Molecular Breeding

, 36:116 | Cite as

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

  • Jonathan Fresnedo-Ramírez
  • Qi Sun
  • Chin-Feng Hwang
  • Craig A. Ledbetter
  • David W. Ramming
  • Anne Y. Fennell
  • M. Andrew Walker
  • James J. Luby
  • Matthew D. Clark
  • Jason P. Londo
  • Lance Cadle-Davidson
  • Gan-Yuan Zhong
  • Bruce I. Reisch
Short Communication
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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.

Keywords

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

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.

Compliance with ethical standards

Conflict of interest

The authors declare that there are no conflicts of interest.

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Copyright information

© Springer Science+Business Media Dordrecht (outside the USA) 2016

Authors and Affiliations

  • Jonathan Fresnedo-Ramírez
    • 1
    • 10
  • Qi Sun
    • 1
  • Chin-Feng Hwang
    • 2
  • Craig A. Ledbetter
    • 3
  • David W. Ramming
    • 3
    • 9
  • Anne Y. Fennell
    • 4
  • M. Andrew Walker
    • 5
  • James J. Luby
    • 6
  • Matthew D. Clark
    • 6
  • Jason P. Londo
    • 7
  • Lance Cadle-Davidson
    • 7
  • Gan-Yuan Zhong
    • 7
  • Bruce I. Reisch
    • 8
  1. 1.BRC Bioinformatics Facility, Institute of BiotechnologyCornell UniversityIthacaUSA
  2. 2.State Fruit Experiment Station at Mountain Grove Campus, Darr School of AgricultureMissouri State UniversitySpringfieldUSA
  3. 3.USDA-ARS San Joaquin Valley Agricultural Sciences CenterParlierUSA
  4. 4.Department of Plant ScienceSouth Dakota State UniversityBrookingsUSA
  5. 5.Department of Viticulture and EnologyUniversity of CaliforniaDavisUSA
  6. 6.Department of Horticultural ScienceUniversity of MinnesotaSt. PaulUSA
  7. 7.USDA-ARS Grape Genetics Research UnitGenevaUSA
  8. 8.Horticulture Section, School of Integrative Plant ScienceCornell UniversityGenevaUSA
  9. 9.Ramming’s Specialty CropsFresnoUSA
  10. 10.Department of Horticulture and Crop ScienceThe Ohio State University/OARDCWoosterUSA

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