Toward the elucidation of cytoplasmic diversity in North American grape breeding programs
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.
KeywordsPlastid genome Mitochondria genome Cytoplasmic differentiation Cytoplasmic lineage Organelle genes Vitis Grapevine
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.
- Adam-Blondon A, Jaillon O, Vezzulli S, Zharkikh A, Troggio M, Velasco R (2011) Genome sequence initiatives. In: Adam-Blondon A-Fo, Martínez-Zapater JM, Kole C (eds) Genetics, genomics and breeding of crop plants. Science Publishers, Enfield, pp 211–234Google Scholar
- Bouvier F, Mialoundama AS, Camara B (2009) A sentinel role for plastids. In: Sandelius A, Aronsson H (eds) The chloroplast, vol 13. Plant cell monographs. Springer Berlin, pp 267–292Google Scholar
- Cingolani P, Platts A, Wang LL, Coon M, Nguyen T, Wang L, Land SJ, Lu XY, Ruden DM (2012) A program for annotating and predicting the effects of single nucleotide polymorphisms, SnpEff: SNPs in the genome of Drosophila melanogaster strain w(1118); iso-2; iso-3. Fly 6(2):80–92CrossRefPubMedPubMedCentralGoogle Scholar
- Cingolani P, Cunningham F, McLaren W, Wang K (2015) Variant annotations in VCF format version 1.0. Available on-line http://snpeff.sourceforge.net/VCFannotationformat_v1.0.pdf
- Hedrick UP, Booth NO, Dorsey MJ, Taylor OM, Wellington R (1908) The grapes of New York, Report of the New York Agricultural Experiment Station for the year 1907. JB Lyon Company, AlbanyGoogle Scholar
- Jaillon O, Aury JM, Noel B, Policriti A, Clepet C, Casagrande A, Choisne N, Aubourg S, Vitulo N, Jubin C, Vezzi A, Legeai F, Hugueney P, Dasilva C, Horner D, Mica E, Jublot D, Poulain J, Bruyere C, Billault A, Segurens B, Gouyvenoux M, Ugarte E, Cattonaro F, Anthouard V, Vico V, Del Fabbro C, Alaux M, Di Gaspero G, Dumas V, Felice N, Paillard S, Juman I, Moroldo M, Scalabrin S, Canaguier A, Le Clainche I, Malacrida G, Durand E, Pesole G, Laucou V, Chatelet P, Merdinoglu D, Delledonne M, Pezzotti M, Lecharny A, Scarpelli C, Artiguenave F, Pe ME, Valle G, Morgante M, Caboche M, Adam-Blondon AF, Weissenbach J, Quetier F, Wincker P, French-Italian Public Consortium for Grapevine Genome C (2007) The grapevine genome sequence suggests ancestral hexaploidization in major angiosperm phyla. Nature 449(7161):463–467CrossRefPubMedGoogle Scholar
- Jansen RK, Kaittanis C, Saski C, Lee SB, Tomkins J, Alverson AJ, Daniell H (2006) Phylogenetic analyses of Vitis (Vitaceae) based on complete chloroplast genome sequences: effects of taxon sampling and phylogenetic methods on resolving relationships among rosids. BMC Evol Biol 6:32. doi: 10.1186/1471-2148-6-32 CrossRefPubMedPubMedCentralGoogle Scholar
- Kupsch C, Ruwe H, Gusewski S, Tillich M, Small I, Schmitz-Linneweber C (2012) Arabidopsis chloroplast RNA binding proteins CP31A and CP29A associate with large transcript pools and confer cold stress tolerance by influencing multiple chloroplast RNA processing steps. Plant Cell 24(10):4266–4280CrossRefPubMedPubMedCentralGoogle Scholar
- Lózsa R, Xia N, Deak T, Bisztray GD (2015) Chloroplast diversity indicates two independent maternal lineages in cultivated grapevine (Vitis vinifera L. subsp vinifera). Genet Resour Crop Evol 62(3):419–429. doi: 10.1007/s10722-014-0169-3
- R development core team (2016) R: a language and environment for statistical computing. R Foundation for Statistical Computing, ViennaGoogle Scholar
- Strefeler MS, Weeden NF, Reisch BI (1992) Inheritance of chloroplast DNA in two full-sib Vitis populations. Vitis 31(4):183–187Google Scholar
- Tomkins JP, Peterson DG, Yang TJ, Main D, Ablett EF, Henry RJ, Lee LS, Holton TA, Waters D, Wing RA (2001) Grape (Vitis vinifera L.) BAC library construction, preliminary STC analysis, and identification of clones associated with flavonoid and stilbene biosynthesis. Am J Enol Viticult 52(4):287–291Google Scholar
- Velasco R, Zharkikh A, Troggio M, Cartwright DA, Cestaro A, Pruss D, Pindo M, Fitzgerald LM, Vezzulli S, Reid J, Malacarne G, Iliev D, Coppola G, Wardell B, Micheletti D, Macalma T, Facci M, Mitchell JT, Perazzolli M, Eldredge G, Gatto P, Oyzerski R, Moretto M, Gutin N, Stefanini M, Chen Y, Segala C, Davenport C, Dematte L, Mraz A, Battilana J, Stormo K, Costa F, Tao Q, Si-Ammour A, Harkins T, Lackey A, Perbost C, Taillon B, Stella A, Solovyev V, Fawcett JA, Sterck L, Vandepoele K, Grando SM, Toppo S, Moser C, Lanchbury J, Bogden R, Skolnick M, Sgaramella V, Bhatnagar SK, Fontana P, Gutin A, Van de Peer Y, Salamini F, Viola R (2007) A high quality draft consensus sequence of the genome of a heterozygous grapevine variety. PLoS ONE 2(12):e1326CrossRefPubMedPubMedCentralGoogle Scholar
- Yang S, Fresnedo-Ramírez J, Wang M, Cote L, Schweitzer P, Barba P, Takacs EM, Clark MD, Luby JJ, Manns DC, Sacks GL, Mansfield AK, Londo JP, Fennell AY, Gadoury D, Reisch BI, Cadle-Davidson LE, Sun Q (2016) A next-generation marker genotyping platform (AmpSeq) in heterozygous crops: a case study for marker assisted selection in grapevine. Horticult Res 3:16002CrossRefGoogle Scholar