Development of the Northern European <i>Ribes</i> core collection based on a microsatellite (SSR) marker diversity analysis

Antonius, Kristiina; Karhu, Saila; Kaldmäe, H.; Lācis, Gunārs; Rugenius, R.; Baniulis, Danas; Sasnauskas, A.; Schulte, E.; Kuras, Anita; Korbin, M.; Gunnarsson, Anita; Werlemark, G.; Ryliškis, Darius; Todam-Andersen, T.; Kokk, L.; Järve, Kadri

doi:10.1017/s1479262111000980

Cited by 23 publications

(19 citation statements)

References 7 publications

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“…International application of molecular markers and comparison of genotypes was supported in the EU project "Core collection of Northern European gene pool of Ribes -RIBESCO" (Karhu et al, 2007) (Antonius et al, 2012b), with the aim of evaluating genetic diversity and to select accessions for the common core collection. Application of selected SSR markers allowed selection of a core collection of Ribes accessions, which represented 64% of black currant, 80% of red and white currant and 61% of gooseberry alleles identified in the region (Antonius et al, 2012b). A similar SSR marker set was used for characterisation of different Ribes species and interspecific hybrids from North Italy and Switzerland (Cavanna et al, 2009).…”

Section: Genotyping Of Berry Crop Grmentioning

confidence: 99%

Characterisation of Latvia Fruit Crop Genetic Resources by Application of Molecular Genetics Methods

Lācis¹

2013

Proceedings of the Latvian Academy of Sciences. Section B. Natural, Exact, and Applied Sciences

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A large diversity of fruit crop accessions is maintained at the Latvia State Institute of Fruit- Growing, which consists of modern cultivars, landraces and selections from local breeding programmes, as well as germplasm that has resulted from scientific exchange and co-operation with other institutes. Presently, the germplasm collection comprises 2509 accessions of 17 fruit crops; 676 accessions are designated as national genetic resources. Conservation of germplasm itself has little value without characterisation and further utilisation of the stored plant material. To intensify these activities, DNA-based technologies have been implemented in the characterisation of germplasm. Two main groups of molecular markers have been utilised: non-specific markers and gene-specific (functional) markers, subsequently applicable for Marker Assisted Selection (MAS). Genotyping protocols based on SSR, RAPD and Methylation-sensitive amplification polymorphism (MSAP) markers have been developed for twelve fruit crops for use in plant material identification, True-to-Type verification and evaluation of genetic diversity and internal collection structure. In total, 790 accessions have been genotyped using any of the mentioned markers. These markers have been harmonised with the European cooperative programme for plant genetic resources working group (ECPGR WG) recommended sets to ensure international data exchange. Gene specific molecular markers have been applied to apple and pear (resistance to scab), strawberry (resistance to Gnomonia fragariae), sweet cherries and plums (self-incompatibility).

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Section: Genotyping Of Berry Crop Grmentioning

confidence: 99%

Characterisation of Latvia Fruit Crop Genetic Resources by Application of Molecular Genetics Methods

Lācis¹

2013

Proceedings of the Latvian Academy of Sciences. Section B. Natural, Exact, and Applied Sciences

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“…SSR (microsatellite) markers are used both in fundamental studies aimed at assessing genetic polymorphism, investigating phylogenetic relationships and creating genetic maps for linkage groups, and for application-oriented purposes, such as genealogy checking, development of identification and certification systems, search for the markers associated with economic characters, and marker-mediated selection of targeted genotypes at early stages of plant development [9]. SSR markers have been used for assessing the diversity of genetic collections of Ribes in Italy and North Europe [10,11].…”

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confidence: 99%

“…In some cases, during genotyping of microsatellite loci of collected black currant varieties from North Europe, it was impossible to confirm genetic identity of same-name specimens from various collections, for example, one of 10 specimens of variety Odzhebin turned out to be non-identical to the other specimens [11]. S. Reim et al used 11 microsatellite loci in order to clarify the origin of the varieties bred in Dresden-Pillnitz [21].…”

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MICROSATELLITE LOCI POLYMORPHISM IN RUSSIAN BLACK CURRANT (Ribes nigrum L.) VARIETIES FROM COLLECTION OF ALL-RUSSIAN RESEARCH INSTITUTE OF BREEDING FRUIT CROPS

Pikunova¹,

Knyazev²,

Bakhotskaya³

et al. 2015

S-h. biol.

