Journal articles: 'Development molecular markers'

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Varshney, R. K., M. Prasad, R. Kota, R. Sigmund, Valkoun Börner A, J, U. Scholz, N. Stein, and A. Graner. "Functional molecular markers in barley: Development and applications." Czech Journal of Genetics and Plant Breeding 41, Special Issue (July 31, 2012): 128–33. http://dx.doi.org/10.17221/6152-cjgpb.

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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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Guthrie, Sarah C. "Molecular markers in sea urchin development." Trends in Neurosciences 8 (January 1985): 185–87. http://dx.doi.org/10.1016/0166-2236(85)90074-8.

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Chinnappareddy, L. R. D., K. Khandagale, A. Chennareddy, and V. G. Ramappa. "Molecular markers in the improvement of Allium crops." Czech Journal of Genetics and Plant Breeding 49, No. 4 (November 26, 2013): 131–39. http://dx.doi.org/10.17221/111/2013-cjgpb.

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The genus Allium (Family: Alliaceae) is the most important among the bulbous vegetable crops. characterization of Alliums based on phenotypic traits is influenced by the environment and leads to biased diversity estimates. Recognizing the potential of DNA markers in plant breeding, researchers have adopted the molecular markers for marker-assisted selection (MAS), quantitative trait loci (QTL) mapping and characterization of different quality traits in Alliums. This review presents details about the use of DNA markers in Alliums for cultivar identification, diversity studies, SSR development, colour improvement, total soluble solids (TSS), cytoplasmic male sterility (CMS) and efforts of DNA sequencing. As there are no such reports to describe the above work under a single heading, we decided to mine literature for those who are working in onion, garlic, chives and leek improvement to generate new insights in the subject.

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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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Hormi-Carver, Kathy, and Rhonda F. Souza. "Molecular Markers and Genetics in Cancer Development." Surgical Oncology Clinics of North America 18, no. 3 (July 2009): 453–67. http://dx.doi.org/10.1016/j.soc.2009.03.002.

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Ipek, M., A. Ipek, and P. W. Simon. "Molecular markers development and application in garlic." Acta Horticulturae, no. 1297 (November 2020): 653–58. http://dx.doi.org/10.17660/actahortic.2020.1297.86.

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Gitler, Aaron D., Min Min Lu, Yue Qin Jiang, Jonathan A. Epstein, and Peter J. Gruber. "Molecular markers of cardiac endocardial cushion development." Developmental Dynamics 228, no. 4 (November 24, 2003): 643–50. http://dx.doi.org/10.1002/dvdy.10418.

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Soriano, Jose Miguel. "Molecular Marker Technology for Crop Improvement." Agronomy 10, no. 10 (September 24, 2020): 1462. http://dx.doi.org/10.3390/agronomy10101462.

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Since the 1980s, agriculture and plant breeding have changed with the development of molecular marker technology. In recent decades, different types of molecular markers have been used for different purposes: mapping, marker-assisted selection, characterization of genetic resources, etc. These have produced effective genotyping, but the results have been costly and time-consuming, due to the small number of markers that could be tested simultaneously. Recent advances in molecular marker technologies such as the development of high-throughput genotyping platforms, genotyping by sequencing, and the release of the genome sequences of major crop plants open new possibilities for advancing crop improvement. This Special Issue collects sixteen research studies, including the application of molecular markers in eleven crop species, from the generation of linkage maps and diversity studies to the application of marker-assisted selection and genomic prediction.

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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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Xuan, Zhou, Hong Dao Zhang, Zheng Hong Li, Cheng Zhang, Ji Lin Li, and Yan Ming Zhang. "The Role of Molecular Marker in Development of Plant Genetic Resources." Advanced Materials Research 955-959 (June 2014): 855–58. http://dx.doi.org/10.4028/www.scientific.net/amr.955-959.855.

