Genetic Profiling Of Moldavian, Crimean and Russian Cultivars Of Vitis Vinifera L. with Nuclear Microsatellite Markers françois lefort1, svetlana gorislavets2, valentina risovannaya2 & leonid troshin3




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Genetic Profiling Of Moldavian, Crimean and Russian Cultivars Of Vitis Vinifera L. with Nuclear Microsatellite Markers
FRANÇOIS LEFORT1, SVETLANA GORISLAVETS2, VALENTINA RISOVANNAYA2 & LEONID TROSHIN3

1Laboratory of Biotechnology and Applied Genetics, Ecole d’Ingénieurs de Lullier, Haute Ecole Spécialisée de Suisse Occidentale, 150, route de Presinge, 1254 Jussy, Switzerland.

2Institute of Vine and Wine Magarach, 31 Kirov St. 98600 Yalta, Crimea, Ukraine.

3Viticulture Department, Kuban State University of Agriculture, 350044 Krasnodar, Kuban, Russia 
Corresponding author : Lefort, F., E-mail : francois.lefort@etat.ge.ch
Key words: grapevine, Moldova, nuclear microsatellites, SSR, Ukraine, Russia, Vitis vinifera.
Introduction
Microsatellite markers have been proved to be a useful tool for assessing genetic identities and genetic relationships between grapevine gene pools (for a review, see Sefc et al., 2001). Characterization of Moldavian, Russian and Crimean genetic resources of grapevine sources with the use of nuclear microsatellite nuclear markers is reported here for the first time.

The 52 Crimean and 27 Moldavian cultivars, included in this study, are conserved in the ampelographic collection of the Institute of Wine and Vines Magarach in Yalta, Crimea, Ukraine and represent a major part of the grapevine genetic resources from these provenances. Crimean cultivars are cultivars from the region of Crimea and not from other regions of Ukraine. The 24 Russian cultivars, are conserved in the new ampelographic collection of Russia, located at the University of Agriculture of the Kuban state in Krasnodar. Cultivars were selected as being potentially the most ancient cultivars cultivated in these regions, without prejudice of their native or foreign origin, since it could be likely for historical reasons that some Greek, Turkish or Caucasian cultivars would have been transmitted to these regions.

Genetic profiling of these cultivars was carried out with 9 nuclear microsatellite loci previously characterized: VVS2, ssrVrZAG21, ssrVrZAG47, ssrVrZAG62, ssrVrZAG 64, ssrVrZAG79, ssrVrZAG83, ssrVvUCH11 and ssrVvUCH29.

These loci have already been used in similar works of genetic characterization in other European countries. Consequently, allele sizing carried out in our laboratory was standardized with profiling results obtained at the same loci by Sefc at the University of Agriculture of Vienna, Austria and by Lefort at the University of Heraklion in Greece. Standardization allowed to compare these Crimean, Moldavian and Russian grapevine cultivars with Western European and Greek genetic resources already characterized at the same loci.


Materials and Methods
Plant material:

Leaves of Vitis vinifera L. cultivars were collected from the ampelographic collections of the Institute of Wine and Vines, Magarach, Yalta, Crimea, Ukraine and of the Viticulture Department of the University of Agriculture of the Kuban state, Krasnodar, Russia.


DNA extraction:

DNA was extracted from 100 to 150 mg fresh weight of leaf tissue according to a previously described micro-method of DNA purification developed for hardwood species and modified for Vitis species. (Lefort and Roubelakis-Angelakis, 2001)


Microsatellite PCR and microsatellite profile analysis:
Amplification primer sequences for 9 nuclear microsatellite loci from Vitis riparia (Sefc et al., 1999), ssrVrZAG 21, ssrVrZAG 47, ssrVrZAG 62, ssrVrZAG 64, ssrVrZAG 79, ssrVrZAG 83, and from Vitis vinifera, VVS2 (Thomas et al., 1994), UCH11, and UCH29 (Lefort et al., 2002), were used for DNA amplification.

