Barcoding DNA, a concept introduced by Heber (2003), is the nucleotide sequence of a short, orthologous, DNA sequence in which a region is little changed (very stable – conserved). defensive) and has a variable region in the evolutionary process. Based on the degree of change in this DNA sequence to assess genetic variation between organisms. Thus, barcoded DNA is a new identification method that uses one or more short standard DNA fragments located in the genome of the organism under study, to determine to which species the organism belongs. After about 10 years of research and development of barcoded DNA, up to now, scientists have published more than thousands of scientific works in specialized scientific journals, with more than 3,483,696 DNA barcode sequences at 215,513 There are 144,402 species of animals, 54,478 species of plants, 16,633 species of fungi and other organisms. Many research results have shown that there are many specific DNA fragments used as barcoded DNA, barcoded DNA fragments can be DNA fragments located in the nucleus such as: 18S, 5,6S, 26S, 5S and ITS region; located in mitochondria such as: Cytb and control region; located in chloroplasts such as: matK, rcbL, atpβ, ndnF (Cuenoud, 2002; Kress et al., 2008; Aron et al., 2008; Spooner et al., 2009). There are about eight gene loci that have been used as DNA barcoding in plants, including the nuclear genome and the chloroplast genome (atpF-atpH intergenic region, matK gene, rbcL gene, rpoC1 gene, psbK- intercalation region) psbI, trnH-psbA intergenic region, and nuclear ITS region).
Li et al. (2018) performed comparative analyzes on 10 different chloroplast genomes of fruiting persimmons of the genus Thi (Dyospyros) collected from Beijing Botanical Garden, Chinese Academy of Sciences and National Persimmon Gene Bank (Faculty of Agriculture, Northwest A&F University, Yanglin, Shaanxi Province, China). Eight highly polymorphic regions including trnH-psbA, rps16-trnQ, rpoB-trnC, rps4-trnT-trnL, ndhF, ndhF-rpl32-trnL, ycf1a, and ycf1b were found. These potential sequences could be developed as chloroplast DNA markers for individual identification at the species level.
D’Agostino et al. (2018) sequenced the full plastid genomes from 8 species of the genus Capsicum. Comparative analyzes show a high degree of diversity resulting from point mutations and insertion or deletion mutations (InDels). In which, accD, ndhB, rpl20, ycf1, and ycf2 are the most valuable genes. The polymorphic sequences found have opened the prospect of developing useful molecular markers for the differentiation of species in the genus Capsicum.
Dillon et al. (2013) evaluated the effectiveness of 11 SSR molecular markers in the study of species identification, identification of seedlings and parents, and judgment of population genetic diversity. Through testing on many different Mangifera indica L. mango cultivars, these molecular markers proved to be optimal in fingerprinting technique with an average of 8.36 alleles at each locus identified. The SSR markers helped to identify the parents of hybrid plants produced by both hand pollination and free pollination with 95% confidence.
Mursyidin and Daryono (2016) conducted a study to evaluate the relationship and genetic diversity of durian varieties (Durio zibethinus Murr.) grown in South Kalimantan (Indonesia) based on RAPD molecular markers. Eleven durian seed samples and six RAPD primers, including PA-01, OPA-02, OPA-07, OPA-16, OPA-18 and OPA-19 were used. Durian samples tested showed high diversity with polymorphism of 82.17%.
Vanijajiva (2011) tested the genetic diversity of durian varieties (Durio zibethinus Murr.) grown in Nonthaburi province (Thailand) by RAPD technique with 9 primers (OPAM-03, OPAM-12, OPAM18) , OPB-01, OPB-14, OPC-01, OPC-05, OPK-05 and OPZ-03). A total of 90 DNA fragments, ranging in size from 100 to 3000 bp were amplified; Among them, 34 products were found to be polymorphic.
