Genetic Diversity
Unravelling the domestication history of crop species.
Genealogy of varieties, structure of the germplasm, and signatures of selection provide useful information for unravelling the history of domestication and improvement of crop species. We investigate these issues in traditional fruit crops such as grapevine, olive, coffee, sweet cherry, and Citrus, as well as in forest species.
Our scientific interest is to :
- describe the level and structure of intraspecific genetic diversity;
- reconstruct the network of pedigree relationships from ancient to modern varieties;
- identify the impact of human selection and breeding on the genome of fruit crops;
- evaluate the extent of crop diversity in recent polyploids
read Nature news coverage of our recent work on the mechanisms generating divesity in coffee
All arabica coffee is genetically similar: how can beans taste so different?
The differences in the flavour notes and other characteristics of coffee varieties from around the world are not down to variations in individual genes, a study has found. Rather, they seem to be mainly the result of wholesale swapping, deletion and rearrangement of chromosomes.
The most complete sequencing yet of the genome of Coffea arabica has revealed that the ‘letters’ in the DNA strands differ only slightly between varieties. Despite this, there is substantial variation in the physical characteristics of the arabica coffee plant, including different flavour profiles in the beans and variations in disease resistance.
The study found evidence of significant chromosomal rearrangements, especially in a varietal of C. arabica called Bourbon. There were deletions, in which fragments of chromosomes were missing — in some cases large chunks — and even instances in which entire chromosomes were absent.
Source: https://doi.org/10.1038/d41586-024-00165-x
References
Scalabrin, S. et al. Nature Commun. https://doi.org/10.1038/s41467-023-44449-8 (2024).
IGA has resequenced the genomes of more than 120 grape varieties, sampled from the whole range of continental distribution of viticulture. Funding was provided by three complementary projects at national, transnational and EU levels. The project Vigneto has funded the resequencing of 51 varieties predominantly cultivated in the Italian peninsula and locally regarded as flagships of local wine districts. The project VISO has funded the resequencing of rare varieties grown in the crossborder area of Italy-Slovenia, a geographical passage that since Roman times has connected viticulture in Western Europe with viticulture in the Danubian basin. This set includes the variety Zametovka, the oldest living specimen of a domesticated grape. The ERC project Novabreed has funded the resequencing of a set of 50 grape varieties that captures phenotypic diversity across the continental range of viticulture, including wine and table grapes from the Atlantic coast to the oasis of Central Asia.
This data revealed insights into the history and genetic ancestry of European wine grapes. We showed that a single domestication event occurred in Western Asia and European wine grapes have originated from the hybridization of western Asian-domesticated table grapes and local wild relatives. By modelling how the ancestry components, including the one provided by interbreeding with European wild relatives, in different regions of Europe related to aspects of the local climate, we propose that introgression from local wild populations contributed traits that enabled the introduced varieties in the Mediterranean coastal areas to adapt to different regions, as they moved northward into cooler climates, and to greatly diversify within and between wine-producing countries.
Magris et al. (2021) The genomes of 204 Vitis vinifera accessions reveal the origin of European wine grapes. Nature Communications 12(1):7240
Funded by the Italian Ministry of Agriculture (MIPAAF), EU Cross-border cooperation Italy-Slovenia, European Research Council
Status: Novabreed project, completed; Vigneto project, completed; VISO project, completed
Thanks to a collaboration with the Centre for GeoGenetics at the Natural History Museum of Denmark in Copenhagen, the Trace and Environmental DNA Laboratory, Curtin University in Perth, and archeologists across Europe, Armenia and Israel, IGA has compared modern grape varieties with ancient DNA recovered from a collection of grape pips and specimens from archeological sites across Eurasia, dating ca. 4000 BC–1500 AD.
