Metacontigs were integrated in the 19 grape LGs based on the genetic map derived from the cross Syrah X Pinot Noir. To improve marker density, polymorphic sites identified during WGS were selected for developing 799 additional SNP-based markers (http://genomics.research.iasma.it) using the SNPlex™ Genotyping System [111] (link). DNA was prepared according to the instructions and the samples were analyzed on the ABI PRISM® 3730xl (Applied Biosystems, Foster City, CA). Data were analyzed by Gene Mapper v. 4.0 (Applied Biosystems, Foster City, CA). The genetic maps were followed a double pseudo-testcross strategy [112] (link). Marker phase was determined by the Phasing algorithm (http://math.berkeley.edu/dustin/tmap/; [113] (link)), which provides LG assignment and ordering of loci. LG were assembled with a minimum LOD of 8.0 and a maximum distance of 35 cM. Homologous LGs of the two parents were merged in a consensus map.
Velasco R., Zharkikh A., Troggio M., Cartwright D.A., Cestaro A., Pruss D., Pindo M., FitzGerald L.M., Vezzulli S., Reid J., Malacarne G., Iliev D., Coppola G., Wardell B., Micheletti D., Macalma T., Facci M., Mitchell J.T., Perazzolli M., Eldredge G., Gatto P., Oyzerski R., Moretto M., Gutin N., Stefanini M., Chen Y., Segala C., Davenport C., Demattè 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 J.A., Sterck L., Vandepoele K., Grando S.M., Toppo S., Moser C., Lanchbury J., Bogden R., Skolnick M., Sgaramella V., Bhatnagar S.K., 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), e1326.
Corresponding Organization : Fondazione Edmund Mach
Other organizations :
Myriad Genetics, Roche (United States), Royal Holloway University of London, VIB-UGent Center for Plant Systems Biology, University of Padua
Polymorphic sites identified during whole-genome sequencing (WGS)
dependent variables
Genetic maps derived from the cross Syrah X Pinot Noir
Marker density
Linkage group (LG) assignment and ordering of loci
control variables
Minimum LOD of 8.0 for LG assembly
Maximum distance of 35 cM for LG assembly
Annotations
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