Sugarcane Research Institute, Yunnan Academy of Agricultural Sciences/Yunnan Key Laboratory of Sugarcane Genetic Improvement, Kaiyuan, Yunnan, 661699, China.
Agronomy Department, University of Florida, Gainesville, FL, 32610, USA.
BMC Genomics. 2023 Jan 25;24(1):42. doi: 10.1186/s12864-023-09139-1.
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.
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.
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.
蔗糖磷酸合酶 B (SPSB) 基因编码在甘蔗中蔗糖合成的重要限速酶，主要在叶片中表达，其等位基因控制蔗糖合成。本研究以高、低糖含量杂交无性系和不同近缘种为材料，调查 SPSB 基因不同单倍型的遗传变异。
从 18 个甘蔗品种中鉴定出 39 个大小为 2824bp 的 SPSB 基因单倍型。这些单倍型主要根据 AP85-441 参考基因组分布在 Chr3B、Chr3C 和 Chr3D 上。39 个单倍型中，单核苷酸多态性(SNPs)和插入/缺失(InDels)非常密集(42bp/序列变异)，包括 44 个转换和 23 个颠换 SNPs。高糖含量(HS)无性系的序列多样性相关 Hd、Eta 和 Pi 值均低于低糖含量(LS)无性系。进化网络分析表明，约一半的 SPSB 单倍型(39 个中的 19 个)聚为一组，包括与 Badila(蔗属栽培种)中鉴定的 HAP26 相比处于正选择的 6 个( HAP4、HAP6、HAP7、HAP9、HAP17 和 HAP20)单倍型，与印度 1 号(蔗属野生种)中鉴定的 HAP18 相比处于纯化选择(除 HAP19 处于中性选择)，后者的糖含量低但耐胁迫能力强。HS 无性系中处于正选择的单倍型平均数量是 LS 无性系的两倍。大多数 SNP 和 InDels 序列变异位点与蔗糖和纤维含量呈正相关，与还原糖呈负相关。
本研究共鉴定出 39 个 SPSB 基因单倍型。鉴定出与高蔗糖合成效率相关的单倍型。HS 中 SPSB 单倍型的突变是有利的，倾向于被选择和固定。本研究结果为今后甘蔗蔗糖合成的分子辅助育种提供了有价值的信息。
