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

Journal of Applied Genetics volume 62, pages 373–387 (2021)Cite this article

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.

References

  • Abuzayed MA, Goktay M, Allmer J, Doganlar S, Frary A (2017 Feb 1) Development of genomic simple sequence repeat markers in faba bean by next-generation sequencing. Plant Mol Biol Report 35(1):61–71

    Article  CAS  Google Scholar 

  • Alghamdi SS, Khan MA, Ammar MH, Sun Q, Huang L, Migdadi HM, El-Harty EH, Al-Faifi SA (2018 Dec) Characterization of drought stress-responsive root transcriptome of faba bean (Vicia faba L.) using RNA sequencing. 3. Biotech. 8(12):1–9

  • Alsamman AM (2019) The art of bioinformatics learning in our Arabic World. Highlights in BioScience. https://doi.org/10.36462/H.BioSci.20193

  • Altschul SF et al (1990) Basic local alignment search tool. J Mol Biol 215(3):403–410

    Article  CAS  PubMed  Google Scholar 

  • Amer A, EL Azab K, Ismail A, El-Shazly M (2018 Dec 1) Saline soil management to improve its fertility and productivity by some agricultural practices application. Journal of Soil Sciences and Agricultural Engineering 9(12):743–751

    Article  Google Scholar 

  • Arun-Chinnappa KS, McCurdy DW (2015) De novo assembly of a genome-wide transcriptome map of Vicia faba (L.) for transfer cell research. Front Plant Sci 6:217

  • Asadi A, Ebrahimi A, Rashidi-Monfared S, Basiri M, Akbari-Afjani J (2020 Feb 1) Comprehensive functional analysis and mapping of SSR markers in the chickpea genome (Cicer arietinum L.). Computational biology and chemistry 84:107169

    Article  CAS  PubMed  Google Scholar 

  • Awan Z, Ali A, Iqbal A (2019 May 5) Plant molecular biology databases. Highlights in BioScience. 2:1–7

    Article  Google Scholar 

  • Biswas MK, Bagchi M, Nath UK, Biswas D, Natarajan S, Jesse DM, Park JI, Nou IS (2020 Oct 29) Transcriptome wide SSR discovery cross-taxa transferability and development of marker database for studying genetic diversity population structure of Lilium species. Sci Rep 10(1):1–3

    Article  Google Scholar 

  • Botstein D, White RL, Skolnick M, Davis RW (1980) Construction of a genetic linkage map in man using restriction fragment length polymorphisms. Am J Hum Genet 32(3):314

    CAS  PubMed  PubMed Central  Google Scholar 

  • Chen J, Li R, Xia Y, Bai G, Guo P, Wang Z, Zhang H, Siddique KH (2017 Sep 13) Development of EST-SSR markers in flowering Chinese cabbage (Brassica campestris L. ssp. chinensis var. utilis Tsen et Lee) based on de novo transcriptomic assemblies. PloS one 12(9):e0184736

    Article  PubMed  PubMed Central  Google Scholar 

  • Dubey H, Rawal HC, Rohilla M, Lama U, Kumar PM, Bandyopadhyay T, Gogoi M, Singh NK, Mondal TK (2020 Jan) TeaMiD: a comprehensive database of simple sequence repeat markers of tea. Database. 1:2020

    Google Scholar 

  • Duc G, Bao S, Baum M, Redden B,Sadiki M, Suso MJ, Vishniakova M, Zong X (2010) Diversity maintenance and use of Vicia faba L. genetic resources. Field Crops Res 115(3):270–278

  • Duhan N, Meshram M, Loaiza CD, Kaundal R (2020) citSATdb: genome-wide simple sequence repeat (SSR) marker database of Citrus species for germplasm characterization and crop improvement. Genes 11(12):1486

  • El-Esawi MA (2017 Nov 1) SSR analysis of genetic diversity and structure of the germplasm of faba bean (Vicia faba L.). Comptes Rendus Biologies 340(11–12):474–480

  • El-Rodeny W, Kimura M, Hirakawa H, Sabah A, Shirasawa K, Sato S, Tabata S, Sasamoto S, Watanabe A, Kawashima K, Kato M (2014) Development of EST-SSR markers and construction of a linkage map in faba bean (Vicia faba). Breed Sci 64(3):252–263

