Haplotype variations of sucrose phosphate synthase B gene among sugarcane accessions with different sucrose content
Abstract Background Sucrose phosphate synthase B (SPSB) gene encoding an important rate-limiting enzyme for sucrose synthesis in sugarcane is mainly expressed on leaves, where its alleles control sucrose synthesis. In this study, genetic variation of SPSB gene represented by different haplotypes in...
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BMC
2023-01-01
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| Series: | BMC Genomics |
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| Online Access: | https://doi.org/10.1186/s12864-023-09139-1 |
| _version_ | 1811175945005957120 |
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| author | Hongbo Liu Xiuqin Lin Xujuan Li Ziliang Luo Xin Lu Qian You Xiping Yang Chaohua Xu Xinlong Liu Jiayong Liu Caiwen Wu Jianping Wang |
| author_facet | Hongbo Liu Xiuqin Lin Xujuan Li Ziliang Luo Xin Lu Qian You Xiping Yang Chaohua Xu Xinlong Liu Jiayong Liu Caiwen Wu Jianping Wang |
| author_sort | Hongbo Liu |
| collection | DOAJ |
| description | Abstract Background Sucrose phosphate synthase B (SPSB) gene encoding an important rate-limiting enzyme for sucrose synthesis in sugarcane is mainly expressed on leaves, where its alleles control sucrose synthesis. In this study, genetic variation of SPSB gene represented by different haplotypes in sugarcane was investigated in hybrid clones with high and low sugar content and various accessory species. Results A total of 39 haplotypes of SPSB gene with 2, 824 bp in size were identified from 18 sugarcane accessions. These haplotypes mainly distributed on Chr3B, Chr3C, and Chr3D according to the AP85-441 reference genome. Single nucleotide polymorphisms (SNPs) and insertion/deletion (InDels) were very dense (42 bp/sequence variation) including 44 transitional and 23 transversional SNPs among the 39 haplotypes. The sequence diversity related Hd, Eta, and Pi values were all lower in clones of high sucrose content (HS) than those in clones of low sucrose content (LS). The evolutionary network analysis showed that about half SPSB haplotypes (19 out of 39) were clustered into one group, including 6 (HAP4, HAP6, HAP7, HAP9, HAP17 and HAP20) haplotypes under positive selection in comparison to HAP26 identified in Badila (S. officinarum), an ancestry noble cane species and under purification selection (except HAP19 under neutral selection) in comparison to HAP18 identified from India1 (S. spontaneum), an ancestry species with low sugar content but high stress tolerance. The average number of haplotypes under positive selection in HS clones was twice as that in LS. Most of the SNPs and InDels sequence variation sites were positively correlated with sucrose and fiber content and negatively correlated with reducing sugar. Conclusions A total of 39 haplotypes of SPSB gene were identified in this study. Haplotypes potentially associated with high sucrose synthesis efficiency were identified. The mutations of SPSB haplotypes in HS were favorable and tended to be selected and fixed. The results of this study are informative and beneficial to the molecular assisted breeding of sucrose synthesis in sugarcane in the future. |
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| institution | Directory Open Access Journal |
| issn | 1471-2164 |
| language | English |
| last_indexed | 2024-04-10T19:45:19Z |
| publishDate | 2023-01-01 |
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| series | BMC Genomics |
| spelling | doaj.art-7f8c379d30784e8a86b23f8fbfe7b2832023-01-29T12:05:10ZengBMCBMC Genomics1471-21642023-01-0124111210.1186/s12864-023-09139-1Haplotype variations of sucrose phosphate synthase B gene among sugarcane accessions with different sucrose contentHongbo Liu0Xiuqin Lin1Xujuan Li2Ziliang Luo3Xin Lu4Qian You5Xiping Yang6Chaohua Xu7Xinlong Liu8Jiayong Liu9Caiwen Wu10Jianping Wang11Sugarcane Research Institute, Yunnan Academy of Agricultural Sciences/Yunnan Key Laboratory of Sugarcane Genetic ImprovementSugarcane Research Institute, Yunnan Academy of Agricultural Sciences/Yunnan Key Laboratory of Sugarcane Genetic ImprovementSugarcane Research Institute, Yunnan Academy of Agricultural Sciences/Yunnan Key Laboratory of Sugarcane Genetic ImprovementAgronomy Department, University