High-resolution genetic mapping and physical map construction for the fertility restorer Rfm1 locus in barley. Oxford: Blackwell Science Publisher; 2014. p. 1634. Using the RNA-seq data against two different conditions of the phenotype, you can create a SNP catalog and evaluate the effects on the protein sequence and which SNPs have a significant change in allele frequency. Open Access is an initiative that aims to make scientific research freely available to all. PCR products can be very small:-Markers will work with extremely degraded DNA samples. 2012;30(5):107188. As genomes of many species are fully sequenced, including human, Arabidopsis, and rice, the discovery of interest-specific sequence differences becomes easier [24]. This will result in the improvement of economically important traits. Advantages and Limitations of SNP Array in the Molecular CAS Marcussen T, Sandve SR, Heier L, Spannagl M, Pfeifer M, Jakobsen KS, et al. Kumar S, Banks TW, Cloutier S. SNP Discovery through Next-generation sequencing and its applications. Am. A single-nucleotide polymorphism (SNP) occurs when a single nucleotide in a DNA sequence differs between . Plant Genetic Resources. Indian J Biotech. 2014;2(3):195212. PubMedGoogle Scholar. 2015;16:92. doi:10.1186/s12863-015-0254-4. With the help of a high-quality reference genome, the fusion sequence and SNPs also provide a stronger analysis of the entire SNP catalog for each species. Somers DJ, Kirkpatrick R, Moniwa M, Walsh A. 49 746756, Ganal MW and Roder MS 2007 Microsatellite and SNP markers in wheat breeding; in Genomic assisted crop improvement, Vol 2: Genomics applications in crops (Eds) RK Varshney and R Tuberosa (Springer, New York) pp 124, Garrido-Cardenas JA, Mesa-Valle C, Manzano-Agugliaro F 2018 Trends in plant research using molecular markers. Genetic differences between wheat and barley arise from the individual origins and evolutionary history of both species. In contrast, Cleaved Amplified Polymorphic Sequences (CAPS) are more widely and successfully employed in small-scale experiments with highly polymorphic genetic regions containing multiple SNPs in barley, but not in wheat. In barley, the presence of highly polymorphic genetic regions containing multiple SNPs allows the simple development of CAPS in small-scale experiments. 2012;10(6):74349. Single nucleotide polymorphism discovery in barley using autoSNPdb. Phil. 2002;48(5-6):52937. 18 65316535, Wu K, Jones R, Dannaeberger L and ScolnikPA 1994 Detection of microsatellite polymorphisms without cloning. 2014;345(6194):2857. Appl. 2011;28(3):281301. BMC Plant Biol 16 J. Sci. 2015;128(1):13143. Disadvantages: Its PIC (polymorphic . Hanemann A, Schweizer GF, Cossu R, Wicker T, Rder MS. Fine mapping, physical mapping and development of diagnostic markers for the Rrs2 scald resistance gene in barley. This technology enables nucleotide diversity studies related to a wide variety of species. High-throughput methods cannot be easily adapted to the study of GOI, where SNPs must be found and assessed on a very short fragment of the coding region. Turk. Genet. The KASP assay utilizes a novel homogeneous fluorescent genotyping system [16], that claims to provide greater flexibility for researchers. 257264, Tautz D 1989 Hypervariability of simple sequences as a general source for polymorphic DNA markers. Restriction Fragment Length Polymorphism (RFLP), Random Amplified Polymorphic DNA (RAPD), Amplified Fragment Length Polymorphism (AFLP), Single-Strand Conformation Polymorphism (SSCP) and Microsatellite DNA. Anyone you share the following link with will be able to read this content: Sorry, a shareable link is not currently available for this article. Therefore, significantly less applied SNP markers in barley revealed similar genetic polymorphism compared to wheat. First, thousands of SNPs can be discovered, and expression levels of millions of functional genes with sequence variations can be observed simultaneously. 36 306, McCouch SR, McNally KL, Wang W and Sackville Hamilton R 2012 Genomics of gene banks: a case study in rice. BMC Genomics. Due to the availability of technologies that provide validation and detection of SNPs, the development of SNP markers has become a routine process, especially in products with a reference genome. On the usefulness of mock genomes to define heterotic pools, testers High-throughput technology is very effective for SNP marker development in both bread wheat and barley despite considerable differences in the rate of their occurrence in the entire genomes: 2.4-3-fold more in barley than in each of three genomes of wheat. 