IDEAS home Printed from https://ideas.repec.org/a/plo/pone00/0202582.html
   My bibliography  Save this article

Population genetic analysis of aquaculture salmonid populations in China using a 57K rainbow trout SNP array

Author

Listed:
  • Han-Yuan Zhang
  • Zi-Xia Zhao
  • Jian Xu
  • Peng Xu
  • Qing-Li Bai
  • Shi-Yong Yang
  • Li-Kun Jiang
  • Bao-Hua Chen

Abstract

Various salmonid species are cultivated in cold water aquaculture. However, due to limited genomic data resources, specific high-throughput genotyping tools are not available to many of the salmonid species. In this study, a 57K single nucleotide polymorphism (SNP) array for rainbow trout (Oncorhynchus mykiss) was utilized to detect polymorphisms in seven salmonid species, including Hucho taimen, Oncorhynchus masou, Salvelinus fontinalis, Brachymystax lenok, Salvelinus leucomaenis, O. kisutch, and O. mykiss. The number of polymorphic markers per population ranged from 3,844 (O. kisutch) to 53,734 (O. mykiss), indicating that the rainbow trout SNP array was applicable as a universal genotyping tool for other salmonid species. Among the six other salmonid populations from four genera, 28,882 SNPs were shared, whereas 525 SNPs were polymorphic in all four genera. The genetic diversity and population relationships of the seven salmonid species were studied by principal component analysis (PCA). The phylogenetic relationships among populations were analyzed using the maximum likelihood method, which indicated that the shared SNP markers provide reliable genomic information for population genetic analyses in common aquaculture salmonid fishes. Furthermore, this obtained genomic information may be applicable for population genetic evaluation, marker-assisted breeding, and propagative parent selection in fry production.

Suggested Citation

  • Han-Yuan Zhang & Zi-Xia Zhao & Jian Xu & Peng Xu & Qing-Li Bai & Shi-Yong Yang & Li-Kun Jiang & Bao-Hua Chen, 2018. "Population genetic analysis of aquaculture salmonid populations in China using a 57K rainbow trout SNP array," PLOS ONE, Public Library of Science, vol. 13(8), pages 1-12, August.
    • Handle: RePEc:plo:pone00:0202582
    DOI: 10.1371/journal.pone.0202582
    as

    Download full text from publisher

    File URL: https://journals.plos.org/plosone/article?id=10.1371/journal.pone.0202582
    Download Restriction: no
    File URL: https://journals.plos.org/plosone/article/file?id=10.1371/journal.pone.0202582&type=printable
    Download Restriction: no
    File URL: https://libkey.io/10.1371/journal.pone.0202582?utm_source=ideas
    LibKey link: if access is restricted and if your library uses this service, LibKey will redirect you to where you can use your library subscription to access this item
    ---><---

    References listed on IDEAS

    as
    1. Weeks, Jonathan P., 2010. "plink: An R Package for Linking Mixed-Format Tests Using IRT-Based Methods," Journal of Statistical Software, Foundation for Open Access Statistics, vol. 35(i12).
    Full references (including those not matched with items on IDEAS)

    Most related items

    These are the items that most often cite the same works as this one and are cited by the same works as this one.
    1. Yang Liu & Jan Hannig & Abhishek Pal Majumder, 2019. "Second-Order Probability Matching Priors for the Person Parameter in Unidimensional IRT Models," Psychometrika, Springer;The Psychometric Society, vol. 84(3), pages 701-718, September.
    2. Alexander Robitzsch, 2020. "L p Loss Functions in Invariance Alignment and Haberman Linking with Few or Many Groups," Stats, MDPI, vol. 3(3), pages 1-38, August.
    3. Daniel M. Bolt & Xiangyi Liao, 2022. "Item Complexity: A Neglected Psychometric Feature of Test Items?," Psychometrika, Springer;The Psychometric Society, vol. 87(4), pages 1195-1213, December.
    4. Rikkert M. van der Lans & Ridwan Maulana & Michelle Helms-Lorenz & Carmen-María Fernández-García & Seyeoung Chun & Thelma de Jager & Yulia Irnidayanti & Mercedes Inda-Caro & Okhwa Lee & Thys Coetze, 2021. "Student Perceptions of Teaching Quality in Five Countries: A Partial Credit Model Approach to Assess Measurement Invariance," SAGE Open, , vol. 11(3), pages 21582440211, August.
    5. Chalmers, R. Philip, 2012. "mirt: A Multidimensional Item Response Theory Package for the R Environment," Journal of Statistical Software, Foundation for Open Access Statistics, vol. 48(i06).
    6. González, Jorge, 2014. "SNSequate: Standard and Nonstandard Statistical Models and Methods for Test Equating," Journal of Statistical Software, Foundation for Open Access Statistics, vol. 59(i07).
    7. Brzezińska Justyna, 2018. "Item Response Theory Models in the Measurement Theory with the Use of ltm Package in R," Econometrics. Advances in Applied Data Analysis, Sciendo, vol. 22(1), pages 11-25, March.

    More about this item

    Statistics

    Access and download statistics

    Corrections

    All material on this site has been provided by the respective publishers and authors. You can help correct errors and omissions. When requesting a correction, please mention this item's handle: RePEc:plo:pone00:0202582. See general information about how to correct material in RePEc.

    If you have authored this item and are not yet registered with RePEc, we encourage you to do it here. This allows to link your profile to this item. It also allows you to accept potential citations to this item that we are uncertain about.

    If CitEc recognized a bibliographic reference but did not link an item in RePEc to it, you can help with this form .

    If you know of missing items citing this one, you can help us creating those links by adding the relevant references in the same way as above, for each refering item. If you are a registered author of this item, you may also want to check the "citations" tab in your RePEc Author Service profile, as there may be some citations waiting for confirmation.

    For technical questions regarding this item, or to correct its authors, title, abstract, bibliographic or download information, contact: plosone (email available below). General contact details of provider: https://journals.plos.org/plosone/ .

    Please note that corrections may take a couple of weeks to filter through the various RePEc services.

    IDEAS is a RePEc service. RePEc uses bibliographic data supplied by the respective publishers.