scholarly journals Genetic Diversity of Peach Cultivars from the Collection of the Nikita Botanical Garden Based on SSR Markers

Plants ◽  
2021 ◽  
Vol 10 (12) ◽  
pp. 2609
Author(s):  
Aya A. Trifonova ◽  
Ksenia V. Boris ◽  
Natalia V. Mesyats ◽  
Valentina A. Tsiupka ◽  
Anatoly V. Smykov ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Ssr Markers ◽  
Prunus Persica ◽  
Geographic Origin ◽  
Botanical Garden ◽  
Fruit Characteristics ◽  
Breeding Center ◽  
Rational Management ◽  
Clear Differentiation ◽  
Polymorphism Level

The Nikita Botanical Garden (NBG) has a unique Prunus L. collection (peach, apricot, plum, cherry) comprising more than 3000 accessions. NBG is also a breeding center for stone fruits, including peach (Prunus persica (L.) Batsch). In the present study a set of 85 peach cultivars bred in NBG, Europe, and North America was analyzed using 12 SSR markers to assess their genetic diversity and relatedness. The detected polymorphism level was comparable to the previous estimates of genetic variability in peach cultivars. The average number of alleles per locus was 5.67, PIC value averaged 0.49, expected, and observed heterozygosity averaged 0.52 and 0.31, respectively. Among the detected alleles, 19 (27.94%) were rare and 12 (17.65%) were unique. All studied accessions except two could be identified with the used marker set. Cluster analysis revealed some groups according to the cultivars’ pedigrees. No clear differentiation of the studied sample according to geographic origin or fruit characteristics of peach cultivars was revealed. The results provide valuable information for identification and rational management of the material preserved in the NBG peach collection.

scholarly journals Genetic Diversity Analysis of Peach [Prunus persica (L.) Batsch] Varieties Using SSR Markers

2013 ◽  
Vol 45 (3) ◽  
pp. 201-211 ◽  
Author(s):  
Jee-Hwa Hong ◽  
Seung-In Yi ◽  
Yong-Sham Kwon ◽  
Young Kim ◽  
Keun-Jin Choi
Keyword(s):  
Genetic Diversity ◽  
Ssr Markers ◽  
Prunus Persica ◽  
Diversity Analysis ◽  
Genetic Diversity Analysis

scholarly journals Genetic Diversity of Local Peach (Prunus persica) Accessions from La Palma Island (Canary Islands, Spain)

Agronomy ◽  
2020 ◽  
Vol 10 (4) ◽  
pp. 457 ◽  
Author(s):  
Verónica Pérez ◽  
Nerea Larrañaga ◽  
Donia Abdallah ◽  
Ana Wünsch ◽  
José I. Hormaza
Keyword(s):  
Genetic Diversity ◽  
Canary Islands ◽  
Prunus Persica ◽  
Genetic Material ◽  
Geographic Origin ◽  
Ex Situ ◽  
Subtropical Climate ◽  
La Palma ◽  
Local Selection ◽  
Ssr Loci

Peach (Prunus persica) is an economically important temperate fruit crop due to its edible fruits. Due to the need to develop new varieties better adapted to climate change, it is of great interest to find germplasm adapted to warmer conditions, such as those found in the Canary Islands. Peach was an important crop during the last century in one of those islands (La Palma), but its cultivation has been abandoned in recent years. Currently, commercial production is relict and isolated trees are relegated to family orchards with little management. With the objective to characterize and prevent the loss of local varieties of this crop, peach trees were sampled along La Palma. A total of 89 local peach accessions were prospected and analyzed with 10 single-sequence repeat (SSR) loci, which permitted 28 different genotype profiles to be detected. These genotypes were compared to 95 Spanish peach landraces conserved in an ex situ collection, and 26 additional samples from eight different countries. Results showed that the peach genetic diversity found in La Palma was low. In addition, a relation between La Palma samples and other Spanish peaches was observed, which could indicate the arrival of genetic material from the Iberian Peninsula and subsequent intercrossing and local selection of the genotypes more adapted to the subtropical climate of the island. The population structure reflects a grouping of the samples based on fruit type and geographic origin.

