were clustered into 28,158 unigenes, ranged from 201 bp to 16,402 bp on the length, of which the average length was 1,284 bp. Of these, the SSR sequence appeared at an average interval of 15.43 kB, and the frequency of SSR was 0.0648 SSR/kB. Polymorphism of 9 primers was observed among 22 populations, and was verified by the Shannon’s index (average = 1.414) and polymorphic information index (> 0.50). The genetic diversity analysis revealed diversity in all host populations and geographical populations. Further, molecular variance analysis (AMOVA) showed that the differences between groups were mainly related to geographical location. Based on cluster analysis, the 7 populations were roughly divided into 3 groups, and the results were highly consistent with those based on the geographical location, ultimately aligning with the results of STRUCTURE analysis.DiscussionThe findings build on current knowledge of the distribution of S. rolfsii in the southwest area of China, adding value to current knowledge base on the population structure and genetic diversity of S. rolfsii, specifically in the context of Chinese herbal medicine cultivation in China. Overall, our findings may provide valuable information for breeding of crops with enhanced resistance toward S. rolfsii. |
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| issn | 1664-302X |
| language | English |
| last_indexed | 2024-03-13T08:03:33Z |
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| spelling | doaj.art-c4fce752a28c46c19200239616f596222023-06-01T10:17:38ZengFrontiers Media S.A.Frontiers in Microbiology1664-302X2023-05-011410.3389/fmicb.2023.11528651152865Development of EST-SSR primers and genetic diversity analysis of the southern blight pathogen Sclerotium rolfsii using transcriptome dataFanfan Wang0Fanfan Wang1Fanfan Wang2Tao Tang3Tao Tang4Ting Mao5Yuanyuan Duan6Yuanyuan Duan7Xiaoliang Guo8Xiaoliang Guo9Jingmao You10Jingmao You11Key Laboratory of Biology and Cultivation of Chinese Herbal Medicines, Ministry of Agriculture and Rural Affairs, Institute of Chinese Herbal Medicines, Hubei Academy of Agricultural Sciences, Enshi, ChinaHubei Engineering Research Center of Under-forest Economy, Hubei Academy of Agricultural Sciences, Wuhan, ChinaHubei Engineering Research Center of Good Agricultural Practices (GAP) Production for Chinese Herbal Medicines, Institute of Chinese Herbal Medicines, Hubei Academy of Agricultural Sciences, Enshi, ChinaKey Laboratory of Biology and Cultivation of Chinese Herbal Medicines, Ministry of Agriculture and Rural Affairs, Institute of Chinese Herbal Medicines, Hubei Academy of Agricultural Sciences, Enshi, ChinaHubei Engineering Research Center of Good Agricultural Practices (GAP) Production for Chinese Herbal Medicines, Institute of Chinese Herbal Medicines, Hubei Academy of Agricultural Sciences, Enshi, ChinaKey Laboratory of Biology and Cultivation of Chinese Herbal Medicines, Ministry of Agriculture and Rural Affairs, Institute of Chinese Herbal Medicines, Hubei Academy of Agricultural Sciences, Enshi, ChinaKey Laboratory of Biology and Cultivation of Chinese Herbal Medicines, Ministry of Agriculture and Rural Affairs, Institute of Chinese Herbal Medicines, Hubei Academy of Agricultural Sciences, Enshi, ChinaHubei Engineering Research Center of Under-forest Economy, Hubei Academy of Agricultural Sciences, Wuhan, ChinaKey Laboratory of Biology and Cultivation of Chinese Herbal Medicines, Ministry of Agriculture and Rural Affairs, Institute of Chinese Herbal Medicines, Hubei Academy of Agricultural Sciences, Enshi, ChinaHubei Engineering Research Center of Good Agricultural Practices (GAP) Production for Chinese Herbal Medicines, Institute of Chinese Herbal Medicines, Hubei Academy of Agricultural Sciences, Enshi, ChinaKey Laboratory of Biology and Cultivation of Chinese Herbal Medicines, Ministry of Agriculture and Rural Affairs, Institute of Chinese Herbal Medicines, Hubei Academy of Agricultural Sciences, Enshi, ChinaHubei Engineering Research Center