| Institution: | 1.BRC Bioinformatics Facility, Institute of Biotechnology,Cornell University,Ithaca,USA;2.State Fruit Experiment Station at Mountain Grove Campus, Darr School of Agriculture,Missouri State University,Springfield,USA;3.USDA-ARS San Joaquin Valley Agricultural Sciences Center,Parlier,USA;4.Department of Plant Science,South Dakota State University,Brookings,USA;5.Department of Viticulture and Enology,University of California,Davis,USA;6.Department of Horticultural Science,University of Minnesota,St. Paul,USA;7.USDA-ARS Grape Genetics Research Unit,Geneva,USA;8.Horticulture Section, School of Integrative Plant Science,Cornell University,Geneva,USA;9.Ramming’s Specialty Crops,Fresno,USA;10.Department of Horticulture and Crop Science,The Ohio State University/OARDC,Wooster,USA |
| 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. |
