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1
Chesnokov, Yu V. "GENETIC MARKERS: COMPARATIVE CLASSIFICATION OF MOLECULAR MARKERS." Vegetable crops of Russia, no. 3 (July 25, 2018): 11–15. http://dx.doi.org/10.18619/2072-9146-2018-3-11-15.
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With the creation of the molecular markers allowing to carry out analysis of genotypes on the level initial genetic information – DNA, onset one of the most multifarious and one of the most large in number class of markers at the present day. It is concerned with that each separate nucleic acid sequence is unique on its structure. Set of molecular and genetic methods, named as DNA-fingerprinting, most wide used in modern investigations for solving different problems in different biological areas. In this connection, necessity in comparative classification of modern molecular and genetic markers is actual. Based on published literature material it shown data on different classifications of molecular markers. Determined definition of term “marker” in genetics and breeding. Gave the characters and distinctive features of genetic markers. It given the definition what is “good” genetic marker as well as kinds, categories, variations and types on heredity of molecular markers. Manifested by means of molecular markers polymorphisms can classified on polymorphism of sequence itself (including nucleotide substitution and insertion-deletion) and polymorphism the number of tandem repeat sequences in repeated regions. Moreover, molecular markers can classify on two variations: anonymous, for which nucleotide acid sequence unknown and for manifestation of the molecular marker its detection not necessary (for example, RAPD, AFLP, RFLP), and announce (or determined), for which nucleic acid sequence is known or can be detect during analysis (for example, SNP, CAPS, STS). However, in independence on using of molecular markers the choice of method of investigation will be depend on investigated plant species as well. The next influence of molecular and genetic methods on genetics and practical breeding of plants will be depend on results, which will be obtain, in particular, on revealing the possibility or not possibility of genotyping of individual on single genetic marker as wel as on economic price of obtain informative data.
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Trent, Ronald J. "DNA markers in genetic disease." Medical Journal of Australia 152, no. 6 (March 1990): 281–82. http://dx.doi.org/10.5694/j.1326-5377.1990.tb120942.x.
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Nam, Vu Tuan, Pham Le Bich Hang, Nguyen Nhat Linh, Luu Han Ly, Huynh Thi Thu Hue, Nguyen Hai Ha, Ha Hong Hanh, and Le Thi Thu Hien. "Molecular markers for analysis of plant genetic diversity." Vietnam Journal of Biotechnology 18, no. 4 (May 24, 2021): 589–608. http://dx.doi.org/10.15625/1811-4989/18/4/15326.
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Genetic diversity plays an important role in diversity conservation at multiple levels and supports to monitor and assess genetic variation. In plants, genetic diversity provides the ability to adapt and respond to environmental conditions that helps plants to survive through changing environments. Genetic diversity analyses based on molecular genetic markers are effective tools for conservation and reintroduction of rare and endangered species. In recent years, the development of various chemical and molecular techniques for studying genetic diversity has received great attention. While biochemical markers are primarily used in the diagnosis of pathogens, DNA markers have been developed and widely applied for identification of species and population based on the genotype of an organism that is more stable and not easily affected by the environmental factors. PCR-based molecular marker tools, such as restriction fragment length polymorphisms (RFLPs), random amplified polymorphic DNA (RAPD), simple sequence repeats (SSRs) are used for analysing the difference in the targeted DNA sequences. With the rapid and robust development of genomic sequencing technology it is now possible to obtain and analyse DNA sequences of the whole genome of studied organisms. However, each type of DNA markers has different principles, as well as the pros and cons of specificity. In this article, we review methods and point out DNA markers, which are considered as reliable and widely used tools for the detection of genetic variation. In addition, we present the application of DNA marker in analysing genetic diversity of wild, domestic and medicinal plants, as well as some perspectives on the future of DNA marker’s application in the analysis of genetic diversity.
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Hallerman, Eric M., and Jacques S. Beckmann. "DNA-Level Polymorphism as a Tool in Fisheries Science." Canadian Journal of Fisheries and Aquatic Sciences 45, no. 6 (June 1, 1988): 1075–87. http://dx.doi.org/10.1139/f88-131.
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Several methods for the visualization of genetic polymorphisms at the nucleic acid level have been developed. Such polymorphisms promise to be exceedingly numerous, and may form the basis for a number of scientific and practical applications in fisheries science. An expanded number of genetic markers should increase the statistical power of marker-based studies in population genetics, for example, improving the sensitivity of biological stock assessments and of studies assessing the impact of stocking programs upon natural populations. Utilization of such genomic markers could contribute to the rapid elaboration of piscine genomic maps and to development of markers for health- and production-related traits in fishes.
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Hanáček, P., T. Vyhnánek, M. Rohrer, J. Cieslarová, and H. Stavělíková. "DNA polymorphism in genetic resources of red pepper using microsatellite markers." Horticultural Science 36, No. 4 (November 20, 2009): 127–32. http://dx.doi.org/10.17221/7/2009-hortsci.
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Genetic variability among 41 accessions of red pepper (<I>Capsicum annuum</I> L.) was assessed using eight microsatellite markers. Three of the microsatellite markers (<I>Hpms 1-1, Hpms 1-168, and Hpms 1-274</I>) had uniform spectra in all the analyzed plants. Two to eight alleles were detected for the remaining loci. In total, 28 alleles were detected, i.e. 3.5 alleles per one microsatellite locus on average. The highest number of different alleles was detected with <I>Hpms 1-5</I> (8 alleles) and <I>Hpms 2-21</I> primers (7 alleles). Molecular data were complemented with morphological measurements according to the descriptor list for the genus <I>Capsicum</I>. A dendrogram based on our genetic analysis suggests a high level of similarity between some of the accessions presumed to be distant and, at the same time, genetic variability between accessions of the same or similar name. These results show the possibility of duplicities in the current Czech collection of red pepper genetic resources.
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Teneva, A., and M. P. Petrovic. "Application of molecular markers in livestock improvement." Biotehnologija u stocarstvu 26, no. 3-4 (2010): 135–54. http://dx.doi.org/10.2298/bah1004135t.
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With recent developments in DNA technologies, a large number of genetic polymorphisms at DNA sequence level has been introduced over the last decades as named DNA-based markers. The discovery of new class of DNA profiling markers has facilitated the development of marker-based gene tags, mapbased cloning of livestock important genes, variability studies, phylogenetic analysis, synteny mapping, marker-assisted selection of favourable genotypes, etc. The most commonly used DNA-based markers have advantages over the traditional phenotypic and biochemical markers since they provide data that can be analyzed objectively. In this article the main applications of molecular markers in present-day breeding strategies for livestock improvement - parentage determination, genetic distance estimation, genetic diversity, gene mapping and marker-assisted selection have been reviewed.
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Stone, W. H., J. J. Ely, G. S. Manis, and J. L. VandeBerg. "Classical genetic markers and DNA markers: A commensal marriage." Primates 34, no. 3 (July 1993): 365–76. http://dx.doi.org/10.1007/bf02382632.
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Thompson, Paul G., Liang L. Hong, Kittipat Ukoskit, and Zhiqiang Zhu. "Genetic Linkage of Randomly Amplified Polymorphic DNA (RAPD) Markers in Sweetpotato." Journal of the American Society for Horticultural Science 122, no. 1 (January 1997): 79–82. http://dx.doi.org/10.21273/jashs.122.1.79.
