Intergenic Spacer Length Variability in Cultivated, Weedy and Wild Rye Species

Skuza, Lidia; Filip, Ewa; Szućko, Izabela

doi:10.1515/biol-2015-0020

Cited by 4 publications

(4 citation statements)

References 34 publications

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“…The introduction of DNA barcoding was a breakthrough in species identification methods. The basis of this technique is the use of a very short, defined genomic sequence that allows obtaining a DNA barcodean image of base pair sequence in the DNA fragment that can be compared to determine individual species classification (Ajmal et al 2014;Skuza et al, 2015). The gene encoding cytochrome oxidase (COI, coxI) subunit of 648 bp, located in the mitochondrial genome is the best gene used for barcoding in animals (Stoeckle and Thaler 2014).…”

Section: Dna Extraction Pcr Amplification and Sequencingmentioning

confidence: 99%

DNA Barcoding in Selected Species and Subspecies of Rye (Secale) Using Three Chloroplast Loci (matK, rbcL, trnH-psbA)

Skuza

Szućko

Filip

et al. 2018

Not Bot Horti Agrobo

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DNA barcoding is a relatively new method of identifying plant species using short sequences of chloroplast DNA. Although there is a large number of studies using barcoding on various plant species, there are no such studies in the genus Secale. In this study the plant material consisted of 10 cultivated and non-cultivated species and subspecies of rye genus. Three chloroplast DNA regions (rbcL, matK, trnH-psbA) were tested for their suitability as DNA barcoding regions. Universal primers were used, and sequenced products were analyzed using Neighbor Joining and the Maximum Likelihood in the MEGA 7.1 program. We did not observe high variability in nucleotide sequences within the matK and rbcL regions. Only 2.2% of the sequences showed polymorphism in the rbcL region, while 6.5% in the matK region. The most variable trnH-psbA (15.6%) intergenic region was the most useful for rye barcoding. Individual application of the studied regions did not provide the expected results. None of the regions used in the study allowed the division of rye species and subspecies according to the adopted classification of the genus Secale. The results confirm that the use of matK and rbcL is insufficient for DNA barcoding in rye species, and better discrimination within the genus Secale can be obtained only in combination with the non-coding trnH-psbA sequence. Our results also indicate the necessity of using a different region. All of the new sequences have been deposited in Genbank.

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Section: Dna Extraction Pcr Amplification and Sequencingmentioning

confidence: 99%

DNA Barcoding in Selected Species and Subspecies of Rye (Secale) Using Three Chloroplast Loci (matK, rbcL, trnH-psbA)

Skuza

Szućko

Filip

et al. 2018

Not Bot Horti Agrobo

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“…The differences in the classification of the genus Secale may result from the use of various experimental methods, as described in detail previously [18]. Establishing phylogenetic relationships is extremely important for the process of breeding new cultivars, which can be enriched with functional traits derived from wild rye species, e.g., resistance to downy mildew and brown rust, resistance to lodging and pre-harvest sprouting and cms [19,20].…”

Section: Introductionmentioning

confidence: 99%

“…In addition, organelle DNA is a useful tool in the search for species-specific molecular markers. However, phylogenetic studies of the genus Secale were almost exclusively based on the analysis of the nuclear and chloroplast genomes [18,24–34]. So far, two works have been published that include mtDNA: Isik et al [33] and Skuza et al [34].…”

Section: Introductionmentioning

confidence: 99%

Genetic diversity and relationship between cultivated, weedy and wild rye species as revealed by chloroplast and mitochondrial DNA non-coding regions analysis

et al. 2019

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The genus Secale is small but very diverse. Despite the high economic importance, phylogenetic relationships of rye species have not been fully determined, and they are extremely important for the process of breeding of new cultivars that can be enriched with functional traits derived from wild rye species. The study analyzed the degree of relationship of 35 accessions of the genus Secale , representing 13 most often distinguished species and subspecies, originating from various seed collections in the world, based on the analysis of non-coding regions of the chloroplast (cpDNA) and mitochondrial genome (mtDNA), widely used in phylogenetic and population plant studies, because of a higher rate of evolution than the coding regions. There was no clear genetic structure between different species and subspecies, which may indicated the introgression between these taxa. The obtained data confirmed that S . vavilovii was very similar to S . cereale , which confirmed the assumption that they might share a common ancestor. The results also confirmed the divergence of S . sylvestre from other species and subspecies of rye. Areas that may be useful molecular markers in studies on closely related species of the genus Secale were also indicated.

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“…DNA barcoding technique has an essential role in the identification of species (Hebert et al 2003) due to the small size of the DNA sequence with a high discriminatory power between the organisms. So, they play an important role in the identification of the plants having a problematic taxonomic identity for the biodiversity investigation and the identification of polymorphic plant species (Ajmal et al 2014;Skuza et al 2015).…”

Section: Introductionmentioning

confidence: 99%

DNA barcoding of different Triticum species

Osman

Ramadan

2019

Bull Natl Res Cent

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Background: The genus Triticum L. includes diploid, tetraploid, and hexaploid species. DNA barcoding is a new method to identify plant taxa by using short sequences of DNA and within a short time. In this investigation, we determined a phylogenetic analysis of 20 different Triticum species by partial chloroplast Maturase encoding gene (matK). Materials and methods: Twenty accessions of different Triticum species diploid, tetraploid, and hexaploid were obtained from different countries. Genomic DNA was isolated from young leaves of studied samples and then used as a template for PCR reaction. PCR products were checked by electrophoresis, purified, sequenced, and submitted in the GenBank nucleotide sequence database, the nucleotide sequence was translated into an amino acid sequence. The nucleotide and amino acid sequences were aligned with Clustal W multiple sequence alignment programs to obtain the phylogenetic tree depending on two statistical data analysis such as bootstrapping and pairwise distance from both nucleotide and amino acid sequences. Results: The phylogenetic tree obtained from both nucleotide and amino acid sequences divided the 20 Triticum species into two groups, A and B. Group A represented the diploid Triticum species. Group B was divided into two subgroup, I and II. Subgroup I represented the hexaploid Triticum species and subgroup II represented the tetraploid species. Conclusion: The matK gene sequence has a critical role in discriminating the closely related Triticum species. So these sequences could be used as a DNA barcode for detecting the evolutionary history of Triticum species.

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Intergenic Spacer Length Variability in Cultivated, Weedy and Wild Rye Species

Cited by 4 publications

References 34 publications

DNA Barcoding in Selected Species and Subspecies of Rye (Secale) Using Three Chloroplast Loci (matK, rbcL, trnH-psbA)

DNA Barcoding in Selected Species and Subspecies of Rye (Secale) Using Three Chloroplast Loci (matK, rbcL, trnH-psbA)

Genetic diversity and relationship between cultivated, weedy and wild rye species as revealed by chloroplast and mitochondrial DNA non-coding regions analysis

DNA barcoding of different Triticum species

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