Mitochondrial genome structural variants and candidate cytoplasmic male sterility-related gene in sugarcane
Abstract Background Sugarcane is a crucial crop for both sugar and bioethanol production. The nobilization breeding and utilization of wild germplasm have significantly enhanced its productivity. However, the pollen sterility in Saccharum officinarum restricts its role to being a female parent in cr...
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2025-01-01
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| Online Access: | https://doi.org/10.1186/s12864-025-11210-y |
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| author | Yihan Li Shuangyu Li Xiuting Hua Yi Xu Shuqi Chen Zehuai Yu Gui Zhuang Yuhong Lan Wei Yao Baoshan Chen Muqing Zhang Jisen Zhang |
| author_facet | Yihan Li Shuangyu Li Xiuting Hua Yi Xu Shuqi Chen Zehuai Yu Gui Zhuang Yuhong Lan Wei Yao Baoshan Chen Muqing Zhang Jisen Zhang |
| author_sort | Yihan Li |
| collection | DOAJ |
| description | Abstract Background Sugarcane is a crucial crop for both sugar and bioethanol production. The nobilization breeding and utilization of wild germplasm have significantly enhanced its productivity. However, the pollen sterility in Saccharum officinarum restricts its role to being a female parent in crosses with Saccharum spontaneum during nobilization breeding, resulting in a narrow genetic basis for modern sugarcane cultivars. Mitochondria, often referred to as the intracellular “energy factories”, provide energy for plant life activities, and are also implicated in cytoplasmic male sterility (CMS). Results We performed mitochondrial genome assembly and structural analysis of two Saccharum founding species. We discovered that the proportions of repeat sequences are the primary factor contributing to the variations in mitochondrial genome structure and size between the two Saccharum species. Heterologous expression of the mitochondrial chimeric gene ORF113, which is highly expressed in male-sterile S. officinarum flowers, significantly inhibits growth and ATP synthesis in yeast cells, making it a key candidate CMS-related gene in sugarcane. Furthermore, we developed two co-dominant simple sequence repeat (SSR) markers based on the mitochondrial genome, which can effectively distinguish the cytoplasmic types of the two Saccharum species. Conclusion In this study, we identified structural variants and developed SSR molecular markers in the mitochondrial genomes of both S. officinarum and S. spontaneum. We also identified a novel mitochondrial chimeric ORF as a key candidate CMS-related gene. These findings offer valuable insights into variety identification, genetic resource development, and cross-breeding strategies in sugarcane. |
| format | Article |
| id | doaj-art-1d7515ce0d0c4758b9f9cbf5af304352 |
| institution | Kabale University |
| issn | 1471-2164 |
| language | English |
| publishDate | 2025-01-01 |
| publisher | BMC |
| record_format | Article |
| series | BMC Genomics |
| spelling | doaj-art-1d7515ce0d0c4758b9f9cbf5af3043522025-01-12T12:09:13ZengBMCBMC Genomics1471-21642025-01-0126111610.1186/s12864-025-11210-yMitochondrial genome structural variants and candidate cytoplasmic male sterility-related gene in sugarcaneYihan Li0Shuangyu Li1Xiuting Hua2Yi Xu3Shuqi Chen4Zehuai Yu5Gui Zhuang6Yuhong Lan7Wei Yao8Baoshan Chen9Muqing Zhang10Jisen Zhang11State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, Guangxi Key Laboratory of Sugarcane Biology, College of Agriculture, Guangxi UniversityFujian Provincial Key Laboratory of Haixia Applied Plant Systems Biology, Center for Genomics and Biotechnology, Fujian Agriculture and Forestry UniversityState Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, Guangxi Key Laboratory of Sugarcane Biology, College of Agriculture, Guangxi UniversityState Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, Guangxi Key Laboratory of Sugarcane Biology, College of Agriculture, Guangxi UniversityFujian Provincial Key Laboratory of Haixia Applied Plant Systems Biology, Center for Genomics and Biotechnology, Fujian Agriculture and Forestry UniversityState Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, Guangxi Key Laboratory