scholarly journals Simple sequence repeat markers revealed genetic divergence and population structure of okra [Abelmoschus esculentus] collections of diverse geographic origin

2020 ◽  
pp. 1032-1041
Author(s):  
Wassu Mohammed ◽  
Beyene Amelework ◽  
Hussein Shimelis
Keyword(s):  
Genetic Diversity ◽  
Population Structure ◽  
Ssr Markers ◽  
Simple Sequence Repeat ◽  
Geographic Origin ◽  
Population Divergence ◽  
Sequence Repeat ◽  
Germplasm Exchange ◽  
Geographic Regions ◽  
Simple Sequence

The study was carried out to assess the genetic diversity and population structure of okra collections from diverse geographic origin using selected polymorphic simple sequence repeat (SSR) markers. Thirty-two okra accessions collected from three geographic regions were genotyped using 16 selected SSR markers. The SSR markers generated a total of 71 loci of which 67% were polymorphic. Genetic distances among accessions ranged from 2.2 to 7.1, with a mean of 4.65. Gene diversity ranged from 0.10 to 0.78 with a mean of 0.52. Genetic clustering classified the accessions into three major clusters and four sub-clusters. Each cluster and sub-cluster consisted of accessions derived from different sources. Analysis of molecular variance revealed that 67%, 81% and 83% of the total genetic variation detected was found within populations of geographic origin, altitude and collection district, respectively. The observed moderate to high population differentiation could partly be attributed to limited germplasm exchange, agro-ecological differences, and partly by selection pressure. The present study revealed the presence of high genetic diversity and population divergence among okra collections from Ethiopia. The study demonstrated that a collection strategy for conservation of okra genetic resources should focus on sampling of representative genotypes covering wide geographic regions and altitudinal ranges of target agro-ecologies.

scholarly journals Genetic Diversity Within and Among Populations of Roseroot (Rhodiola rosea L.) Based on Molecular Markers

2012 ◽  
Vol 40 (2) ◽  
pp. 266 ◽  
Author(s):  
Zsuzsanna GYORGY ◽  
Maria SZABO ◽  
Dmitry BACHAROV ◽  
Andrzej PEDRYC
Keyword(s):  
Genetic Diversity ◽  
Ssr Markers ◽  
Gene Diversity ◽  
Geographic Origin ◽  
Morphological Characteristics ◽  
Population Level ◽  
Shannon Index ◽  
Rhodiola Rosea ◽  
Pharmacologically Active ◽  
Cool Climate

Rhodiola rosea L. is a perennial adaptogenic medicinal plant found in cool climate of the northern hemisphere. The species is very diverse both in terms of morphological characteristics and in the content of the pharmacologically active substances. The genetic diversity of four geographically distant roseroot populations was studied with ISSR and SSR markers. Using 7 ISSR primers 64 DNA fragments were generated and 85,94% of those were found to be polymorphic, indicating high genetic variability at the species level (gene diversity = 0.33, Shannon index = 0.48). Lower level of diversity was detected at the population level (Shannon-index ranged from 0.2173 to 0.2696). Only four out of the eight SSR markers used were informative during this study. The primer pairs for these four SSR markers produced 25 fragments with an average of 6.25 putative alleles per locus. Observed heterozygosity ranged from 0.4 to 1.0, whereas expected heterozygosity ranged from 0.47 to 0.84. Cluster analysis based on both markers revealed the same groups, individuals clustered according to their geographic origin. The Southern-Uralian population was the most genetically isolated. ITS analysis was used for the determination whether these Southern-Uralian individuals belong to the same species.

scholarly journals Analisis Kekerabatan 50 Aksesi Kelapa Sawit (Elaeis guineensis Jacq.) Asal Kamerun Berdasarkan Marka Mikrosatelit

2016 ◽  
Vol 9 (1) ◽  
pp. 19
Author(s):  
I Made Tasma ◽  
Ahmad Warsun ◽  
Dani Satyawan ◽  
Syafaruddin Syafaruddin ◽  
Budi Martono
Keyword(s):  
Genetic Diversity ◽  
Ssr Markers ◽  
Oil Palm ◽  
Germ Plasm ◽  
Elaeis Guineensis ◽  
Study Finding ◽  
Multivariate System ◽  
High Genetic Diversity ◽  
Low Genetic Diversity ◽  
Polymorphism Level

