山桐子转录组SSR特征分析及其分子标记开发与应用

SSR characteristics analysis in transcriptome of Idesia polycarpa and development and application of molecular markers

  • 摘要: 【目的】 基于转录组测序数据从山桐子叶片中挖掘SSR位点并进行分析,评估SSR标记的可用性和多态性,为山桐子种质资源收集与保存及分子标记开发提供理论参考。【方法】 以山桐子叶片为材料,利用MISA对转录组测序数据进行SSR位点检索并分析其特征,使用Primer 5.0设计SSR引物,通过SSR-PCR验证开发其多态性引物。【结果】 利用MISA筛选获得的18300条Unigenes共有8182条含SSR位点,占序列总数的44.71%;共有11767个SSR位点,平均分布距离为1.74 kb。完全型SSR位点数量为10721个,占总SSR位点的91.11%。SSR重复类型中以单核苷酸重复数量最多,共6384个,占总SSR位点的54.25%;二核苷酸次之,共2223个,占总SSR位点的18.89%;五核苷酸重复数量最少,仅36个,占总SSR位点的0.31%。共发现257种重复基元,在单核苷酸重复基元中,A/T数量最多,共6222个,占总SSR位点的52.88%;二核苷酸重复基元中,CT/AG数量最多,共701个,占总SSR位点的5.96%,其次为TC/GA,共664个,占总SSR位点的5.64%。在基元重复次数中,重复次数为10的SSR位点数量最多,共2434个,占总SSR位点的20.68%,且以单核苷酸重复数量最多,为2263个,占比为92.97%。10721个SSR位点长度为10~84 bp,平均长度为14.99 bp,位点长度主要集中在10~42 bp,该区间内共有10697个SSR位点,占总SSR位点的90.91%;具有高多态性(SSR长度≥20 bp)的SSR位点共1941个,占总SSR位点的16.50%。基于16份山桐子种质资源对随机选取的70对SSR引物进行验证,共有65对引物可扩增出目标条带,有效扩增率为92.86%,其中16对引物可扩增出多态性条带。利用6对多态性引物对16份山桐子样品进行聚类分析,在遗传相似系数0.78处,16份样品可分为2类。【结论】 山桐子叶片转录组中SSR位点类型丰富,共获得16对多态性引物,具有开发出高多态性SSR分子标记的潜力,可用于山桐子遗传多样性分析、分子标记育种和资源保护。

     

    Abstract: 【Objective】 Based on the transcriptome sequencing data, SSR loci were excavated and analyzed from the leaves of Idesia polycarpa, and the availability and polymorphism of SSR markers were evaluated, which provided theoretical reference for the collection and preservation of Idesia polycarpa germplasm resources and the development of molecular markers. 【Method】 With Idesia polycarpa leaves as materials, MISA was used to retrieve SSR loci from transcriptome sequencing data and analyze their characteristics. Primer 5.0 was used to design SSR primers, and SSR-PCR was used to verify and develop polymorphic primers. 【Result】 A total of 8182 SSR loci were found in 18300 Unigenes screened by MISA, accounting for 44.71% of the total sequences. A total of 11767 SSR loci were identified, with an average distribution distance of 1.74 kb. There were 10721 complete SSR loci, accounting for 91.11% of the total SSR loci. Among the SSR repeat types, the number of single nucleotide repeats was the largest, with a total of 6384, accounting for 54.25% of the total SSR loci;followed by dinucleotide, a total of 2223 SSR loci, accounting for 18.89% of the total SSR loci; the number of pentanucleotide repeats was the least, only 36, accounting for 0.31% of the total SSR loci. A total of 257 repeat motifs were found. Among the single nucleotide repeat motifs, A/T had the largest number (6222), accoun-ting for 52.88% of the total SSR loci. Among the dinucleotide repeat motifs, CT/AG had the largest number (701), accounting for 5.96% of the total SSR loci, followed by TC/GA, a total of 664, accounting for 5.64% of the total SSR loci. Among the number of motif repeats, the number of SSR loci with a repeat number of 10 was the largest (2434), accounting for 20.68% of the total SSR loci, and the number of single nucleotide repeats was the largest (2263), accoun-ting for 92.97%. The lengths of 10721 SSR loci ranged from 10 to 84 bp, with an average length of 14.99 bp. The length of the loci was mainly concentrated in 10-42 bp. There were 10697 SSR loci in this interval, accounting for 90.91% of the total SSR loci. A total of 1941 SSR loci had high polymorphism (SSR length ≥ 20 bp), accounting for 16.50% of the total SSR loci. Based on 16 germplasm resources of Idesia polycarpa, 70 pairs of SSR primers were randomly selected for verification. A total of 65 pairs of primers could amplify the target bands, with an effective amplification rate of 92.86%, of which 16 pairs of primers could amplify polymorphic bands. Using 6 pairs of polymorphic primers, a cluster analysis was conducted on 16 samples of Idesia polycarpa. At the genetic similarity coefficient of 0.78, the 16 samples could be classified into 2 categories. 【Conclusion】 The SSR loci in the leaf transcriptome of Idesia polycarpa are abundant, and a total of 16 pairs of polymorphic primers have been obtained, which has the potential to be developed into high polymorphic SSR molecular markers. The result lays foundation for genetic diversity analysis, molecular marker bree-ding, and resource protection of Idesia polycarpa.

     

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