基于454测序技术的青藏高原黄绿蜜环菌微卫星引物的开发

Isolation and characterization of 27 polymorphic microsatellite markers in Armillaria luteo-virens (Physalacriaceae)

摘要:

摘要:【目的】本研究利用454 焦磷酸测序技术，对青藏高原黄绿蜜环菌(Armillaria luteo-virens)转录组进行测序，从获得的Expressed sequence tags(EST)序列中开发EST-SSR引物。【方法】利用高通量测序获得的EST序列设计微卫星引物，通过PCR扩增、琼脂糖凝胶电泳和毛细管电泳检测筛选出合格的微卫星引物。【结果】共得到了1997121条reads，总数据量超过80Mb，序列平均长度为449bp。对于所获得的reads 进行拼接后得到了22236条非冗余的EST序列，其中含有2024条contigs(平均读长974bp) 和20212条singletons(平均读长404bp)。在所有序列中共找到321条符合条件的含有SSR的序列，从中随机选择98对，成功开发出27对具有多态性条带的微卫星引物。利用采集自3个不同居群的66个个体对上述27对引物进行验证，有17对引物符合Hardy-Weinberg平衡且没有连锁不平衡现象。【结论】首次成功利用高通量测序技术开发的EST-SSR 引物将会对今后黄绿蜜环菌遗传多样性的研究以及种质资源鉴定、遗传图谱构建等打下了坚实基础。

Abstract:

Abstract:［Objective］The objectives of this study were to use Roche 454 GS FLX system to develop SSR markers for Armillaria luteo-virens． These datasets will be valuable for detecting genetic diversity and population structure of this species．［Methods］We collected Armillaria luteo-virens samples from Yushu in Qinghai province，China．Total RNA was isolated by using the TRIzol reagent，after that we constructed cDNA library and performed one quarter plate of the whole run 454 pyrosequencing．We selected 98 primer pairs randomly from the 321 SSRs to evaluate their application and the polymorphism across 66 individuals (Armillaria luteo-virens) representing 3 wild populations．［Results］Roche 454 sequencing yielded 197，121 reads with a total nucleotide size of 88，585，965bp．27 of 98 SSRs loci were polymorphic．Numbers of alleles (Na) ranged from 2 to 8．Expected heterozygosity (HE) ranged from less than 0. 001 to 0.810 at locus ALV65，while observed heterozygosity (HO) from 0 at loci AIV64 and AIV92 to 0.900 at loci ALV8．We found no evidence of linkage disequiliburium，however 10 of 27 SSR markers showed significant deviation from Hardy-weinberg equilibrium．［Conclusion］These remaining 17 pairs of Armillaria luteo-virens SSＲ markers will be valuable for future research on detecting population structure and conservation of this species．