PCR amplifications were carried out in 96-well propylene plates in 20 l final volume reaction mixtures in a Gradient Mastercycler (Eppendorf, Germany). PCR reactions were as follows: 1 μM of each primer, 100 μM of each dNTPs (Biofinex, Praroman, Switzerland), 1.5 mM MgCl2 in the buffer 75 mm Tris-HCl (pH 9.0), 50 mM KCl, 20 mM (NH4)2 SO4, 0.5 units Taq polymerase (Biotools, Madrid, Spain) and 50 ng DNA template. The forward primer in each case was labeled with the Cy5 fluorochrome (Amersham Biosciences, UK). The following thermal cycling protocol was applied for all loci: 95°C for 5 min, 10 cycles of 15 s at 50°C, 15 s at 94°C, followed by 23 cycles of 15 s at 50°C, 15 s at 89°C and terminated immediately at 4°C, except for ssrVrZAG64, of which the annealing temperature was 58°C. PCR product analysis was carried out on Reprogel template (Amersham Biosciences) in an ALFExpress 2 DNA Sequencer (Amersham Biosciences), and alleles were sized with the software Allele Locator (Amersham Biosciences ). PCR samples were run along with internal size markers 100 bp and 300 bp. Additionnally, external markers scale (50 bp –350 bp) and home made gold markers for each locus were run in the most peripheral wells. Sizing was standardized for all loci with previous works (Sefc et al., 2000, 2002; Lefort and Roubelakis, 2000; Lefort et al., 2001) using the same markers set, in order to allow an easy comparison with other Vitis vinifera germplasm. The phenogram presented in figure 1 was obtained by using MICROSAT software (Minch et al., 1997) for calculating genetic distance in [-log(proportion of shared alleles)]. The distance matrix obtained from MICROSAT was processed with KITSCH from the PHYLIP package (Feselstein, 1989) and the phenogram was drawn with TREEVIEW (Page, 1996). Observed and expected heterozygosity (He = 1 - pi2) (Nei, 1973), probability of identity (PI = pi4 +  [2pipj]2 ) (Paetkau et al., 1995), and probability of null alleles (r = [He –Ho] / [1 + He]) (Brookfield, 1996) were calculated with IDENTITY 1.0 (Wagner and Sefc).


Results and Discussion
Cultivars included in the present study are shown in table 1. According to the transliteration in Latin alphabet, it appears that several cultivars seem to have a name of Turkish origin, which is not a proof of Turkish origin but could indicate that these cultivars could have been transmitted from Turkey or former Turkish dependences. Analysis of microsatellite profiling are given in table 2. The total number of alleles found in these 103 cultivars was high at 105 alleles and consequently the mean number of alleles per locus was high at 11,66 which was much higher than those previously recorded in other gene pools with the same set of markers (Lefort and Roubelakis-Angelakis, 2001; Sefc et al. 2000). Heterozygosity was high and ranged between 0.71 and 0.93, though the estimated frequency of null alleles was surprisingly close to 0.05 at 2 loci VVS2 and ssrVrZAG79, which resulted from a slight excess of homozygous cultivars at these loci. The average heterozygosity was high at 0.80 and expressed an overall high genetic diversity, which was also expressed by a low average genetic similarity of about 37% as calculated from the distance matrix. As shown on figure 1, microsatellite profiling at 9 loci was powerful enough to discriminate 103 cultivars in 102 single identity profiles. Most of the cultivars clustered in groups of branches according to their geographic origins. Russian cultivars seem to be of mixed origins, with some groups closer to Moldavian cultivars while others were closer to Crimean cultivars. Only one pair of synonyms were found among these 103 cultivars and they were two Crimean cultivars. Biyas aibatly and Khachador. Possible parent relationships were only found for 5 combinations of cultivars with four of them involving Moldavian cultivars, which would need further investigation at more loci. Such a low level of possible parent relationship at only 9 loci is congruent with the high observed diversity and could suggest that a large part of these resources were from diverse origins. No synonyms were found between cultivars from these 3 provenances and 305 other cultivars from France, Greece, Switzerland and Albania (data not shown) when comparison were made at 8 loci out of nine.
References
Brookfield JFY. 1996. A simple new method for estimating null allele frequency from heterozygote deficiency. Mol. Ecol. 5:453-455.

Felsenstein, J. 1989. Phylogeny inference package. Cladistics 5:164-166.

Lefort F, Kyvelos CJ, Zervou MI, Edwards KJ and Roubelakis-Angelakis KA. 2002. Characterization of new microsatellite loci from Vitis vinifera and their conservation in some Vitis species and hybrids. Molecular Ecology Notes., 2(1), 20-21.

Lefort F and Roubelakis-Angelakis KA. 2000. The Greek Vitis Database. A multimedia web-backed genetic database for germplasm management of Vitis resources in Greece. J. Wine Res. 11(3):233-242.

Lefort F and Roubelakis-Angelakis KA. 2001. Genetic comparison of Greek cultivars of Vitis vinifera L. by nuclear microsatellite profiling. Am. J. Enol. Vitic., 52(2), 101-108.

Minch E, Ruiz-Linares A, Goldstein D, Feldman M and Cavalli-Sforza LL. 1997. Microsat v.1.5d: a computer program for calculating various statistics on microsatellite allele data.

Nei M. 1973. Analysis of gene diversity in subdivided populations. Proc. Natl. Acad. Sc. USA 70(12):3321-3323.

Paetkau D, Calvert W, Stirling I and Strobeck C. 1995. Microsatellite analysis of population structure in Canadian polar bears. Mol. Ecol. 4: 347-354.

Page RDM. 1996. Treeview: An application to display phylogenetic trees on personal computers. Computer Applications in the Biosciences 12: 357-358.

