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Novel Microsatellite Markers Derived from Arachis pintoi Transcriptome Sequencing for Cross-Species Transferability and Varietal Identification

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Abstract

Forage peanut (Arachis pintoi) is an important leguminous forage that has gained popularity due to increased livestock productivity. Furthermore, the species helps with soil fertility and the restoration of degraded areas. However, A. pintoi has a limited number of molecular markers. The objective of this study was to create and characterize gene-derived microsatellite markers as well as to test their transferability to the peanut (Arachis hypogaea) and other six wild Arachis species. A total of 4461 putative simple sequence repeats (SSR) were identified, and PCR primer pairs were designed for 999 SSR regions after filtering out primers with the same annealing site and searching for sequences related to open reading frames (ORFs). The dinucleotide motif was the most common (628; 62.86%). For validation, 186 primer pairs were chosen at random, of which 63 (33.87%) were polymorphic, with an average of 7.37 alleles per locus. Polymorphic information content (PIC = 0.70) and discriminatory power (D = 0.80) were both high on average. The functional annotation discovered 120 sequences that were assigned to 87 gene ontology functional groups divided into three main categories: molecular function (27 sub-categories), cellular components (21 sub-categories), and biological process (39 sub-categories). Thirty-three SSRs were tested for transferability to peanut and six other wild Arachis species, resulting in variable cross-species amplification (63.64 to 100%). Here, we present the first gene-derived SSR for A. pintoi. These new informative microsatellites may be linked to agronomically important genes to be used in genetic studies.

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Data Availability

The datasets generated during and/or analyzed during the current study are available from the corresponding author upon reasonable request.

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Acknowledgements

The authors are grateful to the staff of the Life Sciences Core Facility (LaCTAD) from the State University of Campinas (UNICAMP) for the Genomics analysis. Also, the authors thanked researcher José Francisco Montenegro Valls from Embrapa Genetic Resources and Biotechnology (CENARGEN) for the plant material provided for this study.

Funding

This work received financial support from Federal Government of Brazil through the “Conselho Nacional de Desenvolvimento Científico e Tecnológico” (CNPq), Government of the State of Acre through the “Fundação de Amparo à Pesquisa do Estado do Acre” (FAPAC—TO 024/2018), and “Empresa Brasileira de Pesquisa Agropecuária” (Embrapa).

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Authors and Affiliations

  1. Federal University of Acre, Rio Branco, Brazil

    Jônatas Chagas de Oliveira, André Lucas Domingos da Silva & Leila Priscila Peters

  2. Embrapa Acre, Rio Branco, Brazil

    Luciélio Manoel da Silva, Giselle Mariano Lessa de Assis & Tatiana de Campos

  3. Embrapa Agroenergia, Brasília, Brazil

    Eduardo Fernandes Formighieri

  4. Center of Molecular Biology and Genetic Engineering, University of Campinas, Campinas, Brazil

    Carla Cristina da Silva & Anete Pereira de Souza

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  1. Jônatas Chagas de Oliveira
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  2. André Lucas Domingos da Silva
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  9. Tatiana de Campos
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Contributions

TC, APS, EFF, and GMLA designed the study and revised the manuscript. JCO, ALDS, LMS, CCS, and EFF performed material preparation, data collection, and analysis. LPP revised the functional annotation and gene ontology. All of the authors have read and approved the final version of the manuscript.

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Correspondence to Tatiana de Campos.

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Key Messages

The study presents the first SSR markers derived from the transcriptome of Arachis pintoi which were highly informative and can access genetic variability, distinguish cultivars, and have a high cross-amplification rate in other Arachis species.

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de Oliveira, J.C., da Silva, A.L.D., da Silva, L.M. et al. Novel Microsatellite Markers Derived from Arachis pintoi Transcriptome Sequencing for Cross-Species Transferability and Varietal Identification. Plant Mol Biol Rep 42, 183–192 (2024). https://doi.org/10.1007/s11105-023-01402-9

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  • DOI: https://doi.org/10.1007/s11105-023-01402-9

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