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RAPD marker analyses were completed on parents and progeny of two sweetpotato [Ipomoea batatas (L.) Lam.] crosses to determine the feasibility of genetic linkage map construction. A total of 100 primers was tested and 96 produced amplified genomic DNA fragments. The average number of polymorphisms per primer was 0.69. A total of 134 polyphorphic markers was observed and 74 (60%) segregated 1 band present : 1 band absent as needed for use in genetic linkage mapping of polyploids. The 60% of RAPD markers that segregated 1:1 shows that genetic linkage mapping of the hexaploid sweetpotato by RAPD marker analysis is feasible. Linkage was determined for all markers that segregated 1:1 and five pairs of linked markers were found. These were the first linked molecular markers found in sweetpotato and they show that construction of a genetic linkage map is feasible. A genetic linkage map will be a valuable tool to assist in genetic improvements.
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Teneva, A., K. Dimitrov, Caro Petrovic, M. P. Petrovic, I. Dimitrova, N. Tyufekchiev, and N. Petrov. "Molecular genetics and SSR markers as a new practice in farm animal genomic analysis for breeding and control of disease disorders." Biotehnologija u stocarstvu 29, no. 3 (2013): 405–29. http://dx.doi.org/10.2298/bah1303405t.
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Molecular genetics investigates the genetic makeup of individuals at the DNA level. That includes the identification and mapping of molecular genetic markers and genetic polymorphisms. Molecular genetic markers (DNA markers) are one of the most powerful means for the genomic analysis and allow the connection of hereditary traits with genomic variation. Molecular marker technology has developed rapidly over the last decade and two shapes of specific DNA based marker, Simple Sequence Repeats (SSRs), also known as microsatellites, and Single Nucleotide Polymorphisms (SNPs) prevail applications in modern genetic analysis. Genomic simple sequence repeats (SSRs, microsatellites) have been used for a variety of purposes, including gene tagging, physical mapping, genome mapping, estimation of genetic diversity, phylogenetic and conservation genetic purposes in farm animal breeding. SSR analyses are applied successfully in parentage verification and pedigree analysis, as disease markers and to locate the mutation in genetic disorders in livestock animals. The ultimate use of SSRs markers is for mapping quantitative trait loci (QTL), marker assisted selection (MAS) in order to practice genomic selection and improve the farm animal health. Developments in ?omics? technologies, such as genomic selection, may help overcome several of the limitations of traditional breeding programmes and will be especially beneficial in breeding for lowly heritable disease traits that only manifest themselves following exposure to pathogens or environmental stressors in adulthood. The current paper provides a brief overview of the present - day application of microsatellites markers in animal breeding and make significant contribution to the overall farm animal health and resistance to disease.
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Toomey, Lola, Dirk Welsford, Sharon A. Appleyard, Andrea Polanowski, Cassandra Faux, Bruce E. Deagle, Mark Belchier, James Marthick, and Simon Jarman. "Genetic structure of Patagonian toothfish populations from otolith DNA." Antarctic Science 28, no. 5 (May 19, 2016): 347–60. http://dx.doi.org/10.1017/s0954102016000183.
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AbstractThe Patagonian toothfish, Dissostichus eleginoides, is a valuable fishery species and has a discontinuous distribution across the Southern Ocean. Identification of the genetic stock structure of toothfish would allow evaluation of the suitability of the spatial scale at which fisheries management operates. Genetic subdivision seems likely given the species distribution. Population genetics studies of this species have been performed; however, they have been limited by sample size, spatial coverage and/or the type of markers investigated. As a potential solution, we developed methods for extracting toothfish DNA from otoliths that are available in large numbers from collections held at several research institutes. Genetic differentiation between the three oceanic sectors was investigated. Four mitochondrial and four nuclear markers with multiple single nucleotide polymorphisms were sequenced by high throughput sequencing for samples from six locations. Genetic differentiation was found between three sectors with nuclear markers. However, only the Pacific sector was differentiated from other sectors with mitochondrial markers. This study demonstrates the usefulness of otolith DNA as a means of increasing sample sizes for population genetics research of fish. Additionally, the combination of nuclear and mitochondrial markers may allow insight into how the observed differences in movements between male and female toothfish impact population structure.
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Sukhareva, A. S., and B. R. Kuluev. "DNA markers for genetic analysis of crops." Biomics 10, no. 1 (2018): 69–84. http://dx.doi.org/10.31301/2221-6197.bmcs.2018-15.
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Carlier, J. D., D. Nancheva, J. M. Leitão, and G. Coppens d'Eeckenbrugge. "GENETIC MAPPING OF DNA MARKERS IN PINEAPPLE." Acta Horticulturae, no. 702 (February 2006): 79–86. http://dx.doi.org/10.17660/actahortic.2006.702.9.
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Owen, M. J., and P. McGuffin. "DNA-and classical genetic markers in schizophrenia." European Archives of Psychiatry and Clinical Neuroscience 240, no. 3 (February 1991): 197–203. http://dx.doi.org/10.1007/bf02190764.
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Lestari, Puji, Reflinur Reflinur, Dody Dwi Handoko, and Mastur Mastur. "KERAGAMAN GENETIK VARIETAS PADI japonica DAN indica BERDASARKAN MARKA DNA TERKAIT MUTU RASA." Scripta Biologica 5, no. 1 (March 1, 2018): 19. http://dx.doi.org/10.20884/1.sb.2018.5.1.751.
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PCR-based markers and evaluation of physicochemical properties should be addressed for the improvement of rice varieties with good eating dan eating quality (EQ). This study aimed to examine the genetic diversity of rice varieties based on DNA markers related to physicochemical properties determining EQ. A total of 46 rice varieties consisting of 22 japonica varieties and 24 indica varieties were examined using 43 PCR-based markers. The results showed that polymorphic information content (PIC) ranged from 0.04 to 0.38, in support of genetic diversity indices which ranged from 0.04 to 0.50 across total markers. Pairwise genetic similarity matrix ranged from 0.40 to 0.98 with the closest genetic distance was observed between two japonica varieties (Dongjin and Hwaseong) and the most distant one was between japonica and indica (Onnuri/Manmi with Cigeulis/Fatmawati). The unweighted neighbor-joining tree clustered the rice varieties into two major clades, indica and japonica, and subsequent subclades were differentiating according to the individual genetic background. The genetic diversity of rice from different subspecies and DNA markers for EQ can effectively be utilized for basic information and marker-assisted selection (MAS) for the development of improved varieties with good EQ in rice breeding program.
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Levi, A., C. E. Thomas, J. Thies, A. Simmons, Y. Xu, X. Zhang, O. U. K. Reddy, A. Davis, S. King, and T. Wehner. "GENETIC LINKAGE MAP FOR WATERMELON: SEGREGATION AND DISTRIBUTION OF DNA MARKERS." HortScience 40, no. 3 (June 2005): 872a—872. http://dx.doi.org/10.21273/hortsci.40.3.872a.
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Genetic linkage map is being constructed for watermelon based on a testcross population and an F2 population. About 51.0% and 31.8% of the markers in the testcross and F2 populations are skewed form the expected segregation ratios. AFLP markers appeared to be clustered on linkage regions, while ISSR and RAPD markers are randomly dispersed on the genome. AFLP markers also have greater genetic distances as compared with ISSR and RAPD markers, resulting in significant increase of map distance. An initial genetic map (based on the testcross population) that contains 27 ISSR and 141 RAPD markers has a total linkage distance of 1,166.2 cM. The addition of 2 ISSR, 8 RAPD and 77 AFLP markers increased the genetic distance of the map to 2,509.9 cM. Similar results with AFLP markers were also shown in mapping experiments with an F2S7 recombinant inbred line (RIL) population that was recently constructed for watermelon. Although the skewed segregation, marker order appeared to be consistent in linkage groups of the testcross and the F2 population. Experiments with SSR, and EST markers are being conducted to saturate the linkage map of watermelon genome.
