PHENOTYPIC AND MOLECULAR ANALYSIS OF CROP NATURAL VARIATION
- Carrasco Gata, David - Technician
- López Román, María Isabel - Postdoctoral Fellow
- Ramírez Parra, Elena - Researcher CSIC-INIA
- Rodríguez Izquierdo, Alberto - PhD Student
How to improve production and adaptation to climate change in crops is one of the key challenges that plant scientist has to address. Our group is focused in developing new genetic and molecular tools to address this challenge. Our research program involved three main fields: 1) Genetic diversity of grapevine and study of the domestication process. 2) Exploiting genetic diversity of wild and cultivated grapevine to manage abiotic stress and to identify natural genotypes tolerant to abiotic stress (drought and salinity). 3) Promoting sustainable viticulture using soil microorganisms with beneficial effects to abiotic stresses.
1.Genetic diversity of grapevine and study of the domestication process
Dual domestication process in grapevine. Glacial cycles and wild adaptations shaped grape domestication and the rise of wine.
This study established that the successive glacial episodes that happened during the Pleistocene split sylvestris into eastern and western ecotypes. The last glacial advance produced the division of the eastern ecotype into two groups that gave rise to a process of dual domestication in grapevine. This process occurred about 11,000 years ago in the Near East and South Caucasus to produce table and wine grapevine, respectively. The researchers found that although the domestication of the South Caucasus is associated with early winemaking, it had limited diffusion and very little additional influence, but the domestication of the Near East came to dominate the entire Mediterranean basin thanks to human trade routes that has been a key factor in promoting gene flow of this specie (Figure 1). The authors state that the origin of wine in Western Europe is associated with cross-fertilization (introgression) between wild populations of Western Europe and domesticated grapes originating in the Near East that were initially used as food sources.
Domestication process caused different methylation strategies in grapevine.
The vegetative propagation of grapevine allowed preserving the phenotype easier than using sexual reproduction. However, in spite of the use of vegetative propagation in grapevine, different phenotypes often appeared in the same vineyard. To explain this effect, the advances in epigenomic knowledge in plants could explain these variations by different epialleles that could produce that phenotypic variance. This study shown that cultivar grapevines methylated genes related to oxidative stress and polyphenols metabolic processes, whereas wild grapevines methylated genes related to response to biotic stress in plants.( Figure 2)
Figure 2: At left, representation of all Genes methylation Body (GmB) and promoters which contain methylated cytosines with no DMR (Differential Methylated Regions) (CMRG, Common Methylated Gene Regions, in green) and DMRs (Wild DMR, in yellow; Cultivated, in red), and their respective percentage of methylated cytosines depending on the gene part (exon, intron or promoter). At right, the number of genes for each type of methylated genes and their correspondent most representative GO term.
2. Exploiting genetic diversity of wild and cultivated grapevine to manage abiotic stress
Analysis of wild and cultivated grapevine genotypes across the Mediterranean basin identified natural genotypes or cultivars tolerant to abiotic stress. Physiological, transcriptomic, and metabolomic analyses were conducted to identify putative genes related to abiotic stress.
In salinity conditions, we have identified a wild grapevine genotype called AS1B that is tolerant to salinity stress. Comparative transcriptomic responses between AS1B and the rootstock Richter 110, demonstrated that AS1B exhibits a greater response to mild increases in salinity and develops specific mechanisms of tolerance under sustained salt stress (Figure 3). In contrast, Richter 110 maintains constitutive expression until faced with high and prolonged saline inputs, where it primarily shows responses to osmotic stress (Figure 3). The genetic basis of AS1B's strategy to cope with salinity could be valuable in breeding programs aimed at expanding the range of salt-tolerant rootstocks, thus improving viticulture adaptation to climate change.
Under drought conditions, commercial varieties such as Merlot are more sensitive to water deprivation compared to local varieties like Callet, which are accustomed to arid climates. The results revealed that ABA sensitivity in grapevines is crucial for drought tolerance. The study demonstrated that Callet exhibits a more modulated gene expression pattern to minimize water loss compared to Merlot. Additionally, the study uncovered a dual response originating from the scion to the rootstock resulting from this modulation, which could influence rootstock behaviour.
3. Sustainable viticulture using soil microorganisms
Promoting sustainable viticulture involves not only efficient use of water using drought-tolerant cultivars, but also the use of innovative agricultural techniques. The beneficial effects of soil microorganisms, such as increased tolerance to drought, can help crops adapt to climate change. Studies in this direction suggest that the bacterial community was more affected by the variety cultivated than by changes in available water. While in the fungal community it is strongly influenced by water stress and a greater number of genera present were detected. In addition, the presence of microorganisms in the rhizospheric soil with potential positive effect on plants under conditions of water stress were observed.
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