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Plants are fundamental to life, being the basis of our food production and an essential part of the global ecosystem on which life on earth depends. Plant genetic resources include primitive forms of cultivated plant species and landraces, modern cultivars, breeding lines and genetic stocks, weedy types and related wild species, which provide the building blocks that, allow classical plant breeders and biotechnologists to develop new commercial varieties and other biological products. Detection and analysis of genetic variation can help us to understand the molecular basis of various biological phenomena in plants. Molecular markers for the detection and exploitation of DNA polymorphism is one of the most significant developments in the field of molecular genetics. The presence of various types of molecular markers, and differences in their principles, methodologies, and applications require careful consideration in choosing one or more of such methods. This article describes the advances of molecular marker in present, introduces the molecular basis in development of plant genetic resources and perspectives the important role of molecular marker in development of plant genetic resources in the future.

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Guo, Baozhu, Manish K. Pandey, Guohao He, Xinyou Zhang, Boshou Liao, Albert Culbreath, Rajeev K. Varshney, Victor Nwosu, Richard F. Wilson, and H. Thomas Stalker. "Recent Advances in Molecular Genetic Linkage Maps of Cultivated Peanut." Peanut Science 40, no. 2 (July 1, 2013): 95–106. http://dx.doi.org/10.3146/ps13-03.1.

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ABSTRACT The competitiveness of peanuts in domestic and global markets has been threatened by losses in productivity and quality that are attributed to diseases, pests, environmental stresses and allergy or food safety issues. Narrow genetic diversity and a deficiency of polymorphic DNA markers severely hindered construction of dense genetic maps and quantitative trait loci (QTL) mapping in order to deploy linked markers in marker-assisted peanut improvement. The U.S. Peanut Genome Initiative (PGI) was launched in 2004, and expanded to a global effort in 2006 to address these issues through coordination of international efforts in genome research beginning with molecular marker development and improvement of map resolution and coverage. Ultimately, a peanut genome sequencing project was launched in 2012 by the Peanut Genome Consortium (PGC). We reviewed the progress for accelerated development of peanut genomic resources in peanut, such as generation of expressed sequenced tags (ESTs) (252,832 ESTs as December 2012 in the public NCBI EST database), development of molecular markers (over 15,518 SSRs), and construction of peanut genetic linkage maps, in particular for cultivated peanut. Several consensus genetic maps have been constructed, and there are examples of recent international efforts to develop high density maps. An international reference consensus genetic map was developed recently with 897 marker loci based on 11 published mapping populations. Furthermore, a high-density integrated consensus map of cultivated peanut and wild diploid relatives also has been developed, which was enriched further with 3693 marker loci on a single map by adding information from five new genetic mapping populations to the published reference consensus map.

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Fang, D. Q., C. T. Federici, and M. L. Roose. "Development of molecular markers linked to a gene controlling fruit acidity in citrus." Genome 40, no. 6 (December 1, 1997): 841–49. http://dx.doi.org/10.1139/g97-809.

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Fruit juice pH, titratable acidity, or citric acid content was measured in 6 populations derived from an acidless pummelo (pummelo 2240) (Citrus maxima (Burm.) Merrill). The acidless trait in pummelo 2240 is controlled by a single recessive gene called acitric. Using bulked segregant analysis, three RAPD markers were identified as linked to acitric. RAPD marker OpZ20410, which mapped 1.2 cM from acitric, was cloned and sequenced, and a sequence characterized amplified region (SCAR) marker (SCZ20) was developed. The SCZ20-410 marker allele that is linked to the acitric allele occurs only in pummelo 2240 and other pummelos, and therefore, this SCAR marker should be useful as a dominant or codominant marker for introgressing acitric into mandarins and other citrus species. Using the cloned OpZ20410 band as a hybridization probe revealed a codominant RFLP marker called RFZ20 that mapped 1.2 cM from acitric. Progeny homozygous (acac) for the acitric allele had citric acid content below 10 μM, the minimum level detectable by high pressure liquid chromatography. The citric acid content of fruit juice from progeny predicted to be heterozygous (Acac) for acitric by the above markers was about 30% lower than that of juice from individuals predicted to be homozygous (AcAc) for the normal acid allele. Markers OpZ20410, SCZ20, and RFZ20 were highly polymorphic among 59 citrus accessions, and using one or more of these markers would allow citrus breeders to select seedling progeny heterozygous for acitric in nearly all crosses between pummelo 2240 or its offspring and other citrus genotypes.Key words: Citrus, fruit acidity, citric acid, RAPD, SCAR, RFLP.