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Martono, Budi, and Laba Udarno. "Keragaman Genetik Beberapa Genotipe Teh Berdasarkan Penanda RAPD (Random Amplified Polymorphic DNA)." Jurnal Tanaman Industri dan Penyegar 1, no. 1 (March 1, 2014): 1. http://dx.doi.org/10.21082/jtidp.v1n1.2014.p1-6.
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<p>Informasi keragaman genetik dan ketersediaan plasma nutfah teh (Camellia sinensis) diperlukan dalam perakitan varietas unggul. Keragaman genetik berdasarkan penanda DNA dapat memberikan hasil yang lebih konsisten karena tidak dipengaruhi lingkungan. Dalam penelitian ini sebanyak 9 genotipe teh dianalisis keragamannya menggunakan enam penanda RAPD (OPA 03, OPA 05, OPB 04, OPB 06, OPC 06, dan OPD 08). Penelitian dilakukan mulai bulan Maret sampai Mei 2013 di Laboratorium Terpadu Biotrop Bogor. Perhitungan koefisien kesamaan genetik dan analisis gerombol dilakukan dengan menggunakan perangkat lunak NTSYSpc versi 2.02. Sebanyak 54 lokus penanda RAPD berhasil diamplifikasi menggunakan enam primer dan 47 lokus di antaranya memiliki alel yang polimorfik (87,04%). Hasil analisis gerombol berdasarkan kesamaan genetiknya mengelompokkan 9 genotipe ke dalam enam kelompok. Empat kelompok (I, II, IV, V) masing-masing terdiri atas satu genotipe, sementara dua kelompok yang lain yaitu kelompok III dan VI masing-masing beranggotakan tiga dan dua genotipe.</p><p>Kata Kunci: Camellia sinensis, diversitas genetik, penanda RAPD</p><p>The availability of diverse tea (Camellia sinensis) germplasms as well as the information about their genetic diversity is required for plant breeding program. Genetic diversity analysis based on DNA marker is known to be more effective since the markers provide more consistent results. In this study, nine tea genotypes were evaluated for their genetic diversity using six Random Amplified Polymorphic DNA (RAPD) markers (OPA 03, OPA 05, OPB 04, OPB 06, OPC 06, and OPD 08). The study was conducted from March to May 2013 in the Integrated Laboratory of Biotrop Bogor. The estimation of genetic similarity and the cluster analysis were done using NTSYSpc version 2.02. Of the six RAPD markers used in this study, a total of 54 RAPD marker loci have been successfully amplified. In which, 47 loci (87.04%) were polymorphic and subsequently used for the evaluation of tea genotypes. The results of cluster analysis showed that those tea genotypes were clustered into six groups. Each of four groups (I, II, IV, V) consisted of only one genotype. Meanwhile, the other two groups (III and VI) had three and two genotypes, respectively.</p>
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Klimenko, Irina, Nikolay Kozlov, Anastasia Shamustakimova, and Vladimir Dushkin. "INVESTIGATION OF FORAGE CROPS GENETIC DIVERSITY USING MOLECULAR DNA MARKERS." Adaptive Fodder Production 2019, no. 4 (December 13, 2019): 89–100. http://dx.doi.org/10.33814/afp-2222-5366-2019-4-89-100.
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Genetic diversity is the precondition for any selection program. The collection and exploitation of natural variation from ecotypes and landraces has played a vital role in the improvement of forage crops. The review is devoted to the most important aspects of studying the genetic variation in populations, cultivars, samples and forms of wild and cultivated forage plants. The factors with negative impact on the biodiversity conservation have been determined. The main types of genetic markers that used for genetic recourses of perennial grasses evaluation were described. Particular attention was focused on the role of molecular DNA markers for the population genetics and phylogenetic studies. The main advantages of DNA markers application for the forage crops, due of its great variability of traits and properties, the complexity of the genetic system and a high degree of plasticity of this group of plants, have been discussed. The latest generation of genetic DNA markers allows conducting the objective and accurate assessment of genetic diversity, provides selection process intensification, increases the possibilities for identification and molecular-genetic certification of the selection achievements.
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Pourmohammad, Alireza. "Application of molecular markers in medicinal plant studies." Acta Universitatis Sapientiae, Agriculture and Environment 5, no. 1 (December 1, 2013): 80–90. http://dx.doi.org/10.2478/ausae-2014-0006.
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Abstract The World Health Organization has estimated that more than 80% of the world’s population in developing countries depends primarily on herbal medicine for basic healthcare needs. Approximately two thirds of the 50 000 different medicinal plant species in use are collected from the wild and only 10% of medicinal species used commercially are cultivated. DNA-based molecular markers have utility in the fields like taxonomy, physiology, embryology, genetics, etc. DNA-based techniques have been widely used for authentication of plant species of medicinal importance. The geographical conditions affect the active constituents of the medicinal plant and hence their activity profiles. Many researchers have studied geographical variation at the genetic level. Estimates of genetic diversity are also important in designing crop improvement programmes for the management of germplasm and evolving conservation strategies. The DNA-based molecular marker helps in the improvement of medicinal plant species. DNA markers are more reliable because the genetic information is unique for each species and is independent of age, physiological conditions and environmental factors.
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McDonald, B. A., R. E. Pettway, R. S. Chen, J. M. Boeger, and J. P. Martinez. "The population genetics of Septoria tritici (teleomorph Mycosphaerella graminicola)." Canadian Journal of Botany 73, S1 (December 31, 1995): 292–301. http://dx.doi.org/10.1139/b95-259.
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The DNA-based markers of molecular genetics were combined with the analytical tools of population genetics to learn about the population biology of the wheat pathogen Mycosphaerella graminicola. DNA-based genetic markers, including restriction fragment length polymorphisms in nuclear and mitochondrial DNA, DNA fingerprints, and electrophoretic karyotypes were used in combination to show that the amount and distribution of genetic variation within and among field populations of M. graminicola is similar around the world. Measures of gametic disequilibrium suggested that the sexual stage of reproduction has a more significant impact on the genetic structure of M. graminicola populations than asexual reproduction. A field experiment conducted over a 3-year period showed that populations had a high degree of genetic stability over time. The potential effects of selection were quantified in a cultivar mixture experiment with four wheat cultivars that varied in resistance to M. graminicola. In combination, these experiments demonstrated the utility of selectively neutral genetic markers to elucidate the population genetics of fungi. Key words: genetic diversity, wheat, gene flow, RFLPs, DNA fingerprinting.
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Szczechura, Wojciech, Mirosława Staniaszek, and Hanna Habdas. "Tomato Molecular Markers." Vegetable Crops Research Bulletin 74, no. 1 (January 1, 2011): 5–23. http://dx.doi.org/10.2478/v10032-011-0001-y.
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Tomato Molecular MarkersTomato (Solanum lycopersicumL.) is one of the most popular vegetable grown in many regions of the world. Due to its high taste quality and nutritional value increase interest in the cultivation of this species and its consumption. Using the latest achievements in fields of genetics, molecular biology and biotechnology, breeders can create new varieties with improved useful traits. Introduction of DNA markers, especially those based on the polymerase chain reaction (PCR) has led to breakthrough in the plants genetic research, including tomato. They are successfully used for plant genomes mapping, phylogenetics studies, selection of parental forms in plant breeding, and above all to identify the genes of important traits. For tomato have been identified and mapped 9309 molecular markers. High-density genetic maps development gives an opportunity to use them in genetic research and breeding programs. Identification of DNA markers closely linked to studied gene can significantly facilitate the identification of desirable traits in material breeding, or accelerate the plants selection for elimination of genotypes with undesirable genes. Material breeding selection using molecular markers, defined as MAS (marker-assisted-selection) is increasingly being used in tomato breeding programs, contributing to facilitated identification of genes or QTL and their transfer into the cultivated species from wild form.
