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园艺学报 ›› 2020, Vol. 47 ›› Issue (8): 1552-1564.doi: 10.16420/j.issn.0513-353x.2019-0840

• 研究报告 • 上一篇    下一篇

油梨转录组SSR分子标记开发与种质资源亲缘关系分析

郭 俊1,2,朱 婕1,2,谢尚潜1,3,张 叶1,2,叶蓓蕾1,2,郑丽燕2,凌 鹏1,3,*   

  1. 1海南大学热带特色林木花卉遗传与种质创新教育部重点实验室,海口 570228;2海南大学园艺学院,海口 570228;3海南大学林学院,海口 570228
  • 出版日期:2020-08-25 发布日期:2020-08-25
  • 基金资助:
    海南省重点研发计划项目(S100007118001012)

Development of SSR Molecular Markers Based on Transcriptome and Analysis of Genetic Relationship of Germplasm Resources in Avocado

GUO Jun1,2,ZHU Jie1,2,XIE Shangqian1,3,ZHANG Ye1,2,YE Beilei1,2,ZHENG Liyan2,and LING Peng1,3,*   

  1. 1Key Laboratory of Genetics and Germplasm Innovation of Tropical Special Forest Trees and Ornamental Plants(Hainan University),Ministry of Education,Haikou 570228,China;2College of Horticulture,Hainan University,Haikou 570228,China;3College of Forestry,Hainan University,Haikou 570228,China
  • Online:2020-08-25 Published:2020-08-25

摘要: 选取海南大学油梨种质资源圃的‘Fuerte’油梨花朵和小果进行转录组测序,获得18 010条序列,总长度为29 422 056 bp。利用MISA软件检索转录组测序数据,获得分布于4 687个序列中的6 312个SSR位点。经统计发现,SSR在所检测的序列中出现的频率为35.05%。分析SSR位点特征显示,所有类型的SSR平均长度为18.90 bp,SSR之间的平均距离为4.66 kb。‘Fuerte’油梨转录组中SSR序列以二核苷酸、三核苷酸重复类型为主,两者占SSR总数的87.15%。二、三、四核苷酸重复类型中优势基元分别为AG/CT、AAG/CTT、AAAT/ATTT。利用Primer 3.0对SSR序列设计引物13 398对。以32份油梨种质资源为研究对象,对随机挑选的100对SSR引物进行有效性验证,并用于对这些油梨种质进行亲缘关系分析。发现其中40对引物具良好多态性,共扩增出219条谱带,其中171条为多态性谱带。经计算,平均每对引物产生4.275个多态性片段。He和PIC均值分别为0.529和0.456。UPGMA聚类和PCA分析结果较一致,在系数设定为0.74时可将32份油梨种质分为4大类,与地理分布有一定的关系。

关键词: 油梨, 转录组, SSR, 多态性引物, 聚类分析

Abstract: The‘Fuerte’(Persea americana Mill.)avocado flowers and small fruits from the avocado germplasm resource nursery of Hainan University were selected for transcriptome sequencing,and 18 010 sequences were obtained,with a total length of 29 422 056 bp. MISA software was used to retrieve the transcriptome sequences data of avocado‘Fuerte’ to obtain 6 312 SSR loci distributed in 4 687 sequences. The frequency of these SSRs was 35.05%. Analysis of SSR locus characteristics showed that the average length of SSRs was 18.90 bp and the average distance between SSRs was 4.66 kb in the unigenes. The major types of SSR repeated motifs were dinucleotide and trinucleotide,which accounted for 87.15% of all the SSRs. AG/CT,AAG/CTT,and AAAT/ATTT were the predominant motifs in dinucleotide,trinucleotide and tetranucleotide groups,respectively. A total of 13 398 primers were designed with Primer 3.0 software for the SSR sequences. Thirty-two avocado germplasm resources were used as experimental subjects to verify the validity of 100 randomly chosen primers,and the genetic relationship of these avocado germplasm was also analyzed. Forty primers showed polymorphism with the He and PIC mean values as 0.529 and 0.456,respectively. A total of 219 bands and 171 polymorphic bands were amplified. On average,each pair of primers produced 4.275 polymorphic fragments. Consistent results were obtanned with the UPGMA clustering and PCA analysis,respectively. When the coefficient was set to 0.74,these avocado germplasms can be divided into 4 groups,which has certain correlation with geographical distribution.

Key words: Persea americana, avocado, transcriptome, SSR, polymorphic primer, cluster analysis

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