<p>Genetic diversity of the<br />Indonesian oil palm collection remains low and collection<br />enrichness through exploration activities from the center of<br />origins is required. In 2009, 103 oil palm accessions from<br />Cameroon were collected at the National Oil Palm Genetic<br />Resources Collection located at the District of Sijunjung,<br />West Sumatera. The objectives of the present study were to<br />analayze the 50 Cameroon-originated oil palm accessions in<br />order to: (1) determine polymorphism levels of the SSR<br />markers used; (2) understand diversity levels of the oil palm<br />accessions tested; and (3) analyze accessions potentially<br />used for germ plasm collection. Fifty oil palm accessions<br />were used in this study. DNA was isolated from leaves of the<br />selected individual plants representing each of the<br />accessions. DNA was analyzed with 12 SSR markers. A<br />dendrogram was constructed using the UPGMA through<br />Numerical Taxonomy and Multivariate System program<br />version 2.1-pc. Results showed that SSR markers used<br />demonstrated the average number of alleles per locus of 3.6<br />(2-6). The polymorphism level was 0.53 (0.21-0.73). The<br />phylogenetic analysis resulted nine clusters with genetic<br />diversity between two accessions ranged from 4-82%. Ten<br />accessions (20%) showed low genetic diversity (&lt;10%) but<br />the accessions demonstrated high diversity in flowering<br />time. Eleven accessions showed medium diversity level (27-<br />42%). Five accessions demonstrated high genetic diversity<br />level (45-82%). A confirmation study using more SSR<br />markers is recommended. This study finding may be useful<br />in planning the oil palm germ plasm collection activities.</p>

scholarly journals Discovery, Characterization, and Linkage Mapping of Simple Sequence Repeat Markers In Hazelnut

2018 ◽  
Vol 143 (5) ◽  
pp. 347-362 ◽  
Author(s):  
Gehendra Bhattarai ◽  
Shawn A. Mehlenbacher
Keyword(s):  
Genetic Diversity ◽  
Linkage Map ◽  
Ssr Markers ◽  
Genome Sequence ◽  
Simple Sequence Repeat ◽  
Genomic Sequence ◽  
Geographic Origin ◽  
Null Alleles ◽  
Sequence Repeat ◽  
Simple Sequence

From the genome sequence of hazelnut (Corylus avellana), 192 new polymorphic simple sequence repeat (SSR) markers were developed, characterized, and used to investigate genetic diversity in 50 accessions. Next-generation sequencing allows inexpensive sequencing of plant genomes and transcriptomes, and efficient development of polymorphic SSR markers, also known as microsatellite markers, at low cost. A search of the genome sequence of ‘Jefferson’ hazelnut identified 9094 fragments with long repeat motifs of 4, 5, or 6 base pairs (bp), from which polymorphic SSR markers were developed. The repeat regions in the ‘Jefferson’ genome were used as references to which genomic sequence reads of seven additional cultivars were aligned in silico. Visual inspection for variation in repeat number among the aligned reads identified 246 as polymorphic, for which primer pairs were designed. Polymerase chain reaction (PCR) amplification followed by agarose gel separation indicated polymorphism at 195 loci, for which fluorescent forward primers were used to amplify the DNA of 50 hazelnut accessions. Amplicons were post-PCR multiplexed for capillary electrophoresis, and allele sizes were determined for 50 accessions. After eliminating three, 192 were confirmed as polymorphic, and 169 showed only one or two alleles in each of the 50 cultivars, as expected in a diploid. At these 169 SSRs, a total of 843 alleles were found, for an average of 4.99 and a range of 2 to 17 alleles per locus. The mean observed heterozygosity, expected heterozygosity, polymorphism information content, and the frequency of null alleles were 0.51, 0.53, 0.47, and 0.03, respectively. An additional 25 primer pairs produced more than two bands in some accessions with an average of 6.8 alleles. The UPGMA dendrogram revealed a wide genetic diversity and clustered the 50 accessions according to their geographic origin. Of the new SSRs, 132 loci were placed on the linkage map. These new markers will be useful for diversity and parentage studies, cultivar fingerprinting, marker-assisted selection, and aligning the linkage map with scaffolds of the genome sequence.