  • FAO Faostat (2021) “Crops”, Food and Agriculture Organization of the United Nations. Available online at http://www.fao.org/faostat

  • Faraji S, Rasouli SH, Kazemitabar SK (2018 Dec) Genome-wide exploration of C2H2 zinc finger family in durum wheat (Triticum turgidum ssp. Durum): insights into the roles in biological processes especially stress response. Biometals. 31(6):1019–1042

    Article  CAS  PubMed  Google Scholar 

  • Gnanasambandam A et al (2012) Impact of molecular technologies on faba bean (Vicia Faba L.) breeding strategies. Agronomy 2(3):132–166

  • Hass B. TransDecoder (find coding regions within transcripts). http://transdecoder.github.io/. 2015

  • Jensen ES, Peoples MB, Hauggaard-Nielsen H (2010) Faba bean in cropping systems. Field Crops Res 115(3):203–216

  • Kaur S, Pembleton LW, Cogan NO, Savin KW, Leonforte T, Paull J, Materne M, Forster JW (2012 Dec) Transcriptome sequencing of field pea and faba bean for discovery and validation of SSR genetic markers. BMC Genomics 13(1):1–2

    Article  Google Scholar 

  • Kaur S, Cogan NOI, Forster JW, Paull JG (2014) Assessment of genetic diversity in faba bean based on single nucleotide polymorphism. Diversity 6(1):88–101

    Article  Google Scholar 

  • Li GQ, Song LX, Jin CQ, Li M, Gong SP, Wang YF (2019 Jun) Genome survey and SSR analysis of Apocynum venetum. Biosci Rep 28:39(6)

    Google Scholar 

  • Li W (2015) Fast program for clustering and comparing large sets of protein or nucleotide sequences. In: Encyclopedia of metagenomics. Springer, pp 173–177

  • Liu H, Wang YX, Li H, Teng RM, Wang Y, Zhuang J (2019 Aug 1) Genome-wide identification and expression analysis of calcineurin B-like protein and calcineurin B-like protein-interacting protein kinase family genes in tea plant. DNA Cell Biol 38(8):824–839

    Article  CAS  PubMed  Google Scholar 

  • Liu K, Muse SV (2005) PowerMarker: an integrated analysis environment for genetic marker analysis. Bioinformatics 21(9):2128–2129

    Article  CAS  PubMed  Google Scholar 

  • Mahmoud AF, Abd El-Fatah BE (2020 Feb) Genetic diversity studies and identification of molecular and biochemical markers associated with fusarium wilt resistance in cultivated faba bean (Vicia faba). The plant pathology journal 36(1):11

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Marondedze C (2020 Sep 30) The increasing diversity and complexity of the RNA-binding protein repertoire in plants. Proc R Soc B 287(1935):20201397

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Mason AS (2015) SSR genotyping. In: Plant genotyping. Humana Press, New York, NY, pp 77–89

    Chapter  Google Scholar 

  • Mindrebo JT, Nartey CM, Seto Y, Burkart MD, Noel JP (2016 Dec 1) Unveiling the functional diversity of the alpha/beta hydrolase superfamily in the plant kingdom. Curr Opin Struct Biol 41:233–246

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Mokhtar MM, Adawy SS, El-Assal SE, Hussein EH (2016 Jul 19) Genic and intergenic SSR database generation, SNPs determination and pathway annotations, in date palm (Phoenix dactylifera L.). PLOS one 11(7):e0159268

    Article  PubMed  PubMed Central  Google Scholar 

  • Mohamed RK, El-Eraky MB, Kandeal MS, El-Sawy MA (2019 Sep 1) An economic study for the important factor on the gap of faba beans in Egypt. Arab Universities Journal of Agricultural Sciences 27(3):1761–1770

    Article  Google Scholar 

  • Morad MM, Atia MAM (2018) SSRome: an integrated database and pipelines for exploring microsatellites in all organisms. Nucleic Acids Res 47(D1):D244–D252

