Genetic diversity in Swedish and Finnish heirloom apple cultivars revealed with SSR markers

Garkava-Gustavsson, Larisa; Mujaju, Claid; Sehic, Jasna; Zborowska, Anna; Backes, Gunter; Hietaranta, Tarja; Antonius, Kristiina

doi:10.1016/j.scienta.2013.07.040

Cited by 45 publications

(27 citation statements)

References 23 publications

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“…In the Finnish and Swedish apple tree gene pool (a total of 101 genotypes), 105 alleles have been identified by 9 loci. In this case, expected (H e ) and observed (H o ) heterozygosity values varied within 0.31-0.88 and 0.41-0.88, respectively [23], whereas in our study they ranged within 0.548-0.897 for H o and 0.602-0.827 for H e (see table). The average values of H o and H e in our study were equal to 0.786 and 0.755, respectively, which exceeded the figures obtained as a result of analysis of Scandinavian apple tree geneplasm (H e = 0.72; H o = 0.74) where the average number of alleles per locus was 11.6 (23).…”

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confidence: 77%

GENETIC DIVERSITY STUDY OF MODERN RUSSIAN APPLE (Malus* domestica Borkh.) CULTIVARS BY THE SSR LOCI ANALYSIS

Супрун¹,

Ushakova²,

Токмаков³

et al. 2015

S-h. biol.

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A b s t r a c tSSRs are one of the most suitable DNA-markers for assessment of genetic diversity of plant genetic resources. Microsatellites were used for development of saturated genetic maps of apple (Malus ½ domestica Borkh.) as well as for wide range of genetic diversity studies. Our study was aimed on the investigation of the genetic relationship within subcollection of modern Russian apple cultivars. Polymorphism of 12 microsatellite loci was estimated for 31 apple cultivars from the SKZNIISiV collection of genetic resources. These cultivars have been bred in North Caucasian Regional Research Institute of Horticulture and Viticulture (SKZNIISiV) and All-Russian Research Institute of Fruit Crop Breeding (VNIISPK). SSR-markers CH01f03b, CH01h01, CH01h10, CH02c06, CH02d08, CH04e05, CH05f06, CH01f02, CH02c11, Hi02c07, CH02c09 and CH03d07, which are recommended by Fruitbreedomics, the European consortium, were used in the study. According to the data of SSR-analysis from 5 to 10 alleles per locus were detected, with an average value of 7.75 alleles per locus. A total of 93 alleles were detected for all 12 loci. All apple cultivars showed individual, distinct SSR-profiles. Comparison with the data on the genetic diversity of the world apple tree gene pool suggests that the SSR-loci polymorphism in studied set of the apple cultivars is relatively high. Expected (H e ) and observed (H o ) heterozygosity varied within the ranges of 0.548-0.897 and 0.602-0.827 for H o and H e , respectively. The average values of these indexes are H o = 0.786 and H e = 0.755. PIC value ranged from 0.571 to 0.806, and 9 loci showed PIC value higher than 0.712. Results of UPGMA-analysis are consistent with the level of genetic heterogeneity of the studied cultivar set. Five clusters were determined. Distribution of cultivars into clusters in most cases is consistent with their genealogy. For example, Svezhest' cultivar, formed a distinct cluster ¹ 1, as well as cultivars Imrus and Zimnee utro which formed cluster ¹ 5 are originated from the cultivars, which are not presented as the parental forms of any studied cultivars. Cultivars of VNIISPK breeding such as Solnishko, Stroevskoe, Yubilei Moskvy, Afrodita and Start, which formed distinct cluster ¹ 3 have one common parental cultivar. The structure of dendrite obtained when performing clustering on the results of SSR-analysis may be due to large number of unique alleles studied in genotypes that in turn is due to the high genetic diversity within the studied set of cultivars. At the same time, the fact of incorporation of cultivars with the same genealogy in the same clusters confirms the high significant genetic similarity within groups of such varieties. Results of the study allows to assess the level of the genetic diversity within the set of modern apple cultivars as well as can be used for confirmation of genealogy of apple cultivars and hybrids in the case of disputes, as well as for identification of varieties.

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confidence: 77%

GENETIC DIVERSITY STUDY OF MODERN RUSSIAN APPLE (Malus* domestica Borkh.) CULTIVARS BY THE SSR LOCI ANALYSIS

Супрун¹,

Ushakova²,

Токмаков³

et al. 2015

S-h. biol.