2012;19(6):44961. Acad. Lai K, Lorenc MT, Lee HC, Berkman PJ, Bayer PE, Visendi P, et al. Graner A, Streng S, Drescher A, Jin Y, Borovkova I, Steffenson BJ. 2012;124(3):55564. The high-throughput technology of SNP markers is very effective in bread wheat (Triticum aestivum L.). - 199.85.209.142. In the case of de novo sequence data, an additional step called as clustering is needed to group the short sequence reads. Barker GLA, Edwards KJ. Botstein D, White RL, Skolnick M and Davis RW 1980 Construction of a genetic linkage map in man using restriction fragment length polymorphisms. Crop improvement is a continuous effort, since some 10,000 years ago when primitive man made the transition from hunting and foraging to domestication and crop cultivation. This is a preview of subscription content, access via Cleaved Amplified Polymorphic Sequences (CAPS) Markers in Plant Biology. In the post-genomic era, SNPs became the commonly used marker systems in many plants with several advantages such as stability, ease of use, considerably low mutation rates, and high-throughput genotyping [41]. Theor. If the data set is based on a reference mapped output, mapping step is required. The most obvious advantages of SNP markers are that they are flexible and fast and provide data management convenience. In addition, de novo and reference-based SNP discovery is carried out in many organisms, including many plants with little or no genetic information [50]. The SNP detection technologies have been evolved with the discovery of new techniques on reporter systems, fluorescent probes, development of enzymatic assays, use of highly sensitive instruments, and mostly the accelerated high-throughput sequencing technology and bioinformatic tools. 31 22742280, Mondini L, Noorani A and Pagnotta MA 2009 Assessing plant genetic diversity by molecular tools. However, the same cannot be applied to CAPS markers. Genet. The effects on plant protein function and gene expression against a changing condition may result from SNPs occurring in coding regions and regulatory sequences, respectively. If the data set is de novo assembly output, clustering step is needed. This mini-review summarises results supporting the development of different strategies for the application of effective SNP and CAPS markers in wheat and barley. Tempos of gene locus deletions and duplications and their relationship to recombination rate during diploid and polyploid evolution in the Aegilops-Triticum alliance. In the next-generation sequencing, the main goal is to parallelize DNA sequencing so that the molecules of thousands or millions of genetic materials could be read simultaneously. The development of SNP markers involves the following approaches (Taillon-Miller et al. CAS Affymetrix and Illumina SNP Chips use the technology to hybridize fragmented single-stranded DNA to arrays containing thousands of nucleotide probe sequences that are designed to bind to a target DNA sequence [35]. The determination of the functionality of the genes of the wild species that have increased and continued in recent years and the presence of beneficial alleles for indirect plant breeding and yield improvement studies still make up an important topic for the future that is open for further improvement. Correspondence to Google Scholar. 2013;6(3): doi:10.3835/plantgenome2013.06.0019. In: Abdurakhmonov I, editor. Theor Appl Genet. Maccaferri M, Ricci A, Salvi S, Milner SG, Noli E, Martelli PL, et al. Comparison of SNP and CAPS markers application in genetic research in wheat and barley, https://doi.org/10.1186/s12870-015-0689-9, Selected articles from PlantGen 2015 conference: Plant biology, http://www.hutton.ac.uk/research/groups/information-and-computational-sciences/tools, http://www.biomedcentral.com/bmcplantbiol/supplements/16/S1, http://creativecommons.org/licenses/by/4.0/, http://creativecommons.org/publicdomain/zero/1.0/. 54 499513, Litt M and Luty JA 1989 A hypervariable microsatellite revealed by in vitro amplification of a dinucleotide repeat within the cardiac muscle actin gene. However, barley SNPs within individual genes occur significantly more frequently than quoted. 