scholarly journals Analysis of Genetic Diversity and Population Structure of Pigeonpea [Cajanus cajan (L.) Millsp] Accessions Using SSR Markers

Plants ◽  
2020 ◽  
Vol 9 (12) ◽  
pp. 1643
Author(s):  
Didas Kimaro ◽  
Rob Melis ◽  
Julia Sibiya ◽  
Hussein Shimelis ◽  
Admire Shayanowako
Keyword(s):  
Genetic Diversity ◽  
Population Structure ◽  
Ssr Markers ◽  
Genetic Improvement ◽  
Polymorphic Information Content ◽  
Geographic Origin ◽  
Germplasm Collection ◽  
Fixation Index ◽  
Population Structure Analysis ◽  
The Mean

Understanding the genetic diversity present amongst crop genotypes is an efficient utilization of germplasm for genetic improvement. The present study was aimed at evaluating genetic diversity and population structure of 48 pigeonpea genotypes from four populations collected from diverse sources. The 48 pigeonpea entries were genotyped using 33 simple sequence repeat (SSR) markers that are polymorphic to assess molecular genetic diversity and genetic relatedness. The informative marker combinations revealed a total of 155 alleles at 33 loci, with an average of 4.78 alleles detected per marker with the mean polymorphic information content (PIC) value of 0.46. Population structure analysis using model based revealed that the germplasm was grouped into two subpopulations. The analysis of molecular variance (AMOVA) revealed that 53.3% of genetic variation existed within individuals. Relatively low population differentiation was recorded amongst the test populations indicated by the mean fixation index (Fst) value of 0.032. The Tanzanian pigeonpea germplasm collection was grouped into three major clusters. The clustering pattern revealed a lack of relationship between geographic origin and genetic diversity. This study provides a foundation for the selection of parental material for genetic improvement.

scholarly journals DNA fingerprinting and genetic relationships among white clover cultivars

2003 ◽  
pp. 163-169 ◽  
Author(s):  
M.Z.Z. Jahufer ◽  
B.A. Barrett ◽  
A.G. Griffiths ◽  
D.R. Woodfield
Keyword(s):  
Genetic Diversity ◽  
Cluster Analysis ◽  
Dna Fingerprinting ◽  
Ssr Markers ◽  
White Clover ◽  
Trifolium Repens ◽  
Genetic Relationships ◽  
Geographic Origin ◽  
Indirect Measure ◽  
Trifolium Repens L

Genetic diversity provides the raw material for plant improvement programmes. The assessment of genetic diversity is commonly based on plant morphology; however, this indirect measure of genetic diversity is often confounded by environmental effects. Microsatellite (SSR) markers are a powerful tool that directly measures variation among plants at the DNA level. We assayed the pattern of relatedness among 32 white clover (Trifolium repens L.) cultivars using 39 SSR markers that are evenly distributed within the white clover genome. The 390 alleles detected were used to quantify the 496 pairwise genetic similarity estimates among the cultivars, detecting a mean value of 0.56 (range 0.44 - 0.68). Cluster analysis assigned the 32 cultivars to 14 clusters based on their genetic similar ity. The resulting clusters revealed strong correlation with known genetic relationships based on pedigree and the geographic origin of the parental germplasm. The development of a DNA fingerprinting technique based on high-throughput SSR markers has potential applications in plant variety rights, seed certification and variety identification in grazed pastures. Keywords: cluster analysis, DNA fingerpr inting, genetic diversity, microsatellite , molecular markers, Trifolium repens L

Genetic diversity and population structure of Populus yunnanensis revealed by SSR markers

2020 ◽  
Vol 52 (6) ◽  
Author(s):  
Anpei Zhou ◽  
Dan Zong ◽  
Peihua Gan ◽  
Yao Zhang ◽  
Dan Li ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Population Structure ◽  
Ssr Markers
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