Specimens from medieval times excavated in the Western Europe belong to the three most frequent chlorotypes A, C, and D found in modern varieties of the same geographical area. Vice versa, specimens predating medieval times do not show evidence of the A chlorotype, the most frequent chlorotype in undomesticated grape populations that survived until the present in Western Europe. Roman-age seeds excavated from the Colosseum have the chlorotype D. Chlorotype D is prevalent in modern varieties from the Balkans, Anatolia, and the Near East. Two specimens from the southeastern tip of the Italian peninsula do not have an exact counterpart in modern chlorotypes The specimen dating 7th-9th century AD is closely related to modern chlorotype C. The specimen dating 4th-2nd century BC has a chlorotype ancestral to modern chlorotype D. All this evidence is compatible with westward spread of eastern varieties and introgression of wild western grapes.
The nuclear genome has even greater promise to compare individual archeological specimens against modern varieties, disclosing their genetic affiliations. We are excited by this look into the past.
Wales N et al (2016) The limits and potential of paleogenomic techniques for reconstructing grapevine domestication. Journal of Archaeological Science 72:57-70
Bud sports are an important source of genetic variation in fruit crops. IGA has developed an efficient bioinformatic pipeline for the detection of somatic mutations in plant varieties. A protocol of validation of somatic variants is available for thousands of variant sites in a single-run experiment. IGA-subsidiary IGATech uses this know-how to offer a service of clone identification to breeding companies and plant nurseries.
We applied Illumina sequencing and this toolkit to investigate SNPs and structural variants in “cultivar” groups of sweet orange, and in ecotypes of different grape varieties.
Through our subsidiary company IGA-Tech, IGA's commitment to explore somaclonal variation in vegetatively propagated crops has extended to citrus fruits.
The assembled genome of a haploid clementine has provided the reference Citrus sequence and insights into the ancient origin of cultivated citrus types. The PON-Citrus project offered IGA the opportunity of producing de novo genome assemblies of the three ancestral species (mandarin, pummelo and citron) that generated different citrus crops.
Genetic variation in twenty cultivated sweet oranges was investigated with our pipeline for somatic variants. All "varieties" of sweet orange arose through somatic mutations. Shared and private SNPs provided enough resolution for inferring clone phylogeny. Blood oranges have highly diverged from blond oranges. Variation within blond oranges (common oranges versus navels) is higher than variation within blood oranges. The extent of SNP variation within each "cultivar group" (common oranges, navels, Moro, Tarocco) is fairly similar.
PON-Citrus is a collaborative project with Parco Tecnologico Padano Lodi, University of Padua, CREA Acireale
Funded to IGA-Tech by PON Ricerca e Competitività 2007-2013, Fondo Europeo di Sviluppo Regionale
Sangiovese is an iconic grapevine in Central Italy. Sangiovese grapes are used for producing the Tuscan red wines Brunello di Montalcino, Chianti Classico and Vino Nobile di Montepulciano, known worldwide for their fine quality. Local ecotypes or somatic variants of Sangiovese have slightly different compositions of berry metabolites. Each wine district claims the peculiarity of local wines derived from the unique combination of local ecotypes grown in the local microclimate.
IGA has applied a proprietary pipeline for identifying somatic mutations in ten ecotypes of Sangiovese. Tuscan ecotypes - grown in Central Italy on the Tyrrenian side of the Apennines - differ from one another for dozens of somatic SNPs. Each Tuscan ecotype has a similar level of somatic diversity with clones grown on the Adriatic side of the Apennines, collectively known as ecotype ‘Romagnolo’. The model of intravarietal diversity in Sangiovese is a star-shaped tree, with predominant private SNPs in each clone and a minority of SNPs shared between pair of clones.
Applied research funded by Vivai Cooperativi Rauscedo
We have used single-primer enrichment technology (SPET) to generate sequence-based genotyping data sets in black poplar (P. nigra). A large-scale study of a natural black poplar population of 540 individuals - sampled from Spain, Italy, France, Germany, and The Netherlands - allowed us to reveal the structure of genetic diversity in Europe and provided the basis for discovering polymorphisms associated with biomass-related traits.
Scaglione et al (2019) Single primer enrichment technology as a tool for massive genotyping: a benchmark on black poplar and maize. Annals of Botany 124:543-552