Extent of wild–to–crop interspecific introgression in grapevine (Vitis vinifera) as a consequence of resistance breeding and implications for the crop species definition

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 known 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.

Phased grapevine genome sequence of anRpv12carrier for biotechnological exploration of resistance toPlasmopara viticola

“…It was identified in several independent introgressions of V. amurensis and is present in the genomes of diverse varieties like ‘Michurinetś, ‘Zarja severá, as well as in ‘Kunbarat’, ‘Petrá, ‘Lelá, ‘Kunleaný and ‘Milá (Venuti et al ., 2013). Recently, it was shown that Rpv12 was inherited by V. amurensis to the grapevine variety ‘Merlot Khoruś based on introgression maps (Foria et al ., 2022).…”

“…In general, some influence of the genetic background on the efficiency of individual resistance loci is possible (Foria et al, 2018). Complementarily, little is known about the interaction of combined resistance loci directed against different pathogens, such as Ren and Rpv-Loci.…”

The Role of Italy in the Use of Advanced Plant Genomic Techniques on Fruit Trees: State of the Art and Future Perspectives

“…With the aim of reducing the massive use of chemical compounds in vineyards against fungal pathogens, in 1998 scientists from the University of Udine and the Institute of Applied Genomics (IGA) of Udine started the genetic improvement program which led in 2015 and 2020 to the registration in the Italian National Catalog of new fungi-resistant wine varieties ( , accessed on 20 December 2022). Evaluations of their agronomic traits, enological features, and field resistance to downy and powdery mildews are reported in literature [ 106 , 107 , 108 ]. In 2020, the Foundation Edmund Mach together with Civit (Consorzio Innovazione Vite) also registered four wine varieties resistant to fungal pathogens ( , accessed on 20 December 2022).…”

Advances in Crop Breeding Through Precision Genome Editing

“…It is also an important breeding strategy for transferring desirable traits from wild species to cultivated varieties. Interspecific gene flow has contributed to the origin of crop plants, restoration of crop diversity after domestication and to the adaptation to challenging environments ( Foria et al, 2022 ). Introgressive hybridization has been used to tap the secondary gene pool for accessing the genetic variation for crop improvement in wheat ( Mujeeb-Kazi and Asiedu, 1990 ), rice ( Jena, 2010 ), potato ( Jansky and Oeloquin, 2006 ), tomato ( Schouten et al, 2019 ), cassava ( Wolfe et al, 2019 ).…”