PHENOTYPIC AND MOLECULAR ANALYSIS OF CROP NATURAL VARIATION

Group leader: Rosa Adela Arroyo García - Research Professor CSIC-INIA
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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) development of genomic tools to identify the genetic bases of the natural variation at quality traits in grape with the purpose to development molecular markers that allow to accelerate the selection in breeding programs; 2) Identify natural genotypes tolerant to abiotic stress (drought and salinity) related to climate change and evaluation of candidate genes responsible of the phenotypic variation. 3) Molecular characterization of plant genetic resources of legume collections (Vicia sativa L) for breeding purposes. In order to identify the genes and the nucleotide variation that it is responsible for the fruit quality variation. We have exploited the possibilities that offer the combination of the genomic information with the different tools of genetic analysis. Elucidation of the molecular basis of these traits can allow increasing the effectiveness of the breeding programs. Other efficient tool in the identification of characters of quality is the characterization of the metaboloma of mature berries of wild accessions and clones of wine grape varieties, with the purpose of determinate biomarkers of quality for the clones and search of new metabolites in the wild accessions. Regarding the abiotic stress tolerance we will exploit the genetic diversity of the European Wild Grape (Vitis sylvestris) for the development of resilient rootstocks. In this context, the final objective is the development of molecular tools that allow to accelerate the selection in future breeding programs of wine grape.


GOALS

  1. The analysis of the genetic diversity and the study of the domestication process in grapevine.
  2. The genetic control of quality traits in grape and tolerance to abiotic stress using the grapevine natural variation.
  3. Origin and consequences of somatic variation in grapevine.
  4. Development of genetic tools for genetic improvement of crops.


RESEARCH ACTIVITY


Genetic diversity analysis in germplasm collection


Grapevine

The wild grapevine, Vitis vinifera L. ssp. sylvestris (Gmelin) Hegi, considered as the ancestor of the cultivated grapevine, is native from Eurasia. In Spain, natural populations of V. vinifera ssp. sylvestris can still be found along river banks. We have performed a wide search of wild grapevine populations in Spain and characterized the amount and distribution of their genetic diversity using 25 nuclear SSR loci. The genetic diversity of wild grapevine populations was similar than that observed in the cultivated group. The molecular analysis showed that cultivated germplasm and wild germplasm are genetically divergent with low level of introgression. We have identified four genetic groups, with two of them fundamentally represented among cultivated genotypes and two among wild accessions. The analyses of genetic relationships between wild and cultivated grapevines could suggest a genetic contribution of wild accessions from Spain to current Western cultivars. Currently, we are carrying out the phenotypic characterization of wild grapevine accessions from the Iberian Peninsula.


Common vetch

The common vetch, Vicia sativa, is one of the most important annual forage-grain legumes due to its economic and ecological advantages. INIA conserves the active Spanish germplasm collection of vetch. These plant resources from native landrace varieties are essential for the selection of characters of agronomic interest. In the current context of climate change, we have a special interest in the improvement focused on the selection and production of new varieties tolerant to drought and aridity. Our aim is the development of molecular tools (functional molecular markers) for breeding programs to select and improve drought tolerant varieties.

 

Figure 1. Grapevine natural populations (Vitis vinifera L ssp sylvestris)

 

Natural variation at quality traits in grapevine

The color is a quality trait determined by the quantity and anthocyanin profile of the berry. The biochemical analysis of these traits in wild grape accessions showed different profiles than cultivated grapevine. In grapevine the transcriptional factors VvmybA1 and VvmybA2 are associated with this trait. We have analyzed the allelic variants present in wild grape accessions from the both end of Mediterranean basin (Iberian Peninsula and Anatolian Peninsula). Results provide evidence that variation in both transcriptional regulators has generated a new allelic series that it has been not found in cultivated grapevine. Furthermore, the allelic series showed correlation with anthocyanins content. At the same time, we have analyzed the biochemical profile of the wild berries compared with the cultivated ones. The results showed a different biochemical profile and we have performed a transcriptomic analysis to evaluate the genes expression patterns and associate them with their phenylpropanoid profiles. Some genes of the phenylpropanoid pathway were up-regulated in wild compared with cultivated grapevine. Most noticeably, transcript levels of stilbene synthase genes showed steady increase. Transcriptional regulation of MYBA1, MYBA2, MYBF, F3'H, F3'5'H, UFGT, OMT, and FLS are in some cases correlated with the characteristic anthocyanin and flavonol profiles in wild berry skin. These results reveal a unique pattern of transcription and biosynthesis pathways regulation underlying the enological characteristics of wild grape. In addition, the expression profiles of stress-related genes showed a specific dynamic modulation during berry development in wild berries. These results yield new knowledge on the distinct chemistry and characteristics of wild berry.

Somatic mutations that affect berry skin color leading to various phenotypes have been one of the major contributors for the current diversity in cultivated grapevines. Our research on grape berry color demonstrates that in white-skinned cultivars the absence of anthocyanins is related with the insertion of the Gret1, a long retrotransposon, in the promotor region of MYBA1 gene, combined with two non-conservative mutations in the coding sequence of MYBA2 gene. Additionally, several molecular and cellular mechanisms have been described as being behind berry skin color reversions occurring on grape varieties, which is linked to the phenolic profiles, specifically with the anthocyanin profile of the cultivars and ultimately with the skin color phenotype diversity.

 

Figure 2. Heat map showing the differentially expressed genes in the full ripening stage of wild and cultivated berries. The color legend represents the abundance of transcripts. In red up regulated and blue down-regulated.

 

Exploiting the genetic diversity of the wild grapevine for adaptive trait

Adaptation to adverse environment is the central survival strategy of plants. As active process, adaptation requires that resources are repartitioned that otherwise would be available for growth. When humans domesticated plants for their own purposes, they selected for high yield and rapid growth which was achieved on the cost of reduced resilience (and the lost of the genetic factors underlying this resilience). Humans compensated this by creating a highly artificial environment, where the crop is cultivated under optimal conditions and environmental challenges are compensated by agricultural means including fertilization, irrigation, weeding, and chemical plant protection. Wild ancestors of crops have to survive without relying on this artificial support and therefore represent valuable resources to mine for resilience genes or alleles. For that reason, we have analyzed wild and cultivated genotypes around the Mediterranean basin and we have identified natural genotypes or cultivars tolerant to abiotic stress (drought and salinity) and better quality of grape characters related to climate change such as higher acidity and resveratrol content. Actually we are performed the transcriptomic analyses in order to identified putative genes related to abiotic stress.


Representative Publications

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.