| 苦荞全基因组SSR位点特征分析与分子标记开发 |
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| 引用本文： | 马名川,刘龙龙,刘璋,周建萍,南成虎,张丽君.苦荞全基因组SSR位点特征分析与分子标记开发[J].作物杂志,2021,37(1):38-109. |
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| 作者姓名： | 马名川 刘龙龙 刘璋 周建萍 南成虎 张丽君 |
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| 作者单位： | 山西农业大学农业基因资源研究中心/农业农村部黄土高原作物基因资源与种质创制重点实验室/杂粮种质资源发掘与遗传改良山西省重点实验室,030031,山西太原 |
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| 基金项目： | 山西省农科院优秀青年基金项目(YCX2020YQ26);国家燕麦荞麦产业技术体系育种技术与方法岗位(CARS-07-A-2);山西省农科院杂粮分子育种平台专项(YGC2019FZ2);山西省农科院国家自然基金支持和培育项目(YGJPY2004)。 |
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| 摘 要： | 目前苦荞SSR多态性标记数量较少,根据已发表的苦荞基因组测序数据,利用MISA软件对1~6核苷酸重复的SSR位点进行了查找和序列特征分析,批量设计引物并对引物进行了有效性和多态性检测。结果表明,苦荞基因组中共检测到1 640个SSR位点,其中三核苷酸重复型SSR最多,占比63.29%,五核苷酸重复型最少,仅占0.12%。AT/TA、AAG/CTT、ACC/GGT和ATC/GAT为出现频率较高的重复基序。苦荞基因组SSR序列长度变化范围为12~476bp,平均长度23.14bp,长度12~19bp的占比71.71%,长度≥20bp的占比28.29%。根据不同类型SSR位点设计并合成引物479对,选择200对引物对5份苦荞资源和3份甜荞资源进行多态性检测,有56对扩增出多态性条带,17对在苦荞种质中产生多态性条带,48对在甜荞种质中产生多态性条带,9对同时在两种种质中产生多态性条带。利用苦荞全基因组序列可实现SSR标记的批量开发,可鉴定出适用于苦荞和甜荞遗传多样性分析、遗传图谱构建和品种鉴定等研究的SSR引物。
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| 关 键 词： | 苦荞 全基因组 SSR |
| 收稿时间： | 2020-04-08 |
Analysis of SSR Loci in Whole Genome and Development of Molecular Markers in Tartary Buckwheat |
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| Ma Mingchuan,Liu Longlong,Liu Zhang,Zhou Jianping,Nan Chenghu,Zhang Lijun.Analysis of SSR Loci in Whole Genome and Development of Molecular Markers in Tartary Buckwheat[J].Crops,2021,37(1):38-109. |
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| Authors: | Ma Mingchuan Liu Longlong Liu Zhang Zhou Jianping Nan Chenghu Zhang Lijun |
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| Institution: | Center for Agricultural Genetic Resources Research, Shanxi Agricultural University/Key Laboratory of Crop Gene Resources and Germplasm Enhancement on Loess Plateau, Ministry of Agriculture and Rural Affairs/Shanxi Key Laboratory of Genetic Resources and Genetic Improvement of Minor Crops, Taiyuan 030031, Shanxi, China |
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| Abstract: | The number of polymorphic SSR markers of tartary buckwheat is limited.In this study,SSRs with 1-6 nucleotide repeats were searched from the published whole genome sequences of tartary buckwheat using MISA software and the characterization of SSR sequences and their polymorphisms were analyzed.A total of 1640 SSR loci were detected in whole genome sequences of tartary buckwheat.The content of tri-nucleotide repeat SSRs was the highest,accounting for 63.29%;the content of penta-nucleotide repeat SSRs was the lowest,only 0.12%.The most abundant repeat motifs were AT/TA,AAG/CTT,ACC/GGT and ATC/GAT.The SSR length ranged from 12 to 476bp,with an average of 23.14bp.The ratio of SSR length ranged from 12 to 19bp was 71.71%,and the SSRs(≥20bp)was 28.29%.Based on the type of SSR loci,479 pairs of primers were designed and synthesised.The 200 pairs of primers were selected for PCR amplification,56 of them showed polymorphism,17 pairs showed polymorphism in five accessions of tartary buckwheat,48 pairs showed polymorphism in three accessions of common buckwheat,and nine pairs showed polymorphism in tartary buckwheat and common buckwheat.SSR markers can be developed in largescale based on whole genome sequences of buckwheat and a large number of SSR primers also can be identified for genetic diversity analysis,genetic mapping and variety identification. |
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| Keywords: | Tartary buckwheat Whole genome SSR |
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