|FRESNEDO-RAMIREZ, JONATHAN - Cornell University|
|SUN, QI - Cornell University|
|HWANG, CHIN-FENG - Missouri State University|
|FENNELL, ANNE - South Dakota State University|
|WALKER, ANDREW - University Of California|
|LUBY, JAMES - University Of Minnesota|
|CLARK, MATTHEW - University Of Minnesota|
|REISCH, BRUCE - Cornell University|
Submitted to: Molecular Breeding
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 7/21/2016
Publication Date: 8/1/2016
Citation: Fresnedo-Ramirez, J., Sun, Q., Hwang, C., Ledbetter, C.A., Ramming, D.W., Fennell, A., Walker, A., Luby, J., Clark, M., Londo, J.P., Cadle Davidson, L.E., Zhong, G., Reisch, B. 2016. Towards the elucidation of the cytoplasmic diversity of North American Grape Breeding Programs. Molecular Breeding. 36:116.
Interpretive Summary: In plants, interactions among genetic material from the nucleus and the so-called “cytoplasmic genomes”, which include DNA from organelles such as mitochondria and plastids, may impact breeding strategies and outcomes. Genetic analysis of cytoplasmic genomes for grape breeding has been limited. The understanding of how diverse grapevine is with respect to cytoplasmic genomes will help to address those limitations. Here, cytoplasmic diversity was analyzed among 6073 grapevines, with 52 DNA markers revealing five distinct cytoplasmic groups. These groups included wine grapes, raisin/table grapes, and three groups of interspecific hybrids. Ten of the 52 DNA markers were predicted to affect gene function, which may have an impact on the traits of known cultivars or breeding selections. The results will aid further study of cytoplasmic genomes and breeding in grapevine.
Technical 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 not been elucidated yet. 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 identified and were suitable to describe the diversity of the germplasm. Ten organelle genes showed distinct SNP annotations and effect predictions, of which six were in the chloroplast and three were mitochondrial genes, in addition to one mitochondrial SNP affecting an open reading frame. The results suggest that the application of GBS will aid in the study of cytoplasmic genomes in grapevine, which will help to design further studies of the role of cytoplasmic genomes in grapevine germplasm, and then allow exploitation of these sources of diversity in breeding.