长江刀鲚选育群体转录组EST-SSR的分布特征分析

Characteristic Analysis of Microsatellites in Selected Coilia ectenes Using a Transcriptome Dataset

关键词:  刀鲚  转录组  微卫星  分子标记

Key words:  Coilia ectenes  Transcriptome  Microsatellites  Molecular markers

摘要:

本研究利用MISA软件挖掘长江刀鲚(Coilia ectenes)肌肉和肝脏转录组中的微卫星标记，为刀鲚选育群体的种质资源评估和分子标记辅助育种奠定基础。结果显示，从71869条Unigenes中共获得33896条重复单元长度为1~6碱基的微卫星序列；刀鲚转录组中不同类型微卫星的重复基序具有不同的分布特征，其中，单核苷酸重复、二核苷酸重复和三核苷酸重复为主要的微卫星重复类型，分别占总微卫星数目的34.94%、49.47%和13.34%；不同微卫星重复类型的优势重复基序亦有所不同，其中，A/T为单核苷酸重复基序的优势重复基序占86.25%，AC/GT为二核苷酸重复基序的为优势重复基序占75.25%，AGG/CCT为三核苷酸重复基序的优势重复基序占28.57%；不同微卫星重复基序核苷酸的数量和重复次数亦有所不同，重复次数伴随着重复单元中核苷酸数量的增加而呈现降低的趋势；从100对四核苷酸重复的SSR引物中筛选获得了16对多态性微卫星标记，并以此为基础，对长江刀鲚选育群体(F3)的遗传学特征进行了初步评估，结果显示，长江刀鲚选育群体F3的平均有效等位基因数(Ne)、平均观测杂合度(Ho)、平均期望杂合度(He)和Shannon多样性指数I分别为1.7580、0.3414、0.3977和0.6278。以上结果表明，基于刀鲚转录组数据批量开发微卫星是切实可行的，所开发的多态性微卫星标记能够应用于长江刀鲚选育群体的遗传背景评估和进一步的遗传育种研究。

Abstract:

The objective of this study was to identify microsatellites from the transcriptome sequences of Coilia ectenes using MISA software. These microsatellites could create very useful resources in the evaluation of germplasm resource and marker-assisted breeding of C. ectenes. The results showed that a total of 33,896 microsatellites were identified with repeating units, at lengths of 1~6 bases, from 71,869 unigenes. Different types of repeat SSRs had considerably different distribution characteristics. The majority of the microsatellite loci consisted of mono-, di-, and tri-nucleotide motifs (34.94%, 49.47%, and 13.34%, respectively). Dinucleotide microsatellite repeating units were the most abundant in the C. ectenes transcriptome, and the AC/GT repeating units were the most ascendant repeating unit (75.25%). The dominant repeating units for the mononucleotide and trinucleotide motifs were A/T (86.25%) and AGG/CCT (28.57%), respectively. Different nucleotide repeat motifs had different repetitions that had a reducing trend, with the increase in the number of nucleotides in repeat motifs. Among the 100 designed primer pairs, 16 pairs proved to be polymorphic microsatellite markers. In the present study, 16 polymorphic microsatellite loci were characterized to evaluate the genetic diversity of the selected C. ectenes (F3). The results showed that the average number of effective alleles (Ne), the average observed heterozygosity (Ho), the average expected heterozygosity (He), and the average Shannon´s information index (I) of the selected C.ectenes (F3) were 1.7580, 0.3414, 0.3977, and 0.6278, respectively. These results indicate that it is feasible to develop microsatellite markers based on the C. ectenes transcriptome and polymorphic microsatellite loci obtained in this study will facilitate further studies on the population genetic management and conservation of C. ectenes.