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Article|31 Jan 2022|OPEN
Extent of wild–to–crop interspecific introgression in grapevine (Vitis vinifera) as a consequence of resistance breeding and implications for the crop species definition
Serena Foria1,2,5 ,† , Gabriele Magris1,2 ,† , Irena Jurman1 , Rachel Schwope1,2 and Massimo De Candido3 , Elisa De Luca3 , Dragoslav Ivanisevi ˇ c4 , Michele Morgante1,2 , , Gabriele Di Gaspero,1 ,
1Istituto di Genomica Applicata, via Jacopo Linussio, 51, 33100 Udine, Italy
2Department of Agricultural, Food, Environmental and Animal Sciences, University of Udine, via delle Scienze 206, 33100 Udine, Italy
3VCR Research Center, Vivai Cooperativi Rauscedo, Via Ruggero Forti 4, 33095 San Giorgio della Richinvelda, Italy
4Faculty of Agriculture, University of Novi Sad, Trg Dositeja Obradovica 8, 21102 Novi Sad, Serbia
5Current address: Dr. Schär R&D Centre, Padriciano 99, 34149 Trieste, Italy
*Corresponding author. E-mail: michele.morgante@uniud.it,digaspero@appliedgenomics.org
Both authors contributed equally to the study.

Horticulture Research 9,
Article number: uhab010 (2022)
doi: https://doi.org/10.1093/hr/uhab010
Views: 176

Received: 26 Jun 2021
Revised: 18 Jan 2022
Accepted: 25 Sep 2021
Published online: 31 Jan 2022

Abstract

Over the past two centuries, introgression through repeated backcrossing has introduced disease resistance from wild grape species into the domesticated lineage Vitis vinifera subsp. sativa. Introgression lines are being cultivated over increasing vineyard surface areas, as their wines now rival in quality those obtained from preexisting varieties. There is, however, a lot of debate about whether and how wine laws defining commercial product categories, which are based on the classification of V. vinifera and interspecific hybrid grapes, should be revised to accommodate novel varieties that do not fit either category. Here, we developed a method of multilocus genotype analysis using short–read resequencing to identify haplotypic blocks of wild ancestry in introgression lines and quantify the physical length of chromosome segments free–of–introgression or with monoallelic and biallelic introgression. We used this genomic data to characterize species, hybrids and introgression lines and show that newly released resistant varieties contain 76.5–94.8% of V. vinifera DNA. We found that varietal wine ratings are not always commensurate with the percentage of V. vinifera ancestry and linkage drag of wild alleles around known resistance genes persists over at least 7.1–11.5 Mb, slowing down the recovery of the recurrent parental genome. This method also allowed us to identify the donor species of resistance haplotypes, define the ancestry of wild genetic background in introgression lines with complex pedigrees, validate the ancestry of the historic varieties Concord and Norton, and unravel sample curation errors in public databases.