SNP-Discovery by RAD-Sequencing in a Germplasm Collection of Wild and Cultivated Grapevines (V. vinifera L.)

Marrano, Annarita; Birolo, Giovanni; Prazzoli, M.L.; Lorenzi, Silvia; Valle, Giorgio; Grando, S.

doi:10.1371/journal.pone.0170655

Cited by 50 publications

(63 citation statements)

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“…All these results are in agreement with previous studies attributing the low level of diversity among sylvestris and the absence of an inter-sylvestris population geneflow to the small size and the isolation of the sylvestris populations, and the high level of diversity within cultivated genotypes to the sexual crossing occurring during the grapevine domestication (This et al, 2006;Di Vecchi-Staraz et al, 2008;Vitti et al, 2013;Marrano et al, 2017;Riaz et al, 2018).…”

Section: Discussionsupporting

confidence: 93%

“…Also the SNPs heterozygosity was higher in the sativa grapevine compared to sylvestris, supporting previous observations based on SNPs analysis (Lijavetzky et al, 2007;Emanuelli et al, 2013;Marrano et al, 2017). With the exclusion of the accessions indicated as non-true-sylvestris, the SNPs heterozygosity of sylvestris further decreased to a range of 37-41% ( Supplementary Table S2).…”

Section: Discussionsupporting

confidence: 86%

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Introgression Among Cultivated and Wild Grapevine in Tuscany

D'Onofrio

2020

Front. Plant Sci.

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Wild grapevine, Vitis vinifera L. subsp. sylvestris (Gmelin, Hegi) is spontaneous to Europe and common in Tuscany. In this study, wild grapevines were identified in 22 populations from eight locations in Tuscan Maremma (Grosseto and Siena province). The plants were propagated by cuttings, collected in a vineyard, genotyped by nuclear simple sequence repeats (SSRs), chloroplast SSRs and single nucleotide polymorphisms (SNPs), and compared to locally cultivated varieties (Vitis vinifera L. subsp. sativa) and to non-vinifera and non-vitis genotypes. The identity analysis revealed that some individuals were redundant genotypes, suggesting natural vegetative propagation. In addition, four of the supposed V.v. sylvestris were in fact naturalized V.v. sativa. The majority of putative sylvestris genotypes had chlorotype A, while the remainder had chlorotype D, as the majority of Vitis vinifera subsp. sativa cultivated in Italy. Some of the recovered sylvestris genotypes appeared to be natural crosses with cultivated grapevine varieties in Tuscany, and their chlorotype suggests a higher pollen flow from sativa to the sylvestris genotypes than in the opposite direction. In addition, other genotypes appeared to be crosses within sylvestris, sylvestris-sativa or sylvestris-sylvestris siblings, or equivalent relationships. These relationships suggest a noticeably level of sexual reproductive activities among sylvestris and sylvestris-sativa genotypes. A cluster and structure analysis clearly differentiated the true sylvestris from the sativa, and the nonvinifera or non-vitis genotypes, and also highlighted a possible introgression of sylvestris into some Italian and French cultivated varieties. The results therefore suggest that, in addition to the primary ancient center of domestication from the Near East to Central Asia, the introgression among cultivated and wild grapevine occurred in other centers of diversification along the migration routes, contributing to the domestication processes, and suggesting that these processes are still ongoing despite the reduction in populations of sylvestris. The results also highlight that the GrapeReSeq 18K Vitis genotyping chip are suitable for non-vitis genotyping and that the range of SNPs heterozygosity in sylvestris appears to be up to 6% less and does not overlap the heterozygosity range of sativa genotypes.

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Section: Discussionsupporting

confidence: 93%

Section: Discussionsupporting

confidence: 86%

Introgression Among Cultivated and Wild Grapevine in Tuscany

D'Onofrio

2020

Front. Plant Sci.

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“…In wild species the percentages were 73% and 27% respectively, while 71% and 29% were the values observed in hybrid/wild species genotypes. The current results slightly diverge from the usual transitions/transversions ratio found in grapevine (~1.5 in Salmaso et al , 2004; Lijavetzky et al , 2007; Vezzulli et al , 2008a; 2008b; ~2 in Marrano et al , 2017) as well as in beetroot (Schneider et al , 2001), potato (Simko, Haynes, & Jones, 2006) and cotton (Byers et al , 2012), while they are much higher than in soybean (Zhu et al , 2003) and almond (Wu et al , 2008).…”

Section: Resultscontrasting

confidence: 88%

“…SNP informativeness depends on their reliability among individuals and species and their high transferability rates probably are not consistent with a direct impact on the genetic sequence (when in coding regions). Considering previous studies in grapevine, a larger representativeness of MAF values <0.1 was found in non- vinifera genotypes and rootstocks, non-cultivated vinifera showed a MAF 0.05<x<0.3 while MAF >0.1 were severely represented by vinifera sativa (Lijavetzky et al , 2007; Vezzulli et al , 2008a; Emanuelli et al , 2013; Marrano et al , 2017). In the current study, the aim to focus on impacting mutations was achieved, since MAF ≤0.05 is a distinguishing mark for rare SNPs, which may be not considered interesting for SNP-arrays but which are most likely affecting the gene sequence and putatively protein activity.…”