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Hu, Jing, Xiaoke Hu, Qian Zhang, Jinhu Zhang, Baoli Fan, and Qiushi Yu. "Development of SSR molecular markers for Allium mongolicum." Genes & Genomics 39, no. 12 (August 8, 2017): 1387–94. http://dx.doi.org/10.1007/s13258-017-0601-0.

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Zhang, Xinzhong, Chao Lu, Rugen Xu, and Meixue Zhou. "Development of molecular markers linked to barley heterosis." Euphytica 203, no. 2 (October 8, 2014): 309–19. http://dx.doi.org/10.1007/s10681-014-1265-3.

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Periyannan, Sambasivam K., Zia U. Qamar, Urmil K. Bansal, and Harbans S. Bariana. "Development and validation of molecular markers linked with stem rust resistance gene Sr13 in durum wheat." Crop and Pasture Science 65, no. 1 (2014): 74. http://dx.doi.org/10.1071/cp13325.

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Stem rust resistance gene Sr13, found frequently in tetraploid wheats, was tested effective against Puccinia graminis f. sp. tritici pathotype Ug99 (TTKSK) and its derivatives. It remains a candidate for developing new cultivars with diverse combinations of stem rust resistance genes. To combine Sr13 with other genes that produce a similar phenotype, linked markers would be required. We used the AFLP approach to identify markers linked closely with Sr13. The STS marker AFSr13, derived from an AFLP fragment, mapped at 3.4–6.0 cM proximal to Sr13 across three mapping populations. Marker dupw167, previously reported to be linked with Sr13, mapped 2.3–5.7 cM distal to Sr13 in four F3 populations. Marker gwm427 mapped proximal to AFSr13 in two populations, and these markers were monomorphic on one population each. The map order dupw167–Sr13–AFSr13–gwm427 was deduced from the recombination data. Markers dupw167 and AFSr13 were validated on 21 durum wheat genotypes. Combination of dupw167 and AFSr13 would facilitate marker-assisted selection of Sr13 in segregating populations. At the hexaploid level, only gwm427 showed polymorphism and differentiated the presence of Sr13 in 10 of the 15 backcross derivatives carrying Sr13 from their Sr13-lacking recurrent parents.

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Stevens, Mikel R., Shawn A. Chrisensen, Ammon B. Marshall, JoLynn J. Stevens, Peter Wenzl, Eric Hunter, Jason Carling, and Andrzej Killian. "Molecular Marker Development and High Throughput with Microarrays using Diversity Array Technology (DArT)." HortScience 40, no. 4 (July 2005): 1113D—1114. http://dx.doi.org/10.21273/hortsci.40.4.1113d.

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Recently, a technology known as DArT (diversity array technology) has been developed to increase throughput in marker assisted selection (MAS). DArT utilizes microarray technology as a method to potentially compare thousands of molecular markers in one test to a single DNA sample. We used DArT on two sets of interspecific tomato [Solanum lycopersicum (Fla 7613) × S. pennellii (LA 716 or LA 2963)] segregating populations (BC, F2, and F1). We compared over 300 segregating plants to 3840 random tomato genomic fragments. After the 3840 markers were prepared, it took about 2 weeks of laboratory time to perform the experiments. With experience, this time can be reduced. We identified a total of 654 polymorphic markers usable for developing a DArT tomato genetic map. Depending on the particular cross, 13 to 17 linkage groups were identified (LOD 3) per population. Most recently, the amplified polymorphic DNA (AFLP) technique has been used for rapid genetic mapping of large numbers of anonymous genomic fragments. Besides the additional effort and reagents using AFLPs compared to DArT, a desired AFLP polymorphic band is often difficult to clone and process into a PCR based marker, whereas in DArT all markers are already cloned and immediately available for such experiments. A drawback to DArT is that it requires specialized software and equipment and is technically demanding. However, once the equipment and software are secured, techniques are optimized, and segregating populations developed, marker throughput is increased by orders of magnitude. Although challenging, the application of DArT can dramatically increase MAS throughput, thus facilitating quantitative trait and saturated mapping research.