22 32573258, Xu Y, Xie C, Wan J, He Z and Prasanna BM 2013 Marker-assisted selection in cereals: platforms, strategies and examples; in Cereal Genomics II (Eds) PK Gupta and RK Varshney (Springer) https://doi.org/10.1007/978-94-007-6401-9-14, Zabeau M and Vos P 1993 Selective restriction fragment amplification, a general method for DNA fingerprinting (European Patent Application Number 0534858 A1), Zane L, Bargelloni L and Patarnello T 2002 Strategies for microsatellite isolation: a review. Moreover, they are less prone to mutation, and they can reveal some. Iimure T, Zhou TS, Hoki T. Development of CAPS markers and its use for malting barley breeding. 246 327333, Mullis KB and Faloona FA 1987 Specific synthesis of DNA in vitro: A polymerase catalyzed chain reaction. Provided by the Springer Nature SharedIt content-sharing initiative, Over 10 million scientific documents at your fingertips, Not logged in Vavilov J Genet Breed. Software tools like CAP3 and Phrap have been extensively used for this purpose. In vitro techniques comprise of non-sequencing, sequencing, and re-sequencing methods. If de novo SNP mining is performed, AutoSNP, QualitySNP, and MAVIANT can be used. The integration of genomic technologies with traditional breeding can have a big impact in dealing with current and future environmental challenges more effectively [32]. SNPs can influence promoter activity for gene expression and finally produce a functional protein by transcription. Fro. Sci. Genet. Effectiveness of microsatellite and SNP markers for parentage and . Tax calculation will be finalised during checkout. UniGene set is designed for mapping transcript data. PDF MICROSATELLITE AND SNP MARKERS IN WHEAT BREEDING - Springer Several members of the European forensic DNA typing community launched a project in 2003 known as SNP for ID that worked to develop SNP assays to directly aid forensic DNA analysis. The marker can be used to modulate the cultivation program for the determination of the relevant feature and improvement of the crop more economically using new-generation technologies than using traditional methods [22]. Kanazin V, Talbert H, See D, DeCamp P, Nevo E, Blake T. Discovery and assay of single-nucleotide polymorphism in barley (Hordeum vulgare). Therefore, we would like to focus on the discovery, current technologies, and applications of SNPs in breeding. Ancient hybridizations among the ancestral genomes of bread wheat. PubMed Central Article In silico methods are easy to apply to the SNPs that are occurring in known genomes or sequences of a species of interest. We also thank Carly Schramm for critical comments in the manuscript. In this case, a service providing a molecular analysis of DNA samples using various high-throughput SNP technologies can be applied. J. Clin. STRs vs. SNPs: thoughts on the future of forensic DNA testing Initial applications of SNP markers were based on the high-throughput platform from the American company Illumina that was very suitable for plants [5]. 1. 2002;3(6):42941. These developments accelerated the whole-genome association studies (WGAS) and the identification of many new SNPs in model and non-model plants. Science. VALIDATION OF SNP BY Tm SHIFT PRIMER short GC tail. Identification of genomic regions involved in tolerance to drought stress and drought stress induced leaf senescence in juvenile barley. Gain or loss of chromosomal regions exceeding 10 Mb occurred in 46 cases (53%), including six cases (7%) with complex chromosomal alterations. Single nucleotide polymorphisms and the future of genetic - PubMed From restriction fragment length polymorphisms (RFLPs) to simple sequence repeats (SSRs) and single nucleotide polymorphisms (SNPs), the types of molecular markers predominantly used have evolved. The integrated approach alongside the recent innovations will allow an increased knowledge and application of SNPs in the future. STRs, mini STRs and SNPs--a comparative study for typing - PubMed Genet. Although other techniques have been previously used in gene expression studies such as northern blot or quantitative PCR, the ability to determine the level of less represented genes of a mixture facilitated the analysis of thousands of genes in the same reaction and increased sensitivity [16]. Food Agric. Your US state privacy rights, SNP markers are the most abundant and robust ones . 16 142147, Rajendrakumar P, Biswal AK, Balachandran SM, Srinivasarao K and Sundaram RM 2007 Simple sequence repeats in organellar genomes of rice: frequency and distribution ingenic and intergenic regions. SNPs are frequently found in the genome with at least one common (>20% allele frequency) SNP density per kilobase pair. New York: Nova Science Publishers; 2014. p. 15165. Target-induced local lesions in genome (TILLING) is a reverse genetics approach that combines chemical mutagenesis with a sensitive mutation detection instrument called denaturing HPLC (DHPLC) [36]. Applications of biotechnology. Why are the development and application of CAPS markers so different in bread wheat compared to barley? Plant phylogenetic and evolutionary researches is traditionally based on sequence genes and hence the knowledge of SNPs [27]. Sometimes it also depends on the substituted amino acid positions because some amino acid controls the activity of the expressed regions. J. Mol Breed. 