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Toward the elucidation of cytoplasmic diversity in North American grape breeding programs

Molecular Breeding volume 36, Article number: 116 (2016) Cite this article

Abstract

Plants have an intriguing tripartite genetic system: Nuclear genome × Mitochondria × Plastids and their interactions may impact germplasm breeding. In grapevine, the study of cytoplasmic genomes has been limited, and their role with respect to grapevine germplasm diversity has yet to be elucidated. In the present study, the results of an analysis of the cytoplasmic diversity among 6073 individuals (comprising cultivars, interspecific hybrids and segregating progenies) are presented. Genotyping by sequencing (GBS) was used to elucidate plastid and mitochondrial DNA sequences, and results were analyzed using multivariate techniques. Single nucleotide polymorphism (SNP) effects were annotated in reference to plastid and mitochondrial genome sequences. The cytoplasmic diversity identified was structured according to synthetic domestication groups (wine and raisin/table grape types) and interspecific-hybridization-driven groups with introgression from North American Vitis species, identifying five cytoplasmic groups and four major clusters. Fifty-two SNP markers were used to describe the diversity of the germplasm. Ten organelle genes showed distinct SNP annotations and effect predictions, of which six were chloroplast-derived and three were mitochondrial genes, in addition to one mitochondrial SNP affecting a nonannotated open reading frame. The results suggest that the application of GBS will aid in the study of cytoplasmic genomes in grapevine, which will enable further studies on the role of cytoplasmic genomes in grapevine germplasm, and then allow the exploitation of these sources of diversity in breeding.

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Acknowledgments

The authors acknowledge the U.S. Department of Agriculture, National Institute of Food and Agriculture, Specialty Crop Research Initiative (Award no. 2011-51181-30635), and the National Grape and Wine Initiative for funding for the VitisGen project (http://www.vitisgen.org/). We also thank Shanshan Yang for discussion and suggestions.

Author information

Author notes

  1. David W. Ramming

    Present address: Ramming’s Specialty Crops, Fresno, CA, 93737, USA

  2. Jonathan Fresnedo-Ramírez

    Present address: Department of Horticulture and Crop Science, The Ohio State University/OARDC, Wooster, OH, 44691, USA

Authors and Affiliations

  1. BRC Bioinformatics Facility, Institute of Biotechnology, Cornell University, Ithaca, NY, 14853, USA

    Jonathan Fresnedo-Ramírez & Qi Sun

  2. State Fruit Experiment Station at Mountain Grove Campus, Darr School of Agriculture, Missouri State University, Springfield, MO, 65897, USA

    Chin-Feng Hwang

  3. USDA-ARS San Joaquin Valley Agricultural Sciences Center, Parlier, CA, 93648, USA

    Craig A. Ledbetter & David W. Ramming

  4. Department of Plant Science, South Dakota State University, Brookings, SD, 57007, USA

    Anne Y. Fennell

  5. Department of Viticulture and Enology, University of California, Davis, CA, 95616, USA

    M. Andrew Walker

  6. Department of Horticultural Science, University of Minnesota, St. Paul, MN, 55108, USA

    James J. Luby & Matthew D. Clark

  7. USDA-ARS Grape Genetics Research Unit, Geneva, NY, 14456, USA

    Jason P. Londo, Lance Cadle-Davidson & Gan-Yuan Zhong

  8. Horticulture Section, School of Integrative Plant Science, Cornell University, Geneva, NY, 14456, USA

    Bruce I. Reisch

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  1. Jonathan Fresnedo-Ramírez
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Correspondence to Jonathan Fresnedo-Ramírez.

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Fresnedo-Ramírez, J., Sun, Q., Hwang, CF. et al. Toward the elucidation of cytoplasmic diversity in North American grape breeding programs. Mol Breeding 36, 116 (2016). https://doi.org/10.1007/s11032-016-0538-z

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Keywords

  • Plastid genome
  • Mitochondria genome
  • Cytoplasmic differentiation
  • Cytoplasmic lineage
  • Organelle genes
  • Vitis
  • Grapevine