scholarly journals The newly developed genomic-SSR markers uncover the genetic characteristics and relationships of olive accessions

PeerJ ◽  
2020 ◽  
Vol 8 ◽  
pp. e8573 ◽  
Author(s):  
Danyang Li ◽  
Cui Long ◽  
Xiaoming Pang ◽  
Delu Ning ◽  
Tao Wu ◽  
...  
Keyword(s):  
Ssr Markers ◽  
Trinucleotide Repeat ◽  
Principal Coordinate Analysis ◽  
Clonal Variation ◽  
Dna Fingerprints ◽  
Genetic Characteristics ◽  
Repeat Sequences ◽  
Genomic Ssr ◽  
Olive Cultivars ◽  
Simple Sequence

Background Olive (Olea europaea L.) is an important oil and fruit crop worldwide, owning a rich germplasm with a large number of cultivars. Simple sequence repeats (SSRs) are excellent markers and have been used for the identification of olive cultivars. However, the limited number of SSR markers and the occurrence of confusion on the names of cultivars, as well as the possible appearance of clonal variation make it difficult to identify cultivars and interpret relationships among olive cultivars. Method SSR markers were designed based on trinucleotide repeat sequences by screening the whole genome of olive, and the polymorphic SSR markers were developed that were applied to the identification of 53 olive accessions. The genetic characteristics and relationships of these olive accessions were evaluated based on the developed SSR markers. Results Twenty-one highly polymorphic genomic-SSR markers were developed, covering most chromosomes of olive. These SSR markers could well distinguish all 53 olive accessions, confirming their effectiveness. DNA fingerprints of the 53 olive accessions were constructed based on the 21 SSR markers. The dendrogram clearly divided the tested accessions into two main groups, which was also supported by the results of principal coordinate analysis. A total of 31 private alleles were detected in 15 olive accessions, which reflected the genetic diversity within 53 olive accessions to some extent. Six homonymy cases were also clarified by genetic analysis. These results suggest that the newly developed olive SSR markers are informative for the exploitation, preservation and breeding of olive.

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 Development of SSR Marker Set to Identify Fourty Two Indonesian Soybean Varieties

2016 ◽  
Vol 11 (2) ◽  
pp. 49
Author(s):  
Andari Risliawati ◽  
Eny I. Riyanti ◽  
Puji Lestari ◽  
Dwinita W. Utami ◽  
Tiur S. Silitonga
Keyword(s):  
Ssr Markers ◽  
Ssr Marker ◽  
Variety Identification ◽  
Polymorphism Analysis ◽  
Dna Fingerprints ◽  
Soybean Variety ◽  
Genetic Purity ◽  
Electrophoresis System ◽  
Simple Sequence ◽  
Genetic Analyzer

<p>Profile of molecular marker can be used for variety identification, genetic purity monitoring of germplasm and additional<br />requirement in proposing intellectual property protection. DNA fingerprinting of soybean had been applied at the ICABIOGRADIAARD<br />since 2004 using simple sequence repeat (SSR) markers which were run automatically by CEQ 8000 Genetic Analyzer<br />platform based on capillary electrophoresis system. This method had produced unique DNA fingerprints of the varieties tested,<br />but the marker set to efficiently identify the varieties had not yet been developed. This study aimed to develop a set of SSR<br />markers as a tool to identify the Indonesian soybean varieties. Fourty two soybean varieties were analyzed using 14 random SSR<br />markersA total of 168 alleles that were obtained from the polymorphism analysis. The average of polymorphic information<br />content (PIC) value observed was 0.7337 per SSR locus. Based on marker reproducibility rate, PIC value, number of rare alleles,<br />frequency of dominant alleles, and percentage of SSR fragment detected by genetic analyzer, we identified five SSR markers i.e.<br />Satt414, Satt147, Satt308, Satt009, and Satt516 as a SSR marker set to be used for soybean variety identification purposes. This<br />marker set was used to develop the identity (ID) of the 42 Indonesian soybean varieties.</p>

scholarly journals Evaluation of Cross-Species Transferability of SSR Markers in Foeniculum vulgare