14 4359, Taillon-Miller P,Gu Z, Li Q, Hillier L and Kwok PY 1998 Overlapping genomic sequences: a treasure trove of single-nucleotide polymorphisms. The Netherlands), Picoult-Newberg L, Ideker TE, Pohl MG, Taylor SL, Donaldson MA, Nickerson DA and Boyce-Jacino M 1999 Mining SNPs from EST databases. Appl. Development and implementation of high-throughput SNP genotyping in barley. Prehistoric people were able to transform crops into crops that serve food for humanity by using traditional treatment techniques. Nat Methods. Patterns of polymorphism and linkage disequilibrium in cultivated barley. Ramesh, P., Mallikarjuna, G., Sameena, S. et al. Theor Appl Genet. PubMed The difference in the expected frequencies in both crops can be illustrated by the rather unusual example of restriction enzyme selection. There is a need for the development of a tool for extracting bulk of data, support for the data analyses, and intelligent decision on the accuracy. It is also important to know the location of SNP in the genome, because if SNP is present in the coding region, it can greatly affect the activity and thermostability level of an enzyme or a similar product [30]. https://doi.org/10.1016/b978-0-12-381466-1.00011-0. The basic idea behind SNP detection is whether identifying a novel polymorphism that is previously not defined or searching for an already-known polymorphism. Genomics 7 524530, Weber JL and May PE 1989 Abundant class of human DNA polymorphisms which can be typed using the polymerase chain reaction. An empirical comparison of population genetic analyses using Kompetitive allele specific PCR ( KASP) is a homogenous, fluorescence-based genotyping variant of polymerase chain reaction. The barley genome is estimated to be about 5.1 Gb with 26,159 high-confidence genes recognised [30]. In: Shavrukov Y, editor. As the most common type of DNA polymorphism, SNPs can also be specific at the genome-wide locus, which can reveal the selection of SNP variants at the target locus as well as informative marker sets for specific germplasm pools. Single Nucleotide Polymorphism - an overview | ScienceDirect Topics Characterization of polyploid wheat genomic diversity using a high-density 90 000 single nucleotide polymorphism array. However, preliminary in silico search databases for assessing the potential value of SNPs have yet to be developed. your institution. Also, the sensitivity, reproducibility and resolution of the AFLP marker are higher as compared with other markers. These cultivated plants, when compared to their wild relatives, differed due to such characteristics that affected the plant breeders directly such as flowering time, sizes of the reproductive organs, and seed loss. Bull. Sallam AH, Endelman JB, Jannink JL, Smith KP. In conjunction with the easy to use and publicly available software FlapJack (http://www.hutton.ac.uk/research/groups/information-and-computational-sciences/tools), SNP can be clearly visualised in the linear arrangement that allows a direct comparison of genotypes, as presented earlier [10]. Single Nucleotide Polymorphisms (SNPs) in Plant Genetics - IntechOpen The diversity and genotyping of the SNP sequence in these protected regions is used to explain a wide variety of phylogenetic and evolutionary relationships and inheritance extraction [28]. BMC Plant Biol. New York: Nova Science Publishers; 2014. p. 3160. Pollen-mediated gene flow in wheat fields in Western Canada. Mol. GM is thankful to UGC India, for providing RGN Fellowship (F1-17.1/2017-18/RGNF-2017-18-SC-AND-37354/ (SA-III/Website), 31-07-2017); SS acknowledge the financial support from the DST-INSPIRE (IF-170752 dated 3 March 2018) and GK acknowledge the financial support from the DST-INSPIRE (IF-140991 dated 31 December 2014). Google Scholar. Further, these functional markers (FMMs), genotype-by-sequencing and association mapping methodologies have opened new avenues for identification of novel genetic resources (lines) that can facilitate accelerated crop breeding programs for increased yield, high nutritional quality, and tolerance