A SNP transferability survey within the genus Vitis

BackgroundEfforts to sequence the genomes of different organisms continue to increase. The DNA sequence is usually decoded for one individual and its application is for the whole species. The recent sequencing of the highly heterozygous Vitis vinifera L. cultivar Pinot Noir (clone ENTAV 115) genome gave rise to several thousand polymorphisms and offers a good model to study the transferability of its degree of polymorphism to other individuals of the same species and within the genus.ResultsThis study was performed by genotyping 137 SNPs through the SNPlex™ Genotyping System (Applied Biosystems Inc.) and by comparing the SNPlex sequencing results across 35 (of the 137) regions from 69 grape accessions. A heterozygous state transferability of 31.5% across the unrelated cultivars of V. vinifera, of 18.8% across the wild forms of V. vinifera, of 2.3% among non-vinifera Vitis species, and of 0% with Muscadinia rotundifolia was found. In addition, mean allele frequencies were used to evaluate SNP informativeness and develop useful subsets of markers.ConclusionUsing SNPlex application and corroboration from the sequencing analysis, the informativeness of SNP markers from the heterozygous grape cultivar Pinot Noir was validated in V. vinifera (including cultivars and wild forms), but had a limited application for non-vinifera Vitis species where a resequencing strategy may be preferred, knowing that homology at priming sites is sufficient. This work will allow future applications such as mapping and diversity studies, accession identification and genomic-research assisted breeding within V. vinifera.

[1]  S Rozen,et al.  Primer3 on the WWW for general users and for biologist programmers. , 2000, Methods in molecular biology.

[2]  T. Lacombe,et al.  Construction of nested genetic core collections to optimize the exploitation of natural diversity in Vitis vinifera L. subsp. sativa , 2008, BMC Plant Biology.

[3]  T. Lacombe,et al.  Historical origins and genetic diversity of wine grapes. , 2006, Trends in genetics : TIG.

[4]  R Higuchi,et al.  Preferential PCR amplification of alleles: mechanisms and solutions. , 1992, PCR methods and applications.

[5]  B. Baum,et al.  Efficient validation of single nucleotide polymorphisms in plants by allele-specific PCR, with an example from barley , 2003, Plant Molecular Biology Reporter.

[6]  Maria Hopf,et al.  Domestication of plants in the old world , 1988 .

[7]  J. Boursiquot,et al.  Development of Stable RAPD Markers for the Identification of Grapevine Rootstocks and the Analysis of Genetic Relationships , 1997, American Journal of Enology and Viticulture.

[8]  E. Maul,et al.  Development of SCAR markers linked to powdery mildew (Uncinula necator) resistance in grapevine (Vitis vinifera L. and Vitis sp.) , 2007, Molecular Breeding.

[9]  S. Otto,et al.  Use of Ecotilling as an efficient SNP discovery tool to survey genetic variation in wild populations of Populus trichocarpa , 2006, Molecular ecology.

[10]  M. S. Grando,et al.  A grapevine (Vitis vinifera L.) genetic map integrating the position of 139 expressed genes , 2008, Theoretical and Applied Genetics.

[11]  P. Cregan,et al.  BARCSoySNP23: a panel of 23 selected SNPs for soybean cultivar identification , 2007, Theoretical and Applied Genetics.

[12]  Dustin A. Cartwright,et al.  A reference integrated map for cultivated grapevine (Vitis vinifera L.) from three crosses, based on 283 SSR and 501 SNP-based markers , 2008, Theoretical and Applied Genetics.

[13]  P. This,et al.  Establishment of a local map of AFLP markers around the powdery mildew resistance gene Run1 in grapevine and assessment of their usefulness for marker assisted selection , 2001, Theoretical and Applied Genetics.

[14]  Roger S Lasken,et al.  Unbiased whole-genome amplification directly from clinical samples. , 2003, Genome research.

[15]  R. Shoemaker,et al.  High-throughput genotyping with the GoldenGate assay in the complex genome of soybean , 2008, Theoretical and Applied Genetics.

[16]  Dustin A. Cartwright,et al.  A High Quality Draft Consensus Sequence of the Genome of a Heterozygous Grapevine Variety , 2007, PloS one.

[17]  Nicolas Peyret,et al.  The SNPlex genotyping system: a flexible and scalable platform for SNP genotyping. , 2005, Journal of biomolecular techniques : JBT.

[18]  Stephen M. Mount,et al.  The draft genome of the transgenic tropical fruit tree papaya (Carica papaya Linnaeus) , 2008, Nature.

