Study of genetic variability in Vitis vinifera L. germplasm by high-throughput Vitis18kSNP array: the case of Georgian genetic resources

Lorenzis, Gabriella De; Chipashvili, R.; Failla, O.; Maghradze, D.

doi:10.1186/s12870-015-0510-9

Cited by 62 publications

(83 citation statements)

References 51 publications

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“…After removing SNPs having a range of NC from 20 to 100 %, the analysis were carried out on the amplified loci showing a GT score lower than 0.6, as well, providing a good coverage of whole genome (79 %). Since the Vitis18kSNP array contains about 25 % of loci identified from different Vitis species (V. aestivalis, V. berlandierii, V. labrusca, V. cinerea, V. lincecumi, and Muscadinia rotundifolia), the percentage of SNP loci (3 %) showing any fragment amplification appeared reasonable, as compared to previous reports (Bekele et al 2013;De Lorenzis et al 2015). The percentage of polymorphic loci was high, and the values of heterozygosity (expected, H e and observed, H o ), very similar among them, lower than those reported for Sicilian collections analyzed by SSR markers (Carimi et al 2010;De Lorenzis et al 2014).…”

Section: Discussionmentioning

confidence: 56%

High-throughput 18K SNP array to assess genetic variability of the main grapevine cultivars from Sicily

Mercati

Lorenzis

Brancadoro

et al. 2016

Tree Genetics & Genomes

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The viticulture of Sicily, for its vocation, is one of the most important and ancient forms in Italy. Autochthonous grapevine cultivars, many of which known throughout the world, have always been cultivated in the island from many centuries. With the aim to preserve this large grapevine diversity, previous studies have already started to assess the genetic variability among the Sicilian cultivars by using morphological and microsatellite markers. In this study, simple sequence repeat (SSR) were utilized to verify the true-to-typeness of a large clone collection (101) belonging to 21 biotypes of the most 10 cultivated Sicilian cultivars. Afterwards, 42 Organization Internationale de la Vigne et du Vin (OIV) descriptors and a high-throughput single nucleotide polymorphism (SNP) genotyping array (Vitis18kSNP) were applied to assess genetic variability among cultivars and biotypes of the same cultivar. Ampelographic traits and high-throughput SNP genotyping platforms provided an accuracy estimation of genetic diversity in the Sicilian germplasm, showing the relationships among cultivars by cluster and multivariate analyses. The large SNP panel defined sub-clusters unable to discern among biotypes, previously classified by ampelographic analysis, belonging to each cultivar. These results suggested that a very large number of SNP did not cover the genome regions harboring few morphological traits. Genetic structure of the collection revealed a clear optimum number of groups for K = 3, clustering in the same group a significant portion of family-related genotypes. Parentage analysis highlighted significant relationships among Sicilian grape cultivars and Sangiovese, as already reported, but also the first evidences of the relationships between Nero d'Avola and both Inzolia and Catarratto. Finally, a small panel of highly informative markers (12 SNPs) allowed us to isolate a private profile for each Sicilian cultivar, providing a new tool for cultivar identification.

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Section: Discussionmentioning

confidence: 56%

High-throughput 18K SNP array to assess genetic variability of the main grapevine cultivars from Sicily

Mercati

Lorenzis

Brancadoro

et al. 2016

Tree Genetics & Genomes

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“…The heterozygosity estimated using in silico SNP genotypes of our discovery panel was on average 0.26 (Table S1), probably because of the differences in levels of polymorphisms between SNPs and SSRs (Emanuelli et al ., ). Similar values of heterozygosity were observed in other highly heterozygous tree species (De Lorenzis et al ., ; Micheletti et al ., ).…”

Section: Resultsmentioning

confidence: 97%

A new genomic tool for walnut (Juglans regia L.): development and validation of the high‐density Axiom™ J. regia 700K SNP genotyping array