Sefc KM, Lopes MS, Lefort F, Botta R, Roubelakis-Angelakis KA, Ibanez J, Pejic I, Wagner HW, Glossl J and Steinkellner H. 2000. Microsatellite variability in grapevine cultivars from different European regions and evaluation of assignment testing to specify the geographic origin of cultivars. Theor. Appl. Genet. 100(3/4):498-505.

Sefc KM, Regner F, Turetschek E, Glössl J and Steinkellner H. 1999. Identification of microsatellite sequences in Vitis riparia and their applicability for genotyping of different Vitis species. Genome 42:367--373.

Sefc KM, Lefort F, Grando MS, Scott K, Steinkellner H and Thomas MR. 2001. Microsatellite markers for grapevine: a state of the art, 433-463. In: Molecular biology and biotechnology of grapevine. Kluwer Publishers, Amsterdam 499 p.

Thomas MR, Cairn P and Scott NS. 1994. DNA typing of grapevines a universal methodology and database for describing cultivars and evaluating genetic relatedness. Plant Mol. Biol., 25, 939-949.

Wagner HW and Sefc KM 2000. IDENTITY 1.0.


Table 1: Moldavian, Crimean and Russian cultivars of Vitis vinifera L. used in the present study. Names of Crimean and Russian cultivars were transliterated from Ukrainian and Russian Cyrillic alphabets according to the appropriate schemes of transliteration.



RUSSIE

CRIMÉE







Agadai

Abla aganyn izium

Ag-izyum

Adgem misket

Alyi terskii

Aibatly

Asyl Kara

Akseit kara

Bulanyi

Alburla

Buryi

Amet Adgi Ibram

Cikrah

Artin zerva

Cimlijanszki chernyi

Asma

Gyulyabi Dagestanski

Biyas aibatly

Kaitangi

Bogos zerva

Klinchatyi

Cherny kuymski

Krasnostop zolotovski

Cornichon crymski

Kumshatskii belyi

Crona

Lesnoi belyi maraginski

Dardagan

Makhbor Tsibil

Demir kara

Makhrovatchic

Dere izium

Narma

Dgevat kara

Plechistik

Firski ranni

Pukhlyakovski

Kapitan Yani kara


Rish Baba

Kapselski

Shavrony

Kastel chernyi

Sibirkovyi

Kefesia

Tygys

Khachador

Varyoshkin

Khalil izium




Khersonesski

MOLDAVIE

Kirmisi sap sudakski

Adgi

Kok khabakh

Akkermanski chernyi

Kok pandas

Ali-ali negru

Kokur belyi

Alimshak

Kokurdes belyi

Alvarna

Kokurdes chernyi

Briazy

Kovalevka

Cabasma

Kurtseit aganyn izium

Cabassia

Mangil al

Chorcutsa rosove

Misgiuli kara

Copchak

Misket

Fet frumos

Murza izium

Fetiaska niagre

Nasurla

Galabura

Pavlo izium

Galbena

Safta durmaz

Gordin verde

Sale aganyn kara

Moldavski belyi

Sary kokur

Muscat bessarabski

Sary pandas

Muscat de Codru

Shira izium

Muscat moldavski

Soldaya

Seyna

Solnechnodolinski

Sgigarda

Sykh dane

Sgigardai krasnoplodnyi

Tanagoz

Tidveska

Tashly

Tiras

Tergulmek

Tsisa caprian

Yanykh zerva

Turba plotnyi belyi

Zerva

Turba rykhlyi




Table 2: Analysis of 102 profiles found in 103 cultivars: Number of alleles, observed and expected heterozygosity, probability of identity, and estimated frequency of null alleles at 9 nuclear microsatellite loci.

Loci

Number

of alleles



Ho

He

Probability

of identity (PI)



Estimated frequency

of null alleles




















VVS2


11

0.7254

0.8259

0.0952

0.0550

SsrVrZAG21

14

0.9313

0.8745

0.0533

- 0.0303

SsrVrZAG47

10

0.8627

0.815

0.0751

- 0.0063

SsrVrZAG62

10

0.9117

0.8352

0.0883

- 0.0417

SsrVrZAG64

9

0.8431

0.8156

0.1128

- 0.0151

SsrVrZAG79

12

0.7843

0.7862

0.105

0.0011

SsrVrZAG83

9

0.6274

0.6610

0.3029

0.0202

UCH11

11

0.7156

0.8292

0.0932

0.0620

UCH29

19

0.8627

0.8187

0.0827

- 0.0241




105 alleles




0.8068







Mean

MNA = 11.66


0.8071

0.8068

PI for all loci

9.35 x 10-10






Figure 1. Phenogram of Moldavian, Ukrainian and Russian grapevine cultivars. Moldavian cultivars are shown in italics underlined, Crimean cultivars are shown in bold and Russian cultivars are shown in black. The genetic distance used was (-log [proportion of shared alleles]) and the scale is a function of this distance.










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