Plant diversity and transcriptional variability assessed by retrotransposon-based molecular markers

Kalendar, Ruslan; Aizharkyn, K. S.; Хапилина, О.Н.; Amenov, Asset; Tagimanova, Damelya

doi:10.18699/vj17.231

Cited by 11 publications

(9 citation statements)

References 48 publications

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“…Bearing this is mind, molecular markers such as retrotransposons and simple sequence repeats (SSR) or microsatellites, which are more informative for the discrimination of closely related genotypes and are considered to be of great value in fingerprinting, mapping, and genetic analysis of plants can be used for discriminating between and within the two groups of plantains evaluated in this study. Thus far, retrotransposon- and microsatellite-based molecular markers have been readily utilized for purposes of genetic analysis, including an estimation of the genetic diversity of plants [33], determination of the relationships between plant accessions, elucidation of evolutionary relationships, as an aid in the taxonomic classification of many plants including tropical pasture grasses [34–37] as well as in the molecular genotyping of important crops such as rice [38], orphan legume species [39, 40] and banana and plantain [12]. Consequently, their use in the evaluation of dichotomous bunching plantain cultivars will be in order and highly recommended as this will help to pinpoint the degree of divergence within them on the one hand and between them and the single bunching cultivar of False Horn plantains on the other.…”

Section: Discussionmentioning

confidence: 99%

Ploidy level and nucleotide variations in inflorescence dichotomous cultivars of plantain (Musa spp. AAB genome)

Brisibe

Ekanem

2019

BMC Genomics

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Background Inflorescence dichotomy in Musa species is a rare developmental event which leads to the production of multiple bunches on a single pseudostem at fruiting. In spite of its fascinating attraction and seductive appeal, little is known about the cytogenetic basis and molecular mechanisms that could be ascribed to this phenomenon. To bridge this gap in information, an integrative approach using cytological fingerprinting and DNA ploidy level profiling (based on chromosome counting and flow cytometry) were assayed on five inflorescence dichotomous plantain varieties and a single-bunching cultivar that served as control. This was done to assess the number and behaviour of chromosomes on the one hand and single nucleotide polymorphisms identified during analysis of nucleotide variations on the other. Results Chromosomes stained with aceto-orcein were very tiny, compact, metacentric and acrocentric, and differed both in number and ploidy level between the inflorescence dichotomous and single-bunching cultivars. The dichotomous plantains were mainly diploid (2n = 2x = 22) while the single-bunching ‘Agbagba’ cultivar was consistently a triploid (2n = 3x = 33), as revealed by histological chromosome counting and flow cytometry, implying that there was a high incidence of genomic divergence on account of ploidy variations among the different Musa cultivars. Molecular genotyping using single nucleotide polymorphisms detected on the GTPase-protein binding gene of the leaf tissue gene complex provided further evidence indicating that differences in the number of bunches among the inflorescence dichotomous cultivars could be ascribed to nucleotide diversity that was elicited by changes in amino acid sequences in the genome of the crops. Non-synonymous nucleotide substitutions resulted mainly from transversion (from purine to pyramidine and vice versa), tacitly implying that these changes were crucial and promoted a cascade of reactions in the genome that were, probably, responsible for the non-persistence of the dichotomization event(s) or the reversals in the bunch phenotype detected among the inflorescence dichotomous cultivars. Conclusions This is the first report of cytogenetic fingerprints and nucleotide diversity detection among single- and multiple-bunching Musa cultivars. A clear distinction between the two groups was found that is indicative of variations both in ploidy level and nucleotide sequences. The pattern of single nucleotide polymorphisms provided profound clues suggesting that there was a high incidence of genomic divergence, due to random and unstable genetic events that were triggered by frequent spontaneous somatic mutations.

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Section: Discussionmentioning

confidence: 99%

Ploidy level and nucleotide variations in inflorescence dichotomous cultivars of plantain (Musa spp. AAB genome)

Brisibe

Ekanem

2019

BMC Genomics

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“…The RLX-based genetic marker techniques rely on PCR amplification between features such as the LTR that are conserved in RLXs, or between these features and other dispersed and conserved motifs in the genome. The methods include retrotransposonbased insertion polymorphism (RBIP) [21], sequencespecific amplified polymorphism (S-SAP) [22], interretrotransposon-amplified polymorphism (IRAP) [19], retrotransposon-microsatellite-amplified polymorphism (REMAP), and inter-primer binding site (iPBS) amplification [17][18][19][23][24][25][26][27].…”