Marrano

Martínez-García

Bianco

et al. 2018

Plant Biotechnology Journal

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Summary Over the last 20 years, global production of Persian walnut ( Juglans regia L.) has grown enormously, likely reflecting increased consumption due to its numerous benefits to human health. However, advances in genome‐wide association ( GWA ) studies and genomic selection ( GS ) for agronomically important traits in walnut remain limited due to the lack of powerful genomic tools. Here, we present the development and validation of a high‐density 700K single nucleotide polymorphism ( SNP ) array in Persian walnut. Over 609K high‐quality SNP s have been thoroughly selected from a set of 9.6 m genome‐wide variants, previously identified from the high‐depth re‐sequencing of 27 founders of the Walnut Improvement Program ( WIP ) of University of California, Davis. To validate the effectiveness of the array, we genotyped a collection of 1284 walnut trees, including 1167 progeny of 48 WIP families and 26 walnut cultivars. More than half of the SNP s (55.7%) fell in the highest quality class of ‘ Poly High Resolution ’ ( PHR ) polymorphisms, which were used to assess the WIP pedigree integrity. We identified 151 new parent‐offspring relationships, all confirmed with the Mendelian inheritance test. In addition, we explored the genetic variability among cultivars of different origin, revealing how the varieties from Europe and California were differentiated from Asian accessions. Both the reconstruction of the WIP pedigree and population structure analysis confirmed the effectiveness of the Applied Biosystems™ Axiom™ J. regia 700K SNP array, which initiates a novel genomic and advanced phase in walnut genetics and breeding.

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“…Chemical strategies have included the concentration of anthocyanins to discriminate Barbera (Ferrandino and Guidoni ), Sangiovese (Rustioni et al ) and Syrah (Roggero et al ) clones. Other secondary metabolites used to study the intra‐varietal diversity include: flavonols for Barbera (Ferrandino and Guidoni ) and Cabernet Sauvignon (Burin et al ), and volatile compounds for Chardonnay (Duchêne et al ) and Muscat of Alexandria (De Lorenzis et al ). Applying genetic strategies based on DNA molecular markers, slightly divergent genotypes have been identified for clones of cultivars, such as Chardonnay (Riaz et al ) by simple sequence repeats (SSR), Sangiovese (D'Onofrio et al ) by specific sequence amplified polymorphism (S‐SAP) and Manto Negro, Callet and Moll (Cretazzo et al ) by selective amplification of microsatellite loci.…”

Section: Introductionmentioning

confidence: 99%

Study of intra-varietal diversity in biotypes of Aglianico and Muscat of Alexandria (Vitis viniferaL.) cultivars

Lorenzis

Squadrito²,

Rossoni

et al. 2016

Australian Journal of Grape and Wine Research

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Background and Aims: Somatic mutations are the major source of intra-varietal variability in some species such as grapevine (Vitis vinifera L.) that are propagated vegetatively. Aglianico and Muscat of Alexandria are two cultivars mostly cultivated in the south of Italy, showing great intra-varietal diversity. The variability of 15 clones of Aglianico belonging to three biotypes, Taburno, Taurasi and Vulture, and 21 clones of Muscat of Alexandria, coming from France, Greece, Italy and Spain, was investigated. Methods and Results: The intra-varietal diversity was investigated by ampelographic and eno-carpological (berry characteristics of oenological interest) methods (nine OIV descriptors, related to bunch and berry morphology, sugar content, total acid content and pH of must), chemical (anthocyanins, aromatic compounds and phenolic substances) and genetic analysis [18 K SNPs, single nucleotide polymorphisms (SNP)]. Intra-varietal diversity has been detected in both cultivars, mainly based on differences in the accumulation of secondary metabolites. The Taurasi biotype was discriminated by linear discrimination analysis mainly for the proportion of malvidin-3-O-glucoside acetate and methoxylated anthocyanins, while the Spanish Muscat biotype was discriminated based on the proportion of flavanols and hydroxycinnamic acids. Conclusions: Ampelography and the concentration of secondary metabolites have proved to be the best tools for the characterisation of the intra-varietal variability of grapevine germplasm. The high-throughput genetic analysis based on 18 K SNP loci did not highlight a polymorphism sufficient to distinguish among biotypes of the same cultivar, suggesting that a different molecular approach has to be adopted. Significance of the Study: This study confirms that intra-varietal diversity is better examined with a multidisciplinary approach.

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Study of genetic variability in Vitis vinifera L. germplasm by high-throughput Vitis18kSNP array: the case of Georgian genetic resources

Cited by 62 publications

References 51 publications

High-throughput 18K SNP array to assess genetic variability of the main grapevine cultivars from Sicily

High-throughput 18K SNP array to assess genetic variability of the main grapevine cultivars from Sicily

A new genomic tool for walnut (Juglans regia L.): development and validation of the high‐density Axiom™ J. regia 700K SNP genotyping array

Study of intra-varietal diversity in biotypes of Aglianico and Muscat of Alexandria (Vitis viniferaL.) cultivars

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