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Levi, Amnon, Claude E. Thomas, Xingping Zhang, Tarek Joobeur, Ralph A. Dean, Todd C. Wehner, and Bruce R. Carle. "A Genetic Linkage Map for Watermelon Based on Randomly Amplified Polymorphic DNA Markers." Journal of the American Society for Horticultural Science 126, no. 6 (November 2001): 730–37. http://dx.doi.org/10.21273/jashs.126.6.730.
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A genetic linkage [randomly amplified polymorphic DNA (RAPD)-based] map was constructed for watermelon [Citrullus lanatus (Thunb.) Matsum and Nakai] using a BC1 population [PI 296341-fusarium wilt resistant × New Hampshire Midget (fusarium susceptible)] × `New Hampshire Midget'. The map contains 155 RAPD markers, and a 700-base pair sequenced characterized amplified region (SCAR) marker that corresponds to a fragment produced by the RAPD primer GTAGCACTCC. This marker was reported previously as linked (1.6 cM) to race 1 fusarium wilt resistance in watermelon. The markers segregated to 17 linkage groups. Of these, 10 groups included nine to 19 markers, and seven groups included two to four markers. The map covers a genetic linkage distance of 1295 cM. Nine of the 10 large linkage groups contained segments with low (or no) level of recombination (0 to 2.6 cM) among markers, indicating that the watermelon genome may contain large chromosomal regions that are deficient in recombination events. The map should be useful for identification of markers linked closely to genes that control fruit quality and fusarium wilt (races 1 and 2) resistance in watermelon.
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MacGregor, Terry, Madan Bhattacharyya, Brett Tyler, Ravindra Bhat, August F. Schmitthenner, and Mark Gijzen. "Genetic and Physical Mapping of Avr1a in Phytophthora sojae." Genetics 160, no. 3 (March 1, 2002): 949–59. http://dx.doi.org/10.1093/genetics/160.3.949.
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Abstract The interaction between soybean and the phytopathogenic oomycete Phytophthora sojae is controlled by host resistance (Rps) genes and pathogen avirulence (Avr) genes. We have mapped the Avr1a locus in F2 populations derived from four different P. sojae races. Four RAPD and nine AFLP markers linked to Avr1a were initially identified. Nine markers were used to compare genetic linkage maps of the Avr1a locus in two distinct F2 populations. Distorted segregation ratios favoring homozygous genotypes were noted in both crosses. Segregation analysis of all the markers in one F2 population of 90 progeny generated a map of 113.2 cM encompassing Avr1a, with one marker cosegregating with the gene. The cosegregating DNA marker was used to isolate P. sojae BAC clones and construct a physical map covering 170 kb, from which additional DNA markers were developed. Three markers occurring within the BAC contig were mapped in an enlarged population of 486 F2 progeny. Avr1a was localized to a 114-kb interval, and an average physical to genetic distance ratio of 391 kb/cM was calculated for this region. This work provides a basis for the positional cloning of Avr1a.
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Kozina, T. D., E. T. Ilnitskaya, and M. V. Makarkina. "PROSPECTS OF USING DNA-MARKERS IN GRAPEVINE BREEDING." Russian Vine 16 (June 2021): 18–26. http://dx.doi.org/10.32904/2712-8245-2021-16-18-26.
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DNA-markers are actively used for the fin-gerprinting of genotypes, identification of va-rieties, in phylogenetic studies, for assessing genetic diversity, for mapping genes, etc. The article presents an analytical review of the achievements in the use of molecular markers in grape genetics as a basis for breeding works. Information is given about mapped genes and quantitative traits loci of grapes (QTL), about identified DNA-markers. It is shown that, using DNA-markers, was imple-mented the identification of genetic determi-nants determining such traits as resistance to pathogens (Agrobacterium sp. Plasmopara viticola, Erysiphe necator, Guignardia bidwellii, etc.), as well as grape quality indica-tors (berry pulp structure, berry size, seedless-ness, etc).Also, sets of DNA-markers have been developed for many of the identified genes. DNA-markers are used to identify genes of valuable traits in hybrid populations and to select the parental forms - gene donors. The DNA-marking method is used in the breeding to accelerate the transfer of econom-ically valuable genes and create new varieties with the required traits. The progress of mo-lecular genetic research in recent decades opens up new opportunities for grape breed-ing. The expediency of using DNA-markers and their selection for research should be as-sessed precisely for a specific breeding pro-gram.
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Satriani, Gloria Ika, Dinar Tri Soelistyowati, Dian Hardianto, and Ratu Siti Aliah. "Genetic variability of the fifth generation of nile tilapia Oreochromis niloticus using microsatellite DNA markers." Jurnal Akuakultur Indonesia 10, no. 2 (March 30, 2015): 124. http://dx.doi.org/10.19027/jai.10.124-130.
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<p>ABSTRACT</p><p><br />Fifth generations of Nile tilapia from several strains have been produced by using selective breeding program in Main Centre for Freshwater Aquaculture Development (MCFAD) Sukabumi, West Java. This research was aimed to evaluate the impact of family selection program of some highly economic traits on its genetic variability using microsatellite DNA markers. The total of 180 specimens have been collected from fifth generation of nine reciprocal mating between three families selected from fourth generation of Nile tilapia and were screened for genetic variability at three microsatellite loci (UNH 123*, UNH 172*, UNH 216*). The results showed that the amount of genetic variability on fifth generations of Nile tilapia from three strains was ranged between 33 to 100% and the highest genetic distance relationship between families was 0.3875. This research approved that females and males issued from the family which have more amount of genetic variability and higher distance to others could be considered as genetic materials to produce the next generation.</p><p><br />Keywords: microsatellite DNA, genotype, genetic variability, genetic distance, Oreochromis nilotiocus</p><p><br /> ABSTRAK</p><p><br />Beberapa strain ikan nila generasi kelima telah dihasilkan dalam program pemuliaan di Main Centre untuk Freshwater Aquaculture Development (MCFAD) Sukabumi, Barat Jawa. Riset ini bertujuan untuk mengevaluasi pengaruh seleksi famili terhadap performa karakter ekonomis penting berdasarkan keragaman genetiknya menggunakan penanda microsatellite DNA. Spesimen dari 180 individu generasi kelima hasil persilangan resiprokal antara tiga famili generasi keempat dianalisis dengan penanda tiga microsatellite loci (UNH 123*, UNH 172*, UNH 216*). Hasil penelitian menunjukkan bahwa keragaman genetik ikan nila generasi kelima berkisar antara 33 sampai 100% dan hubungan kekerabatan genetik antar famili yang paling jauh adalah 0,3875. Individu betina dan jantan yang berasal dari famili dengan tingkat keragaman genetik dan kekerabatan yang lebih tinggi dapat dipertimbangkan sebagai sumber genetik berkualitas untuk menghasilkan generasi berikutnya.<br />Kata kunci: microsatellite DNA, genotipe, keragaman genetik, jarak genetik, Oreochromis nilotiocus</p>
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Conner, Patrick J., Susan K. Brown, and Norman F. Weeden. "Randomly Amplified Polymorphic DNA-based Genetic Linkage Maps of Three Apple Cultivars." Journal of the American Society for Horticultural Science 122, no. 3 (May 1997): 350–59. http://dx.doi.org/10.21273/jashs.122.3.350.
