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Developing a new genic SSR primer database in faba bean (Vicia faba L.)

  • Plant Genetics • Original Paper
  • Published:
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Abstract

The goal of this research was to develop a new genetic database of simple sequence repetition (SSR) primers for faba and classify them according to their target genes and respective biological processes. Approximately 75,605 and 148,196 previously published genomic and transcriptomic faba sequences, respectively, have been used to detect possible SSRs. The numbers of identified SSRs from each dataset were 25,502 and 12,319, respectively. The distribution of different repeat classes indicated that trinucleotides represent the largest number of repeat counts, followed by dinucleotides. The extracted genic SSR sequences were used to design 1091 polymerase chain reaction (PCR) primers, of which only 238 (21.8%) primers target genomic sequences and the other 853 PCR primers targeted transcriptomic sequences. The annotation of gene-targeted SSRs showed that approximately 897 genes were targeted by our SSR primers. Approximately 1890 gene ontology (GO) identification codes have been obtained. The GO keywords were distributed among distinct molecular cell features. The highest redundancies involved 554 technical words, 196 domains, and 160 molecular feature phrases. These GO codes belonged to the general level of GO and included molecular function, cellular component, and biological process (544, 670, and 676 GOs, respectively). Twenty-seven SSR PCR primers were synthesized to 12 Egyptian faba bean genotypes. Approximately 11 SSR provided one to two PCR bands, whereas other SSRs provided only one sharp band with polymorphic band size. There were 13 polymorphic primers. The polymorphism information content was 0.3, which implied moderate informativeness.

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Data availability

All relevant data are within the manuscript and its Supporting Information files. The data are also uploaded to Zenodo and publicly accessible via the following URL: https://doi.org/10.5281/zenodo.3629145.

Code availability

Not applicable.

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Author information

Authors and Affiliations

  1. Agricultural Genetic Engineering Research Institute, PO Box 12619, Giza, Egypt

    Kareem A. Khalifa, Shafik D. Ibrahim & Alsamman M. Alsamman

  2. Department of Genetics and Genetic Engineering, Faculty of Agricultural, Benha University, Benha, Egypt

    Hoda A. S. El-Garhy & Mahmoud M. M. Moustafa

  3. International Center for Agricultural Research in the Dry Areas (ICARDA), PO Box 2416, Cairo, Egypt

    Aladdin Hamwieh

  4. International Center for Agricultural Research in the Dry Areas (ICARDA) , Terbol, Lebanon

    Fouad Maalouf

  5. African Genome Center, Mohammed VI Polytechnic University, Ben Guerir, Morocco

    Achraf El Allali

Authors
  1. Kareem A. Khalifa
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  2. Shafik D. Ibrahim
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  3. Hoda A. S. El-Garhy
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  4. Mahmoud M. M. Moustafa
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  5. Fouad Maalouf
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  6. Alsamman M. Alsamman
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  7. Aladdin Hamwieh
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  8. Achraf El Allali
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Contributions

K.H. implementation and validation; F.M., A.M.A., I.S.D., and A.EA.: writing—original draft and validation; E.H., M.M., and A.EA.: design of methodology and supervision; F.M., H.A., and A.EA.: development and design of methodology, supervision, and resources.

Corresponding author

Correspondence to Achraf El Allali.

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Communicated by: Izabela Pawłowicz

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Khalifa, K.A., Ibrahim, S.D., El-Garhy, H.A.S. et al. Developing a new genic SSR primer database in faba bean (Vicia faba L.). J Appl Genetics 62, 373–387 (2021). https://doi.org/10.1007/s13353-021-00626-3

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  • DOI: https://doi.org/10.1007/s13353-021-00626-3

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