A high-throughput pipeline for detecting locus-specific polymorphism in hexaploid wheat (Triticum aestivum L.)

文献类型： 外文期刊

第一作者： Ma, Jian

作者： Ma, Jian;Liu, Ya-Xi;Wei, Yuming;Zheng, You-Liang;Ma, Jian;Stiller, Jiri;Zheng, Zhi;Liu, Chunji;Zheng, Zhi;Liu, Chunji;Zheng, Zhi

作者机构：

关键词： Allopolyploid;Multiple sequence alignment;blastn;Primer design;Genome-specificity;Sequence polymorphism

期刊名称：PLANT METHODS （ 影响因子：4.993； 五年影响因子：5.312 ）

ISSN： 1746-4811

年卷期： 2015 年 11 卷

页码：

收录情况： SCI

摘要： Background: Bread wheat (Triticum aestivum L., 2n = 6x = 42) is an allohexaploid with a huge genome. Due to the presence of extensive homoeologs and paralogs, generating locus-specific sequences can be challenging, especially when a large number of sequences are required. Traditional methods of generating locus-specific sequences are rather strenuous and time-consuming if large numbers of sequences are to be handled. Results: To improve the efficiency of isolating sequences for targeted loci, a time-saving and high-throughput pipeline integrating orthologous sequence alignment, genomic sequence retrieving, and multiple sequence alignment was developed. This pipeline was successfully employed in retrieving and aligning homoeologous sequences and 83% of the primers designed based on the pipeline successfully amplified fragments from the targeted subgenomes. Conclusions: The high-throughput pipeline developed in this study makes it feasible to efficiently identify locus-specific sequences for large numbers of sequences. It could find applications in all research projects where locus-specific sequences are required. In addition to generating locus-specific markers, the pipeline was also used in our laboratory to identify differentially expressed genes among the three subgenomes of bread wheat. Importantly, the pipeline is not only valuable for research in wheat but should also be applicable to other allopolyploid species.

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