scholarly journals Genetic Diversity of Fig (Ficus Carica L.) Germplasm From The Mediterranean Basin As Revealed by SSR Markers

2021 ◽  
Author(s):  
Athanasios Sclavounos ◽  
Petros Roussos ◽  
Sotiria Milla ◽  
Panagiotis Kostas ◽  
Yiannis Samaras ◽  
...  
Keyword(s):  
Geographical Origin ◽  
Allelic Variation ◽  
Principal Coordinate Analysis ◽  
Ficus Carica ◽  
Ex Situ ◽  
Mediterranean Countries ◽  
Ssr Loci ◽  
Genetic Makeup ◽  
Simple Sequence ◽  
The Mediterranean Basin

Abstract Fig (Ficus carica L.) tree is cultivated worldwide and is highly appreciated for its fruit, which is consumed fresh or dried, having high nutritional and pharmaceutical value and for these reasons there is an increasing interest for its cultivation. In the present study, an ex situ collection of 60 fig accessions (41 indigenous Greek and 19 from other Mediterranean countries) was established and its diversity was analyzed using eight simple sequence repeat (SSR) loci. Greek fig genotypes showed relatively low allelic variation (average number of SSR alleles per locus was 3.3), an excess of heterozygosity (mean He = 0.449 and Ho = 0.537), and extensive outbreeding (mean F index -0.184). Cluster analysis showed that the established fig population exhibited weak genetic structure with the majority of the genetic variation (69%) being present within individual members of the clusters. Both cluster and principal coordinate analysis confirmed that there is no correlation between genetic makeup and geographical origin of the fig accessions. Polymorphism information content (PIC) with an average of 0.398 was reasonably informative. An identification key scheme for fig cultivars that will be useful in cultivar discrimination and intellectual property protection was developed. This work will contribute to a sustainable fig production regionally and worldwide, through the establishment and conservation of a reference fig collection, providing germplasm for future breeding efforts.

scholarly journals Evaluation of Olives Cultivated in Southern Italy by Simple Sequence Repeat Markers

HortScience ◽  
2009 ◽  
Vol 44 (3) ◽  
pp. 582-588 ◽  
Author(s):  
Innocenzo Muzzalupo ◽  
Francesca Stefanizzi ◽  
Enzo Perri
Keyword(s):  
Mediterranean Basin ◽  
Clustering Algorithm ◽  
Southern Italy ◽  
Ex Situ ◽  
Group Method ◽  
Breeding Programs ◽  
Olive Cultivars ◽  
The Mediterranean ◽  
Simple Sequence ◽  
The Mediterranean Basin

Olive (Olea europaea L.) is a species of great economic importance in the Mediterranean basin. Italy is very important for the olive industry; in fact, olive's genetic patrimony is very rich and characterized by an abundance of cultivars. At present, the majority of ancient landraces are vegetatively propagated by farm. It is likely that the number of cultivars is underestimated because of inadequate information on minor local cultivars that are widespread in different olive-growing areas. The existence of many cultivars reinforces the need for a reliable identification method. It is important to improve the ex situ plant germplasm collection and fairly to characterize all cultivars for future breeding programs. In the present report, we used 11 loci microsatellites to characterize 211 olive cultivars of an olive collection cultivated in six regions of southern Italy. These regions represent the major area for olive cultivation in Italy and have a strategic geographical location in the Mediterranean basin. The dendrogram obtained, using the unweighted pair group method with arithmetic mean clustering algorithm, depicts the pattern of relationships between the studied cultivars. There is a clear structuring of the variability relative to the geographic origin of olive cultivars. This work, for the very high number of the Italian olive cultivars analyzed, highlights the degree and distribution of genetic diversity of this species for better exploitation of olive resources and for the design of plant breeding programs. Besides, the use of molecular markers, like simple sequence repeats, is imperative to build a database for cultivar analysis, for traceability of processed food, and for appropriate management of olive germplasm collections.

scholarly journals Application of Microsatellite and Inter Simple Sequence Markers for Certifying Trueness to Type of Grafted Ramets and Clustering of Persian Walnut Varieties