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Genetic linkage maps were created for three apple (Malus ×domestica Borkh.) cultivars using data from two progenies (`Wijcik McIntosh' xNY 75441-67 and `Wijcik McIntosh' xNY 75441-58). The maps consist primarily of randomly amplified polymorphic DNA (RAPD) markers, but also contain six isozyme loci and four morphological markers (Rf, fruit skin color; Vf, scab resistance; Co, columnar growth habit; Ma, malic acid). Maps were constructed using a double pseudotestcross mapping format and JoinMap mapping software. An integrated `Wijcik McIntosh' map was produced by combining marker data from both progenies into a single linkage map. Homologous linkage groups from paternal maps were paired with their counterparts in the `Wijcik McIntosh' map using locus bridges composed of markers heterozygous in both parents of a progeny. The `Wijcik McIntosh' map consists of 238 markers arranged in 19 linkage groups spanning 1206 cM. The NY 75441-67 map contains 110 markers in 16 linkage groups and the NY 75441-58 map consists of 183 markers in 18 linkage groups. The average distance between markers in the maps was ≈5.0 cM.
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Vitoševic, Katarina, Danijela Todorovic, Zivana Slovic, Radica Zivkovic-Zaric, and Milos Todorovic. "Forensic Genetics and Genotyping." Serbian Journal of Experimental and Clinical Research 20, no. 2 (June 1, 2019): 75–86. http://dx.doi.org/10.1515/sjecr-2016-0074.
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Abstract Forensic genetics represents a combination of molecular and population genetics. Personal identification and kinship analysis (e.g. paternity testing) are the two main subjects of forensic DNA analysis. Biological specimens from which DNA is isolated are blood, semen, saliva, tissues, bones, teeth, hairs. Genotyping has become a basis in the characterization of forensic biological evidence. It is performed using a variety of genetic markers, which are divided into two large groups: bi-allelic (single-nucleotide polymorphisms, SNP) and multi-allelic polymorphisms (variable number of tandem repeats, VNTR and short tandem repeats, STR). This review describes the purpose of genetic markers in forensic investigation and their limitations. The STR loci are currently the most informative genetic markers for identity testing, but in cases without a suspect SNP can predict offender’s ancestry and phenotype traits such as skin, eyes and hair color. Nowadays, many countries worldwide have established forensic DNA databases based on autosomal short tandem repeats and other markers. In order for DNA profile database to be useful at a national or international level, it is essential to standardize genetic markers used in laboratories.
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Bukreev, Yu M., E. N. Kosobokova, S. S. Kardashova, M. V. Pinyugina, and V. S. Kosorukov. "DNA-markers for genetic monitoring of laboratory mouse." Russian Journal of Biotherapy 16, no. 3 (September 30, 2017): 86–91. http://dx.doi.org/10.17650/1726-9784-2017-16-3-86-91.
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Introduction. The use of standardized model is required at preclinical researches of drug safety and efficiency. Apart of veterinary control the leading laboratories of the world use genetic monitoring of animals. Objective: to develop the method for detecting genetic contamination of laboratory mouse based on microsatellite DNA markers analysis. Materials and methods. We tested two lines of mice C57BL/6J and BALB/cJLac. We used 5 primers: (GAG)6C, (CTC)6C, (CTC)6A, AG9-1, AG9-2. We weighted the results of рolymerase chain reaction using 1.5 % agarous gel. Results. Three of tested primers allowed to distinguish 2 lines of mice statistically reliably. Two mice lines were bred to control the results. Our data shows track of every line gives a boots in assortment of alleles in locuses. We composed a table of alleles assortment in locuses for every line based of results. Conclusion. Our results prove that this method provides fast, reliable and cost-effective way of genetic monitoring.
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Kobayashi, Eiji. "For genetic improvement using DNA markers in pigs." Journal of animal genetics 23, no. 2 (1995): 41–47. http://dx.doi.org/10.5924/abgri1993.23.41.
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Lee, Sun-Young, and Sang-Min Chung. "Genetic Analysis of Polymorphic DNA Markers in Cucumber." Journal of Life Science 21, no. 3 (March 30, 2011): 468–72. http://dx.doi.org/10.5352/jls.2011.21.3.468.
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Gasser, Robin B., Louise E. Stewart, and Richard Speare. "Genetic markers in ribosomal DNA for hookworm identification." Acta Tropica 62, no. 1 (September 1996): 15–21. http://dx.doi.org/10.1016/s0001-706x(96)00015-0.
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Monden, Yuki, and Makoto Tahara. "Genetic linkage analysis using DNA markers in sweetpotato." Breeding Science 67, no. 1 (2017): 41–51. http://dx.doi.org/10.1270/jsbbs.16142.
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Tingey, S. V., and J. P. del Tufo. "Genetic Analysis with Random Amplified Polymorphic DNA Markers." Plant Physiology 101, no. 2 (February 1, 1993): 349–52. http://dx.doi.org/10.1104/pp.101.2.349.
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Lee, W. "Microsatellite DNA markers for genetic mapping inOreochromis niloticus." Journal of Fish Biology 49, no. 1 (July 1996): 169–71. http://dx.doi.org/10.1006/jfbi.1996.0145.
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Imad, Hadi Hameed, Abdullah Jebor Mohammed, Jaber Ommer Aamera, Yoke Cheah, K. Zadian Haider, H. Al-Saadi Ali, and A. Abdulazeez Muataz. "Genetic variation and DNA markers in forensic analysis." African Journal of Biotechnology 13, no. 31 (July 30, 2014): 3122–36. http://dx.doi.org/10.5897/ajb2013.13160.
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SEIZINGER, B. R., R. E. TANZI, T. C. GILLIAM, J. L. BADER, D. M. PARRY, M. A. SPENCE, M. L. MARAZITA, K. GIBBONS, W. HOBBS, and J. F. GUSELLA. "Genetic Linkage Analysis of Neurofibromatosis with DNA Markers." Annals of the New York Academy of Sciences 486, no. 1 Neurofibromat (December 1986): 304–10. http://dx.doi.org/10.1111/j.1749-6632.1986.tb48083.x.
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Nicholas, F. W. "Discovery, validation and delivery of DNA markers." Australian Journal of Experimental Agriculture 46, no. 2 (2006): 155. http://dx.doi.org/10.1071/ea05228.
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Early attempts at finding markers for quantitative trait loci (QTL) in the 1950s and 1960s involved searching for associations between production traits and polymorphisms at loci encoding blood groups, milk proteins and blood proteins. Overall, this work identified many small and/or non-significant associations, insufficient to warrant their use in marker-assisted selection. It was not until the discovery of microsatellites in the early 1990s that a really useful form of DNA marker became available. By the mid-1990s, linkage maps comprising mainly microsatellites covered most regions of most chromosomes of the cow, and it was then possible to hunt for QTL using a mapping approach first proposed in Drosophilia back in 1961. Fine-mapping of QTL has eventually resulted in the identification of markers in or near particular genes. Some of these markers have been commercialised. In most cases, the actual causative quantitative trait nucleotide (QTN) remains elusive. The recent development of technologies for large-scale detection and genotyping for single nucleotide polymorphisms (SNPs) and for placing the entire genome on a chip have opened up exciting possibilities for the future: geneticists should begin contemplating how best to use SNP and genome chips, which will surely become a reality. Just as one must estimate genetic and phenotypic correlations for every new quantitative trait that is introduced into a genetic evaluation scheme, so must the correlated effects of new DNA markers be evaluated before their commercial use. Researchers and their funders must resist the temptation to cut corners in getting markers to market.