Section: Resultsmentioning

confidence: 62%

Mining downy mildew susceptibility genes: a diversity study in grapevine

Pirrello

Zeilmaker²,

Bianco

et al. 2020

Preprint

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AcknowledgmentsCP acknowledges funding from a FEM PhD fellowship at University of Udine, including a support from SciENZA Biotechnologies bv. Conflict of Interest StatementThe authors declare no conflict of interest. AbstractSeveral pathogens continuously threaten viticulture worldwide. Until now, the investigation on resistance loci has been the main trend to understand the interaction between grapevine and mildew causal agents. Dominantly inherited gene-based resistance has shown to be race-specific in some cases, to confer partial immunity and to be potentially overcome within a few years since its introgression. Recently, on the footprint of research conducted on Arabidopsis, the putative hortologues of genes associated with downy mildew susceptibility in this species, have been discovered also in the grapevine genome. In this work, we deep-resequenced four putative susceptibility genes in 190 highly genetically diverse grapevine genotypes to discover new sources of broad-spectrum recessively inherited resistance. The scouted genes are VvDMR6-1, VvDMR6-2, VvDLO1, VvDLO2 and predicted to be involved in susceptibility to downy mildew. From all identified mutations, 56% were Single Nucleotide Polymorphisms (SNPs) in heterozygosity, while the remaining 44% were homozygous. Regarding the identified mutations with putative impact on gene function, we observed ~4% genotypes mutated in VvDMR6-1 and ~8% mutated in VvDMR6-2, only a handful of genotypes that were mutated in both genes. ~2% and ~7% genotypes showed mutations in VvDLO1 and VvDLO2 respectively, and again a few genotypes resulted mutated in both genes. In particular, 80% of impacting mutations were heterozygous while 20% were homozygous.The current results will inform grapevine genetics and corroborate genomic-assisted breeding programs for resistance to biotic stresses.A survey on the genetic diversity of downy mildew susceptibility genes in grapevine varieties and wild species reveals a potential valuable for genomic-assisted breeding as well as tailored gene editing to induce disease resistance.

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“…Furthermore, collections of clones may represent a wider sampling of variation in the species than a population from a single geographic area. Our observations are not entirely uncommon-for instance, cultivated grapevine (Marrano et al, 2017) was more heterozygous than its wild counterpart and a study using microsatellites found that genetic diversity in hazelnut cultivars was similar or higher than wild populations in southern Europe (Boccacci et al, 2013).…”

Section: No Strong Domestication Bottleneck In Hazelnutmentioning

confidence: 48%

Genetic diversity and domestication of hazelnut (Corylus avellana L.) in Turkey

Helmstetter

Oztolan‐Erol

Lucas

et al. 2020

Plants People Planet

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Hazelnut is consumed worldwide and is of critical economic importance to the rural communities of Turkey's northern coast. A new disease outbreak has drastically decreased yields across Turkey and climate change is emerging as a new threat to cultivation. Our study is the first to provide a genomic perspective on diversity in this vulnerable crop, which will prove valuable for future breeding efforts. Such research into perennial crops like hazelnut can help to improve farmer livelihoods and ensure the sustainability of crop production in a changing world. Summary• Assessing and describing genetic diversity in crop plants is a crucial first step toward their improvement. The European hazelnut, Corylus avellana L., is one of the most economically important tree nut crops worldwide. It is primarily produced in Turkey where rural communities depend on it for their livelihoods. Despite this, we know little about its domestication history and the genetic diversity it holds.• We use double digest restriction-site associated DNA (ddRAD) sequencing to produce a genome-wide dataset containing wild and domesticated hazelnut. We uncover patterns of population structure and diversity, determine levels of crop-wild gene flow, and estimate the relationships among different genetic clusters.• We use a dataset of over 60k single nucleotide polymorphisms to find that genetic clusters of cultivars do not reflect their given names and that there is limited evidence for a reduction in genetic diversity in domesticated individuals. We find evidence that hazelnut may have been domesticated more than once and that admixture has likely occurred multiple times between wild and domesticated hazelnut.• We provide the first genomic assessment of Turkish hazelnut diversity and suggest that there has not been an extreme bottleneck during the domestication of this crop, leading to cultivars at different stages of domestication. Our study provides a platform for further research that will protect hazelnut from the threats of climate change and an emerging fungal disease. | 327 HELMSTETTER ET aL.

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SNP-Discovery by RAD-Sequencing in a Germplasm Collection of Wild and Cultivated Grapevines (V. vinifera L.)

Cited by 50 publications

References 65 publications

Introgression Among Cultivated and Wild Grapevine in Tuscany

Introgression Among Cultivated and Wild Grapevine in Tuscany

Mining downy mildew susceptibility genes: a diversity study in grapevine

Genetic diversity and domestication of hazelnut (Corylus avellana L.) in Turkey

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