The FaRE1 LTR-retrotransposon Based SSAP Markers Reveal Genetic Polymorphism of Strawberry (Fragaria x ananassa) Cultivars

Melnikova, Nataliya V.; Kudryavtseva, Anna V.; Speranskaya, A.S.; Krinitsina, A.A.; Dmitriev, Alexey A.; Belenikin, Maxim S.; Upelniek, V. P.; Batrak, Elena R.; Kovaleva, Irina S.; Kudryavtsev, A. M.

doi:10.5539/jas.v4n11p111

Cited by 9 publications

(10 citation statements)

References 40 publications

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“…Compared to other retrotransposon-based markers, iPBS-retrotransposons have higher reproducibility and are useful for a broader spectrum of organisms, since Effective number of alleles (n e ), gene diversity (h), Shannon information index (I), and polymorphic information content (PIC). they amplify regions not only of endogenous retroviruses but also of both Gypsy and Copia LTR retrotransposons (Melnikova et al, 2012). Very recently, Ali et al (2019) investigated the genetic diversity of a world collection of safflower, confirming the universality of iPBS markers for diversity, taxonomic, and evolutionary studies.…”

Section: Discussionmentioning

confidence: 88%

Genetic diversity analysis in the Turkish pepper germplasm using iPBS retrotransposon- based markers

Yıldız¹,

Koçak²,

Nadeem³

et al. 2020

Turk J Agric For

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Capsicum is one of the most important and diverse plant taxa, widely used as a spice and vegetable worldwide, including Turkey. Germplasm characterization is an essential step for crop breeding. In the present study, we characterized the genetic diversity and population structure of a collection of 94 pepper accessions using inter-primer binding site (iPBS) retrotransposon-based markers. A total of 20 iPBS primers were used that generated 172 bands (mean = 8.6 bands/primer), of which ~92% were polymorphic in the entire germplasm collection, whereas 83%, 69%, and 80% of the bands were polymorphic within the C. annuum, C. chinense, and C. frutescens subsets, respectively. All of the taxa analyzed were clearly differentiated by the iPBS markers. The polymorphism information content of the markers ranged between 0.15 and 0.99, with an average of 0.66. Cluster analyses by different methods (UPGMA, STRUCTURE, and principal coordinate analysis) revealed a clear separation of all of the C. annuum accessions from the other pepper species, with a few subclusters observed among the latter, including groups with accessions of both C. frutescens and C. chinense. At the interspecies level, the 3 clustering methods clearly discriminated C. annuum from C. frutescens and C. chinense. No clear association was found between the iPBS-based clustering and geographical origin or fruit characteristics of the accessions. This is the first report characterizing the genetic diversity and population structure in the Turkish pepper germplasm using iPBS markers. It is expected that these data will serve as a foundation for the development of new and improved pepper varieties.

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Section: Discussionmentioning

confidence: 88%

Genetic diversity analysis in the Turkish pepper germplasm using iPBS retrotransposon- based markers

Yıldız¹,

Koçak²,

Nadeem³

et al. 2020

Turk J Agric For

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“…Several kinds of molecular marker have been developed based on these retrotransposon insertion polymorphisms (Fig. 2), including inter-retrotransposon amplification polymorphism (IRAP) (Antonius-Klemola et al, 2006;Belyayev et al, 2010;Kalendar et al, 1999;Nasri et al, 2013;Smýkal et al, 2011), retrotransposon microsatellite amplification polymorphism (REMAP) (Antonius-Klemola et al, 2006;Kalendar et al, 1999Kalendar et al, , 2000Nasri et al, 2013), retrotransposon-based insertion polymorphism (RBIP) (Flavell et al, 1998) and sequence-specific amplified polymorphism (S-SAP) (Konovalov et al, 2010;Lou and Chen, 2007;Melnikova et al, 2012;Petit et al, 2010;Syed et al, 2005;Waugh et al, 1997).…”

Section: Application Of Retrotransposons As Molecular Markersmentioning

confidence: 99%

Plant Transposable Elements and Their Application to Genetic Analysis via High-throughput Sequencing Platform

