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云南栘[木衣]果实转录组SSR、SNP、InDel特征分析

SSR,SNP and InDel Analysis based on Transcriptome Data of Docynia delavayi(Franch.)Fruits
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摘要 对云南栘[木衣]果实转录组中的简单重复序列(SSR)、单核苷酸多态性(SNP)和插入/缺失多态性(InDel)位点的特征进行分析,为开发特异性分子标记、遗传多样性分析和分子标记辅助育种奠定理论基础。基于7个不同发育时期的云南栘[木衣]果实转录组数据对SSR、SNP和InDel位点进行挖掘,并对其位点特征进行分析。结果显示:在云南栘[木衣]果实转录组中共发现25 796个SSR位点,分布于39 185条转录本(Unigenes)上,发生频率为22.88%;共发现249种SSR重复基元类型,单碱基重复数量最多,六碱基重复数量最少,出现频率最高的基元为A/T,占总SSR数量的37.47%;各类型基元的重复次数均集中在5~11次,SSR序列长度为10~48 bp。21个样品检测到的SNP位点数为255 301~361 860个,平均每个样品含有311 094个SNP位点,转换与颠换比值平均为1.56,且分布在外显子区的位点最多,发生错义突变的位点数量最多。InDel位点数则为36 135~54 655个,平均每个样品包含45 921个,插入型位点数大于缺失型,在内含子区分布最多,发生移码插入的位点最多。研究结果表明:云南栘[木衣]果实转录组中的SSR、SNP和InDel位点丰富,并且具有较高的多态性,为后续的特异性分子标记开发提供数据支撑。 Characterization of SSR,SNP and InDel sites was analyzed in the transcriptome of Docynia delavayi fruit.To lay a theoretical foundation for the development of D.delavayi fruit-specific molecular markers,genetic diversity analysis and molecular marker-assisted breeding.SSR,SNP and InDel sites were mined based on the transcriptome data of D.delavayi fruits at seven different developmental periods,and SSR,SNP and InDel sites characteristics were statistically analysed.A total of 25796 SSR sites were found in the D.delavayi fruit transcriptome,distributed on 39185 unigenes,with a frequency of 22.88%;a total of 249 SSR repeat motif types were found,with the highest number of single-base repeats and the lowest number of hexabase repeats,and the motif with the highest frequency of occurrence was A/T,which accounted for 37.47%of the total number of SSR;the repeat number of each type of motifs were concentrated in 5-11,and the length of SSR sequences ranged from 10-48 bp.The number of SNP sites detected in the 21 samples ranged from 255301 to 361860,with an average of 311094 SNP sites per sample,an average of 1.56 for the conversion to subversion ratio,and the highest number of sites distributed in the exon region,and the highest number of sites with missense mutations.The number of InDel sites ranged from 36135 to 54655,with an average of 45921 contained in each sample.The numbers of insertion-type sites were larger than those of deletion-type,with the highest distribution in the intronic region,and the most sites in which shifted insertions occurred.The abundance of SSR,SNP and InDel sites in the transcriptome of D.delavayi fruits indicates high polymorphism,which provides data support for the subsequent development of specific molecular markers for D.delavayi.
作者 舒国荣 田金红 杨林 王大玮 SHU Guorong;TIAN Jinhong;YANG Lin;WANG Dawei(College of Forestry,Southwest Forestry University,Key Laboratory of Ministry of Education for Conservation and Utilization of Mountain Forest Resources in the Southwest China,Kunming Yunnan 650224,P.R.China;College of Forestry,Southwest Forestry University,Kunming Yunnan 650224,P.R.China)
出处 《西部林业科学》 CAS 北大核心 2024年第5期84-91,99,共9页 Journal of West China Forestry Science
基金 国家自然科学基金项目(32060350) 云南省“万人计划”青年拔尖人才专项(YNWR-QNBJ-2020-230)。
关键词 云南栘[木衣] 转录组 SSR SNP INDEL Docynia delavayi Transcriptome SSR SNP InDel
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