2021 ◽  
Author(s):  
Masoomeh Hosseini Nickravesh ◽  
Kourosh Vahdati ◽  
fatemeh amini ◽  
Reza Amiri ◽  
Keith Woeste
Keyword(s):  
Ssr Markers ◽  
Issr Markers ◽  
Principal Coordinate Analysis ◽  
Dna Fingerprint ◽  
Polymorphic Ssrs ◽  
Persian Walnut ◽  
Inter Simple Sequence Repeats ◽  
Ssr Loci ◽  
Ssrs Markers ◽  
Simple Sequence

Abstract The utility of seventeen Microsatellite (SSR) markers and fifteen inter simple sequence repeats (ISSR) markers for the identification of twenty eight ramets of 11 varieties of walnut (Juglans regia) was explored. Thirty nine individual genomes were screened using 61 and 38 scorable fragments from SSR and ISSR markers, respectively. The least polymorphic SSR locus was WGA004 (two alleles) and the most polymorphic (5 alleles) was WGA276. Polymorphism information content values ranged from 0.08 (WGA004) to 0.43 (WGA032) in SSR markers and from 0.11 (AGA (AC)7) to 0.49 (CAC(TGT)5) in ISSR markers, with an average of 0.29 and 0.19, respectively. In most cases, grafted varieties with identical names also had the same microsatellites profile. The principal coordinate analysis and clustering (UPGMA) based on the combined marker set emphasized two failures in grafting or off-types, ramets identified as Serr 4 (S4) and Vina 1 (V1). The presence of two off-type ramets in the walnut research orchard emphasizes the importance of using molecular certification for proving true-to-type of walnut orchards. Using 13 polymorphic SSRs, we tabulated a DNA fingerprint chart of 11 walnut varieties. Except for ‘Chandler’, each cultivar could be distinguished using a combination of only two SSR loci. The 13 SSRs markers evaluated in this study could be used in future to identify clones produced from the varieties.

scholarly journals Molecular Analysis of Genetic Diversity and Geographic Origin within an Ex Situ Germplasm Collection of Cherimoya by Using SSRs

2007 ◽  
Vol 132 (3) ◽  
pp. 357-367 ◽  
Author(s):  
P. Escribano ◽  
M.A. Viruel ◽  
J.I. Hormaza
Keyword(s):  
Genetic Diversity ◽  
Geographic Origin ◽  
Germplasm Collection ◽  
Ex Situ ◽  
Group Method ◽  
Pair Group ◽  
Ssr Primers ◽  
Upgma Cluster Analysis ◽  
Ssr Loci ◽  
Simple Sequence

Cherimoya (Annona cherimola Mill.) is an underused fruit crop with a clear niche for expansion in subtropical climates. In this study, 16 simple sequence repeat (SSR) loci were used to find molecular polymorphisms among 279 cherimoya accessions from a worldwide ex situ field germplasm collection. A total of 79 amplification fragments were amplified with 16 pairs of SSR primers, with an average of 4.9 bands/SSR. Mean expected and observed heterozygosities averaged 0.53 and 0.44, respectively. The total value for the probability of identity was 4.34 × 10−8. The SSRs studied resulted in 267 different fingerprinting profiles, of which 258 were unique genotypes; the rest were putative cases of synonymies or mislabeling errors. Unweighted pair group method with arithmetic averages (UPGMA) cluster analysis indicated the relationships among the analyzed accessions, showing some specific groups related to their geographical origins. Analysis of molecular variance (AMOVA) was performed to examine the distribution of genetic variation of the 148 accessions collected from putative cherimoya origin areas in Ecuador and Peru, showing that the major variations occurred within valleys in each country. The results confirmed the usefulness of microsatellites for identification of genetic diversity and geographic origin of cherimoya and are discussed in terms of their implications for ex situ conservation of cherimoya genetic resources.

scholarly journals Utilization of Identified Simple Sequence Repeats (SSRs) in Malus ×domestica (Apple) for Germplasm Characterization