of FloridaSugarcane Research Institute, Yunnan Academy of Agricultural Sciences/Yunnan Key Laboratory of Sugarcane Genetic ImprovementAgronomy Department, University of FloridaAgronomy Department, University of FloridaSugarcane Research Institute, Yunnan Academy of Agricultural Sciences/Yunnan Key Laboratory of Sugarcane Genetic ImprovementSugarcane Research Institute, Yunnan Academy of Agricultural Sciences/Yunnan Key Laboratory of Sugarcane Genetic ImprovementSugarcane Research Institute, Yunnan Academy of Agricultural Sciences/Yunnan Key Laboratory of Sugarcane Genetic ImprovementSugarcane Research Institute, Yunnan Academy of Agricultural Sciences/Yunnan Key Laboratory of Sugarcane Genetic ImprovementAgronomy Department, University of FloridaAbstract Background Sucrose phosphate synthase B (SPSB) gene encoding an important rate-limiting enzyme for sucrose synthesis in sugarcane is mainly expressed on leaves, where its alleles control sucrose synthesis. In this study, genetic variation of SPSB gene represented by different haplotypes in sugarcane was investigated in hybrid clones with high and low sugar content and various accessory species. Results A total of 39 haplotypes of SPSB gene with 2, 824 bp in size were identified from 18 sugarcane accessions. These haplotypes mainly distributed on Chr3B, Chr3C, and Chr3D according to the AP85-441 reference genome. Single nucleotide polymorphisms (SNPs) and insertion/deletion (InDels) were very dense (42 bp/sequence variation) including 44 transitional and 23 transversional SNPs among the 39 haplotypes. The sequence diversity related Hd, Eta, and Pi values were all lower in clones of high sucrose content (HS) than those in clones of low sucrose content (LS). The evolutionary network analysis showed that about half SPSB haplotypes (19 out of 39) were clustered into one group, including 6 (HAP4, HAP6, HAP7, HAP9, HAP17 and HAP20) haplotypes under positive selection in comparison to HAP26 identified in Badila (S. officinarum), an ancestry noble cane species and under purification selection (except HAP19 under neutral selection) in comparison to HAP18 identified from India1 (S. spontaneum), an ancestry species with low sugar content but high stress tolerance. The average number of haplotypes under positive selection in HS clones was twice as that in LS. Most of the SNPs and InDels sequence variation sites were positively correlated with sucrose and fiber content and negatively correlated with reducing sugar. Conclusions A total of 39 haplotypes of SPSB gene were identified in this study. Haplotypes potentially associated with high sucrose synthesis efficiency were identified. The mutations of SPSB haplotypes in HS were favorable and tended to be selected and fixed. The results of this study are informative and beneficial to the molecular assisted breeding of sucrose synthesis in sugarcane in the future.https://doi.org/10.1186/s12864-023-09139-1SugarcaneSucrose phosphate synthase B (SPSB) geneHaplotypeSucrose |
| spellingShingle | Hongbo Liu Xiuqin Lin Xujuan Li Ziliang Luo Xin Lu Qian You Xiping Yang Chaohua Xu Xinlong Liu Jiayong Liu Caiwen Wu Jianping Wang Haplotype variations of sucrose phosphate synthase B gene among sugarcane accessions with different sucrose content BMC Genomics Sugarcane Sucrose phosphate synthase B (SPSB) gene Haplotype Sucrose |
| title | Haplotype variations of sucrose phosphate synthase B gene among sugarcane accessions with different sucrose content |
| title_full | Haplotype variations of sucrose phosphate synthase B gene among sugarcane accessions with different sucrose content |
| title_fullStr | Haplotype variations of sucrose phosphate synthase B gene among sugarcane accessions with different sucrose content |
| title_full_unstemmed | Haplotype variations of sucrose phosphate synthase B gene among sugarcane accessions with different sucrose content |
| title_short | Haplotype variations of sucrose phosphate synthase B gene among sugarcane accessions with different sucrose content |
| title_sort | haplotype variations of sucrose phosphate synthase b gene among sugarcane accessions with different sucrose content |
| topic | Sugarcane Sucrose phosphate synthase B (SPSB) gene Haplotype Sucrose |
| url | https://doi.org/10.1186/s12864-023-09139-1 |
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