| 金荞麦转录组SSR位点分析及分子标记开发 |
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| 引用本文：贾 琼，石茂竹，薛贤滨，黎瑞源，陈庆富，黄 娟，邓 娇，石桃雄.金荞麦转录组SSR位点分析及分子标记开发[J].西北农业学报,2024,(11):2028~2037 |
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| 基金项目:国家自然科学基金委员会-贵州省人民政府喀斯特中心项目(U1812401)；国家现代农业产业体系荞麦育种岗位科学家专项资金(CARS-07-A5)；云南省重大科技专项与重点研发计划（202202AE090020）；贵州省科技计划项目（黔科合基础-ZK\[2023\]一般 278）。 |
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| 中文摘要:金荞麦具有较高的医疗保健价值，目前缺乏相应的分子工具用于系统评价金荞麦资源以保护及利用种质资源，SSR标记能够应用于植物多样性评价、品种鉴定以及遗传图谱构建等领域。为揭示金荞麦根系转录组SSR分布特征，开发更多有价值的SSR标记，本研究利用Krait软件对其46 923个Uingenes序列的SSR位点进行检索和标记开发。结果显示，在1 783个Unigenes序列中包含1 961个SSR位点，SSR分布频率为3.80%，平均分布间距为1/17.00 kb；其中三核苷酸重复基序数量最多（54.92%），其次是单核苷酸重复基序（23.36%）和二核苷酸重复基序（10.76%）；共发现104种重复基序，其中A/T的出现频率最高 （23.10%），其次是AAG/CTT（16.32%）和AG/CT（5.61%）。随机合成了115对SSR引物，基于12份金荞麦种质资源检测其多态性，结果得出98对引物（85.2%）能扩增出目标条带，其中36对引物有多态性。单个SSR引物平均能检测到3.83个变异位点，多态信息含量（PIC）为0.15~0.96，平均为0.53；12个金荞麦之间的遗传相似系数为0.47～0.76，平均值为0.55，表明12个金荞麦种质具有一定的遗传多样性。本研究鉴定金荞麦根系转录组SSR标记，有效增加了金荞麦遗传多样性评价、品种鉴定和重要性状遗传机制的解析等研究中可用的分子标记，为金荞麦分子育种的深入研究奠定了基础。 |
| 中文关键词:金荞麦种质 转录组 SSR分子标记 聚类分析 |
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| Transcriptome SSR Loci Analysis and Molecular MarkerDevelopment in Fagopyrum cymosum |
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| Abstract:The medical and healthcare value of Fagopyrum cymosum is widely acknowledged.However, the systematic evaluation and conservation of its germplasm resources face challenges due to a lack of molecular tools.SSR markers, crucial for assessing plant diversity, identifying species, and mapping genes, offer a solution.This study explored the distribution of SSR loci within the root transcriptomes of Fagopyrum cymosum to develop valuable SSR markers.Krait software was utilized to analyze 46 923 Unigene sequences,identifying 1 961 SSR loci across 1 783 Unigenes, indicating a 3.80% occurrence rate with an average spacing of 1 per 17.00 kb.Trinucleotide repeats emerged as the predominant form, accounting for 54.92%, overshadowing mononucleotide (23.36%) and dinucleotide (10.76%) repeats.Among 104 distinct repeat motifs, A/T motifs were the most common at 23.10% , followed by AAG/CTT (16.32%) and AG/CT (5.61%).The synthesis of 115 SSR primer pairs led to polymorphic screening across 12 Fagopyrum cymosum germplasm samples, resulting in 98 pairs (85.2%) amplifying expected bands and 36 pairs exhibiting polymorphism.The average allelic variation detected by a single SSR primer was 3.83, with polymorphic information content (PIC) ranging from 0.15 to 0.96, averaging 0.53.Genetic similarity coefficients among the 12 analyzed Fagopyrum cymosum germplasms ranged from 0.47 to 0.76, with a mean of 0.55, demonstrating notable genetic diversity.This study not only identifies SSR markers within the root transcriptome of Fagopyrum cymosum but also significantly enriches the repository of molecular markers for comprehensive genetic diversity studies, species identification, and the investigation of significant trait genetic mechanisms.This foundation supports the advancement of molecular breeding research in Fagopyrum cymosum. |
| keywords:Fagopyrum cymosum germplasms Transcriptome SSR molecular marker Cluster analysis |
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