HortScience ◽  
1996 ◽  
Vol 31 (4) ◽  
pp. 619b-619 ◽  
Author(s):  
Amy K. Szewc-McFadden ◽  
Warren F. Lamboy ◽  
James R. McFerson
Keyword(s):  
Germplasm Collection ◽  
Ex Situ ◽  
Dna Library ◽  
The Core ◽  
Core Subset ◽  
Ssr Loci ◽  
Dna Fragment ◽  
Simple Sequence

To comprehend genetic identity and relatedness in Malus germplasm held in situ and ex situ, we are employing simple sequence repeat (SSR) DNA fragment information in combination with passport and horticultural data. SSRs offer certain advantages for characterizing large arrays of germplasm efficiently. They are abundantly dispersed throughout plant genomes and are exceedingly polymorphic. In addition, they can be PCR-amplified and detected by automated fluorescence-based technology. A size-fractionated DNA library of M. ×domestica cv Golden Delicious was screened to identify SSR loci. Eight loci were found to be reliably informative and were used to prepare locus-specific primer pairs. Characterization of the 75 M. ×domestica accessions included in the core subset of the USDA-ARS Malus germplasm collection revealed six of the eight loci were polymorphic within the array. The number of alleles per locus ranged from two to 21. Throughput was enhanced by multiplexing, allowing simultaneous use of two or three primer pairs. With improved genetic characterization of Malus germplasm, we intend to better develop and relate the core subset to the rest of the collection and to in situ Malus genetic resources. SSR markers appear to be an efficient and reliable tool to expedite this process.

Microsatellite DNA as shared genetic markers among conifer species

1999 ◽  
Vol 29 (3) ◽  
pp. 365-371 ◽  
Author(s):  
C S Echt ◽  
G G Vendramin ◽  
C D Nelson ◽  
P Marquardt
Keyword(s):  
Pinus Radiata ◽  
Picea Glauca ◽  
Ssr Marker ◽  
Allelic Variation ◽  
Conifer Species ◽  
Ssr Loci ◽  
Polymerase Chain ◽  
Shared Alleles ◽  
Simple Sequence ◽  
Shared Genetic

Polymerase chain reaction (PCR) primer pairs for 21 simple sequence repeat (SSR) loci in Pinus strobus L. and 6 in Pinus radiata D. Don. were evaluated to determine whether SSR marker amplification could be achieved in 10 other conifer species. Eighty percent of SSR primer pairs for (AC)n loci that were polymorphic in P. strobus also amplified SSR loci in two other soft pines of the subgenus Strobus but not in seven hard pines of the subgenus Pinus, nor in Picea glauca (Moench) Voss or Pseudotsuga menziesii (Mirb.) Franco. The six P. strobus SSR primer pairs that did amplify loci from conifers other than soft pines were those that were specific to loci monomorphic within P. strobus. These six loci were also monomorphic within seven other species tested, but four of the loci were polymorphic among species. A comparison of allelic variation among the three soft pine species found only 25 shared alleles among a total of 122 alleles at eight loci. Primer pairs for dinucleotide SSR loci that were polymorphic in Pinus radiata also specifically amplified loci from various other hard pines but not from the soft pines or from the other conifers tested.

scholarly journals Optimization of the Management of an Ex-situ Germplasm Bank in Common Fig with SSRs

2008 ◽  
Vol 133 (1) ◽  
pp. 69-77 ◽  
Author(s):  
Esther Giraldo ◽  
Margarita Lopez-Corrales ◽  
Jose Ignacio Hormaza
Keyword(s):  
Geographic Distance ◽  
Germplasm Collection ◽  
Ex Situ ◽  
Group Method ◽  
Germplasm Management ◽  
Pair Group ◽  
Common Fig ◽  
Mediterranean Countries ◽  
Upgma Cluster Analysis ◽  
Ssr Loci

Common fig (Ficus carica L.) is an underused fruit crop cultivated in Mediterranean countries since antiquity. In this study, 20 simple sequence repeat (SSR) loci were used to characterize 209 fig accessions conserved in an ex-situ field germplasm collection. A total of 78 fragments were amplified with the 20 pairs of SSR primers, with an average of 3.9 alleles per locus and a size between 120 and 376 bp. The mean expected and observed heterozygosities were 0.36 and 0.41, respectively. The total value for the probability of identity was 6.8 × 10−4. The SSRs studied resulted in identification of 98 unique genotypes (46.86% of all accessions preserved in the bank), indicating a high number of synonyms. Unweighted pair group method with arithmetic averages (UPGMA) cluster analysis did not show clear groups based on geographic distance, although some specific groups related to fruit type were observed. The results confirm the usefulness of microsatellites for the identification of genetic diversity and potential value of germplasm management for fig.

