园艺学报 ›› 2021, Vol. 48 ›› Issue (5): 1013-1022.doi: 10.16420/j.issn.0513-353x.2020-0497

• 研究报告 • 上一篇    下一篇


蒋爽*(), 张学英, 安海山, 徐芳杰, 章加应   

  1. 上海农业科学院林木果树研究所,上海市园艺重点实验室,上海 201403
  • 收稿日期:2020-12-15 修回日期:2021-02-08 出版日期:2021-05-25 发布日期:2021-06-07
  • 作者简介:*E-mail:
  • 基金资助:

Development and Analysis of Polymorphism of SSR Markers in the Whole Genome of Loquat

JIANG Shuang*(), ZHANG Xueying, AN Haishan, XU Fangjie, ZHANG Jiaying   

  1. Shanghai Key Laboratory of Protected Horticultural Technology,Forestry and Fruit Tree Research Institute,Shanghai Academy of Agricultural Sciences,Shanghai 201403,China
  • Received:2020-12-15 Revised:2021-02-08 Online:2021-05-25 Published:2021-06-07


搜索枇杷全基因组范围内的SSR位点,分析其分布特点,同时使用10个枇杷品种的重测序数据对这些位点的基因型进行分析。结果显示共获得103 509个SSR位点,二核苷酸重复类型有73 604个,占71.1%,以AT/TA为主。三核苷酸重复类型占15.0%,以AAG/CTT为主。对10个枇杷样本进行重测序,分别获得32 ~ 206 Mb的reads,测序深度为12.9× ~ 81.3×。本研究中新开发2个脚本程序(Flank和SSRtype),对重测序数据Reads中包含的SSR位点长度进行了分析,确定基因型。‘早钟6号’的测序深度达到12.9×,能够覆盖80%的SSR位点,说明12×以上的测序深度能够满足SSR位点的分析。枇杷中大量SSR位点为多拷贝(占78.4%),为单个品种单个位点产生3条以上的条带,而在所有品种中呈现两拷贝的SSR位点有12 962个(占12.5%),这些位点产生的多态性条带分别为2 ~ 10条不等,多态性信息含量的中位数为0.269,大于0.5的位点有526个。从中挑选20对引物进行荧光PCR,结果显示这些引物的多态性与重测序分析结果一致。

关键词: 枇杷, SSR标记, 全基因组, 多态性, 重测序


In this study,we searched the SSR loci in the whole loquat genome and analyzed its distribution characteristics. The resequencing data of 10 cultivars were used to analyze the genotypes of these loci. The results showed that 103 509 SSR sites were obtained,of which 73 604 SSRs were dinucleotide repeat,accounting for 71.1% of total discovered SSRs. The main dinucleotide repeat motif was AT/TA. The trinucleotide repeat type of SSRs accounts for 15.0%,with AAG/CTT as the main type. Ten cultivars of loquat were resequenced,and 32-206 Mb reads were obtained with a depth of 12.9×-81.3×. Two new scripts(Flank and SSRtype)were developed to analyze the length of SSR sites embedded in the resequencing data reads. The sequencing depth of Zaozhong 6 loquat was 12.9×,covering 80% of SSR sites,indicating that a sequencing depth of more than 12 times was enough to the analysis of the SSR loci. A large number of SSR loci in loquat are multiple copies(accounting for 78.4%),producing more than three bands in a locus in a cultivar. There are 12 962 SSR loci with two copies in all cultivars(accounting for 12.5%). The polymorphic bands generated by these loci range from two to 10. The median of the polymorphism information content(PIC)is 0.269. The PIC value of 526 SSR sites was more than 0.5. Twenty pairs of primers were screened to perform fluorescent PCR. The results of polymorphism of these primers were consistent with the resequencing analysis.

Key words: loquat, SSR marker, whole genome, polymorphism, re-sequencing data