| 摘要: |
| 为揭示草莓开花习性分化的遗传基础,本研究通过全基因组重测序技术,对‘章姬’、‘雪里香’、‘香野’3个短日型品种及波特拉’、‘阿尔比’、‘圣安德瑞斯’3个日中型品种进行基因组变异特征比较分析,基于Illumina平台重测序并比对森林草莓参考基因组。结果显示,日中型品种变异数量整体高于短日型,4号染色体变异密度尤为突出。InDel分析表明,日中型品种的插入缺失总数更多,编码区37.21%的InDel引发移码突变,可能显著影响蛋白功能。结构变异(SV)检测发现,日中型品种外显子区SV比例达25.46%,高于短日型的23.73%。功能注释显示,差异变异基因显著富集于植物激素信号转导、昼夜节律及次生代谢产物生物合成等通路。GO分类揭示这些基因多参与代谢过程、催化活性及膜系统功能。进一步筛选出18个昼夜节律相关基因(如GIGANTEA、光敏色素B、早花蛋白3等),其中在日中型品种中存在非同义SNP或移码InDel变异,且在“植物-环境互作”及“生物节律”通路中的显著富集。本研究首次在基因组层面证实,日中型草莓通过积累关键基因的结构变异,改变光周期信号传导通路,从而获得连续开花能力,为解析草莓开花时间变异的分子机制提供了新视角,并为分子标记辅助育种提供理论支撑。 |
| 关键词: 草莓 全基因组重测序 开花习性 单核苷酸多态性 小片段插入缺失 结构变异，光周期调控 |
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| Comparative Study of Genomic Variations by Whole-Genome Resequencing in Short-Day and Day-Neutral Strawberry Cultivars |
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Liang Hongmin1, Wang Yue1, Yu Xiaoyu1, Cui Gang2, Xu Bo2, Sun Jiabo1
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1.Institute of Leisure Agriculture,Shandong Academy of Agricultural Sciences/Key Laboratory of East China Urban Agriculture,Ministry of Agriculture and Rural Affairs/ Shandong Engineering Research Center of Ecological Horticultural Plant Breeding;2.Shandong Plant Agricultural Technology Co,Ltd
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| Abstract: |
| A comparative analysis of genomic variations was conducted through whole-genome resequencing to systematically investigate the genetic basis underlying the divergence in flowering habits between short-day (seasonal flowering) and day-neutral (perpetual flowering) strawberry (Fragaria × ananassa) cultivars. Three short-day cultivars (‘Akihime’, ‘Xuelixiang’, and ‘Kaorino’) and three day-neutral cultivars (‘Portola’, ‘Albion’, and ‘San Andreas’) were selected for high-throughput sequencing using the Illumina platform. The sequencing reads were aligned to the Fragaria vesca reference genome (v4.0) for subsequent genomic analysis. A higher overall number of genetic variants was observed in day-neutral cultivars compared to short-day cultivars, with a notably increased density of polymorphisms detected on chromosome 4. Analysis of insertions and deletions (InDels) revealed that a greater number of InDels were present in day-neutral genotypes, among which 37.21% were identified as frameshift mutations within coding regions, suggesting potential impacts on protein function. Structural variations (SVs) were examined, and a higher prevalence of exonic SVs was found in day-neutral accessions (25.46%) than in short-day accessions (23.73%). Functional annotation of the variant sets demonstrated significant enrichment of genes associated with phytohormone signal transduction, circadian rhythm, and biosynthesis of secondary metabolites. Gene Ontology (GO) classification indicated that these genes were primarily involved in metabolic processes, catalytic activity, and membrane-related functions. Notably, 18 circadian rhythm-associated genes—including GIGANTEA, phytochrome B, and EARLY FLOWERING 3—were identified as carrying nonsynonymous single-nucleotide polymorphisms (SNPs) or frameshift InDels that were specific to day-neutral cultivars. These genes are considered central components of the photoperiodic flowering regulatory network. Significant enrichment of these genes was further validated by KEGG pathway analysis in pathways related to plant-environment interaction and circadian rhythm. This study provides the first genome-scale evidence that continuous flowering in day-neutral strawberries is achieved through the accumulation of structural variants in key regulatory genes, leading to modifications in photoperiodic signaling pathways. These findings offer novel insights into the molecular mechanisms governing flowering time variation in strawberry and establish a foundation for marker-assisted breeding strategies aimed at developing cultivars adapted to diverse photoperiodic conditions. |
| Key words: Strawberry Whole-genome resequencing Flowering habit Single nucleotide polymorphism (SNP) Insertion-deletion (InDel) Structural variation (SV) Photoperiod regulation |