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A b s t r a c tBlack currant is the main berry crop in Russia. The need to improve its assortment requires new effective methods to be involved in breeding. Application of DNA markers as a modern approach in dealing with germplazm is intensively used abroad in works on black currant plants. We are the first in Russia who used SSR DNA markers in studying black currant gene pool. In this paper we report genotyping 27 black currant accessions from the collection of the All-Russian Research Institute of Breeding Fruit Crops, including 16 varieties originated from this institute, on 14 microsatellite loci. Electrophoresis in 6 % denaturing PAAG followed by staining with silver nitrate was used for separation of PCR products. All tested SSR loci, except MS06g03, have been found to be polymorphic. On average 4.9 alleles were amplified per locus. Three fragments have been amplified on DNA of some accessions at one SSR locus that is probably due to the duplication of these microsatellite loci in genome of these accessions. A total of 66 % of all amplified fragments were rare alleles with a frequency of occurrence equal to or less than 0.2. Eight unique alleles have been found. The observed heterozygosity ranged from 0.259 (g2-H21) to 1 (e4-D03) and averaged 0.608. Combinations of alleles at one locus allowed to distinguish from 3 (g2-H21, e1-O21) to 15 (g2-G12) genotypes. The minimum set of four loci (e4-D03, g1-M07, g1-E03, g2-B20) allowed to distinguish all the tested accessions, i.e. unique multilocus profile has been found for each sample. Pairwise genetic similarity coefficients ranged from 0.11 (between Odzhebin and Sharovidnaya varieties) to 0.95 (between Govtva and Rtishchevskaya varieties) and averaged 0.346. Cluster analysis of genetic similarity has been done. The dendrogram shows a few clusters with high bootstrap support. Distribution of alleles between related varieties was consistent with the pedigrees in the most cases, but discrepancies between pedigrees and SSR data also were found. Thus, the varieties Ocharovanie (¹ 1168 ½ Ekzotika variety) and Ekzotika had no common alleles in three loci (e4-D03, g1-E03, g2-B20). It probably is due to pollination by other pollen or error in reproduction and transplantation or mutations in these loci. The varieties Odzhebin and Binar (Odzhebin ½ Naryadnaya) had no common alleles in two loci (g1-M07, g1-E03). Our results allow to recommend SSR markers for evaluation of domestic gene pool of black currant on genetic diversity, and to develop methods for the identification and certification of varieties of black currant.

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“…There are several thousand gooseberry cultivars [30], but they are poorly characterized genetically. Some studies assessed the genetic diversity of some gooseberry cultivars using random genomic SSR markers [12,32,33]. Yet, no genetic diversity studies used markers located in genes responsible for any economically valuable traits.…”

Section: Introductionmentioning

confidence: 99%

The Development of the Genic SSR Markers for Analysis of Genetic Diversity in Gooseberry Cultivars

et al. 2021

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Gooseberry is one of the most promising and underrated small fruit crops. There is a need to improve and genotype the existing cultivars, and this work requires the use of new efficient DNA marking techniques. Marker-assisted selection (MAS) is a modern approach for work with genetic resources. However, the genetic determinants of key qualitative traits are poorly studied. Therefore, we developed SSR markers located in flavonoid biosynthesis genes that can affect the resistance of plants to biotic and abiotic stresses to study the genetic diversity of gooseberry cultivars grown in the Russian Federation and varying in genetic and geographical origin. We have genotyped 22 gooseberry cultivars using a set of 19 of our original microsatellite markers and two neutral previously published ones. A total of 53 alleles were found. Nine of the 21 analyzed loci were polymorphic. The most polymorphic loci of flavonoid biosynthesis were found in the DFR gene (RucDFR1-2, RucDFR1-3, RucDFR2-1), their mean PIC (polymorphism information content) being 0.65, comparable to the PIC values of neutral markers. Our set of gene-targeted SSR markers showed that most of all the studied gooseberry cultivars differed in origin, based on which they were divided into three groups: European cultivars, Russian cultivars, and interspecies hybrids. Thus, the polymorphic markers can be used for cultivar identification and certification as well as for the marker-assisted selection of gooseberry plants having different origins and phenotypic traits.

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Development of the Northern European Ribes core collection based on a microsatellite (SSR) marker diversity analysis

Cited by 23 publications

References 7 publications

Characterisation of Latvia Fruit Crop Genetic Resources by Application of Molecular Genetics Methods

Characterisation of Latvia Fruit Crop Genetic Resources by Application of Molecular Genetics Methods

MICROSATELLITE LOCI POLYMORPHISM IN RUSSIAN BLACK CURRANT (Ribes nigrum L.) VARIETIES FROM COLLECTION OF ALL-RUSSIAN RESEARCH INSTITUTE OF BREEDING FRUIT CROPS

The Development of the Genic SSR Markers for Analysis of Genetic Diversity in Gooseberry Cultivars

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