scholarly journals Microsatellites are Used to Examine Apple and Pear Identities and Genetic Relationships

HortScience ◽  
2006 ◽  
Vol 41 (4) ◽  
pp. 993B-993
Author(s):  
Nahla Bassil ◽  
Kim Hummer ◽  
Joseph Postman
Keyword(s):  
Cluster Analysis ◽  
Ssr Markers ◽  
Simple Sequence Repeat ◽  
Genetic Relationships ◽  
Ex Situ ◽  
Pome Fruit ◽  
Germplasm Collections ◽  
Asian Pear ◽  
Ssr Loci ◽  
Simple Sequence

Simple Sequence Repeat (SSR) markers developed in apple and pear were used to determine genetic relationships among heritage apple and pear cultivars from Portugal's Azore Islands, and to develop identity fingerprints for European and Asian pear accessions at the USDA–ARS National Clonal Germplasm Repository (NCGR). We used 11 SSR markers (six from apple and five from pear) to examine 18 heritage apple and 9 heritage pear cultivars from the Azores. Eight additional Portuguese and economically important cultivars of apple and eight of pear were used as standards. Cluster analysis separated the apple and pear accessions into two distinct groups. Among apple genotypes, 12 unique accessions and five groups of synonyms were identified, while, in pear, seven unique genotypes and three pairs of synonyms were found. None of the accessions obtained from the Azores corresponded to widely grown standard Portuguese apple or pear cultivars. To examine 144 NCGR pear accessions, we used nine polymorphic SSR loci that were developed from GenBank sequences. Cluster analysis identified five sets of synonyms (four in P. communis L. and one in P. ussuriensis Maxim.) and four pairs of homonyms (three in P. communis and one in P. pyrifolia Burm. f. Nakai), and confirmed three clonal sets. Morphological evaluations and additional SSR markers will be used to confirm these results, and to genetically document the identities of pear genotypes. SSR markers will greatly assist the management of ex situ pome fruit germplasm collections by helping to eliminate duplicate accessions and expanding the genetic diversity represented.

scholarly journals ECPGR recommended SSR loci for analyses of European plum (Prunus domestica) collections

2020 ◽  
Vol 1 (1) ◽  
pp. 40-48
Author(s):  
Hilde Nybom ◽  
Daniela Giovannini ◽  
Matt Ordidge ◽  
Stein Harald Hjeltnes ◽  
Jasmin Grahić ◽  
...  
Keyword(s):  
Genetic Structure ◽  
Working Group ◽  
Simple Sequence Repeat ◽  
Geographical Origin ◽  
Sensu Stricto ◽  
Sequence Repeat ◽  
Prunus Domestica ◽  
Ssr Loci ◽  
Standard Set ◽  
Simple Sequence

A set of nine Simple Sequence Repeat (SSR) loci, approved by the ECPGR Prunus working group, are proposed as a standard set for genotyping European plum accessions. These loci show sufficient reliability in spite of problems caused by hexaploidy. Polymorphism in the loci is high and enables differentiation between unique plum accessions as well as analyses of genetic grouping and overall genetic structure. A set of seven reference accessions are described. A compiled dataset with allelic information for 165 accessions is presented. Genetic structure reveals three different K-values (2, 4 and 9) demonstrating a major dichotomy between Prunus insititia-related accessions and cultivars belonging to Prunus domestica sensu stricto, as well as differentiation among minor subgroups defined by pomological traits and geographical origin.

scholarly journals Diversity and Relationships among Neglected Apricot (Prunus armeniaca L.) Landraces Using Morphological Traits and SSR Markers: Implications for Agro-Biodiversity Conservation

