PHENOTYPIC AND MOLECULAR ANALYSIS OF CROP NATURAL VARIATION

 

Personnel:



GENERAL OVERVIEW

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.


RESEARCH ACTIVITY

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.



Figure 1. Geographic distribution of CG1 and CG2 in relation to the domestication centers. Human dispersal routes shown.

 

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.



Figure 3. General transcriptomic profiles between the wild grapevine genotype AS1B and the rootstock, Richter 110 over increasing salt concentration and exposure.

 

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.

 

 


Representative Publications

Zhang, C., Dai, Z., Ferrier, T., Orduña, L., Santiago, A., Peris, A., Wong, D.C.J., Kappel, C., Savoi, S., Loyola, R., Amato, A., Kozak, B., Li, M., Liang, A., Carrasco, D., Meyer-Regueiro, C., Espinoza, C., Hilbert, G., Figueroa-Balderas, R., Cantu, D., Arroyo-Garcia, R., Arce-Johnson, P., Claudel, P., Errandonea, D., Rodríguez-Concepción, M., Duchêne, E., Huang, S.C., Castellarin, S.D., Tornielli, G.B., Barrieu, F., Matus, J.T. 2023. MYB24 orchestrates terpene and flavonol metabolism as light responses to anthocyanin depletion in variegated grape berries. The Plant Cell koad228. DOI: 10.1093/plcell/koad228

Jiménez-Cantizano, A., Puig-Pujol, A., Arroyo-García, R. 2023. Identification of Vitis vinifera L. Local Cultivars Recovered in Andalusia (Spain) by Using Microsatellite Markers. Horticulturae 9, 316. DOI: 10.3390/horticulturae9030316

Ramírez-Parra, E., De la Rosa, L. 2023. Designing Novel Strategies for Improving Old Legumes: An Overview from Common Vetch. Plants 12, 1275. DOI: 10.3390/plants12061275

Dong, Y., Duan, S., Xia, Q., Liang, Z., Dong, X., Margaryan, K., Musayev, M., Goryslavets, S., Zdunić, G., Bert, P.-F., Lacombe, T., Maul, E., Nick, P., Bitskinashvili, K., Bisztray, G.D., Drori, E., De Lorenzis, G., Cunha, J., Popescu, C.F., Arroyo-Garcia, R., Arnold, C., Ergül, A., Zhu, Yifan, Ma, C., Wang, Shufen, Liu, S., Tang, L., Wang, C., Li, D., Pan, Y., Li, J., Yang, L., Li, X., Xiang, G., Yang, Z., Chen, B., Dai, Z., Wang, Yi, Arakelyan, A., Kuliyev, V., Spotar, G., Girollet, N., Delrot, S., Ollat, N., This, P., Marchal, C., Sarah, G., Laucou, V., Bacilieri, R., Röckel, F., Guan, P., Jung, A., Riemann, M., Ujmajuridze, L., Zakalashvili, T., Maghradze, D., Höhn, M., Jahnke, G., Kiss, E., Deák, T., Rahimi, O., Hübner, S., Grassi, F., Mercati, F., Sunseri, F., Eiras-Dias, J., Dumitru, A.M., Carrasco, D., Rodriguez-Izquierdo, A., Muñoz, G., Uysal, T., Özer, C., Kazan, K., Xu, M., Wang, Yunyue, Zhu, S., Lu, J., Zhao, M., Wang, L., Jiu, S., Zhang, Y., Sun, L., Yang, H., Weiss, E., Wang, Shiping, Zhu, Youyong, Li, S., Sheng, J., Chen, W. 2023. Dual domestications and origin of traits in grapevine evolution. Science 379, 892–901. DOI: 10.1126/science.add8655

Álvarez-Aragón, R., Palacios, J.M., Ramirez-Parra, E. 2023. Rhizobial symbiosis promotes drought tolerance in Vicia sativa and Pisum sativum. Environmental and Experimental Botany 105268. DOI: 10.1016/j.envexpbot.2023.105268

