引用本文:	杨铭,于洋,张晓军,王全超,刘敬文,李富花,相建海.基于转录组数据的凡纳滨对虾微卫星标记开发[J].海洋科学,2017,41(2):96-102.

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基于转录组数据的凡纳滨对虾微卫星标记开发
杨铭^1,2, 于洋¹, 张晓军¹, 王全超^3,4, 刘敬文^3,4, 李富花¹, 相建海¹
1.中国科学院海洋研究所;2.福州市海洋与渔业技术中心;3.中国科学院海洋研究所, 实验海洋生物学重点实验室;4.中国科学院大学

摘要:

对虾遗传多样性和育种研究需要大量的分子标记。作者利用凡纳滨对虾(Litopenaeus vannamei)转录组测序数据, 采用MISA软件进行微卫星序列挖掘, 共获得14 767条微卫星序列。统计发现在凡纳滨对虾中微卫星出现的频率为16.76%; 在所有的微卫星序列中, 2碱基微卫星最多, 占59.53%; 其次是3碱基微卫星, 占35.78%。随机选取其中74条序列设计引物, 通过DNA混池扩增和分型的方法进行微卫星标记的开发, PCR扩增的显示有54对(72.97%)能扩增出清晰的目的条带, 进一步分型的结果显示27条(36.49%)微卫星显示出多态性, 从这些多态性的微卫星位点中选择11个位点在“科海1号”种质库材料中进行个体分型, 结果显示在该群体中微卫星标记的等位基因数目为2～11个不等, 期望杂合度值为0.256～0.858, 观察杂合度为0.213～0.875, 多态性信息含量为0.221～0.830, 在11个位点中有4个位点显著偏离HWE (P<0.05)。本研究结果为后续使用微卫星标记进行对虾遗传学研究, 促进对虾的遗传选育和种质资源保护提供了重要基础。

关键词: 凡纳滨对虾(Litopenaeus vannamei) 微卫星转录组遗传多样性

DOI：10.11759/hykx20160322002

分类号:

基金项目:国家自然科学基金资助项目(31502161, 31672632); 国家“863”高技术研究发展计划资助项目(2012AA10A404)

Development of microsatellite markers from the transcriptome sequences of Pacific white shrimp (Litopenaeus vannamei)

YANG Ming,YU Yang,ZHANG Xiao-jun,WANG Quan-chao,LIU Jing-wen,LI Fu-hua,XIANG Jian-hai

Abstract:

The Pacific white shrimp, Litopenaeus vannamei, is one of the most economically important marine aquaculture species in China, as well as the world. A large number of molecular markers are required for the studies of genetic diversity and breeding in shrimp. In the present investigation, 14 767 SSRs were detected in L. vannamei unigenes derived from transcriptome sequencing. Among these, dinucleotide SSRs were the most abundant motif (59.53%), followed by trinucleotide (35.78%) SSRs. A total of 74 primer pairs were designed and validated using DNA pools. 54 pairs (72.97%) were amplified with clear band, and 27 pairs (36.49%) were found to be polymorphic. The genetic diversity was analyzed using 11 highly polymorphic SSR markers in the breeding population of “Kehai No.1, ” a selected new variety of L. vannamei. Consequently, the allele number of these microsatellites ranged from 2 to 11. Expected heterozygosity and observed heterozygosity ranged from 0.256 to 0.858 and 0.213 to 0.875, respectively. The polymorphic information varied from 0.221 to 0.830. Four loci deviated significantly from Hardy-Weinberg equilibrium (HWE) (P<0.05). The large number of genetic markers developed in the present study would be highly beneficial to the researches to understand genetic diversity, selective breeding, and germplasm conservation in shrimp.

Key words: Litopenaeus vannamei microsatellite transcriptome polymorphism