Physical mapping in highly heterozygous genomes: a physical contig map of the Pinot Noir grapevine cultivar
1 Dipartimento di Matematica e Informatica, Università di Udine, Via delle Scienze 206, 33100 Udine, Italy
2 Istituto di Genomica Applicata, Parco Scientifico e Tecnologico di Udine "Luigi Danieli", Via J Linussio 51, 33100 Udine, Italy
3 IASMA Research and Innovation Centre, Foundation Edmund Mach, Via E Mach 1, 38010 San Michele all'Adige (TN), Italy
4 Dipartimento di Scienze Agrarie ed Ambientali, Università degli Studi di Udine, Via delle Scienze 208, 33100 Udine, Italy
5 Keygene NV, PO Box 216, 6700 Wageningen, The Netherlands
6 Dipartimento di Biologia, Università degli Studi di Padova, Via Ugo Bassi 58b, 35121 Padova, Italy
BMC Genomics 2010, 11:204 doi:10.1186/1471-2164-11-204Published: 26 March 2010
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. 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.
We 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.
We 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.