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A Toolbox of Potato Genetic and Genomic Resources

Abstract

Access to genetic and genomic resources can greatly facilitate biological understanding of plant species leading to improved crop varieties. While model plant species such as Arabidopsis have had nearly two decades of genetic and genomic resource development, many major crop species have seen limited development of these resources due to the large, complex nature of their genomes. Cultivated potato is among the ranks of crop species that, despite substantial worldwide acreage, have seen limited genetic and genomic tool development. As technologies advance, this paradigm is shifting and a number of tools are being developed for important crop species such as potato. This review article highlights numerous tools that have been developed for the potato community with a specific focus on the reference de novo genome assembly and annotation, genetic markers, transcriptomics resources, and newly emerging resources that extend beyond a single reference individual.

Resumen

El acceso a los recursos genéticos y genómicos puede facilitar en gran medida el entendimiento biológico de las especies de plantas, lo que conduce a variedades mejoradas de cultivos. Mientras que el modelo de las especies de plantas como Arabidopsis ha tenido cerca de dos décadas de desarrollo de recursos genéticos y genómicos, muchas especies de cultivos principales han visto desarrollo limitado de estos recursos debido a la naturaleza grande, compleja, de sus genomios. La papa cultivada está ubicada entre las especies de plantas que a pesar de su superficie substancial mundial, ha visto limitado el desarrollo de las herramientas genéticas y genómicas. A medida que avanzan las tecnologías, este paradigma está girando y se han estado desarrollando un número de herramientas para especies importantes de cultivo tales como la papa. Este artículo de revisión resalta las numerosas herramientas que se han desarrollado para la comunidad de la papa con un enfoque específico en la referencia de ensamblaje y registro de genomio de novo, marcadores genéticos, recursos transcriptómicos, y nuevas fuentes emergentes que se extienden más allá de la referencia de un único individuo.

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Acknowledgments

This work was supported by a National Science Foundation National Plant Genome Initiative Postdoctoral Fellowship in Biology (Grant No. 1202724) to CDH, a National Science Foundation Plant Genome Research Program award (ISO-1237969) to CRB, and by funds from the U.S. Department of Agriculture, National Institute of Food and Agriculture, Agriculture and Food Research Initiative Plant Breeding, Genetics, and Genome grant (2009-85606-05673) to CRB.

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Correspondence to C. Robin Buell.

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Hirsch, C.D., Buell, C.R. & Hirsch, C.N. A Toolbox of Potato Genetic and Genomic Resources. Am. J. Potato Res. 93, 21–32 (2016). https://doi.org/10.1007/s12230-015-9486-0

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Keywords

  • Genome assembly
  • Genome annotation
  • Markers
  • Transcriptomics