| 摘要: |
| 【目的】对小果甜柿果实转录组中的SSR、SNP和InDel位点进行分析，为开发中国甜柿特异性分子标记、早期鉴定和遗传多样性分析奠定基础。【方法】以中国甜柿传统小果类型种质为材料，在果实发育的5个时期采样，抽提RNA，采用MISA和GATK3软件对小果甜柿果实转录组进行SSR、SNP和InDel位点特征分析。【结果】在小果甜柿果实转录组中共发现42 427个SSR位点，分布于26 928条unigenes上，发生频率为31.52%；在重复基元类型中，单碱基重复数量最多，六碱基重复最少，其中出现频率最高的基元为A/T，占总SSR数量的40.91%；各类型重复基元的重复次数集中在5～20次，SSR序列长度介于10～74 bp。共检测到1 070 614个SNP位点和167 924个InDel位点，其中SNP位点平均每kb出现11.46个，InDel位点平均0.556 kb出现1个，且均以含1个位点的unigenes数最多。【结论】小果甜柿转录组中SSR、SNP和InDel位点丰富，具有潜在较高的多态性，有助于后续中国甜柿特异性分子标记的开发。 |
| 关键词: 小果甜柿；果树育种 转录组；SSR；SNP；InDel |
| DOI： |
| 分类号: |
| 基金项目:国家重点研发计划项目（2019YFD1001200） |
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| SSR,SNP and InDel analysis based on transcriptome data of Diospyros kaki ‘Xiaoguo-tianshi’ fruit |
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WANG Yiru,SUO Yujing,FU Jianmin
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| Abstract: |
| 【Objective】This study analyzed the SSR,SNP and InDel sites of Diospyros kaki ‘Xiaoguo tianshi’ fruit to provide the basis for development of specific molecular markers for early identification and genetic diversity analysis of Chinese PCNA persimmon.【Method】C-PCNA type ‘Xiaoguo-tianshi’ fruits sampled at 5 development stages were used to extract RNA,and MISA and GATK3 software was used to analyze SSR,SNP and InDel sites based on transcriptome data.【Result】A total of 42 427 SSR sites were identified on 26 928 unigenes in the transcriptome data of ‘Xiaoguo-tianshi’ fruits,with the incidence ratio of 31.52%.Mononucleotide type had the largest number of repeat motifs,and hexanucleotide type had the least.Among them,the dominant repeating motif was A/T with contribution of 40.91%.The motif repeats of SSR mainly concentrated in 5-20 times and the length of SSR was mainly 10－74 bp.A total of 1 070 614 SNP sites were detected,with an average of 11.46 SNP sites per kb.A total of 167 924 InDel sites were also detected,with an average of 0.556 kb per InDel sites,and most unigenes only contained 1 site.【Conclusion】SSR,SNP and InDel sites were abundant in the transcriptome data of ‘Xiaoguo-tianshi’ with high potential polymorphism,and were beneficial for the development of C PCNA specific molecular markers. |
| Key words: ‘Xiaoguo-tianshi’ fruit breeding transcriptome SSR SNP InDel |
