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Simple Sequence Repeat-Based Genetic Diversity and Analysis of Molecular Variance among on-Farm Native Potato Landraces from the Influence Zone of Camisea Gas Project, Northern Ayacucho, Peru

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Abstract

The Andean native potato is an important food security crop and constitutes a gene pool for potato-breeding. To establish the current state of the native potatoes diversity in the influence zone of the Camisea Gas Project, North Ayacucho, Peru, landraces (n = 144) were collected. Three sampling populations (Anco, Chungui and Ticllas) were resolved using 10 simple sequence repeats (SSRs) markers that amplified 67 polymorphic alleles. Principal component, correspondence and cluster analysis revealed a minimum set of six SSRs to achieve DNA fingerprinting and cost-effective genetic diversity analysis. Analysis of molecular variance (AMOVA), average fixation index (FST = 0.279), and genetic distance index (SB) indicated that the genetic diversity of the native potatoes is high at the intra- and inter-population levels, and each of the three sampling populations constituted closed populations. The three populations were genetically distinct and contained unique genotypes and exclusive alleles. Misidentified native potatoes (10.41%) were found.

Resumen

La papa nativa andina, es importante para la seguridad alimentaria, constituye un reservorio de genes para el mejoramiento del cultivo. Con el objetivo de establecer el estado actual de la diversidad de papas nativas en la zona de influencia del Proyecto Peruano Gas de Camisea en el norte del departamento de Ayacucho, Perú se colectaron 144 variedades locales en tres distritos (Anco, Chungui y Ticllas). Usando diez marcadores SSR se amplificaron 67 alelos polimórficos. Los análisis de componentes principales, de correspondencia múltiple y de agrupamiento revelaron que se podría usar un set mínimo de seis SSR para el ADN fingerprintig y análisis de diversidad genética costo-efectivo. El AMOVA, el índice promedio de fijación (FST = 0.279) y el índice de distancia genética (SB) muestran que la diversidad genética a nivel intra e inter-poblacional es alto, las tres poblaciones difieren genéticamente, contienen genotipos únicos y alelos exclusivos. El 10.41% de papas nativas estaban mal identificados.

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Acknowledgements

The authors wish to thank Dr. William Roca Pizzini (International Potato Center (CIP), Peru) for his review and analysis of the first draft of this manuscript. The authors too would like to thank Enago (www.enago.com) for the English language review. This work was supported by the Socioeconomic Development Fund of Camisea (ley N° 28451-MEF-PERU) of the Universidad Nacional San Cristóbal de Huamanga, Ayacucho, Peru. The work was carried out through inter-institutional collaboration with Universidad Peruana Cayetano Heredia (UPCH).

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  1. Programa Doctoral de Ciencias e Ingeniería Biológica, Universidad Nacional Agraria La Molina (UNALM), Avenida La Molina, Lima, Peru

    Germán De la Cruz

  2. Laboratorio de Genética y Biotecnología Vegetal, Universidad Nacional San Cristóbal de Huamanga, Portal Constitución N° 57, Ayacucho, Peru

    Germán De la Cruz & Tomás Yuret Miranda

  3. Instituto de Biotecnología, Universidad Agraria La Molina (UNALM), Avenida La Molina, Lima, Peru

    Raúl Humberto Blas

  4. Unidad de Genómica, Universidad Peruana Cayetano Heredia (UPCH), Av. Honorio Delgado 430, San Martín de Porres, Lima, Peru

    Gisella Orjeda

  5. Facultad de Medicina, Universidad Peruana Cayetano Heredia, Av. Honorio Delgado 430, San Martín de Porres, Lima, Peru

    Edgar Neyra

  6. Instituto Nacional de Investigación en Glaciares y Ecosistemas de Montaña (INAIGEM), Juan Bautista N° 887, Huaraz, Peru

    Gisella Orjeda

Authors
  1. Germán De la Cruz
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  2. Tomás Yuret Miranda
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  3. Raúl Humberto Blas
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  4. Edgar Neyra
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  5. Gisella Orjeda
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Contributions

GO, TY, and GDC conceived the project; TY and GDC collected the field samples; TY, EN, and GDC performed the molecular marker LI-COR analysis; RB, EN, and GDC performed the calculations and statistical analysis. GDC, EN, and GO wrote the article. All authors read and approved the final manuscript.

Corresponding author

Correspondence to Edgar Neyra.

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Conflict of Interests

The authors declare that they have no conflict of interests.

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De la Cruz, G., Miranda, T.Y., Blas, R.H. et al. Simple Sequence Repeat-Based Genetic Diversity and Analysis of Molecular Variance among on-Farm Native Potato Landraces from the Influence Zone of Camisea Gas Project, Northern Ayacucho, Peru. Am. J. Potato Res. 97, 143–161 (2020). https://doi.org/10.1007/s12230-020-09763-7

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  • DOI: https://doi.org/10.1007/s12230-020-09763-7

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