Plants ◽  
2021 ◽  
Vol 10 (7) ◽  
pp. 1341
Author(s):  
Giandomenico Corrado ◽  
Marcello Forlani ◽  
Rosa Rao ◽  
Boris Basile
Keyword(s):  
Prunus Armeniaca ◽  
Ex Situ ◽  
Skin Colour ◽  
Maintenance Breeding ◽  
Prunus Armeniaca L ◽  
Ex Situ Collection ◽  
Loss Of Diversity ◽  
Ssrs Markers ◽  
On Farm ◽  
Simple Sequence

Apricot (Prunus armeniaca L.) is an economically important tree species globally cultivated in temperate areas. Italy has an ample number of traditional varieties, but numerous landraces are abandoned and at risk of extinction because of increasing urbanization, agricultural intensification, and varietal renewal. In this work, we investigated the morphological and genetic diversity present in an ex-situ collection of 28 neglected varieties belonging to the so-called “Vesuvian apricot”. Our aim was to understand the level of diversity and the possible link between the promotion of specific fruit types (e.g., by public policies) and the intraspecific variation in apricot. The combination of five continuous and seven categorical traits allowed us to phenotypically distinguish the varieties; while fruit quality-related attributes displayed high variation, both apricot size and skin colour were more uniform. The twelve fluorescent-based Simple Sequence Repeats (SSRs) markers identified cultivar-specific molecular profiles and revealed a high molecular diversity, which poorly correlated with that described by the morphological analysis. Our results highlighted the complementary information provided by the two sets of descriptors and that DNA markers are necessary to separate morphologically related apricot landraces. The observed morphological and genetic differences suggest a loss of diversity influenced by maintenance breeding of specific pomological traits (e.g., skin colour and size). Finally, our study provided evidence to recommend complementary strategies to avoid the loss of diversity in apricot. Actions should pivot on both the promotion of easily identified premium products and more inclusive biodiversity-centred on-farm strategies.

scholarly journals Simple Sequence Repeat and S-Locus Genotyping to Assist the Genetic Characterization and Breeding of Polyploid Prunus Species, P. spinosa and P. domestica subsp. insititia

2021 ◽  
Author(s):  
Júlia Halász ◽  
Noémi Makovics-Zsohár ◽  
Ferenc Szőke ◽  
Sezai Ercisli ◽  
Attila Hegedűs
Keyword(s):  
Simple Sequence Repeat ◽  
Principal Component ◽  
Sequence Repeat ◽  
Breeding Programs ◽  
Allele Number ◽  
Genetic Potential ◽  
Ssr Loci ◽  
High Level ◽  
Diversity Studies ◽  
Simple Sequence

AbstractPolyploid Prunus spinosa (2n = 4 ×) and P. domestica subsp. insititia (2n = 6 ×) represent enormous genetic potential in Central Europe, which can be exploited in breeding programs. In Hungary, 16 cultivar candidates and a recognized cultivar ‘Zempléni’ were selected from wild-growing populations including ten P. spinosa, four P. domestica subsp. insititia and three P. spinosa × P. domestica hybrids (2n = 5 ×) were also created. Genotyping in eleven simple sequence repeat (SSR) loci and the multiallelic S-locus was used to characterize genetic variability and achieve a reliable identification of tested accessions. Nine SSR loci proved to be polymorphic and eight of those were highly informative (PIC values ˃ 0.7). A total of 129 SSR alleles were identified, which means 14.3 average allele number per locus and all accessions but two clones could be discriminated based on unique SSR fingerprints. A total of 23 S-RNase alleles were identified and the complete and partial S-genotype was determined for 10 and 7 accessions, respectively. The DNA sequence was determined for a total of 17 fragments representing 11 S-RNase alleles. ‘Zempléni’ was confirmed to be self-compatible carrying at least one non-functional S-RNase allele (SJ). Our results indicate that the S-allele pools of wild-growing P. spinosa and P. domestica subsp. insititia are overlapping in Hungary. Phylogenetic and principal component analyses confirmed the high level of diversity and genetic differentiation present within the analysed accessions and indicated putative ancestor–descendant relationships. Our data confirm that S-locus genotyping is suitable for diversity studies in polyploid Prunus species but non-related accessions sharing common S-alleles may distort phylogenetic inferences.

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