Molecular Characterisation of the Swiss Fruit Genetic Resources

Bühlmann, Andreas; Gaßmann, Jennifer; Ingenfeld, Anke; Hunziker, K.; Kellerhals, M.; Frey, Jürg E.

doi:10.1007/s10341-015-0230-1

Cited by 16 publications

(13 citation statements)

References 21 publications

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“…The high level of diversity and heterozygosity in apple germplasm at a European level agreed with previous results obtained at collection-scale in several European countries, e.g., Italy [ 24 ], Spain [ 26 ], France [ 23 ], Sweden [ 22 ], Czech Republic [ 25 ] or Switzerland [ 14 ]. The large diversity found is consistent with the weak bottleneck effect reported in connection with the domestication of this species [ 35 – 37 ].…”

Section: Discussionsupporting

confidence: 89%

“… a DCA_I05 'Mele Ubriache' duplicate with 'Calville Rouge d'Hiver' [ 23 ] b based on 11 SSR [ 64 ] the accession CZ_LJ_0045 'Malinové podzimní' was shown to be duplicated with 'Danziger Kantapfel' c based on 11 SSR [ 64 ] the accession CZ_LC_0411 'Hlaváčkovo' duplicate with 'Northen Spy' d based on 11 SSR [ 64 ] the accession CZ_GF_0415 'Evino' duplicate with 'Mank's Codlin' e based on 11 SSR [ 64 ] the accession CZ_BoN_0424 'Trevínské červené' duplicate with 'King David' f based on 11 SSR [ 64 ] the accession CZ_GS_0478 'Ušlechtilé žluté' duplicate with 'Golden Noble' g based on 11 SSR [ 64 ] the accession CZ_GG_0438 'Malinové hornokrajské' duplicate with 'Framboise' h based on 11 SSR [ 64 ] and on 13 SSR [ 14 ] the accession CZ_BB_0466 'Podzvičinské' duplicate with 'Altlander Pfannkuchenapfel' and 'Thurgauer Kent' i based on 11 SSR [ 64 ] the accession DCA_F74 'Limoncella' (TN) duplicate with 'Cola' j recent or old cultivars ; doc. = inferred parentage already documented in [ 23 ] …”

Section: Resultsmentioning

confidence: 99%

“…h based on 11 SSR [ 64 ] and on 13 SSR [ 14 ] the accession CZ_BB_0466 'Podzvičinské' duplicate with 'Altlander Pfannkuchenapfel' and 'Thurgauer Kent'…”

Section: Resultsmentioning

confidence: 99%

“…Until now, the studies of diversity and genetic structure conducted in European apple have been based on the analyses of material from limited geographic areas (mostly nation-scale) [ 11 , 14 , 22 – 26 ]. By contrast, the extent and structure of the apple genetic diversity conserved at a European level have remained largely unknown.…”

Section: Introductionmentioning

confidence: 99%

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Analysis of the genetic diversity and structure across a wide range of germplasm reveals prominent gene flow in apple at the European level

et al. 2016

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BackgroundThe amount and structure of genetic diversity in dessert apple germplasm conserved at a European level is mostly unknown, since all diversity studies conducted in Europe until now have been performed on regional or national collections. Here, we applied a common set of 16 SSR markers to genotype more than 2,400 accessions across 14 collections representing three broad European geographic regions (North + East, West and South) with the aim to analyze the extent, distribution and structure of variation in the apple genetic resources in Europe.ResultsA Bayesian model-based clustering approach showed that diversity was organized in three groups, although these were only moderately differentiated (FST = 0.031). A nested Bayesian clustering approach allowed identification of subgroups which revealed internal patterns of substructure within the groups, allowing a finer delineation of the variation into eight subgroups (FST = 0.044). The first level of stratification revealed an asymmetric division of the germplasm among the three groups, and a clear association was found with the geographical regions of origin of the cultivars. The substructure revealed clear partitioning of genetic groups among countries, but also interesting associations between subgroups and breeding purposes of recent cultivars or particular usage such as cider production. Additional parentage analyses allowed us to identify both putative parents of more than 40 old and/or local cultivars giving interesting insights in the pedigree of some emblematic cultivars.ConclusionsThe variation found at group and subgroup levels may reflect a combination of historical processes of migration/selection and adaptive factors to diverse agricultural environments that, together with genetic drift, have resulted in extensive genetic variation but limited population structure. The European dessert apple germplasm represents an important source of genetic diversity with a strong historical and patrimonial value. The present work thus constitutes a decisive step in the field of conservation genetics. Moreover, the obtained data can be used for defining a European apple core collection useful for further identification of genomic regions associated with commercially important horticultural traits in apple through genome-wide association studies.Electronic supplementary materialThe online version of this article (doi:10.1186/s12870-016-0818-0) contains supplementary material, which is available to authorized users.