Rosmaina et al. (2016) evaluated the relationship and genetic diversity of Indonesian durian (Durio zibethinus Murr.) varieties based on RAPD molecular markers. Six primers including OPT-09, OPO-05 OPY-16, OPY-15, OPD-08 and OPY-14 gave the best recognition results on 5 durian varieties: Bakul, Ome Kampar, Tembaga, Sijantung and Keong Mas .
Siew et al. (2018a) used the molecular marker SSR to study the genetic differences of 27 durian varieties in the variety collection of Putra University Malaysia. Based on the DNA sequences found from GenBank, seven primer pairs were designed to amplify the SSR regions. The results showed a high diversity among the durian samples examined. Specific DNA fingerprints were found for 21 out of 27 durian varieties studied thanks to 5 (out of 7) SSR molecular markers with high polymorphism. The results of this study not only demonstrate the feasibility of SSR molecular markers in DNA fingerprinting on durian seed samples, but also pose a new challenge in individual identification at the subspecies level.
Wang et al. (2018) conducted a study on the chloroplast genome of Conyza bonariensis [L.] Cronquist (flaxleaf fleabane), a difficult-to-control weed common in many countries around the world, with the aim of finding codes new DNA barcodes and use the entire chloroplast genome as a super-barcode for molecular identification. From the obtained sequence, an efficient DNA barcode, rps16 and trnQ-UUG, was designed and successfully distinguished three common species of Conzya (C. bonariensis, C. canadensis and C. sumatrensis). The chloroplast genome-based genealogical analyzes of C. bonariensis, C. canadensis and 18 species of the Asteraceae family demonstrated the potential of the chloroplast genome as a distinguishable plant supercoder. closely related species.
Nemeckova et al. (2018) conducted genotyping analysis using SSR molecular markers, ITS1-5.8S-ITS2 sequence molecular analysis and chromosomal distribution of ribosomal DNA sequences to assess genetic diversity. transmission of East African highland bananas (EAHBs). The results of genotyping with 19 SSR markers showed that the studied banana varieties belonged to 4 branches in the pedigree analysis. Internal transcribed spacer regions (ITS) sequence analyzes demonstrated the relationship of EAHBs to Musa acuminata and M. Schizocarpa. The results suggest that the EAHBs banana varieties are derived from a single cross with the parent M. acuminata ssp. Zebrina and ssp. Banksii.
Gálvez-López et al. (2009) analyzed the diversity and genetic relationship of 112 indigenous mango (Mangifera indica) samples collected from 16 different Mexican states and 4 control samples (3 mango varieties Ataulfo, Manila and Tommy, and another mango species Mangifera odorata) by molecular markers AFLP (amplified fragment length polymorphism) and SSR (simple sequence repeat). Both AFLP and SSR showed high genetic similarity between mango populations and constituted two main groups of mangoes from the Gulf of Mexico coast and from the coastal or off-Pacific regions. The highest genetic diversity was found among individuals in each state. The heterozygosity value ranged from low (0.38) to moderate (0.68). The obtained data suggest that natural or induced pollination often occurs in mangoes leading to genetic segregation as well as recombination that plays a key role in the diversification process. Genetics of Mexican mango populations. AFLP was evaluated to be more effective than SSR in analyzing genetic relationships among indigenous Mexican mango cultivars.
Siew et al. (2018) used 25 ISSR (inter-simple sequence repeat) primers with the aim of evaluating the genetic diversity of 27 durian varieties from 4 fruit gardens of Putra University Malaysia. Twelve out of a total of 25 primers used resulted in 133 clearly amplified DNA fragments and of which 122 products were evaluated as polymorphic. Primers were designed to amplify four regions of chloroplast DNA (the spacer region between the trnL-trnF, atpB-rbcL and trnH-psbA genes and part of the matK gene). In which, spacer gene trnL-trnF and matK gene, although amplified successfully in PCR reaction, did not give polymorphic results, even when using durian samples from Vietnam.
Fitmawati et al. (2017) conducted nucleotide sequence analysis and comparison of different mango cultivars of the genus Mangifera from central Sumatra based on the spacer region between trnL and trnF genes. The results showed that a monophyletic group of two clade separates M. kemanga from other species including M. foetida, M. odorata, M. laurina and Mangifera sp. In addition, the study also showed that M. kemanga is the closest ancestor and also the first species to appear in central Sumatra.