of Sugarcane Biology, College of Agriculture, Guangxi UniversityState Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, Guangxi Key Laboratory of Sugarcane Biology, College of Agriculture, Guangxi UniversityState Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, Guangxi Key Laboratory of Sugarcane Biology, College of Agriculture, Guangxi UniversityState Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, Guangxi Key Laboratory of Sugarcane Biology, College of Agriculture, Guangxi UniversityState Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, Guangxi Key Laboratory of Sugarcane Biology, College of Agriculture, Guangxi UniversityState Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, Guangxi Key Laboratory of Sugarcane Biology, College of Agriculture, Guangxi UniversityState Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, Guangxi Key Laboratory of Sugarcane Biology, College of Agriculture, Guangxi UniversityAbstract Background Sugarcane is a crucial crop for both sugar and bioethanol production. The nobilization breeding and utilization of wild germplasm have significantly enhanced its productivity. However, the pollen sterility in Saccharum officinarum restricts its role to being a female parent in crosses with Saccharum spontaneum during nobilization breeding, resulting in a narrow genetic basis for modern sugarcane cultivars. Mitochondria, often referred to as the intracellular “energy factories”, provide energy for plant life activities, and are also implicated in cytoplasmic male sterility (CMS). Results We performed mitochondrial genome assembly and structural analysis of two Saccharum founding species. We discovered that the proportions of repeat sequences are the primary factor contributing to the variations in mitochondrial genome structure and size between the two Saccharum species. Heterologous expression of the mitochondrial chimeric gene ORF113, which is highly expressed in male-sterile S. officinarum flowers, significantly inhibits growth and ATP synthesis in yeast cells, making it a key candidate CMS-related gene in sugarcane. Furthermore, we developed two co-dominant simple sequence repeat (SSR) markers based on the mitochondrial genome, which can effectively distinguish the cytoplasmic types of the two Saccharum species. Conclusion In this study, we identified structural variants and developed SSR molecular markers in the mitochondrial genomes of both S. officinarum and S. spontaneum. We also identified a novel mitochondrial chimeric ORF as a key candidate CMS-related gene. These findings offer valuable insights into variety identification, genetic resource development, and cross-breeding strategies in sugarcane.https://doi.org/10.1186/s12864-025-11210-ySugarcaneMitochondrial genomeRepeat sequencesCytoplasmic male sterility (CMS)Simple sequence repeat (SSR) |
| spellingShingle | Yihan Li Shuangyu Li Xiuting Hua Yi Xu Shuqi Chen Zehuai Yu Gui Zhuang Yuhong Lan Wei Yao Baoshan Chen Muqing Zhang Jisen Zhang Mitochondrial genome structural variants and candidate cytoplasmic male sterility-related gene in sugarcane BMC Genomics Sugarcane Mitochondrial genome Repeat sequences Cytoplasmic male sterility (CMS) Simple sequence repeat (SSR) |
| title | Mitochondrial genome structural variants and candidate cytoplasmic male sterility-related gene in sugarcane |
| title_full | Mitochondrial genome structural variants and candidate cytoplasmic male sterility-related gene in sugarcane |
| title_fullStr | Mitochondrial genome structural variants and candidate cytoplasmic male sterility-related gene in sugarcane |
| title_full_unstemmed | Mitochondrial genome structural variants and candidate cytoplasmic male sterility-related gene in sugarcane |
| title_short | Mitochondrial genome structural variants and candidate cytoplasmic male sterility-related gene in sugarcane |
| title_sort | mitochondrial genome structural variants and candidate cytoplasmic male sterility related gene in sugarcane |
| topic | Sugarcane Mitochondrial genome Repeat sequences Cytoplasmic male sterility (CMS) Simple sequence repeat (SSR) |
| url | https://doi.org/10.1186/s12864-025-11210-y |
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