Characterization and Identification of Indigenous Olive Germplasm from Cyprus Using Morphological and Simple Sequence Repeat Markers

Implementation of the recently developed Cyprus National Register of Commercial Varieties mandates proper cataloguing of the material conserved in the ex situ Olive Collection at the Agricultural Research Institute of Cyprus. A total of 125 trees belonging to 32 accessions were analyzed using 11 morphological endocarp traits and 14 microsatellite [simple sequence repeat (SSR)] markers. The SSR variability allowed segregation of 16 genotypes among accessions, which were clustered into three main groups based on genetic similarity. Similarity indexes among groups ranged from 0.63 to 0.65 and within groups were ≥0.9. Lower morphological variability was detected among accessions, which conformed to three morphological profiles; moreover, the three morphological profiles corresponded to the three groups of genetic similarity obtained by SSR markers. The identification, based on the unique combination of SSR genotypes and endocarp morphologies, revealed the presence of three cultivars and 15 molecular variants that presented limited molecular differences but morphological profiles identical to their catalogued cultivars. Two cultivars, ‘Ladoelia’ and ‘Kato Drys’, demonstrated molecular variation. The current study underpins the efficient management of olive germplasm collections based on combined molecular and phenotypic characterization of their accessions. The complete cataloguing of olive germplasm ensures the correct distribution of identified and authenticated material across national or international institutions.

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Genetic Diversity of Local Maize Germplasm of Tana Toraja South Sulawesi Using SSR (Simple Sequence Repeat) Markers

Ilmu Pertanian (Agricultural Science) ◽

10.22146/ipas.33085 ◽

2018 ◽

Vol 2 (3) ◽

pp. 144

Author(s):

Ramlah Ramlah ◽

Isna Rasdianah Aziz ◽

Cut Muthiadin ◽

Mashuri Masri ◽

Muhammad Khalifah Mustami ◽

...

Keyword(s):

Genetic Diversity ◽

Genetic Distance ◽

Simple Sequence Repeat ◽

Genetic Similarity ◽

Agricultural Research ◽

Similarity Coefficient ◽

Sequence Repeat ◽

Maize Germplasm ◽

South Sulawesi ◽

Simple Sequence

Plant genetic diversity is an emerging variation in a crop group caused by its genetic factors. Local corn germplasm as a source of plant genes that are able to adapt to the local environment. The purpose of this research is to obtain information on genetic variation of Tana Toraja local maize germ plasm using SSR (Simple Sequence Repeat) marker. This research was conducted at Balitsereal Molecular Biology Laboratory, Agricultural Research Agency in Maros Regency, South Sulawesi. A total of 4 local maize populations were analyzed by laboratory experimental method with observation with NTSYS pc 2.1 program. The results showed that the average number of alleles was 3.72 alleles per locus and the polymorphism rate of 0.53 with the genetic similarity coefficient was in the range of 0.47 to 0.85. 2 main clusters formed in the genetic similarity coefficient 0.47. Klaster I is Local DallePondan and Local Purple. Klaster II is Local Bebo and Kandora. The genetic distance is in the range of 0.15 to 0.74 with an average genetic distance of 0.46. From the data obtained shows that the 4th germplasm of the population of Tana Toraja Local maize diteleti has a very informative level of genetic diversity. Genetic diversity of local maize germplasm of Tana Toraja, can be used as a source of genes in the assembly of improved varieties in the future.

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SSR molecular marker analysis of the grapevine germplasm of Montenegro

OENO One ◽

10.20870/oeno-one.2014.48.2.1562 ◽

2014 ◽

Vol 48 (2) ◽

pp. 87 ◽

Cited By ~ 2

Author(s):

Vesna Maraš ◽

Vladan Bozovic ◽

Sabrina Giannetto ◽

Manna Crespan

Keyword(s):

Molecular Marker ◽

Detailed Analysis ◽

Ssr Markers ◽

Simple Sequence Repeat ◽

Genetic Relationships ◽

Morphological Variability ◽

Sequence Repeat ◽

Molecular Databases ◽

Molecular Marker Analysis ◽

Simple Sequence

Aim: Given that the information about the origin, genetic relationships, and diversity of Montenegrin grapevines is still partial, we performed a detailed analysis of the germplasm in this country using simple sequence repeat (SSR) markers. Our main goal was to determine the identity of cultivars unique to Montenegro and those shared with other countries, especially the neighbouring ones.Methods and results: Seventy samples were collected and 14 genotypes were found. After SSR profile comparison with available molecular databases and literature data, the identity of each genotype was established. Five well-known cultivars were found, the others being minor, lesser-known cultivars.Conclusion: This research provides an overview of the Montenegrin grapevine assortment. There are cultivars shared with other countries, mainly the neighbouring ones, while others are likely native to Montenegro. The Kratošija population (alias Primitivo, Zinfandel and Crljenak Kaštelanski) has a large number of different names in Montenegro and also a wide morphological variability. Therefore, Montenegro is the best candidate as the origin and spreading point of this cultivar.Significance and impact of the study: The present study adds information on the identity, origin, diffusion and variability of some grapevine cultivars, allowing us to reconstruct the history and evolution of national and transnational ampelographic assortment of Montenegro.