Paprocka, M., Dancewicz, K., Kordan, B., Damszel, M., Sergiel, I., Biesaga, M., Mroczek, J., Arroyo Garcia, R.A., Gabryś, B. 2023. Probing behavior of Aphis fabae and Myzus persicae on three species of grapevines with analysis of grapevine leaf anatomy and allelochemicals. The European Zoological Journal 90, 83–100. DOI: 10.1080/24750263.2022.2162615

Carrasco, D., Zhou-Tsang, A., Rodriguez-Izquierdo, A., Ocete, R., Revilla, M.A., Arroyo-García, R. 2022. Coastal Wild Grapevine Accession (Vitis vinifera L. ssp.sylvestris) Shows Distinct Late and Early Transcriptome Changes under Salt Stress in Comparison to Commercial Rootstock Richter 110. Plants 11, 2688. DOI: 10.3390/plants11202688

De la Rosa, L., López-Román, M.I., González, J.M., Zambrana, E., Marcos-Prado, T., Ramírez-Parra, E. 2021. Common Vetch, Valuable Germplasm for Resilient Agriculture: Genetic Characterization and Spanish Core Collection Development. Frontiers in Plant Science 12, 282. DOI: 10.3389/fpls.2021.617873

Grassi, F., Arroyo-Garcia, R. 2020. Editorial: Origins and Domestication of the Grape. Frontiers in Plant Science 11, 1176. DOI: 10.3389/fpls.2020.01176

De la Rosa, L., Zambrana, E., Ramirez-Parra, E. 2020. Molecular bases for drought tolerance in common vetch: designing new molecular breeding tools. BMC Plant Biology 20, 71. DOI: 10.1186/s12870-020-2267-z

Ferreira, V., Matus, J.T., Pinto-Carnide, O., Carrasco, D., Arroyo-García, R., Castro, I. 2019. Genetic analysis of a white-to-red berry skin color reversion and its transcriptomic and metabolic consequences in grapevine (Vitis vinifera cv. ‘Moscatel Galego’). BMC Genomics 20, 952. DOI: 10.1186/s12864-019-6237-5

Ocete, C.A., Arroyo, R., Lovicu, G., Rodríguez-Miranda, Á., Valle, J.M., Cantos, M., Garciá, J.L., Lara, M., De Canales, F.G., Llompart, J., Rodríguez, E.M., Weiland, C.M., Ocete, R. 2019. An inventory of the relic eurasian wild grapevine populational nuclei in huelva province (andalusia, Spain). Vitis - Journal of Grapevine Research 58, 53–57. DOI: 10.5073/vitis.2019.58.53-57

Ferreira, V., Castro, I., Carrasco, D., Pinto-Carnide, O., Arroyo-García, R. 2019. Molecular characterization of berry color locus on the portuguese cv. ‘Fernão Pires’ and cv. ‘Verdelho’ and their red-berried somatic variant cultivars. Ciência e Técnica Vitivinícola 33, 184–190. DOI: 10.1051/ctv/20183302184

Jiménez-Cantizano, A; García De Luján, A; Arroyo-García, R. 2018. "Molecular characterization of table grape varieties preserved in the Rancho de la Merced Grapevine Germplasm Bank (Spain)". Vitis - Journal of Grapevine Research. DOI: 10.5073/vitis.2018.57.93-101".

Ferreira, V; Pinto-Carnide, O; Arroyo-García, R; Castro, I. 2018. "Berry color variation in grapevine as a source of diversity". Plant Physiology and Biochemistry. DOI: 10.1016/j.plaphy.2018.08.021".

Ferreira, V; Castro, I; Carrasco, D; Pinto-Carnide, O; Arroyo-García, R. 2018. "Molecular characterization of berry skin color reversion on grape somatic variants". Journal of Berry Research. DOI: 10.3233/JBR-170289".

