S. Grando

BACKGROUND: Worldwide, grapes and their derived products have a large market. The cultivated grape species Vitis vinifera has potential to become a model for fruit trees genetics. Like many plant species, it is highly heterozygous, which is an additional challenge to modern whole genome shotgun sequencing. In this paper a high quality draft genome sequence of a cultivated clone of V. vinifera Pinot Noir is presented. PRINCIPAL FINDINGS: We estimate the genome size of V. vinifera to be 504.6 Mb. Genomic sequences corresponding to 477.1 Mb were assembled in 2,093 metacontigs and 435.1 Mb were anchored to the 19 linkage groups (LGs). The number of predicted genes is 29,585, of which 96.1% were assigned to LGs. This assembly of the grape genome provides candidate genes implicated in traits relevant to grapevine cultivation, such as those influencing wine quality, via secondary metabolites, and those connected with the extreme susceptibility of grape to pathogens. Single nucleotide polymorphism (SNP) distribution was consistent with a diffuse haplotype structure across the genome. Of around 2,000,000 SNPs, 1,751,176 were mapped to chromosomes and one or more of them were identified in 86.7% of anchored genes. The relative age of grape duplicated genes was estimated and this made possible to reveal a relatively recent Vitis-specific large scale duplication event concerning at least 10 chromosomes (duplication not reported before). CONCLUSIONS: Sanger shotgun sequencing and highly efficient sequencing by synthesis (SBS), together with dedicated assembly programs, resolved a complex heterozygous genome. A consensus sequence of the genome and a set of mapped marker loci were generated. Homologous chromosomes of Pinot Noir differ by 11.2% of their DNA (hemizygous DNA plus chromosomal gaps). SNP markers are offered as a tool with the potential of introducing a new era in the molecular breeding of grape.

Abstract The domestication of the Eurasian grape ( Vitis vinifera ssp. sativa ) from its wild ancestor ( Vitis vinifera ssp. sylvestris ) has long been claimed to have occurred in Transcaucasia where its greatest genetic diversity is found and where very early archaeological evidence, including grape pips and artefacts of a ‘wine culture’, have been excavated. Whether from Transcaucasia or the nearby Taurus or Zagros Mountains, it is hypothesized that this wine culture spread southwards and eventually westwards around the Mediterranean basin, together with the transplantation of cultivated grape cuttings. However, the existence of morphological differentiation between cultivars from eastern and western ends of the modern distribution of the Eurasian grape suggests the existence of different genetic contribution from local sylvestris populations or multilocal selection and domestication of sylvestris genotypes. To tackle this issue, we analysed chlorotype variation and distribution in 1201 samples of sylvestris and sativa genotypes from the whole area of the species’ distribution and studied their genetic relationships. The results suggest the existence of at least two important origins for the cultivated germplasm, one in the Near East and another in the western Mediterranean region, the latter of which gave rise to many of the current Western European cultivars. Indeed, over 70% of the Iberian Peninsula cultivars display chlorotypes that are only compatible with their having derived from western sylvestris populations.

SUMMARY Climate change is now unequivocal, particularly in terms of increasing temperature, increasing CO 2 concentration, widespread melting of snow and ice and rising global average sea level, while the increase in the frequency of drought is very probable but not as certain. However, climate changes are not new and some of them have had dramatic impacts, such as the appearance of leaves about 400 million years ago as a response to a drastic decrease in CO 2 concentration, the birth of agriculture due to the end of the last ice age about 11 000 years ago and the collapse of civilizations due to the late Holocene droughts between 5000 and 1000 years ago. The climate changes that are occurring at present will have – and are already having – an adverse effect on food production and food quality with the poorest farmers and the poorest countries most at risk. The adverse effect is a consequence of the expected or probable increased frequency of some abiotic stresses such as heat and drought, and of the increased frequency of biotic stresses (pests and diseases). In addition, climate change is also expected to cause losses of biodiversity, mainly in more marginal environments. Plant breeding has addressed both abiotic and biotic stresses. Strategies of adaptation to climate changes may include a more accurate matching of phenology to moisture availability using photoperiod-temperature response, increased access to a suite of varieties with different duration to escape or avoid predictable occurrences of stress at critical periods in crop life cycles, improved water use efficiency and a re-emphasis on population breeding in the form of evolutionary participatory plant breeding to provide a buffer against increasing unpredictability. ICARDA, in collaboration with scientists in Iran, Algeria, Jordan, Eritrea and Morocco, has recently started evolutionary participatory programmes for barley and durum wheat. These measures will go hand in hand with breeding for resistance to biotic stresses and with an efficient system of variety delivery to farmers.