[19]  J. Aronson.  Grapes , 1998, BMJ.

[20]  Riccardo Velasco,et al.  SNP high-throughput screening in grapevine using the SNPlex™ genotyping system , 2008, BMC Plant Biology.

[21]  Kathryn F. Beal,et al.  The Staden package, 1998. , 2000, Methods in molecular biology.

[22]  J. Bohlmann,et al.  Efficient Genetic Mapping of Single Nucleotide Polymorphisms Based Upon DNA Mismatch Digestion , 2005, Molecular Breeding.

[23]  N. Mejía,et al.  A NEW, HIGHLY ASSERTIVE SCAR MARKER POTENTIALLY USEFUL TO ASSIST SELECTION FOR SEEDLESSNESS IN TABLE GRAPE BREEDING , 2003 .

[24]  T. Lacombe,et al.  Wine grape (Vitis vinifera L.) color associates with allelic variation in the domestication gene VvmybA1 , 2007, Theoretical and Applied Genetics.

[25]  L. Gianfranceschi,et al.  Towards a marker assisted breeding for resistance against apple scab , 1994 .

[26]  Ralph Rapley,et al.  Molecular analysis and genome discovery , 2004 .

[27]  L. Gianfranceschi,et al.  1994 Kluwer Academic Publishers. Towards a marker assisted breeding for resistance against apple scab , 1994, Euphytica.

[28]  P. This,et al.  An integrated SSR map of grapevine based on five mapping populations , 2006, Theoretical and Applied Genetics.

[29]  Dustin A. Cartwright,et al.  A Dense Single-Nucleotide Polymorphism-Based Genetic Linkage Map of Grapevine (Vitis vinifera L.) Anchoring Pinot Noir Bacterial Artificial Chromosome Contigs , 2007, Genetics.

[30]  K. Gunderson,et al.  High-throughput SNP genotyping on universal bead arrays. , 2005, Mutation research.

[31]  Virander S. Chauhan,et al.  Novel genetic mapping tools in plants , 2002 .

[32]  J. Rafalski.  Novel genetic mapping tools in plants: SNPs and LD-based approaches , 2002 .

[33]  R. Velasco,et al.  Genome diversity and gene haplotypes in the grapevine (Vitis vinifera L.), as revealed by single nucleotide polymorphisms , 2004, Molecular Breeding.

[34]  D. Bhattramakki,et al.  A comparison of simple sequence repeat and single nucleotide polymorphism marker technologies for the genotypic analysis of maize (Zea mays L.) , 2007, Theoretical and Applied Genetics.

[35]  The Arabidopsis Genome Initiative.  Analysis of the genome sequence of the flowering plant Arabidopsis thaliana , 2000, Nature.

[36]  Huanming Yang,et al.  A Draft Sequence of the Rice Genome (Oryza sativa L. ssp. indica) , 2002, Science.

[37]  M. S. Grando,et al.  Generation of a Common Set of Mapping Markers to Assist Table Grape Breeding , 2007, American Journal of Enology and Viticulture.

[38]  A. Brookes.  The essence of SNPs. , 1999, Gene.

[39]  J. Martínez-Zapater,et al.  High throughput SNP discovery and genotyping in grapevine (Vitis vinifera L.) by combining a re-sequencing approach and SNPlex technology , 2007, BMC Genomics.

[40]  J. Poulain,et al.  The grapevine genome sequence suggests ancestral hexaploidization in major angiosperm phyla , 2007, Nature.

[41]  M. Gribskov,et al.  The Genome of Black Cottonwood, Populus trichocarpa (Torr. & Gray) , 2006, Science.

[42]  E. Maul,et al.  Genetic mapping and localization of quantitative trait loci affecting fungal disease resistance and leaf morphology in grapevine (Vitis vinifera L) , 2007, Molecular Breeding.

[43]  A. Bouquet.  Resistance to grape fanleaf virus in muscadine grape inoculated with Xiphinema index. , 1981 .

[44]  R. Varshney,et al.  Single nucleotide polymorphisms in rye (Secale cereale L.): discovery, frequency, and applications for genome mapping and diversity studies , 2007, Theoretical and Applied Genetics.

[45]  W. Williams,et al.  Evolution of Crop Plants. , 1977 .

[46]  A. Oliphant,et al.  A draft sequence of the rice genome (Oryza sativa L. ssp. japonica). , 2002, Science.

[47]  P. Green,et al.  Identification of candidate coding region single nucleotide polymorphisms in 165 human genes using assembled expressed sequence tags. , 1999, Genome research.