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Simple-sequence Repeat Marker Analysis of Genetic Relationships within Hydrangea paniculata

HortScience ◽

10.21273/hortsci.44.1.27 ◽

2009 ◽

Vol 44 (1) ◽

pp. 27-31 ◽

Cited By ~ 4

Author(s):

Sandra M. Reed ◽

Timothy A. Rinehart

Keyword(s):

Ssr Markers ◽

Simple Sequence Repeat ◽

Genetic Similarity ◽

Genetic Relationships ◽

Early Flowering ◽

Sequence Repeat ◽

Breeding Lines ◽

Diversity Studies ◽

Simple Sequence

Genetic diversity studies using 26 simple-sequence repeat (SSR) markers were conducted with 36 cultivars, breeding lines, and wild-collected accessions of Hydrangea paniculata Sieb. The SSR markers were highly variable among the genotypes, producing a mean of 5.8 alleles per marker. Three cultivars (Boskoop, Compact Grandiflora, and Webb) were either identical to or sports of the popular cultivar Grandiflora. The name ‘Pee Wee’ appears to have been applied to two phenotypically different compact forms of H. paniculata, one of which seems to be a sport of ‘Tardiva’, whereas the other is likely derived from ‘Grandiflora’. No close genetic similarity was observed among several cultivars from a long-term Belgium breeding program, although many had one parent in common. Early-flowering genotypes clustered separately from genotypes that flower in midsummer, but close genetic relationships were not observed among early-flowering cultivars. Two genotypes from Taiwan were genetically similar but were distinctly different from the Japanese genotypes. These, along with the early-flowering genotypes and a new collection from Japan, may represent unexploited sources of germplasm for improvement of H. paniculata.

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Genome survey sequencing and characterization of simple sequence repeat (SSR) markers in Platostoma palustre (Blume) A.J.Paton (Chinese mesona)

Scientific Reports ◽

10.1038/s41598-021-04264-x ◽

2022 ◽

Vol 12 (1) ◽

Author(s):

Zhao Zheng ◽

Nannan Zhang ◽

Zhenghui Huang ◽

Qiaoying Zeng ◽

Yonghong Huang ◽

...

Keyword(s):

Ssr Markers ◽

Simple Sequence Repeat ◽

Genetic Similarity ◽

Genetic Improvement ◽

Similarity Coefficient ◽

Sequence Repeat ◽

Genome Survey ◽

Simple Sequence ◽

Genome Survey Sequencing

AbstractPlatostoma palustre (Blume) A.J.Paton is an annual herbaceous persistent plant of the Labiatae family. However, there is a lack of genomic data for this plant, which severely restricts its genetic improvement. In this study, we performed genome survey sequencing of P. palustre and developed simple sequence repeat (SSR) markers based on the resulting sequence. K-mer analysis revealed that the assembled genome size was approximately 1.21 Gb. A total of 15,498 SSR motifs were identified and characterized in this study; among them, dinucleotide, and hexanucleotide repeats had the highest and lowest, respectively. Among the dinucleotide repeat motifs, AT/TA repeat motifs were the most abundant, and GC/CG repeat motifs were rather rare, accounting for 44.28% and 0.63%, respectively. Genetic similarity coefficient analysis by the UPMGA methods clustered 12 clones, of P. palustre and related species into two subgroups. These results provide helpful information for further research on P. palustre resources and variety improvements.

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

HortScience ◽

10.21273/hortsci.41.4.993b ◽

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.

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Genotyping of Peach and Nectarine Cultivars with SSR and SRAP Molecular Markers

Journal of the American Society for Horticultural Science ◽

10.21273/jashs.129.2.0204 ◽

2004 ◽

Vol 129 (2) ◽

pp. 204-210 ◽

Cited By ~ 37

Author(s):

Riaz Ahmad ◽

Dan Potter ◽

Stephen M. Southwick

Keyword(s):