Riaz, S; De Lorenzis, G; Velasco, D; Koehmstedt, A; Maghradze, D; Bobokashvili, Z; Musayev, M; Zdunic, G; Laucou, V; Andrew Walker, M; Failla, O; Preece, JE; Aradhya, M; Arroyo-Garcia, R. 2018. "Genetic diversity analysis of cultivated and wild grapevine (Vitis vinifera L.) accessions around the Mediterranean basin and Central Asia". BMC Plant Biology. DOI: 10.1186/s12870-018-1351-0".

Revilla, E; Arroyo-Garcia, R; Bellido, A; Carrasco, D; Puig, A; Ruiz-Garcia, L. 2018. "Fingerprints of anthocyanins and flavonols in wild grapes (Vitis vinifera L. ssp. sylvestris (Gmelin) Hegi)". In A. M. Jordão and F. Cosme (eds.), Grapes and Wines - Advances in Production, Processing, Analysis and Valorization. DOI: 10.5772/intechopen.70861".

Lara, M; Iriarte-Chiapusso, MJ; Cantos, M; García Jiménez, JL; Morales, R; Ocete, CA; López, MA; Salinas, JA; Rubio, I; Hidalgo, J; Íñiguez, M; Rodríguez, A; Valle, JM; Arroyo-García, R; Ayala, MC; Armendáriz, I; Maghradze, D; Arnold, C; Ocete, R. 2017. "La vid silvestre. Un importante recurso fitogenético sin protección legal en España. The wild vine. An important phytogenetic resource without legal protection in Spain.". Revista Iberoamericana de Viticultura, Agroindustria y Ruralidad.

Ferreira, V; Fernandes, F; Carrasco, D; Hernandez, MG; Pinto-Carnide, O; Arroyo-García, R; Andrade, P; Valentão, P; Falco, V; Castro, I. 2017. "Spontaneous variation regarding grape berry skin color: A comprehensive study of berry development by means of biochemical and molecular markers". Food Research International. DOI: 10.1016/j.foodres.2017.03.050".

Cantos, M; Arroyo-García, R; García, JL; Lara, M; Morales, R; López, MÁ; Gallardo, A; Ocete, CA; Rodríguez, Á; Valle, JM; Vaca, R; González-Maestro, M; Bánáti, H; Ocete, R. 2017. "Current distribution and characterization of the wild grapevine populations in Andalusia (Spain)". Comptes Rendus Biologies. DOI: 10.1016/j.crvi.2017.01.004".

Arroyo-García, R; Cantos, M; Lara, M; López, M-Á; Gallardo, A; Ocete, CA; Pérez, Á; Bánáti, H; García, JL; Ocete, R. 2016. "Characterization of the largest relic Eurasian wild grapevine reservoir in Southern Iberian Peninsula". Spanish Journal of Agricultural Research. DOI: 10.5424/sjar/2016143-8929".

Carrasco, D; De Lorenzis, G; Maghradze, D; Revilla, E; Bellido, A; Failla, O; Arroyo-García, R. 2015. "Allelic variation in the VvMYBA1 and VvMYBA2 domestication genes in natural grapevine populations (Vitis vinifera ssp sylvestris)". Plant Syst and Evol. DOI: 10.1007/s00606-014-1181-y".

Ferreira, V; Fernandes, F; Pinto-Carnide, O; Valentão, P; Falco, V; Martín, JP; Ortiz, JM; Arroyo-García, R; Andrade, PB; Castro, I. 2016. "Identification of Vitis vinifera L. grape berry skin color mutants and polyphenolic profile". Food Chemistry. DOI: 10.1016/j.foodchem.2015.07.142".

de Andrés, M.T.; Benito, A.; Perez-Rivera, G.; Ocete, R.; Lopez, M.A.; Gaforio, L.; Muñoz, G.; Cabello, F.; Martínez-Zapater, J.M.; Arroyo-Garcia, R. 2012. "Genetic diversity of wild grapevine populations in Spain and their genetic relationship with cultivated grapevines". Molecular Ecology. 21(4):800-816.