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布渣叶,岭南特色“药食两用”植物,广泛分布于广东、广西和海南等省区。为评价布渣叶的基因型多态性,加强种质资源保护与开发,本研究基于布渣叶转录组数据,筛选和分析了其SSR位点,并进行了相应的引物设计。研究首先采用RNA-Seq技术分析了布渣叶花、果、芽、茎和叶样品,de novo组装了布渣叶转录组。然后,采用MISA软件在布渣叶转录组数据中搜索SSR位点,分析其组成特征。最后,通过Primer 3设计并筛选相应的引物。结果,RNA-Seq高通量测序所得到的clean reads经Trinity组装后得到48 094个unigene,在4 868(10.12%)条unigene共检出5 841个SSR位点。其中,二核苷酸和三核苷酸串联重复单元的含量达到80%以上。AG/CT和GA/TC占二核苷酸串联重复单元总体的48.43%;三核苷酸串联重复单元中,GAA/TTC、AGA/TCT和AAG/CTT占到39.02%。总体而言,此次检索得到的串联重复单元大多长度短且重复次数高,SSR长度主要在12~20 bp间,具有可用性强,高多态率的特点,为布渣叶的遗传图谱构建与遗传多样性研究等提供了参考依据。
Cloth residue leaves, Lingnan features “Edible & dual purpose ” plants, are widely distributed in Guangdong, Guangxi and Hainan provinces. In order to evaluate the genetic polymorphism of Cloth leaves and to enhance the protection and development of germplasm resources, SSR loci were screened and analyzed based on the transcriptome data of Cloth leaves, and the corresponding primers were designed. In the present study, samples of flowers, fruits, shoots, stems and leaves were analyzed by RNA-Seq technique and de novo was assembled with the cloth-leaves transcriptome. Then, MISA software was used to search SSR loci in the clonal leaf transcriptome data to analyze its compositional characteristics. Finally, the corresponding primers were designed and screened by Primer 3. As a result, 48,094 unigene were obtained after clean reads of RNA-Seq high throughput sequencing were assembled by Trinity, and 5,841 SSR sites were detected in 4868 (10.12%) unigene. Among them, dinucleotide and trinucleotide tandem repeat units content of more than 80%. AG / CT and GA / TC accounted for 48.43% of the total dinucleotide tandem repeat units; GAA / TTC, AGA / TCT and AAG / CTT accounted for 39.02% of the total tandem repeat units. Overall, the tandem repeat units obtained from this search were mostly short in length and repetitive in number, and the SSR length was mainly between 12 and 20 bp. The tandem repeat units were characterized by strong availability and high polymorphism. Genetic diversity research provides a reference.