文章摘要
基于转录组数据的毛蚶(Scapharca kagoshimensis)SSR分子标记开发与评价
Development and evaluation of SSR markers based on transcriptome sequencing in Scapharca kagoshimensis
投稿时间:2021-02-06  修订日期:2021-02-26
DOI:
中文关键词: 毛蚶  转录组  SSR  遗传多样性
英文关键词: Scapharca kagoshimensis  transcriptome  SSR  genetic diversity
基金项目:现代农业产业技术体系建设专项资金资助项目,山东省现代农业产业技术体系建设专项资金资助项目,天津市企业特派员项目
作者单位邮编
陈丽梅 天津农学院水产学院 天津市水产生态及养殖重点实验室 天津 300384
李莉 山东省海洋生物研究院 青岛 
石栩蔚 天津农学院水产学院 天津市水产生态及养殖重点实验室 天津 
秦艺铭 天津农学院水产学院 天津市水产生态及养殖重点实验室 天津 
刘利华 天津农学院水产学院 天津市水产生态及养殖重点实验室 天津 
郭永军 天津农学院水产学院 天津市水产生态及养殖重点实验室 天津 300384
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中文摘要:
      本研究基于毛蚶(Scapharca subcrenata)的转录组数据,利用MISA软件对其中的SSR位点进行挖掘。从35555条Unigene中共获得3987个SSR,SSR出现频率达到11.21%。SSR重复类型主要以二核苷酸重复为主(58.06%),其次为三核苷酸重复(19.04%)。共有182种重复基元,不同类型SSR的重复基元分布特征不同,其中,二核苷酸重复基元中AC/GT类型比例最高,为45.70%。毛蚶转录组中SSR重复次数主要集中在5~7次,且SSR数量随着重复次数的增加逐渐减少;SSR长度主要集中在12~29 bp,多态性均在中等以上。利用筛选出的14对SSR引物在毛蚶山东潍坊野生群体中进行遗传多样性分析,结果显示,平均有效等位基因数(Na)、平均观测杂合度(Ho)、平均期望杂合度(He)和多态性信息含量(PIC) 分别为15.4、0.682、0.852和0.817,从PIC值来看,本研究开发的14个微卫星标记均属高多态性标记(PIC≥0.5)。此外,有7个位点显著偏离哈迪温伯格平衡(Hardy-Weinberg equilibrium, HWE) (P<0.05)。以上结果表明,基于毛蚶转录组数据开发微卫星标记是切实可行的,研究结果丰富了毛蚶的分子标记数量,对毛蚶的种群遗传学分析、遗传图谱构建及分子辅助育种等研究都具有重要意义。
英文摘要:
      Scapharca kagoshimensis is a marine shellfish that has high economic values. In recent decades, the natural resource of S. kagoshimensis has declined due to the environment destruction and overfishing. To further understand the level of genetic diversity and population genetic structure of S. kagoshimensis, microsatellite loci were detected based on the transcriptome data of S. kagoshimensis by MISA software. The results show that a total of 3987 SSRs were identified from 35555 unigenes and the frequency of occurrence was 11.21%. Among them, the main types of repeats were dinucleotides and trinucleotides, which accounted for 58.06% and 19.04% respectively. A total of 182 types of repeat motifs were classified in all SSRs, and AC/GT was the most abundant among dinucleotide repeats (45.70%). The repeat numbers of SSRs were mainly from 5 to 7,and the number of SSRs gradually decreased along with the repeat numbers increased.Besides,the motif length mostly distributed in 12 to 29 bp,and the polymorphism of SSRs was all above medium level.Among the designed 60 primer pairs, 14 pairs proved to be polymorphic microsatellite markers and were amplified in 30 wild individuals sampled from Weifang in Shandong Province. The results showed that the average number of alleles (Na), the average observed heterozygosity (Ho), the average expected heterozygosity (He), and the polymorphism information content (PIC) were 15.4、0.682、0.852 and 0.817 respectively. All of the 14 loci were highly polymorphic (PIC≥0.5). After a Bonferroni correction, 7 of the 14 loci deviated significantly from HWE (P<0.05). These results indicate that it is feasible to develop microsatellite markers based on the S. kagoshimensis transcriptome and polymorphic microsatellite loci obtained in this study will facilitate further studies on the population genetic management, genetic mapping and molecular assisted breeding of S. kagoshimensis.
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