Genome resequencing and custom genotyping elucidates the origin and dissemination history of an emblematic grapevine cultivar, ‘Tempranillo Tinto’

Abstract

Grapevine cultivars are vegetatively propagated to maintain their varietal characteristics. However, long periods of cultivar multiplication result in the accumulation of spontaneous somatic mutations that can differ among clonal lines. Here, we explored this intravarietal genetic diversity to trace back the origin and dissemination history of ‘Tempranillo Tinto’, the third most cultivated wine grape variety worldwide. A stringent somatic variant calling over whole-genome resequencing data of 35 ‘Tempranillo Tinto’ grapevines from seven Iberian winemaking regions revealed 158 somatic single nucleotide variants (SNVs) shared by some of the plants. Among them, 56 highly informative SNVs were used to custom-design a high-throughput intravarietal genotyping assay, which was validated and used to analyze 185 vines representing a broader geographic distribution. Phylogenetic analyses revealed three major clonal lineages in ‘Tempranillo Tinto’ that grouped the samples according to their geographic origin. By inferring the ancestral SNV alleles in ‘Tempranillo Tinto’ from whole-genome resequencing data of its parents, we determined the Ebro River Valley in Northeast Spain as the most likely birthplace of the cultivar. Derived alleles revealed one major historical human-mediated westward dissemination route from this original site towards the winemaking regions following the Duero River Valley and then, to the South in Portugal. Clonal lineages also revealed the polyphyletic nature of somatic variant traits of interest for grape and wine quality production under climate change conditions. Our findings elucidate the origin and historical dispersal of ‘Tempranillo Tinto’ and underscore genomic strategies for advancing clonal improvement to ensure the sustainability of valuable traditional grapevine cultivars.

Acknowledgments

This work is part of the research projects BIO-2017-86375-R and PID2020-120183RB-I00 funded by MICIU/AEI/10.13039/501100011033, and PID2023-152513OB-I00 funded by MICIU/AEI/10.13039/501100011033 and by ERDF/EU. We acknowledge funding from the ERDF granted to the Autonomous Community of La Rioja within the ERDF Operational Program 2021-2027 (project number: PR-05-24). JT was supported by the Ramón y Cajal Programme (RYC2022-037758-I) funded by MCIU/AEI/10.13039/501100011033 and the ESF+. We are grateful to the many institutions, companies and collaborators that provided the plant material used in this work, namely A. Martins (Universidade de Lisboa), G. Santesteban (UPNa), J. Yuste (ITACYL), M. Mena (UCLM), C. Hernández (VCR Agromillora), C. Villanueva (Viveros Villanueva Vides S.L.), E. Regull (Enric Regull S.L.), I. Provedo (Viveros Provedo S.A.), J. Eraso (Vitis Navarra S.A.T.), L. Martínez (Bodegas Roda S.A.), and R. Jiménez (Bodegas Luis Cañas S.A.). The authors also thank the technical and human support provided by SGIker (UPV/EHU/ERDF, EU) and CIBIR for SNV and SSR genotyping, respectively.

Author contributions

J.T. participated in the formal analysis, data curation, methodology, investigation, writing—original draft, writing—review, funding acquisition. P.C.B. participated in the data curation, methodology, investigation, writing—review. R.T.P. participated in the methodology, investigation. Y.F. participated in the investigation. C.R. participated in the investigation. J.P. participated in the resources, investigation, funding acquisition. J.F.C. participated in the resources, investigation. J.C.O. participated in the methodology. J.I. participated in the conceptualization, methodology, writing—review, funding acquisition, project administration. J.M.M.Z. participated in the conceptualization, methodology, supervision, writing—review, funding acquisition, project administration. All authors approved the final version of the manuscript.

Data availability

Raw sequencing data generated for this work can be found in the NCBI SRA database as BioProject ID PRJNA1224223.

Conflict of interest statement

The authors declare no conflicts of interest.

Supplementary data

Supplementary data is available at Horticulture Research online.

References

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