Transcriptome Sequencing of Different Avocado Ecotypes: de novo Transcriptome Assembly, Annotation, Identification and Validation of EST-SSR Markers
文献类型： 外文期刊
作者： Ge, Yu 1 ; Tan, Lin 1 ; Wu, Bin 1 ; Wang, Tao 2 ; Zhang, Teng 3 ; Chen, Haihong 4 ; Zou, Minghong 5 ; Ma, Funing 1 ; Xu, Zin 1 ;
作者机构： 1.Chinese Acad Trop Agr Sci, Haikou Expt Stn, Haikou 570102, Hainan, Peoples R China
2.Liaoning Acad Agr Sci, Inst Vegetables, Shenyang 110161, Liaoning, Peoples R China
3.Tianjin Derit Seed Ind Co Ltd, Tianjin 300384, Peoples R China
4.Guangxi Vocat & Tech Coll, Coll Agr, Nanning 530226, Peoples R China
5.Chinese Acad Trop Agr Sci, South Subtrop Crops Res Inst, Zhanjiang 524091, Peoples R China
关键词： Persea americana; ecological races; next-generation sequencing; microsatellites; genetic diversity
期刊名称：FORESTS （ 影响因子：2.633； 五年影响因子：2.804 ）
ISSN： 1999-4907
年卷期： 2019 年 10 卷 5 期
页码：
收录情况： SCI
摘要： Avocado (Persea americana Mill.) could be considered as an important tropical and subtropical woody oil crop with high economic and nutritional value. Despite the importance of this species, genomic information is currently unavailable for avocado and closely related congeners. In this study, we generated more than 216 million clean reads from different avocado ecotypes using Illumina HiSeq high-throughput sequencing technology. The high-quality reads were assembled into 154,310 unigenes with an average length of 922 bp. A total of 55,558 simple sequence repeat (SSR) loci detected among the 43,270 SSR-containing unigene sequences were used to develop 74,580 expressed sequence tag (EST)-SSR markers. From these markers, a subset of 100 EST-SSR markers was randomly chosen to identify polymorphic EST-SSR markers in 28 avocado accessions. Sixteen EST-SSR markers with moderate to high polymorphism levels were detected, with polymorphism information contents ranging from 0.33 to 0.84 and averaging 0.63. These 16 polymorphic EST-SSRs could clearly and effectively distinguish the 28 avocado accessions. In summary, our study is the first presentation of transcriptome data of different avocado ecotypes and comprehensive study on the development and analysis of a set of EST-SSR markers in avocado. The application of next-generation sequencing techniques for SSR development is a potentially powerful tool for genetic studies.
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