Monden

Tahara

2015

Hortic J

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Transposable elements (TEs) are mobile genetic elements in the eukaryotic genome. They are divided into two classes (class I: retrotransposons and class II: DNA transposons) based on their structure and manner of transposition. TEs are major components of the eukaryotic genome and retrotransposons are especially abundant in higher-plant genomes. As retrotransposon insertions with high copy numbers are dispersed throughout the genome and are inherited genetically, insertion polymorphisms among crop cultivars have been used as molecular markers. Recently, we developed an efficient method for screening the long terminal repeats (LTRs) of retrotransposon families that exhibit high levels of insertion polymorphisms among crop cultivars using a next-generation sequencing (NGS) platform. This method focuses on the primer binding site (PBS) that is adjacent to the 5' LTR and has a conserved DNA sequence among different LTR retrotransposon families. Construction of a sequencing library through PCR amplification using the PBS conserved sequence allowed us to acquire a large number of LTR sequences and their insertion sites throughout the genome. From our data analysis, we screened the LTR sequences that showed high levels of insertion polymorphism among closely related cultivars. In addition, we identified the insertion sites of these identified LTR retrotransposon families at the genome-wide scale in a number of cultivars with an NGS platform, which enabled us to reveal the genetic relationships among the cultivars and acquire a number of molecular markers for cultivar screening. Our results indicated that the target sequencing of these retrotransposon insertion sites was highly effective for DNA genotyping and marker development without requiring any whole-genome sequence information. This review describes the genomic structure and evolutionary aspects of TEs and discusses the development of molecular markers based on retrotransposon insertion polymorphisms.

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“…But it has been well established that the use of fruits, berries, vegetables significantly improves digestibility of food products especially in case of meat, bread and cereals. In addition, low content of proteins allows extensive use of vegetables and fruits in diets with restricted amounts of protein (Melnikova et al, 2012;Moshe et al, 2013, Ostroumov et al, 2013.…”

Section: Introductionmentioning

confidence: 99%

Total Protein and Amino Acid Composition in Selected Fruits of Russia

Prosekov¹,

Moskvina²,

Golubtsova³

2018

JEBAS

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This article attempts to identify specific features of some commonly used Russian fruit and berry raw materials (raspberry, dewberry, gooseberry, dogrose, strawberry, cherry, kiwi, bananas) by estimating the content of total protein, its fractional and amino acid composition. It has been proven that among the studied fruit and berry raw materials, the most protein-rich fruit is banana (0.92%), while the lowest mass fraction of protein is observed in kiwifruit and cherries (0.49 and 0.51%, respectively). Further, in the rest of the fruit and berries, the mass fraction of protein is in the range between 0.53 and 0.81%. Studying the generic peculiarities showed that out of the studied raw materials, raspberries and gooseberries were rich in albumin (the mass fraction was 0.24 and 0.25%); the maximum number of glutelins was observed in gooseberry and banana (the mass fraction was 0.52 and 0.63%, respectively). In cherry and kiwi, the lowest albumin content was observed (0.09 and 0.07%, respectively). Despite the low mass fraction of globulins in the samples of raw materials, it was maximum in banana (0.09%), which, together with the high content of glutelins, ensured high enough contents of total protein (0.9%) in it. The experimental data obtained during analysis of protein in fruit and berry raw materials revealed that these fruits contain both nonessential (valine, leucine, isoleucine, lysine, methionine, threonine, tryptophan, phenylalanine) as well as essential (alanine, arginine, aspartic acid, glutamic acid, glycine, histidine, proline, serine, tyrosine, cysteine) amino acids, and the content of these are varies as per the fruits types.

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The FaRE1 LTR-retrotransposon Based SSAP Markers Reveal Genetic Polymorphism of Strawberry (Fragaria x ananassa) Cultivars

Cited by 9 publications

References 40 publications

Genetic diversity analysis in the Turkish pepper germplasm using iPBS retrotransposon- based markers

Genetic diversity analysis in the Turkish pepper germplasm using iPBS retrotransposon- based markers

Plant Transposable Elements and Their Application to Genetic Analysis via High-throughput Sequencing Platform

Total Protein and Amino Acid Composition in Selected Fruits of Russia

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