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Rootstocks resistant to this pest are hybrids of American vine species with different levels of compatibility with European<jats:italic>Vitis vinifera<\/jats:italic>varieties. Aiming to understand what drives grafting compatibility in grapevine, a transcriptomic approach was used to search for master regulators of graft success. Two scion\/rootstock combinations, with different levels of compatibility, were compared in a nursery-grafting context at two stages, at 21 and 80\u2009days after grafting.<\/jats:p><\/jats:sec><jats:sec><jats:title>Results<\/jats:title><jats:p>In the most compatible combination, an earlier and higher expression of genes signaling the metabolic and hormonal pathways as well as a reduced expression of genes of the phenolic metabolism and of the oxidative stress response was observed. At 80\u2009days after grafting a higher expression of transcription factors regulating vascular maintenance, differentiation and proliferation was obtained in the most compatible combination. Moreover, lower expression levels of microRNAs potentially targeting important transcription factors related to plant development was observed in the more compatible combination when compared to the less compatible one.<\/jats:p><\/jats:sec><jats:sec><jats:title>Conclusion<\/jats:title><jats:p>In this context, a set of regulators was selected as potential expression markers for early prediction of a compatible grafting.<\/jats:p><\/jats:sec>","DOI":"10.1186\/s12870-019-1967-8","type":"journal-article","created":{"date-parts":[[2019,9,11]],"date-time":"2019-09-11T06:52:46Z","timestamp":1568184766000},"update-policy":"https:\/\/doi.org\/10.1007\/springer_crossmark_policy","source":"Crossref","is-referenced-by-count":47,"title":["Understanding the molecular mechanisms underlying graft success in grapevine"],"prefix":"10.1186","volume":"19","author":[{"ORCID":"https:\/\/orcid.org\/0000-0003-3143-7427","authenticated-orcid":false,"given":"M.","family":"Assun\u00e7\u00e3o","sequence":"first","affiliation":[]},{"given":"C.","family":"Santos","sequence":"additional","affiliation":[]},{"given":"J.","family":"Braz\u00e3o","sequence":"additional","affiliation":[]},{"given":"J. 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