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

J. Ma, J. Stiller, Zhi Zheng, Y.X. Liu, Y. Wei, Y.L. Zheng, Chunji Liu

    Research output: Contribution to journalArticle

    3 Citations (Scopus)

    Abstract

    © 2015 Ma et al. 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.
    Original languageEnglish
    Pages (from-to)1-7
    JournalPlant Methods
    Volume11
    Issue number39
    DOIs
    Publication statusPublished - 2015

    Fingerprint

    hexaploidy
    Triticum
    Triticum aestivum
    genetic polymorphism
    loci
    wheat
    Sequence Alignment
    Bread
    sequence alignment
    Research
    allopolyploidy
    Genome
    research projects
    Genes
    genomics
    genome
    genes

    Cite this

    Ma, J. ; Stiller, J. ; Zheng, Zhi ; Liu, Y.X. ; Wei, Y. ; Zheng, Y.L. ; Liu, Chunji. / A high-throughput pipeline for detecting locus-specific polymorphism in hexaploid wheat (Triticum aestivum L.). In: Plant Methods. 2015 ; Vol. 11, No. 39. pp. 1-7.
    @article{fdd3b321194044a28e63491faf95c088,
    title = "A high-throughput pipeline for detecting locus-specific polymorphism in hexaploid wheat (Triticum aestivum L.)",
    abstract = "{\circledC} 2015 Ma et al. 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.",
    author = "J. Ma and J. Stiller and Zhi Zheng and Y.X. Liu and Y. Wei and Y.L. Zheng and Chunji Liu",
    year = "2015",
    doi = "10.1186/s13007-015-0082-6",
    language = "English",
    volume = "11",
    pages = "1--7",
    journal = "Plant Methods",
    issn = "1746-4811",
    publisher = "BioMed Central",
    number = "39",

    }

    A high-throughput pipeline for detecting locus-specific polymorphism in hexaploid wheat (Triticum aestivum L.). / Ma, J.; Stiller, J.; Zheng, Zhi; Liu, Y.X.; Wei, Y.; Zheng, Y.L.; Liu, Chunji.

    In: Plant Methods, Vol. 11, No. 39, 2015, p. 1-7.

    Research output: Contribution to journalArticle

    TY - JOUR

    T1 - A high-throughput pipeline for detecting locus-specific polymorphism in hexaploid wheat (Triticum aestivum L.)

    AU - Ma, J.

    AU - Stiller, J.

    AU - Zheng, Zhi

    AU - Liu, Y.X.

    AU - Wei, Y.

    AU - Zheng, Y.L.

    AU - Liu, Chunji

    PY - 2015

    Y1 - 2015

    N2 - © 2015 Ma et al. 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.

    AB - © 2015 Ma et al. 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.

    U2 - 10.1186/s13007-015-0082-6

    DO - 10.1186/s13007-015-0082-6

    M3 - Article

    VL - 11

    SP - 1

    EP - 7

    JO - Plant Methods

    JF - Plant Methods

    SN - 1746-4811

    IS - 39

    ER -