Abstract
BackgroundMost of the grapevine (Vitis vinifera L.) cultivars grown today are those selected centuries ago, even though grapevine is one of the most important fruit crops in the world. Grapevine has therefore not benefited from the advances in modern plant breeding nor more recently from those in molecular genetics and genomics: genes controlling important agronomic traits are practically unknown. A physical map is essential to positionally clone such genes and instrumental in a genome sequencing project.ResultsWe report on the first whole genome physical map of grapevine built using high information content fingerprinting of 49,104 BAC clones from the cultivar Pinot Noir. Pinot Noir, as most grape varieties, is highly heterozygous at the sequence level. This resulted in the two allelic haplotypes sometimes assembling into separate contigs that had to be accommodated in the map framework or in local expansions of contig maps. We performed computer simulations to assess the effects of increasing levels of sequence heterozygosity on BAC fingerprint assembly and showed that the experimental assembly results are in full agreement with the theoretical expectations, given the heterozygosity levels reported for grape. The map is anchored to a dense linkage map consisting of 994 markers. 436 contigs are anchored to the genetic map, covering 342 of the 475 Mb that make up the grape haploid genome.ConclusionsWe have developed a resource that makes it possible to access the grapevine genome, opening the way to a new era both in grape genetics and breeding and in wine making. The effects of heterozygosity on the assembly have been analyzed and characterized by using several complementary approaches which could be easily transferred to the study of other genomes which present the same features.
Highlights
Most of the grapevine (Vitis vinifera L.) cultivars grown today are those selected centuries ago, even though grapevine is one of the most important fruit crops in the world
A total of 49,104 Bacterial Artificial Chromosome (BAC) clones from two BAC libraries representing approximately 11.4 genome equivalents [35] (Table 1) of the red wine cultivar Pinot Noir, one of the most widely grown in the world, were fingerprinted, adapting to grape a fluorescence-based, high-throughput method developed for wheat and rice [30]
The recent sequencing of the genome of grape cv Pinot Noir showed an average 11.2% of allelic difference between homologous chromosomes by considering both single nucleotide polymorphisms (SNPs) and indels, with important variations according to the genomic region [33]
Summary
Most of the grapevine (Vitis vinifera L.) cultivars grown today are those selected centuries ago, even though grapevine is one of the most important fruit crops in the world. With a production of 67.1 millions tons obtained from 7.9 millions hectares in 2004, grapevine (Vitis vinifera L.) is by far the most important fruit tree crop in the world http://www.oiv.org. The release of new varieties is a considerably slow process This is mainly due to some peculiar genetic and physiological features which are shared with most of the tree crops and which significantly hamper the adoption of modern breeding strategies.
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