Section: Introductionmentioning

confidence: 99%

High-throughput retrotransposon-based genetic diversity of maize germplasm assessment and analysis

et al. 2020

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Maize is one of the world's most important crops and a model for grass genome research. Long terminal repeat (LTR) retrotransposons comprise most of the maize genome; their ability to produce new copies makes them efficient high-throughput genetic markers. Inter-retrotransposon-amplified polymorphisms (IRAPs) were used to study the genetic diversity of maize germplasm. Five LTR retrotransposons (Huck, Tekay, Opie, Ji, and Grande) were chosen, based on their large number of copies in the maize genome, whereas polymerase chain reaction primers were designed based on consensus LTR sequences. The LTR primers showed high quality and reproducible DNA fingerprints, with a total of 677 bands including 392 polymorphic bands showing 58% polymorphism between maize hybrid lines. These markers were used to identify genetic similarities among all lines of maize. Analysis of genetic similarity was carried out based on polymorphic amplicon profiles and genetic similarity phylogeny analysis. This diversity was expected to display ecogeographical patterns of variation and local adaptation. The clustering method showed that the varieties were grouped into three clusters differing in ecogeographical origin. Each of these clusters comprised divergent hybrids with convergent characters. The clusters reflected the differences among maize hybrids and were in accordance with their pedigree. The IRAP technique is an efficient high-throughput genetic marker-generating method.

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“…Similarly to plants, activation of retrotransposons contributes to faster microbial evolution and increased environmental plasticity [9][10][11]. LTR retrotransposon sequences are used to detect mycelial fungal polymorphism using PCR fingerprinting [10][11][12][13][14][15][16].…”

Section: Introductionmentioning

confidence: 99%

“…Since many retrotransposons are embedded, recombined, inverted, or truncated, they can be easily amplified using conservative PBS primers in almost any organism, this allows this method to be used as a universal and highly effective method for direct detection of polymorphism (figure 1) [13]. The iPBS method has shown the usefulness of a wide range for plants and animals and has recently been used to characterize the genetic variability of fungal pathogens [12,[14][15][16][17].…”

Section: Introductionmentioning

confidence: 99%

The Study of Genetic Polymorphism of Fungal Pathogens Using iPBS Assays

Хапилина¹,

Turzhanova²,

Shevtsov³

et al. 2020

Eurasian Journal of Applied Biotechnology

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Species of the genus Alternaria are widely distributed as saprophytes on plant residues, as well as pathogens of various plant species. On wheat seeds, Alternaria fungi are localized in the endosperm and fruit shells, causing symptoms of "black germ" disease, and are a dominant component of the wheat seed microbiome. Recently, due to the high potential danger of these fungi, much attention has been paid to the study of the genetic variability of populations that exist in certain climatic conditions. Using retrotransposon sequences as markers increase knowledge about phylogenetic relationships within populations of phytopathogenic fungi, as well as their biodiversity. The iPBS (inter-priming binding sites) method used in this work was applied to detect genetic polymorphism of isolates of the genus Alternaria, as the most frequently encountered genus (the frequency of isolation was more than 50%). The isolates were isolated from wheat seeds that were cultivated in various ecological regions. The 4 iPBS primers used in this study amplified 387 fragments, 352 of which were polymorphic. The level of detected polymorphism varied from 66% when using primer 2224 to 100% when using primer 2242. The information content index of the PIC (polymorphism information content) primers varied in the range of 0.894-0.987. Analysis of genetic polymorphism revealed significant genetic variability among fungal isolates. Genetic analysis of amplification profiles of isolates of fungi of the genus Alternaria conducted using the GenAlex 6.5 software differentiated all isolates into 2 large groups. Isolates of A. infectoria were isolated in a separate cluster. Isolates of A. alternata and A. tennuissima were grouped in a different cluster depending on the species. Research results show that the iPBS method is highly effective for the genetic differentiation of phytopathogenic fungi at both intraspecific and interspecific levels.

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Plant diversity and transcriptional variability assessed by retrotransposon-based molecular markers

Cited by 11 publications

References 48 publications

Ploidy level and nucleotide variations in inflorescence dichotomous cultivars of plantain (Musa spp. AAB genome)

Ploidy level and nucleotide variations in inflorescence dichotomous cultivars of plantain (Musa spp. AAB genome)

High-throughput retrotransposon-based genetic diversity of maize germplasm assessment and analysis

The Study of Genetic Polymorphism of Fungal Pathogens Using iPBS Assays

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