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Section: Discussionsupporting

confidence: 89%

Section: Resultsmentioning

confidence: 99%

“…h based on 11 SSR [ 64 ] and on 13 SSR [ 14 ] the accession CZ_BB_0466 'Podzvičinské' duplicate with 'Altlander Pfannkuchenapfel' and 'Thurgauer Kent'…”

Section: Resultsmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

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Analysis of the genetic diversity and structure across a wide range of germplasm reveals prominent gene flow in apple at the European level

et al. 2016

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“…Their use in breeding programs would significantly extend the crossing components. To protect the national cultural heritage, collections of old apple cultivars have been developed by several countries in Europe (Garkava-Gustavsson et al, 2008;van Treuren et al, 2010;Patzak et al, 2012;Urrestarazu et al, 2012;Bühlmann et al, 2015;Liang et al, 2015;Lassois et al, 2016). SSR markers have been used for assessment of genetic diversity among apple germplasm (Liebhard et al, 2002;Ramos-Cabrer et al, 2007) and cultivar genotyping (Garkava-Gustavsson et al, 2008;Sikorskaite et al, 2012).…”

Section: Introductionmentioning

confidence: 99%

SSR analysis based on molecular characterisation of apple germplasm in Lithuania

Mažeikienė

Šikšnianienė

Baniulis

et al. 2019

Zemdirbyste-Agriculture

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The survival of apple trees in old and abandoned orchards over 100 years indicates their adaptation to the local environment. These plants have passed an economic and ecological selection over the years. The structure of genetic diversity of apple germplasm in the old orchards of Lithuania is largely unknown. We applied a common set of 7 simple sequence repeat (SSR) markers to genotype 292 accessions across more than 50 geographic locations representing all Lithuanian geographic regions with the aim of analysing the distribution and structure of variation of the apple genetic resources. Eighty-one polymorphic alleles were identified. Of these, 5 alleles were unique, identified only in four individual genotypes. The COL locus was the most homozygous (44.7%) among the cultivars and clones of the apple; however, the part of the germplasm may be heterozygous for nullalleles and those individuals cannot be distinguished from the homozygous ones. The CH02c11 locus was the most heterozygous (90.0%) in the reference cultivars; meanwhile the CH04e05 locus was the most heterozygous (84.4%) among the analysed genotypes. Triploid genotypes constituted 12.5% among the analysed genotypes. A cluster analysis revealed 5 distinct clusters among the 182 diploid apple genotypes collected from the old orchards. According to molecular marker data, the names of 12 apple cultivars were attributed to 45 analysed unknown genotypes. It was found that traditional apple cultivars 'Popierinis', 'Paprastasis antaninis' and 'Pilkasis molinis' were the most prevalent cultivars in the old orchards. The apple genotypes that have survived in old orchards are valuable sources of traits for breeding as well as of high ecological, economic and heritage importance. Their use in breeding programs would significantly extend the diversity of adaptive genes of the domestic apple.

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A Century of Practice and Experiences of the Restoration of Land-Use Types and Ecosystems

Zerbe

2022

Landscape Series

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Molecular Characterisation of the Swiss Fruit Genetic Resources

Cited by 16 publications

References 21 publications

Analysis of the genetic diversity and structure across a wide range of germplasm reveals prominent gene flow in apple at the European level

Analysis of the genetic diversity and structure across a wide range of germplasm reveals prominent gene flow in apple at the European level

SSR analysis based on molecular characterisation of apple germplasm in Lithuania

A Century of Practice and Experiences of the Restoration of Land-Use Types and Ecosystems

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