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Javed, A. M., Ch H. Cannon, and R. Wickneswari. "Microsatellite DNA markers in Shorea platyclados (Dipterocarpaceae): genetic diversity, size homoplasy and mother trees." Journal of Forest Science 60, No. 1 (January 30, 2014): 18–27. http://dx.doi.org/10.17221/71/2013-jfs.
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Cross-specific amplification of microsatellite loci greatly enhances the effectiveness of this marker system. This shortcut would greatly enhance our examination of the gene flow and population structure of trees in diverse tropical rainforests. To explore the effectiveness and limitations of this approach, we examined allelic diversity at six microsatellite loci, originally developed in a congeneric species, in three populations of Shorea platyclados from Peninsular Malaysia. Fragment sizing was performed by an efficient and sensitive (1 bp resolution) technique using capillary electrophoresis, ethidium bromide detection, and minimal clean-up. Fragment size ranges were conserved between species and null allele frequencies were low. Higher overall levels of genetic diversity were detected in our study. Variation among populations was directly related to geographic distance. Fragment size class distributions suggest that each locus should be studied using different evolutionary models. Direct sequencing of SSR fragments revealed that size differences were due to changes in both the flanking regions and repeat motifs. Several clear examples of size homoplasy were observed, along with the disruption of perfect repeats, suggesting that cross-specific amplification of microsatellite loci requires an additional level of confirmation at the DNA sequence level before the influence of size homoplasy and changes in repeat structure can be assessed. Simulation studies demonstrate that the increasing intensity of timber harvest leads to higher variability in levels of potential heterozygosity and decreasing total number of alleles in the remnant "mother trees" The careful selection of "mother" trees can greatly enhance the future genetic diversity of populations.
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Yu, H. F., J. S. Wang, Z. Q. Zhao, X. G. Sheng, and H. H. Gu. "DNA fingerprinting and genetic purity testing of a new broccoli hybrid using SSR markers." Seed Science and Technology 41, no. 3 (December 1, 2013): 464–68. http://dx.doi.org/10.15258/sst.2013.41.3.13.
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Bielikova, О. Y., A. E. Mariutsa, A. I. Mruk, S. I. Tarasjuk, and V. M. Romanenko. "Genetic structure of rainbow trout Oncorhynchus mykiss (Salmoniformes, Salmonidae) from aquaculture by DNA-markers." Biosystems Diversity 29, no. 1 (February 17, 2021): 28–32. http://dx.doi.org/10.15421/012104.
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The rational use of valuable fish species from aquaculture is difficult to implement without knowledge of the state of the genetic structure of local stocks. Different types of DNA markers can be used to achieve the goals of selection and breeding work. The genetic structure of a local stock of rainbow trout (Oncorhynchus mykiss Walbaum, 1792) (Salmoniformes, Salmonidae) farmed in Ukraine was studied using DNA-markers: microsatellite (SSR-markers – simple-sequence repeats-markers) and intermicrosatellite (ISSR – inter-simple sequence repeat). Five fragments of trinucleotide microsatellite motifs with a single anchor nucleotide at the 3'-end were used as a primer for analysis by the ISSR-PCR method. Totally, 85 amplicons were obtained across the five loci, of which 92.9% were polymorphic. The total number of alleles ranged from 10 (marker (ACC)₆G) to 23 (marker (AGC)₆G). The following monomorphic amplicons were determined for the studied local stock of rainbow trout: according to marker (CTC)₆C – 770 and 520 bp bands, for the marker (GAG)₆C – 345, 295 and 260 bp, and for the marker (AGC)₆C – 350 bp. The average number of polymorphic bands per locus was 15.8. The selected ISSR primers had a level of polymorphic information content above the average. The most effective markers for molecular-genetic analysis of rainbow trout were (AGC)₆G and (AGC)₆C according to the percentage of polymorphic bands, marker index, effective multiplex ratio and resolving power. The selected ISSR loci allow the genetic structure of the studied local stock to be characterized using the total and the effective number of alleles per locus (Na and Ne were 1.9 and 1.4, respectively), the Shannon index (average value I was 0.4) and the unbiased expected heterozygosity (mean uHe = 0.3). Microsatellite-based analysis showed features of the genetic structure of the local stock of rainbow trout at six microsatellite loci (OMM 1032, OMM 1077, OMM 1088, Str 15, Str 60, Str 73). Allelic diversity was established and alleles with the highest frequency and most typical for the given stock were identified. The Shannon index and unbiased expected heterozygosity were determined using SSR-markers and were 1.42 and 0.79, respectively. This depicts the complexity of the population structure, a high level of genetic diversity and indicates a high level of heterozygosity of local stock. The “gene pool profile” established as a result of ISSR-PCR in the future will help to differentiate local stocks of rainbow trout in aquaculture of Ukraine. Microsatellite markers provide the ability to determine individual features of genetic variation of local populations and to conduct the management of genetic resources on fish farms.
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Beeman, Richard W., and Susan J. Brown. "RAPD-Based Genetic Linkage Maps of Tribolium castaneum." Genetics 153, no. 1 (September 1, 1999): 333–38. http://dx.doi.org/10.1093/genetics/153.1.333.
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Abstract A genetic map of the red flour beetle (Tribolium castaneum) integrating molecular with morphological markers was constructed using a backcross population of 147 siblings. The map defines 10 linkage groups (LGs), presumably corresponding to the 10 chromosomes, and consists of 122 randomly amplified polymorphic DNA (RAPD) markers, six molecular markers representing identified genes, and five morphological markers. The total map length is 570 cM, giving an average marker resolution of 4.3 cM. The average physical distance per genetic distance was estimated at 350 kb/cM. A cluster of loci showing distorted segregation was detected on LG9. The process of converting RAPD markers to sequence-tagged site markers was initiated: 18 RAPD markers were cloned and sequenced, and single-strand conformational polymorphisms were identified for 4 of the 18. The map positions of all 4 coincided with those of the parent RAPD markers.
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Yang, Xiaofeng, and Carlos F. Quiros. "Characterizing the Celery Genome with DNA-based Genetic Markers." Journal of the American Society for Horticultural Science 120, no. 5 (September 1995): 747–51. http://dx.doi.org/10.21273/jashs.120.5.747.
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To characterize the celery (Apium graveolens L. var. dulce, 2n = 2x = 22) genome, 126 celery cDNA clones and 340 random 10-mer primers were used to generate restriction fragment-length polymorphism (RFLP) and randomly amplified polymorphic DNA (RAPD) markers between two cultivated types. Different abundance classes of the genomic sequences represented by the cDNA clones and the RAPD markers were observed. Most of the cDNA clones were single-copy sequences, suggesting the true diploid nature of the celery genome. Nearly half of the 39 RAPD markers tested by Southern hybridization were multiple-copy sequences. Of the RAPD markers tested, 28% was single- and low-copy, and 26% was high-copy sequences. The polymorphism level of the cDNA clones was 23% when tested with four restriction enzymes (Eco RI, Eco RV, Hin dIII, and Hae III). A positive association was observed between RFLP level and the size of cDNA inserts or hybridized restriction fragments. Deletion, insertion, and base substitution were important in the formation of the RFLP markers. Eighty-two (23%) of the 340 primers tested yielded useful RAPD markers, but only 3.8% of the amplified products were polymorphic. Base substitution may be the most important mechanism for the RAPD markers in celery. The RAPD fragments revealed no RFLP markers when tested by Southern hybridization, implying that RAPD markers are an important complement to RFLP markers in genomic mapping in celery. Random methylation of cytosine was determined in 5S rDNA on Bam HI and Hin dIII cutting sites that produced ladder patterns characteristic of tandem repeats.