  • Nahas LD, Alsamman AM, Hamwieh A, Al-Husein N, Lababidi G (2020 May 11) Characterization of EST-SSR markers in bread wheat EST related to drought tolerance and functional analysis of SSR-containing unigenes. Highlights in BioScience 3:1–2

    Article  Google Scholar 

  • Noman M, Aysha J, Ketehouli T, Yang J, Du L, Wang F, Li H (2021 Jan 1) Calmodulin binding transcription activators: an interplay between calcium signalling and plant stress tolerance. J Plant Physiol 256:153327

    Article  CAS  PubMed  Google Scholar 

  • Oliveira HR et al (2016) Genetic diversity and population structure in Vicia baba L. landraces and wild related species assessed by nuclear SSRs. PloS one 11(5):e0154801

    Article  PubMed  PubMed Central  Google Scholar 

  • Pan G, Chen A, Li J, Huang S, Tang H, Chang L, Zhao L, Li D (2020 Apr) Genome-wide development of simple sequence repeats database for flax (Linum usitatissimum L.) and its use for genetic diversity assessment. Genet Resour Crop Evol 67(4):865–874

    Article  CAS  Google Scholar 

  • Portis E, Lanteri S, Barchi L, Portis F, Valente L, Toppino L, Rotino GL, Acquadro A (2018 Mar 28) Comprehensive characterization of simple sequence repeats in eggplant (Solanum melongena L.) genome and construction of a web resource. Frontiers in plant science 9:401

    Article  PubMed  PubMed Central  Google Scholar 

  • Redden B (2018) Efficient and sustainable production of faba bean. Burleigh Dodds Science Publishing, Cambridge

  • Rozen, Steve, and Helen Skaletsky. 2000. “Primer3 on the WWW for general users and for biologist programmers.” In Bioinformatics Methods and Protocols, Springer, 365–386

  • Tan C, Chapman B, Wang P, Zhang Q, Zhou G, Zhang XQ, Barrero RA, Bellgard MI, Li C (2020 Jan) BarleyVarDB: a database of barley genomic variation. Database. 1:2020

    Google Scholar 

  • Tufan H, Erdoğan C (2017) Genetic diversity in some faba bean (Vicia faba L.) genotypes assessed by simple sequence repeats. Biotechnology & Biotechnological Equipment 31(1):29–35

    Article  Google Scholar 

  • Tulsani NJ, Hamid R, Jacob F, Umretiya NG, Nandha AK, Tomar RS, Golakiya BA (2020) Transcriptome landscaping for gene mining and SSR marker development in Coriander (Coriandrum sativum L.). Genomics 112(2):1545–1553

  • Wang L, Gong X, Jin L, Li H, Lu J, Duan J, Ma L (2019 Aug) Development and validation of EST-SSR markers of Magnolia wufengensis using de novo transcriptome sequencing. Trees. 33(4):1213–1223

    Article  CAS  Google Scholar 

  • Wang S, Wang B, Liu J, Ren J, Huang X, Zhou G, Wang A (2017 Nov 27) Novel polymorphic EST-based microsatellite markers characterized in lettuce (Lactuca sativa). Biologia. 72(11):1300–1305

    Article  CAS  Google Scholar 

  • Wang X, Yang S, Chen Y, Zhang S, Zhao Q, Li M, Gao Y, Yang L, Bennetzen JL (2018) Comparative genome-wide characterization leading to simple sequence repeat marker development for Nicotiana. BMC Genomics. https://doi.org/10.1186/s12864-018-4878-4

  • Wu Q, Zang F, Xie X, Ma Y, Zheng Y, Zang D (2020 Oct 1) Full-length transcriptome sequencing analysis and development of EST-SSR markers for the endangered species Populus wulianensis. Sci Rep 10(1):1–1

    Article  Google Scholar 

  • Yang T et al (2012) High-throughput novel microsatellite marker of faba bean via next generation sequencing. BMC Genomics 13(1):602

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Zheng Y, Zhang Z, Wan Y, Tian J, Xie W (2020 Oct) Development of EST-SSR markers linked to flowering candidate genes in Elymus sibiricus L. Based on RNA Sequencing Plants 9(10):1371

    CAS  Google Scholar 

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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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