Plants ◽  
2020 ◽  
Vol 9 (2) ◽  
pp. 175 ◽  
Author(s):  
Domenico Aiello ◽  
Nicoletta Ferradini ◽  
Lorenzo Torelli ◽  
Chiara Volpi ◽  
Joep Lambalk ◽  
...  
Keyword(s):  
Ssr Markers ◽  
Genomic Information ◽  
Foeniculum Vulgare ◽  
Breeding Programs ◽  
Breeding Lines ◽  
Transcriptomic Data ◽  
Genomic Ssr ◽  
Ssr Loci ◽  
Ssr Transferability ◽  
Simple Sequence

Fennel (Foeniculum vulgare) is a species belonging to the Apiaceae family, well known for its nutritional and pharmacological properties. Despite the economic and agricultural relevance, its genomic and transcriptomic data remain poor. Microsatellites—also known as simple sequence repeats (SSRs)—are codominant markers widely used to perform cross-amplification tests starting from markers developed in related species. SSRs represent a powerful tool, especially for those species lacking genomic information. In this study, a set of primers previously designed in Daucus carota for polymorphic SSR loci was tested in commercial varieties and breeding lines of fennel in order to: (i) test their cross-genera transferability, (ii) look at their efficiency in assessing genetic diversity, and (iii) identify their usefulness for marker-assisted selection (MAS) in breeding programs. Thirty-nine SSR markers from carrot were selected and tested for their transferability score, and only 23% of them resulted suitable for fennel. The low rate of SSR transferability between the two species evidences the difficulties of the use of genomic SSR in cross-genera transferability.

scholarly journals Identification of Simple Sequence Repeat Markers that Differentiate Bermudagrass Cultivars Derived from ‘Tifgreen’

2011 ◽  
Vol 136 (3) ◽  
pp. 211-218 ◽  
Author(s):  
Karen R. Harris-Shultz ◽  
Brian M. Schwartz ◽  
Jeff A. Brady
Keyword(s):  
Ssr Markers ◽  
Simple Sequence Repeat ◽  
Triploid Hybrid ◽  
Sequence Repeat ◽  
Microsatellite Repeat ◽  
Polymorphic Fragment ◽  
Shoot Tissue ◽  
Genomic Ssr ◽  
Insight Into ◽  
Simple Sequence

The release of the bermudagrass (Cynodon spp.) triploid hybrid ‘Tifgreen’ revolutionized southeastern U.S. golf course greens. Off-types within this cultivar began to be identified soon after the initial plantings, and through the last 50 years, many of the best performing off-types have been released as new cultivars. Examination of some of the most popular somatic mutants with a new set of 47 simple sequence repeat (SSR) markers and 23 previously discovered genomic SSR markers identified five polymorphic fragments (as compared with ‘Tifgreen’) among three cultivars, TifEagle, MiniVerde, and Tifdwarf. Each polymorphism appears to be a slight increase/decrease in microsatellite repeat number and the polymorphic fragments are unique for each cultivar. Two polymorphic fragments were identified that were unique to ‘Tifdwarf’, one polymorphic fragment was unique to ‘TifEagle’, and two polymorphic fragments were unique to ‘MiniVerde’. Furthermore, three of the five polymorphic markers display an additional allele only in the shoot tissue but not in the root tissue of ‘TifEagle’ and ‘Tifdwarf’. This finding suggests that ‘TifEagle’ and ‘Tifdwarf’ are somatic chimeras. This set of SSR markers identifies repeatable polymorphic fragments among multiple ‘Tifgreen’-derived cultivars and gives insight into the nature of the mutations that exist within ‘Tifgreen’.

Polymorphism of PCR-based markers targeting exons, introns, promoter regions, and SSRs in maize and introns and repeat sequences in oat

Genome ◽  
2001 ◽  
Vol 44 (6) ◽  
pp. 1065-1076 ◽  
Author(s):  
J B Holland ◽  
S J Helland ◽  
N Sharopova ◽  
D C Rhyne
Keyword(s):  
Ssr Markers ◽  
Inbred Lines ◽  
Amplification Product ◽  
Promoter Regions ◽  
Repeat Sequences ◽  
Sequence Tagged Sites ◽  
Maize Genotype ◽  
Oat Cultivars ◽  
Ssr Polymorphism ◽  
Simple Sequence