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Khatoon, Arifa, Sumeet Verma, Gayatri Wadiye, and Anuprita Zore. "Molecular markers and their potentials." International Journal of Bioassays 5, no. 01 (January 1, 2016): 4706. http://dx.doi.org/10.21746/ijbio.2016.01.003.
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The use of molecular markers, revealing polymorphism at the DNA level, has been playing an increasing part in plant molecular biotechnology and their genetic studies. There are three different types of markers viz. morphological, biochemical and DNA based molecular markers. These DNA based markers are differentiating in two types 1. Non PCR based (RFLP) and 2. PCR based markers (RAPD, AFLP, SSR, SNP etc.). Amongst others, the microsatellite DNA marker is one of the most widely used marker due to its easy use by simple PCR, followed by a denaturing gel electrophoresis. SNP (Single Nucleotide Polymorphism) is nowadays is the one which is used mainly. In this review, we are going to discuss about the biochemical and molecular markers which are recently developed, the important characteristics of molecular markers their advantages, disadvantages and the applications of these markers in comparison with other markers types.
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Keiper, F. J., and R. McConchie. "561 Using AFLPs to Examine Genetic Diversity in Umbrella Fern." HortScience 34, no. 3 (June 1999): 543A—543. http://dx.doi.org/10.21273/hortsci.34.3.543a.
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Umbrella fern [Sticherus flabellatus (R. Br.) St John] is a successful Australian native foliage product. Currently, all umbrella fern sold on the market is bush-harvested. To meet the growing demand for this product on local and international markets, a commercially viable method for its production must be developed, with effective management of the germplasm resource in terms of conservation and exploitation. To manage this resource, breeders require a detailed knowledge of the amount and distribution of genetic variability within the species. Traditionally, plant breeders focus on a combination of agronomic and morphological traits (phenotype) to measure genetic diversity. In umbrella fern there are a limited number of morphological traits, and these are influenced by environmental factors and therefore do not reflect true genetic diversity. To overcome these problems, molecular techniques such as PCR-based DNA markers are used to complement traditional strategies for genotype assessment. DNA markers have the advantages of being independent of environmental effects, as well as being fast, cost-effective, reproducible, and largely accessible to the nonmolecular geneticist. Amplified fragment length polymorphisms (AFLPs) fulfil many of the desirable features of molecular markers, as well as requiring little knowledge of the genome to be investigated. AFLPs have been used widely in the analysis of breeding systems, ecogeographical variation, and genetic variation within and between natural populations. To date there are no published accounts of DNA molecular marker research on umbrella fern. A DNA extraction protocol has been developed for this species, and AFLP markers have been used to analyse genetic diversity within and between natural populations sampled in the Sydney Basin. A large number of polymorphic loci were revealed using 11 primer combinations. The genetic variation detected was partitioned between rather than within populations, suggesting that the mating system in Sticherus is primarily inbreeding. Data will be presented illustrating AFLPs as useful molecular markers for assessing genetic diversity within and between populations of umbrella fern and providing insight on the breeding system used by the species.
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Bonnin, Isabelle, Jean-Marie Prosperi, and Isabelle Olivieri. "Genetic Markers and Quantitative Genetic Variation in Medicago truncatula (Leguminosae): A Comparative Analysis of Population Structure." Genetics 143, no. 4 (August 1, 1996): 1795–805. http://dx.doi.org/10.1093/genetics/143.4.1795.
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Abstract Two populations of the selfing annual Medicago truncatula Gaertn. (Leguminoseae), each subdivided into three subpopulations, were studied for both metric traits (quantitative characters) and genetic markers (random amplified polymorphic DNA and one morphological, single-locus marker). Hierarchical analyses of variance components show that (1) populations are more differentiated for quantitative characters than for marker loci, (2) the contribution of both within and among subpopulations components of variance to overall genetic variance of these characters is reduced as compared to markers, and (3) at the population level, within population structure is slightly but not significantly larger for markers than for quantitative traits. Under the hypothesis that most markers are neutral, such comparisons may be used to make hypotheses about the strength and heterogeneity of natural selection in the face of genetic drift and gene flow. We thus suggest that in these populations, quantitative characters are under strong divergent selection among populations, and that gene flow is restricted among populations and subpopulations.
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Ruņgis, Dainis, Ilze Gaile, Ilze Veinberga, Sanita Zute, Vija Strazdiņa, Māra Bleidere, and Arta Kronberga. "Use of DNA markers for cereal line uniformity assessment." Proceedings of the Latvian Academy of Sciences. Section B. Natural, Exact, and Applied Sciences. 66, no. 1-2 (January 1, 2012): 21–25. http://dx.doi.org/10.2478/v10046-011-0041-1.
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Use of DNA markers for cereal line uniformity assessment Prior to the registration of a new variety, it is required to undergo Distinctness, Uniformity and Stability (DUS) testing. Preparing a newly developed variety to meet the requirements of DUS testing is a lengthy process, particularly regarding aspects of uniformity and stability. Field testing of a large number of lines is time and resource intensive. In addition, the expression of certain traits may be influenced by environmental conditions. The use of DNA markers may allow rapid assessment of the level of genetic diversity within a particular line or variety, and to remove individuals that are genetically differentiated, thus accelerating the homogenisation of a newly developed variety. In this study, we utilised AFLP and the iPBS marker techniques to assess genetic variation within advanced breeding lines of several cereal species (triticale, wheat, barley). The combined use of molecular and morphological selection over three years of analysis and selection resulted in the reduction of genetic diversity within breeding lines.
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Afifah, Ismayati, Dedy Duryadi Solihin, and Arzyana Sunkar. "Karakteristik Molekuler Kelelawar (Microchiroptera), berdasarkan DNA Mitokondria (Gen COI) di Gua Sukabumi dan Sentul Jawa Barat." Al-Kauniyah: Jurnal Biologi 14, no. 1 (April 30, 2021): 20–28. http://dx.doi.org/10.15408/kauniyah.v14i1.14147.
