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Unveiling the demographic background and genetic diversity of Urochloa mosambicensis (Poaceae) through genome-wide identification of simple sequence repeats and molecular marker development

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Abstract

The first set of simple sequence repeat (SSR) markers for Urochloa mosambicensis (Hack.) Dandy is described in this study. SSRs were isolated from a genomic library with 3491 contigs obtained by high-throughput sequencing. Primers were designed for twenty loci, and all primer pairs were successfully amplified in 39 genotypes, yielding an average of 4.95 alleles per locus. The mean polymorphic information content (PIC) was 0.559, and the mean discriminating power (DP) was 0.520 for all loci considering also all U. mosambicensis genotypes. The non‐Bayesian clustering analysis has confirmed clustering consistency of the individuals and provides enough support for the existence of the pattern that also emerged from PCoA and UPGMA. These markers demonstrated potential transferability to U. advena, U. oligotricha, U. brachyura and U. xantholeuca. Our findings showed that the set of molecular markers described here have strong potential for fingerprinting and characterizing genetic diversity in intra-specific plant collections, whose breeding programs could be accelerated by the effective use of these molecular tools, not only in U. mosambicensis, but also within the genus Urochloa.

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Data availability

The datasets generated or analyzed during the current study are available in the GenBank repository (accession numbers MH742936–MH742955) but restrictions apply to the availability of these data, so they are not publicly available until article publication.

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Acknowledgements

The authors would like to thank the Genomics and Bioinformatics Center of Drug Research and Development Center of Federal University of Ceará for technical support.

Funding

The Brazilian Agricultural Research Corporation–Embrapa and The Foundation for Scientific and Technological Development of Ceará–FUNCAP funded this study through the project grant no. MP 22.16.04.018.00 (MegFor) and BP5-0197-00214.01.00/22, respectively. FMD would like to thank FUNCAP for a Research Productivity Scholarship.

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Authors and Affiliations

  1. Northeast Biotechnology Network - RENORBIO, Universidade Federal do Piauí, Teresina, Piauí, CEP: 64049-550, Brazil

    Ueslei S. Leão & Aline B. Negreiros

  2. EMBRAPA Caprinos e Ovinos, Sobral, Ceará, CEP: 62010-970, Brazil

    Luice G. Bueno, Geice R. Silva, Diego B. Galvani & Fábio M. Diniz

  3. Institute of Marine Sciences, LABOMAR, Universidade Federal do Ceará, Fortaleza, Ceará, CEP: 60165-081, Brazil

    Rodrigo Maggioni

  4. Departamento de Zootecnia e Ciências Biológicas, Universidade Federal do Piauí, Universitário Ministro Petrônio Portella, Campus, Teresina, Piauí, CEP: 64049-550, Brazil

    Fabio B. Britto & Jose L. R. Sarmento

Authors
  1. Ueslei S. Leão
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  2. Luice G. Bueno
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  3. Aline B. Negreiros
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  4. Geice R. Silva
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  5. Rodrigo Maggioni
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  8. Diego B. Galvani
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  9. Fábio M. Diniz
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Contributions

USL, LGB, DBG, ABN, and GRS were involved in sample collection, methodology, laboratory work, data curation, formal analysis, manuscript writing. FBB and JLRS contributed to data curation, manuscript reviewing and editing. LGB, DBG, RM and FMD carried out fieldwork, partial funding acquisition and manuscript reviewing. USL and FMD supported laboratory work, LGB and DBG contributed to conceptualization, fieldwork, methodology, resources, supervision, writing original draft and editing. All authors read and approved the final manuscript.

Corresponding author

Correspondence to Fábio M. Diniz.

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Leão, U.S., Bueno, L.G., Negreiros, A.B. et al. Unveiling the demographic background and genetic diversity of Urochloa mosambicensis (Poaceae) through genome-wide identification of simple sequence repeats and molecular marker development. Conservation Genet Resour 15, 135–143 (2023). https://doi.org/10.1007/s12686-023-01312-8

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