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“…Microsatellites, or SSRs, are the DNA markers of choice to uncover the genetic diversity between and within fruit species (Gupta et al, 1996), due to their high polymorphism level, abundance and co-dominant inheritance and reproducibility, as well as relative easiness of analysis (Madesis et al, 2013). Previously, many authors used this technique to determine the genetic diversity in order to identify duplicates and genetic relationships within and between Malus × domestica accessions (Garkava-Gustavsson et al, 2013;Gaši et al, 2010;Lassois et al, 2015;Liang et al, 2015;Oraguzie et al, 2005;Patzak et al, 2012;Pina et al, 2014;Urrestarazu et al, 2012). Nevertheless, only a few reports have demonstrated basic and detailed data on adaptability and fruit quality traits of Malus × domestica cultivars from different geographical areas, especially from species grown under the Greek climatic conditions.…”

Section: Introductionmentioning

confidence: 99%

Phenotypic and molecular characterization of apple (Malus × domestica Borkh) genetic resources in Greece

Ganopoulos¹,

Tourvas

Xanthopoulou

et al. 2018

Sci. agric. (Piracicaba, Braz.)

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ABSTRACT:The phenotypic and genetic analysis of apple (Malus × domestica Borkh) genotypes is essential for breeding species. Information on the morphology and genetic structure of apple offers significant help for germplasm maintenance and selection of suitable material to breed superior cultivars. This study shows the results of an investigation on the morphology and the genetic diversity for 19 apple cultivars, which are preserved in an ex situ collection in Naoussa, Central Macedonia, Greece. Information was recorded over a 5-year period for 47 traits describing plant morphology and phenotype, as well as leaf and fruit quality. Data were analyzed using the principal component analysis (PCA) method. The Euclidean distance metric and the Ward's agglomeration method were used in an unsupervised hierarchical cluster analysis of all cultivars. The cultivars were grouped into four main clusters, suggesting that the characterized apple collection has a high potential for specific breeding goals. Furthermore, the cultivars were genotyped using seven microsatellite primers. Moderate levels of polymorphism were detected, and 38 distinctive alleles (5.4 alleles per primer pair) were identified. Both multivariate clustering approach (phenotypic data) and the genetic distance clustering approach (genetic data) grouped the apple cultivars according to their type. Hence, these data could be used for protection or patenting processes of existing or new apple cultivars carried out by the EU-Community Plant Variety Office.

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“…SSR markers have a number of advantages, such as the high level of polymorphisms, locus specificity, co-dominance, reproducibility, convenience through using PCR, and random distribution throughout the genome (Powell et al, 1997). As such, they have become a popular marker system in rice, wheat, almond, peach, and apple (Jain et al, 2004;Khlestkina et al, 2004;Xie et al, 2010;Garkava-Gustavsson et al, 2013). ISSR markers use primers based on di-, tetra-, or pentanucleotide sequence repeats and anchored nucleotides.…”

Section: Introductionmentioning

confidence: 99%

Genetic diversity analysis of sweet kernel apricot in China based on SSR and ISSR markers

et al. 2015

Genet. Mol. Res.

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ABSTRACT. Simple sequence repeat (SSR) and inter-simple sequence repeat (ISSR) markers were used to evaluate genetic diversity among 22 sweet kernel apricot accessions and 12 cultivars in China to provide information on how to improve the utilization of kernel apricot germplasms. The results showed that 10 pairs of SSR primers screened from 40 primer pairs amplified 43 allelic variants, all of which were polymorphic (100%), and 9 ISSR primers selected from 100 primers amplified 67 allelic variants with 50 polymorphic bands (74.63%). There was a relatively distant genetic relationship between the 34 samples, where their genetic similarity coefficient was between 0.62 and 0.99. The UPGMA dendrogram constructed using combined data of the two marker systems separated the genotypes into three main clusters.

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Genetic diversity in Swedish and Finnish heirloom apple cultivars revealed with SSR markers

Cited by 45 publications

References 23 publications

GENETIC DIVERSITY STUDY OF MODERN RUSSIAN APPLE (Malus* domestica Borkh.) CULTIVARS BY THE SSR LOCI ANALYSIS

GENETIC DIVERSITY STUDY OF MODERN RUSSIAN APPLE (Malus* domestica Borkh.) CULTIVARS BY THE SSR LOCI ANALYSIS

Phenotypic and molecular characterization of apple (Malus × domestica Borkh) genetic resources in Greece

Genetic diversity analysis of sweet kernel apricot in China based on SSR and ISSR markers

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