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AbstrakCytochrome Oxidase I (COI) merupakan salah satu gen mitokondria untuk membantu konstruksi dari pohon filogeni yang dapat bertindak sebagai gen marker. Gen COI memiliki keakuratan dalam mengidentifikasi spesies dan umumnya digunakan sebagai “DNA Barcoding”. Informasi mengenai karakteristik genetik berdasarkan DNA mitokondria pada kelelawar di Sukabumi dan Sentul belum banyak dilaporkan. Tujuan dari penelitian ini untuk mengetahui keragaman genetik kelelawar berdasarkan DNA mitokondria dengan penanda Cytochrome Oxidase I (COI) sebagai DNA barcoding. Isolasi DNA total dilakukan menggunakan Kit Dneasy® Blood and Tissue Kit cat no 69504 (50) berdasarkan prosedur Spin-Column Protocol dengan modifikasi. Hasil penelitian ini menunjukkan bahwa gen COI telah berhasil mengidentifikasi karakteristik spesies. Dua haplotipe didapatkan dari masing-masing populasi. Berdasarkan barcode DNA menunjukkan populasi Sukabumi merupakan spesies Chaerephon plicatus dengan nilai identitas genetik sebesar 97,08%, sedangkan populasi Sentul menunjukkan perbedaan secara genetik dengan spesies Hipposideros larvatus dengan nilai identitas genetik sebesar 94,85%. Identifikasi secara genetik dengan menggunakan gen COI menunjukkan bahwa kelelawar yang berasal Sukabumi adalah spesies Chaerephon plicatus dengan jarak genetik sebesar 3,1%. Kelelawar yang berasal dari Sentul memiliki kedekatan dengan spesies Hipposideros larvatus namun memiliki jarak genetik sebesar 5,2%. AbstractCytochrome Oxidase I (COI) is one of the mitochondrial genes to help the construction of phylogeny trees that can act as marker genes. The COI gene has accuracy in identifying species and is commonly used as "DNA Barcoding". Information about genetic characteristics based on mitochondrial DNA in bats in Sukabumi and Sentul has not been widely reported. The purpose of this study was to determine the genetic diversity of bats based on Mitochondrial DNA with Cytochrome Oxidase I (COI) markers as DNA barcoding. Total DNA isolation was carried out using the Dneasy® Blood and Tissue Kit paint no. 69504 (50) based on the Spin-Column Protocol procedure with modifications. The results of this study indicate that the COI gene has successfully identified species characteristics. Two haplotypes were obtained from each population. Based on DNA barcodes, the population of Sukabumi is a species of Chaerephon plicatus with a genetic identity value of 97.08%, while the Sentul population shows genetic differences with the Hipposideros larvatus species with a genetic identity value of 94.85%. Genetic identification using the COI gene shows that the bats originating from Sukabumi is a spesies Chaerephon plicatus with a genetic distance of 3.1%. The bats originating from Sentul are closely related to the species Hipposideros larvatus but have a genetic distance of 5.2%.
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Runģis, Dainis, Linards Ļubinskis, and Veneranda Stramkale. "Agronomic Trait and Genetic Analysis of Latvian Flax Germplasm." Environment. Technology. Resources. Proceedings of the International Scientific and Practical Conference 2 (August 5, 2015): 260. http://dx.doi.org/10.17770/etr2011vol2.1000.
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There is a long history of flax cultivation in Latvia, and breeding programs were active until 1970’s, when flax breeding in Latvia was halted. Since 1992, the Agriculture Science Centre of Latgale (ASCL) has repatriated Latvian flax germplasm from various genebanks, as well as renewed limited breeding activities in flax. Currently, the ASCL holds a collection of 497 flax accessions, as well as 9865 accessions of various lines and hybrids developed at the LLZC since 1993. To assist in the characterization of this Latvian flax germplasm, we have utilised DNA markers to assess genetic diversity and relatedness, as well as surveying functional polymorphism. We have utilised Simple sequence repeat (SSR) markers developed from both genomic libraries as well as expressed sequences. The results of the DNA marker survey were utilised to determine the genetic polymorphism and relatedness within Latvian flax germplasm, and these results were compared with the analysis of agronomic traits carried out in field trials at the ASCL. The development of DNA markers linked to traits of agronomic importance will assist in the development of a Latvian flax breeding program. The use of DNA marker technology will allow more efficient assessment and rational utilization of Latvian flax germplasm.
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Waldron, Julie, Cameron P. Peace, Iain R. Searle, Agnelo Furtado, Nick Wade, Ian Findlay, Michael W. Graham, and Bernard J. Carroll. "Randomly Amplified DNA Fingerprinting: A Culmination of DNA Marker Technologies Based on Arbitrarily-Primed PCR Amplification." Journal of Biomedicine and Biotechnology 2, no. 3 (2002): 141–50. http://dx.doi.org/10.1155/s1110724302206026.
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Arbitrarily-primed DNA markers can be very useful for genetic fingerprinting and for facilitating positional cloning of genes. This class of technologies is particularly important for less studied species, for which genome sequence information is generally not known. The technologies include Randomly Amplified Polymorphic DNA (RAPD), DNA Amplification Fingerprinting (DAF), and Amplified Fragment Length Polymorphism (AFLP). We have modified the DAF protocol to produce a robust PCR-based DNA marker technology called Randomly Amplified DNA Fingerprinting (RAF). While the protocol most closely resembles DAF, it is much more robust and sensitive because amplicons are labelled with either radioactive33P or fluorescence in a 30-cycle PCR, and then separated and detected on large polyacrylamide sequencing gels. Highly reproducible RAF markers were readily amplified from either purified DNA or alkali-treated intact leaf tissue. RAF markers typically display dominant inheritance. However, a small but significant portion of the RAF markers exhibit codominant inheritance and represent microsatellite loci. RAF compares favorably with AFLP for efficiency and reliability on many plant genomes, including the very large and complex genomes of sugarcane and wheat. While the two technologies detect about the same number of markers per large polyacrylamide gel, advantages of RAF over AFLP include: (i) no requirement for enzymatic template preparation, (ii) one instead of two PCRs, and (iii) overall cost. RAF and AFLP were shown to differ in the selective basis of amplification of markers from genomes and could therefore be used in complementary fashion for some genetic studies.
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Yang, Cong Cong, Jian Ma, Cong Li, Min Sun, Ya Ya Zou, Ting Li, Yang Mu, Hua Ping Tang, and Xiu Jin Lan. "The development and validation of new DNA markers linked to the thousand-grain weight QTL in bread wheat (Triticum aestivum L.)." Czech Journal of Genetics and Plant Breeding 56, No. 2 (March 17, 2020): 52–61. http://dx.doi.org/10.17221/35/2019-cjgpb.
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Thousand-grain weight (TGW) is an important trait affecting wheat production. We previously identified a major quantitative trait loci (QTL) controlling the TGW on the 2D chromosome of wheat using a recombinant inbred line (RIL) population constructed by the cross between Tibetan semi-wild wheat Q1028 (Q1028) and Zhengmai 9023 (ZM9023). The positive allele at this QTL is from ZM9023. To further characterise this QTL, here, we try to develop and validate the high-resolution melting (HRM) and sequence-characterised amplified region (SCAR) markers. One HRM marker (0C98-411) and two SCAR markers (E301-700 and B0BB-10470) were developed and integrated into the genetic map. All of these three markers were validated in three populations with different genetic backgrounds. 0C98-411 is the most closely linked marker that could trace QTgw.sau-2D in molecular marker assisted breeding.
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Sarao, Navraj Kaur, Mamta Pathak, Neha Kaur, and Kirandeep. "Microsatellite-based DNA fingerprinting and genetic diversity of bottle gourd genotypes." Plant Genetic Resources 12, no. 1 (September 6, 2013): 156–59. http://dx.doi.org/10.1017/s1479262113000385.
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In India, the registration and protection of new and notified/extant plant varieties are based on the criteria of distinctness, uniformity and stability (DUS) of morphological characteristics. However, these morphological traits have not been helpful in resolving closely related genotypes. The molecular markers can very well support the DUS testing in such cases. Therefore, in the present study, 20 accessions of bottle gourd were fingerprinted using 20 simple sequence repeat (SSR) primers. Of these, ten primers exhibited polymorphic profiles, while nine exhibited monomorphic patterns and one revealed a null allele. The number of alleles ranged from 2 to 4 with an average of 2.6 alleles per locus. Unique DNA profiles of all the accessions could be created using a set of five polymorphic primers. Therefore, SSR markers used in the present study could precisely distinguish all the 20 accessions from each other, and these SSR markers can be further used to differentiate the future genotypes from the existing ones. The dendrogram depicting the genetic relationships as revealed by NTSYS-pc 2.02 and the tree diagram generated using the DARwin 5.0 program classified the accessions into two main clusters. There is no strong association between the clustering pattern and geographical origin of these accessions. This SSR marker-based diversity would facilitate the implementation of marker-assisted breeding schemes for efficient introduction of the desired traits into bottle gourd.