Sequence databases could be efficiently exploited for development of DNA markers if it were known which gene regions reveal the most polymorphism when amplified by PCR. We developed PCR primer pairs that target specific regions of previously sequenced genes from Avena and Zea species. Primers were targeted to amplify 40 introns, 24 exons, and 23 promoter regions within 54 maize genes. We surveyed 48 maize inbred lines (previously assayed for simple-sequence repeat (SSR) polymorphism) for amplification-product polymorphism. We also developed primers to target 14 SSRs and 12 introns within 18 Avena genes, and surveyed 22 hexaploid oat cultivars and 2 diploid Avena species for amplification-product polymorphism. In maize, 67% of promoter markers, 58% of intron markers, and 13% of exon markers exhibited amplification-product polymorphisms. Among polymorphic primer pairs in maize, genotype diversity was highest for SSR markers (0.60) followed by intron markers (0.46), exon markers (0.42), and promoter markers (0.28). Among all Avena genotypes, 64% of SSR markers and 58% of intron markers revealed polymorphisms, but among the cultivars only, 21% of SSR markers and 50% of intron markers were polymorphic. Polymorphic-sequence-tagged sites for plant-breeding applications can be created easily by targeting noncoding gene regions.Key words: Avena, Zea, genetic diversity, DNA sequence.

Genetic variation and population structure of Rosa roxburghii by EST-based and genomic SSR markers

2020 ◽  
Vol 52 (4) ◽  
Author(s):  
Min Lu ◽  
Huaishan Zhang ◽  
Huaming An ◽  
Wen Zhou
Keyword(s):  
Population Structure ◽  
Genetic Variation ◽  
Ssr Markers ◽  
Genomic Ssr ◽  
Rosa Roxburghii

Transferability Analysis of Cassava EST-SSR and Genomic-SSR Markers in Jatropha and Rubber Tree

2011 ◽  
Vol 37 (1) ◽  
pp. 74-78 ◽  
Author(s):  
Ming-Fu WEN ◽  
Xin CHEN ◽  
Hai-Yan WANG ◽  
Cheng LU ◽  
Wen-Quan WANG
Keyword(s):  
Ssr Markers ◽  
Rubber Tree ◽  
Genomic Ssr

LEGITIMACY OF PROGENIES USING SSR MARKERS AS CONTROLLING SYSTEM AND EARLIER SELECTION IN THE OIL PALM NURSERY (Elaeis guineensis JACQ.)

2018 ◽  
Vol 25 (1) ◽  
pp. 21-30
Author(s):  
Rokhana Faizah ◽  
Sri Wening ◽  
Abdul Razak Purba
Keyword(s):  
Dna Fingerprinting ◽  
Ssr Markers ◽  
Oil Palm ◽  
Dna Markers ◽  
Elaeis Guineensis ◽  
Gene Marker ◽  
Controlling System ◽  
Crossing Probability ◽  
Simple Sequence

Information of legitimacy of oil palm progenies is important to guaranty the quality and to control commercial seeds procedures. A true and legitimate cross will produce progeny which has a combination of their parent's allele. The information could be obtained early in the nursery stage through DNA fingerprinting analysis. Simple Sequence Repeats (SSR) is one of DNA markers used for DNA fingerprinting, since the marker system has advantages to acquire information of allele per individual in population and efficiency diverse allele of progeny and their parents. The aim of the research is to obtain legitimacy of 12 progenies analyzing in the oil palm nursery stage. Thirteen SSR markers were used to analyze 12 crossings number of oil palm. The genotypes data by alleles of SSR inferred and quantified using Gene Marker® Software version 2.4.0 Soft Genetics® LLC and analyzed based on Mendel's Law of Segregation. The result showed based on heredity pattern of progeny and their parent's allele that progenies H were indicated genetically derived from their known parents while progenies from A and G indicated as illegitimate crossing. Probability value for legitimacy of progenies of 9 other crosses has 0.031 and 0.5. Legitimacy analysis of progeny using SSR markers could be used to control the quality of crossing material and earlier selection in the oil palm nursery.

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

2004 ◽  
Vol 129 (2) ◽  
pp. 204-210 ◽  
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.

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

Plants ◽  
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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