to a variety of abiotic and biotic stresses. volume45, Articlenumber:123 (2020) Mol. Wehner GG, Balko CC, Enders MM, Humbeck KK, Ordon FF. Furthermore, a large proportion of the microsatellite markers is genome-specific, thus amplifying a defined single product from one of the three wheat genomes. An entire wheat genome analysis of bread wheat reported one true SNP per 540-569bp [11, 12, 51] within one of three genomes. https://doi.org/10.1186/s12870-015-0689-9, DOI: https://doi.org/10.1186/s12870-015-0689-9. Kumpatla SP, Buyyarapu R, Abdurakhmonov IY, Mammadov JA. And this is the aim of the article: to offer to the reader a state of the art of SNP genotyping technologies and chemistries showing the advantages and disadvantages for the different forensic applications. In bread wheat, CAPS markers are reportedly much rarer [3537] but they have been found in tetraploid Triticum dicoccoides [38] and Aegilops tauschii Coss, the wild progenitor of D genome [39]. Screening of 200 Core SNPs and the Construction of a Systematic SNP-DNA Close TJ, Bhat PR, Lonardi S, Wu Y, Rostoks N, Ramsay L, et al. Our own experience of Next Generation Sequencing (NGS) with 9K Illumina Infinium SNP array in wheat [10] confirmed the supreme effectiveness of this technology in crops [11]. Recent technological advances make it easier to identify various SNPs that can be used for product developments. A topic of great interest when examining the differences observed in the frequencies of SNPs in both barley and wheat is to debate the possible biological origins behind these differences, as is discussed in the following section. 2015;19(2):20513. The Recent Topics in Genetic Polymorphisms, Reviewed: February 25th, 2020 Published: March 28th, 2020, Edited by Mahmut alkan, Osman Erol and Gl Cevahir z, Total Chapter Downloads on intechopen.com. BioTechnology 7 257264, Bardakci F 2001 Random amplified polymorphic DNA (RAPD) markers. With the advantages of stability, budget friendly improvements, and high-throughput assays, SNP has become increasingly important in crop genetic studies. Am. The choice of the methods for SNP detection is diverse. More common in genome. Most recently, a 9M SNP array in a single homeologous group of chromosome 7 in bread wheat has been reported [15]. Publishing on IntechOpen allows authors to earn citations and find new collaborators, meaning more people see your work not only from your own field of study, but from other related fields too. (Allele 2) ADVANTAGES & DIS-ADVANTAGES OF SNP It is a co- dominant marker. 9 167174, Powell W, Machray GC and Provan J 1996 Polymorphism revealed by simple sequence repeats. 8 29, Edwards A, Civitello A, Hammond HA and Caskey CT 1991DNA typing and genetic mapping with trimeric and tetrameric tandem repeats. Trends Biotechnol. RK Varshney and R Tuberosa (Springer, Dordrecht) pp 1329, Varshney RK, Nayak SN, May GD and Jackson SA 2009 Next generation sequencing technologies and their application for crop genetics and breeding. Theor .Appl. Beckie HJ, Warwick SI, Hall LM, Harker KN. 2010;49(2):14958. By using this website, you agree to our In contrast, barley SNPs within individual barley GOI may be significantly more frequent than quoted. A common workflow schema for in silico SNP mining. 183 935966, Khan F 2015 Molecular markers: an excellent tool for genetic analysis. Plant Breeding. Nucleic Acid Res. In vitro SNP detection methods are often composed of several laborious steps or require specialized instruments which makes the process high-cost and compound. your institution, https://doi.org/10.1016/b978-0-12-381466-1.00011-0, https://doi.org/10.1007/978-94-007-6401-9-14. Advantages And Disadvantages Of Snps - Forensic Science Yuri Shavrukov. Rostoks N, Mudie S, Cardle L, Russell J, Ramsay L, Booth A, et al. Regardless of the technique used, it identifies a large number of markers, allowing the development of high-density genetic maps [17]. Barley and bread wheat show large differences in frequencies of Single Nucleotide Polymorphism (SNP) as determined from genome-wide studies. Google Scholar. Genetic Markers: RFLP, RAPD, AFLP, ISSR, STR, SCAR, EST, SSR and SNP Genetics. Integration of the next-generation sequencing (NGS) technologies with precise phenotyping, association mapping, proteome and metabolome studies has increased the chances of finding candidate genes and their allelic variants controlling a trait of interest. 