The grape genome
Progress on the grapevine genome has been of great interest since the International Grapevine Genome Program was funded with the aim of stimulating innovation in grape breeding and biology. Due to its cultural and economic importance, wine grape was an obvious candidate for the first woody plant to have its genome deciphered. Research at IASMA focused on the elite cultivar Pinot Noir with the multiple goals of genome assembly, gene identification and annotation, and identification of a maximum number of polymorphisms. Of special interest to biologists and breeders are polymorphisms in and around the coding regions.
The sequencing of Pinot Noir
Pinot Noir is highly polymorphic, with two clearly distinguishable haplotypes that reveal several million single nucleotide polymorphisms SNPs and small insertion/deletion (In/Dels). These polymorphisms, along with trait and QTL marker association, represent a substantial resource for molecular breeding programs. A total coverage of seven genome equivalents of libraries of ascending size sequenced by the Sanger method, coupled with systematic highly parallel automated primer walking and 4.2 genome equivalents of 454 Life ScienceTM sequences, allowed us to create an effective genome sequence. Assembly was then achieved by adding sequences of two BAC libraries and a fosmid library which were end-sequenced to assemble large meta-contigs. Contigs were oriented and ordered on appropriate chromosomes by high throughput marker development and genotyping in an F1 cross of Syrah x Pinot Noir (IASMA Genomics).
Genetic and physical maps
A dense genetic map containing 1006 markers (SSRs, SNPs, and AFLPs) which refers to the Pinot Noir physical map cited below and to the Pinot Noir genome has recently been published (NCBI). The genetic and physical maps, as well as the genome sequence are available at IASMA Genomics.