of Under-forest Economy, Hubei Academy of Agricultural Sciences, Wuhan, ChinaIntroductionSclerotium rolfsii Sacc. is a globally dispersed pathogenic fungus that causes southern blight disease in many crops and Chinese herbal medicine. The high degree of variation and diversity in the fungi altered population genetic structure. Therefore, the important factors of variation within the pathogen population should be considered during the development of management strategies for the disease.MethodsIn this study, S. rolfsii isolates from 13 hosts in 7 provinces of China were collected and analyzed to identify their morphological features and perform molecular characterization. To develop EST-SSR primers, transcriptome sequencing was performed on isolated CB1, and its SSR loci were comprehensively analyzed. In addition, we analyzed the polymorphisms among different populations based on screened EST-SSR primers.ResultsThe results showed that all of these clean reads with total 36,165,475 assembled bases were clustered into 28,158 unigenes, ranged from 201 bp to 16,402 bp on the length, of which the average length was 1,284 bp. Of these, the SSR sequence appeared at an average interval of 15.43 kB, and the frequency of SSR was 0.0648 SSR/kB. Polymorphism of 9 primers was observed among 22 populations, and was verified by the Shannon’s index (average = 1.414) and polymorphic information index (> 0.50). The genetic diversity analysis revealed diversity in all host populations and geographical populations. Further, molecular variance analysis (AMOVA) showed that the differences between groups were mainly related to geographical location. Based on cluster analysis, the 7 populations were roughly divided into 3 groups, and the results were highly consistent with those based on the geographical location, ultimately aligning with the results of STRUCTURE analysis.DiscussionThe findings build on current knowledge of the distribution of S. rolfsii in the southwest area of China, adding value to current knowledge base on the population structure and genetic diversity of S. rolfsii, specifically in the context of Chinese herbal medicine cultivation in China. Overall, our findings may provide valuable information for breeding of crops with enhanced resistance toward S. rolfsii.https://www.frontiersin.org/articles/10.3389/fmicb.2023.1152865/fullsouthern blightSclerotium rolfsiimolecular markersgenetic diversitytranscriptome |
| spellingShingle | Fanfan Wang Fanfan Wang Fanfan Wang Tao Tang Tao Tang Ting Mao Yuanyuan Duan Yuanyuan Duan Xiaoliang Guo Xiaoliang Guo Jingmao You Jingmao You Development of EST-SSR primers and genetic diversity analysis of the southern blight pathogen Sclerotium rolfsii using transcriptome data Frontiers in Microbiology southern blight Sclerotium rolfsii molecular markers genetic diversity transcriptome |
| title | Development of EST-SSR primers and genetic diversity analysis of the southern blight pathogen Sclerotium rolfsii using transcriptome data |
| title_full | Development of EST-SSR primers and genetic diversity analysis of the southern blight pathogen Sclerotium rolfsii using transcriptome data |
| title_fullStr | Development of EST-SSR primers and genetic diversity analysis of the southern blight pathogen Sclerotium rolfsii using transcriptome data |
| title_full_unstemmed | Development of EST-SSR primers and genetic diversity analysis of the southern blight pathogen Sclerotium rolfsii using transcriptome data |
| title_short | Development of EST-SSR primers and genetic diversity analysis of the southern blight pathogen Sclerotium rolfsii using transcriptome data |
| title_sort | development of est ssr primers and genetic diversity analysis of the southern blight pathogen sclerotium rolfsii using transcriptome data |
| topic | southern blight Sclerotium rolfsii molecular markers genetic diversity transcriptome |
| url | https://www.frontiersin.org/articles/10.3389/fmicb.2023.1152865/full |
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