2009;7(4):32633. Diag. Home > Microsatellite and SNP Markers in Wheat Breeding DNA typing methodologies Global J. Sci. New York: Nova Science Publishers; 2014. Biotechnol. Raats D, Yaniv E, Distelfeld A, Ben-David R, Shanir J, Bocharova V, et al. Zool. Trebbi D, Maccaferri M, Heer P, Srensen A, Giuliani S, Salvi S, et al. In summary, different strategies are required for the development of the most suitable molecular markers in the cereal species. Its based on principles of collaboration, unobstructed discovery, and, most importantly, scientific progression. The work of many researchers focuses on individual genes that are of significance to their area of study. J. Exp. The final step is the SNP calling or validation. The frequencies for such false SNP in bread whet are quite high and are reported as one SNP per 20bp [50], per 24bp [51] and up to 61bp [52]. Planta 247 543557, Gupta PK and Varshney RK 2004 Cereal genomics: an overview (Kluwer Gupta Academic Press, Dordrecht, The Netherlands), Gupta M, Chyi YSJ, Romero-Severson and Owen JL 1994 Amplification of DNA markers from evolutionarily diverse genomes using single primers of simple-sequence repeats. Mapping by admixture linkage disequilibrium: advances, limitations and This allows plant growers to improve crop plants and protect germplasm. Intern J Plant Genomics. Schnurbusch T, Collins NC, Eastwood RF, Sutton T, Jefferies SP, Langridge P. Fine mapping and targeted SNP survey using rice-wheat gene colinearity in the region of the Bo1 boron toxicity tolerance locus of bread wheat. . High-throughput snp genotyping to accelerate crop improvement. A genome-wide analysis of single nucleotide polymorphism diversity in the worlds major cereal crops. Many different types of molecular markers are based on SNP identification and each has accompanying advantages and disadvantages. Zhang WS, Li X, Liu JB. J. Genet. Understanding the distribution and diversity of plant species is increasingly important to meet the demands of the growing population. 2003;46(3):4317. According to the input data type, the steps and the algorithms change. volume16, Articlenumber:11 (2016) Genetics. . We are a community of more than 103,000 authors and editors from 3,291 institutions spanning 160 countries, including Nobel Prize winners and some of the worlds most-cited researchers. The selection of SNPs enables the selection of desired lines in large-scale populations. Rijeka: InTech; 2012. p. 13184. Breed. The recently developed open-source and freely available bioinformatic software have speed up the SNP detection and reduced the costs. Thousands of SNP markers can be identified at a time and analyse hundreds of accessions. However, several newly developed approaches provide greater efficiencies. USA 796 4656469, Henry RJ 2013 Molecular markers in plants (Wiley-Blackwell, Ames, IA) pp 200, Jacob HJ, Lindpaintnesr K, Kusumir EL, Bunkery K, Mao IP, Gantenv D, Dzau J and Lander ES 1991 Genetic mapping of a gene causing hypertension in the stroke-prone spontaneously hypertensive rat. (Suppl 1), 11 (2016). However, the emergence of new and third-generation technologies allows the genome to assess SNP-based genetic diversity at scale and can be useful in conserving diversity in domesticated populations. 2. CAS If the fragments are from a trace file or a base quality score, PolyBayes, PolyPhred, novoSNP, and SNPdetector are very well-known tools. PubMed Theor Appl Genet. SNPs are particularly useful for the analysis of highly degraded DNA, as they can be analysed using short amplicons 140 . Mol Breed. R. Soc. There are two strategies for creating a SNP marker map for linkage mapping: (1) . 99 407423, PubMed Comadran J, Ramsay L, MacKenzie K, Hayes P, Close TJ, Muehlbauer G, et al. Single nucleotide polymorphism (SNP) causes genetic diversity among individuals of the species and can occur at different frequencies in different species throughout the entire genome. Perkel J. SNP genotyping: six technologies that keyed a revolution. A new allele of acid soil tolerance gene from a malting barley variety. Disadvantages: The AFLP marker is not co-dominant hence it can not distinguish homozygous from heterozygous. These polymorphisms can be used as simple genetic markers that can be identified around almost any gene. Single nucleotide polymorphisms (SNPs) are polymorphisms that are caused by point mutations that give rise to different alleles containing alternative bases at a given position of nucleotide within a locus. 1 215222, Provan J, Powell W and Hollingsworth PM 2001 Chloroplast microsatellites: new tools for studies in plant ecology and evolution.
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