Genetic Diversity, Population Structure and Construction of a Core Collection of Apple Cultivars from Italian Germplasm

Liang, Wei; Dondini, Luca; Franceschi, Paolo De; Paris, Roberta; Sansavini, S.; Tartarini, Stefano

doi:10.1007/s11105-014-0754-9

Cited by 105 publications

(114 citation statements)

References 79 publications

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“…Furthermore, the Shannon's information index (I) maximum (1.620) was recorded for ch01f02, while the lowest value (1.299) was recorded for locus 28f4, with an average of 1.335. Our results revealed a decreased number of alleles per locus than those reported previously for apple (Gharghani et al, 2009;Liang et al, 2015;Urrestarazu et al, 2012), which could be attributed to the smaller number of cultivars tested in our study. Moreover, the diversity level of heterozygosity in our collection (0.627) is slightly lower compared with heterozygosity (0.73) described for apples from the regions of Asturias, the Basque Country, and Galicia in northern and northwestern Spain (Pereira-Lorenzo et al, 2003) and 0.75 in Portuguese apple germplasm collections (Ferreira et al, 2016).…”

Section: Molecular Characterization Using Microsatellite Markerscontrasting

confidence: 73%

“…Moreover, the diversity level of heterozygosity in our collection (0.627) is slightly lower compared with heterozygosity (0.73) described for apples from the regions of Asturias, the Basque Country, and Galicia in northern and northwestern Spain (Pereira-Lorenzo et al, 2003) and 0.75 in Portuguese apple germplasm collections (Ferreira et al, 2016). In contrast, the diversity observed here was lower than that observed in local cultivars of northeastern Spain (0.82) (Urrestarazu et al, 2012) and 0.80 (Pina et al, 2014), Italy (0.80) (Liang et al, 2015) and Portuguese Azores Islands, (0.81) (Foroni et al, 2012). This result indicates a moderate genetic diversity (Hamrick and Godt, 1996) between the apple germplasm established in a Greek Pomology Institute collection.…”

Section: Molecular Characterization Using Microsatellite Markerscontrasting

confidence: 65%

“…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%

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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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Section: Molecular Characterization Using Microsatellite Markerscontrasting

confidence: 73%

Section: Molecular Characterization Using Microsatellite Markerscontrasting

confidence: 65%

Section: Introductionmentioning

confidence: 99%

See 1 more Smart Citation

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

Ganopoulos¹,

Tourvas

Xanthopoulou

et al. 2018

Sci. agric. (Piracicaba, Braz.)

View full text Add to dashboard Cite

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“…stanford.edu/group/rosenberglab/distruct.html). Genotypes were assigned to the subgroup for which they had the highest membership coefficient, considering strong affinity when the assignment probability (qI) was ≥0.8 (Liang et al 2015;Urrestarazu et al 2012).…”

Section: Analysis Of Genetic Structurementioning

confidence: 99%

“…(Zhen et al 2004). These markers have proved advantageous for diversity studies on apple (Garkava-Gustavsson et al 2008;Gasi et al 2010;Gross et al 2014;Hokanson et al 2001;Liang et al 2015;Moriya et al 2011;Pereira-Lorenzo et al 2008;Song et al 2006;Urrestarazu et al 2012;van Treuren et al 2010), and several hundred SSR markers have been developed and genetically mapped across the 17 linkage groups of the apple genome (Gianfranceschi et al 1998;Liebhard et al 2002;Silfverberg-Dilworth et al 2006).…”

Section: Introductionmentioning

confidence: 99%

Genetic Diversity, Population Structure, Parentage Analysis, and Construction of Core Collections in the French Apple Germplasm Based on SSR Markers

et al. 2016

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In-depth characterization of apple genetic resources is a prerequisite for genetic improvement and for germplasm management. In this study, we fingerprinted a very large French collection of 2163 accessions with 24 SSR markers in order to evaluate its genetic diversity, population structure, and genetic relationships, to link these features with cultivar selection date or usage (old or modern, dessert or cider cultivars), and to construct core collections. Most markers were highly discriminating and powerful for varietal identification, with a probability of identity P (ID) over the 21 retained SSR loci close to 10 −28. Pairwise comparisons revealed 34 % redundancy and 18.5 % putative triploids. The results showed that the germplasm is highly diverse with an expected heterozygosity H e of 0.82 and observed heterozygosity H o of 0.83. A Bayesian model-based clustering approach revealed a weak but significant structure in three subgroups (F ST = 0.014-0.048) corresponding, albeit approximately, to the three subpopulations defined beforehand (Old Dessert, Old Cider, and Modern Cultivars). Parentage analyses established already known and yet unknown relationships, notably between old cultivars, with the frequent occurrence of cultivars such as BKing of Pippin^and BCalville Rouge d'Hiver^as founders. Finally, core collections based on allelic diversity were constructed. A large dessert core collection of 278 cultivars contained 90 % of the total dessert allelic diversity, whereas a dessert subcore collection of 48 cultivars contained 71 % of diversity. For cider apples, a 48-cultivar core collection contained 83 % of the total cider allelic diversity.

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SSR‐based DNA fingerprinting of fruit crops

et al. 2023

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The DNA fingerprinting of fruit crops, based on DNA microsatellite markers that are considered to be the key markers for the molecular analysis of germplasm collections, is reviewed. Simple sequence repeats (SSRs) remain the markers of choice for fingerprinting in humans, animals, plants, and other living organisms. This review, that considers 44 fruit species, provides a set of markers that are suitable for profiling accessions and that should make the databases produced in different laboratories more comparable. Every effort has been made to select SSR markers that are robust and easily scorable considering that such analyses are sometimes used in legal cases. The review first describes the basic protocols, procedures, and methods of data analyses; it then describes the fingerprinting of individual species or groups of species, providing a set of SSR markers and appropriate guidance based on the revised literature and on the authors' experience.

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Genetic Diversity, Population Structure and Construction of a Core Collection of Apple Cultivars from Italian Germplasm

Cited by 105 publications

References 79 publications

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

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

Genetic Diversity, Population Structure, Parentage Analysis, and Construction of Core Collections in the French Apple Germplasm Based on SSR Markers

SSR‐based DNA fingerprinting of fruit crops

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