Hidayat et al. (2012) used the gene encoding maturaseK located on the chloroplast genome to analyze 19 species of the genus Mangifera collected from Indonesia and Thailand. Genealogical analysis showed that matK was able to identify and divide the genus Mangifera into three main groups. In addition, the matK barcode is capable of identifying mango varieties from Thailand. The analysis results also showed the difference in the matK gene sequences of the two species M. laurina and M. macrocarpa between Indonesia and Thailand.
Yu et al. (2011) conducted research to find a suitable DNA barcoding marker for species identification. Four coding regions of the plastid genome including matK, rpoB, rpoC1 and rbcL collected from 59 specimens of the citrus group and closely related plants were used. matK showed the best performance compared to other regions while rpoB and rpoC1 showed no significant difference, and rbcL showed average efficiency.
Pagliaccia et al. (2015) used the AFLP molecular marker to check genetic diversity as well as re-identify many different dragon fruit samples. Although many varieties of dragon fruit have different names, the analysis results show that they have a high similarity.
Fazekas et al. (2008) compared eight plant barcode regions derived from the chloroplast genome and one from the mitochondrial genome to evaluate their effectiveness in distinguishing monophyly from 92 species belonging to 32 different genera of terrestrial plants. The markers located on the chloroplast genome include five rpoB-coding regions (rpoC1, rbcL, matK and 23S rDNA) and three non-coding regions (trnH-psbA, atpF-atpH and psbK-psbI). The sequence regions in the study have different capacities when it comes to species discrimination, amplification capacity, and sequencing efficiency. Single-locus analyzes ranged from 7% (23S rDNA) to 59% (trnH-psbA). Sequence recovery depends mainly on amplification efficiency (85-100% on chloroplast loci) while matK requires more work to achieve adequate recovery (88% using 10 primer pairs) matK, psbK-psbI and trnH-psbA had problems in bidirectional sequencing. If technical problems in amplification and sequencing efficiency are ignored, the combination of many different chloroplast markers can be of great benefit in species identification.
Tripathi et al. (2013) tested the effectiveness of 5 plant barcode loci (rbcL, matK, ITS, trnH-psbA and ITS2) on 300 tropical plant samples. rbcL was the best locus with amplification in PCR and sequencing. ITS and trnH-psbA were the second most effective loci after rbcL. ITS species discrimination and identification ranged from 24.4% to 74.3%, from 25.6% to 67.7% for trnH-psbA depending on the data and method used matK and ITS2 gave the worst PCR amplification efficiency. Species breakdown using ITS2 and rbcL ranged from 9.0-48.7% and 13.2-43.6%. The combination of ITS and trnH-psbA gives some efficiency in genetic diversity analysis, especially for tropical plants, when compared with the standard efficiency of the reported DNA barcoding program. at now. The use of rbcL and matK does not give good results when used as barcoding for tropical plants.
The research direction of building a barcoded DNA database is being developed by many countries and scientists around the world, especially in recent years and will be a research trend in the coming time. . Barcode DNA is considered a new tool, effectively assisting in taxonomic research, new species discovery, species identification and samples derived from living or dead or even processed organisms. , so DNA barcodes have many applications in research as well as practice (Nimis, 2010; Bruni, 2010; Bell, 2011; Hebert, 2003; Lahaye, 2008; Liu, 2010). The advantage of this technology is rapid species identification. If the standard sample is built, within 4 hours, it gives very accurate results. It can be developed and applied in organizations operating in the field of accreditation.
Thus, based on studies showing that the sequences rbcL, matK, ITS, trnH-psbA, atpF-atpH, psbK-psbI can identify differences in the sequences of plant species. Therefore, these sequences will be used to determine the specific sequence region of Ha Chau strawberry.References
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Nguyen Thi Van
Đăng ngày: 14/11/2020