Molecular Markers ◽

Ssr Markers ◽

Simple Sequence Repeat ◽

Sweet Cherry ◽

Prunus Persica ◽

Sequence Repeat ◽

Srap Markers ◽

Upgma Cluster Analysis ◽

Commercially Important ◽

Simple Sequence

Simple sequence repeat (SSR) and sequence related amplified polymorphism (SRAP) molecular markers were evaluated for detecting intraspecific variation in 38 commercially important peach and nectarine (Prunus persica) cultivars. Out of the 20 SSR primer pairs 17 were previously developed in sweet cherry and three in peach. The number of putative alleles revealed by SSR primer pairs ranged from one to five showing a low level of genetic variability among these cultivars. The average number of alleles per locus was 2.2. About 76% of cherry primers produced amplification products in peach and nectarine, showing a congeneric relationship within Prunus species. Only nine cultivars out of the 38 cultivars could be uniquely identified by the SSR markers. For SRAP, the number of fragments produced was highly variable, ranging from 10 to 33 with an average of 21.8 per primer combination. Ten primer combinations resulted in 49 polymorphic fragments in this closely related set of peaches and nectarines. Thirty out of the 38 peach and nectarine cultivars were identified by unique SRAP fingerprints. UPGMA Cluster analysis based on the SSR and SRAP polymorphic fragments was performed; the relationships inferred are discussed with reference to the pomological characteristics and pedigree of these cultivars. The results indicated that SSR and SRAP markers can be used to distinguish the genetically very close peach and nectarine cultivars as a complement to traditional pomological studies. However, for fingerprinting, SRAP markers appear to be much more effective, quicker and less expensive to develop than are SSR markers.

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Assessment of the Genetic Diversity of Rice Germplasms Characterized by Black-Purple and Red Pericarp Color Using Simple Sequence Repeat Markers

Plants ◽

10.3390/plants8110471 ◽

2019 ◽

Vol 8 (11) ◽

pp. 471

Author(s):

Jae-Ryoung Park ◽

Won-Tae Yang ◽

Yong-Sham Kwon ◽

Hyeon-Nam Kim ◽

Kyung-Min Kim ◽

...

Keyword(s):

Genetic Diversity ◽

Ssr Markers ◽

Simple Sequence Repeat ◽

Germplasm Collection ◽

Group Method ◽

Sequence Repeat ◽

Rice Varieties ◽

Red Pericarp ◽

Simple Sequence ◽

Colored Rice

The assessment of the genetic diversity within germplasm collections can be accomplished using simple sequence repeat (SSR) markers and association mapping techniques. The present study was conducted to evaluate the genetic diversity of a colored rice germplasm collection containing 376 black-purple rice samples and 172 red pericarp samples, conserved by Dong-A University. There were 600 pairs of SSR primers screened against 11 rice varieties. Sixteen informative primer pairs were selected, having high polymorphism information content (PIC) values, which were then used to assess the genetic diversity within the collection. A total of 409 polymorphic amplified fragments were obtained using the 16 SSR markers. The number of alleles per locus ranged from 11 to 47, with an average of 25.6. The average PIC value was 0.913, ranging from 0.855 to 0.964. Four hundred and nine SSR loci were used to calculate Jaccard’s distance coefficients, using the unweighted pair-group method with arithmetic mean cluster analysis. These accessions were separated into several distinctive groups corresponding to their morphology. The results provided valuable information for the colored rice breeding program and showed the importance of protecting germplasm resources and the molecular markers that can be derived from them.

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Characterization and compilation of polymorphic simple sequence repeat (SSR) markers of peanut from public database

BMC Research Notes ◽

10.1186/1756-0500-5-362 ◽

2012 ◽

Vol 5 (1) ◽

pp. 362 ◽

Cited By ~ 27

Author(s):

Yongli Zhao ◽

Channapatna S Prakash ◽

Guohao He

Keyword(s):

Ssr Markers ◽

Simple Sequence Repeat ◽

Sequence Repeat ◽

Public Database ◽

Simple Sequence

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Grass Hosts Harbor More Diverse Isolates of Puccinia striiformis Than Cereal Crops

Phytopathology ◽

10.1094/phyto-07-15-0155-r ◽

2016 ◽

Vol 106 (4) ◽

pp. 362-371 ◽

Cited By ~ 20

Author(s):

P. Cheng ◽

X. M. Chen ◽

D. R. See

Keyword(s):

Ssr Markers ◽

Stripe Rust ◽

Simple Sequence Repeat ◽

Puccinia Striiformis ◽

The United States ◽

Grass Species ◽

Cereal Crops ◽

Sequence Repeat ◽

Grass Hosts ◽

Simple Sequence

Puccinia striiformis causes stripe rust on cereal crops and many grass species. However, it is not clear whether the stripe rust populations on grasses are able to infect cereal crops and how closely they are related to each other. In this study, 103 isolates collected from wheat, barley, triticale, rye, and grasses in the United States were characterized by virulence tests and simple sequence repeat (SSR) markers. Of 69 pathotypes identified, 41 were virulent on some differentials of wheat only, 10 were virulent on some differentials of barley only, and 18 were virulent on some differentials of both wheat and barley. These pathotypes were clustered into three groups: group one containing isolates from wheat, triticale, rye, and grasses; group two isolates were from barley and grasses; and group three isolates were from grasses and wheat. SSR markers identified 44 multilocus genotypes (MLGs) and clustered them into three major molecular groups (MG) with MLGs in MG3 further classified into three subgroups. Isolates from cereal crops were present in one or more of the major or subgroups, but not all, whereas grass isolates were present in all of the major and subgroups. The results indicate that grasses harbor more diverse isolates of P. striiformis than the cereals.

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