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Lee, Tong Geon, Reza Shekasteband, Naama Menda, Lukas A. Mueller, and Samuel F. Hutton. "Molecular Markers to Select for the j-2–mediated Jointless Pedicel in Tomato." HortScience 53, no. 2 (February 2018): 153–58. http://dx.doi.org/10.21273/hortsci12628-17.

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The jointless pedicel trait of tomato conferred by the j-2 gene is widely used in processing markets for stem-free removal of fruit to accommodate mechanized harvest. Although current utilization of j-2 for fresh-market tomato breeding is limited, interest in this trait may increase as breeders seek to address high labor costs through the development of mechanically harvestable cultivars for the fresh market. Yet, the introduction of this trait into new market classes heavily relies on phenotypic selection because there are presently no high-throughput methods available to genotype j-2. Reliable, high-throughput molecular markers to genotype the presence/absence of j-2 for selective breeding were developed. The molecular markers described here use the high-resolution DNA melting analysis (HRM) genotyping with single-nucleotide polymorphism (SNP) and derived cleaved amplified polymorphic sequence (dCAPS)–based genotyping. Two separate HRM-based markers target the j-2 on chromosome 12 or a linked sequence region 3.5 Mbp apart from the gene, and a dCAPS marker resides on the latter. We demonstrate the association between each marker and the jointless pedicel phenotype using segregating populations of diverse filial generations in multiple genetic backgrounds. These markers provide a useful resource for marker-assisted selection of j-2 in breeding populations.

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Li, Xiaomei, Dale R. Gardner, Michael H. Ralphs, and Richard R.-C. Wang. "Development of STS and CAPS markers for identification of three tall larkspurs (Delphinium spp.)." Genome 45, no. 2 (April 1, 2002): 229–35. http://dx.doi.org/10.1139/g01-149.

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One cleaved amplified polymorphic sequence (CAPS) and nine sequence tagged site (STS) markers were developed for identifying tall larkspur (Delphinium spp.) plants in three species based on the DNA sequence of known species-specific RAPD markers. Four STS markers were used for identification of Delphinium occidentale, three STS markers for Delphinium barbeyi, and one CAPS and two STS markers for Delphinium glaucum. One hundred sixty-six individual plants collected at 19 locations in the western U.S.A. were tested using the STS and CAPS markers. Over 95% of the D. occidentale plants contained all four D. occidentale specific STS markers, whereas the remaining plants contained three of the four STS markers. Approximately 97% of D. barbeyi plants contained all three D. barbeyi specific STS markers, and the rest had two of the three STS markers. A small percentage of D. barbeyi plants contained one D. occidentale specific STS marker. Hybrid populations were characterized as having more D. occidentale specific than D. barbeyi specific STS markers, suggesting that the three hybrid populations are composed not of F1 hybrid plants of the parental species but of segregating offspring of different generations from original hybrids. This set of STS and CAPS markers for larkspur species should be useful in classification of unknown plant materials and the identification of hybrid populations.Key words: poisonous plants, RAPD, molecular marker, PCR.

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Risliawati, Andari, Eny I. Riyanti, Puji Lestari, Dwinita W. Utami, and Tiur S. Silitonga. "Development of SSR Marker Set to Identify Fourty Two Indonesian Soybean Varieties." Jurnal AgroBiogen 11, no. 2 (August 9, 2016): 49. http://dx.doi.org/10.21082/jbio.v11n2.2015.p49-58.

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Profile of molecular marker can be used for variety identification, genetic purity monitoring of germplasm and additional requirement in proposing intellectual property protection. DNA fingerprinting of soybean had been applied at the ICABIOGRADIAARD since 2004 using simple sequence repeat (SSR) markers which were run automatically by CEQ 8000 Genetic Analyzer platform based on capillary electrophoresis system. This method had produced unique DNA fingerprints of the varieties tested, but the marker set to efficiently identify the varieties had not yet been developed. This study aimed to develop a set of SSR markers as a tool to identify the Indonesian soybean varieties. Fourty two soybean varieties were analyzed using 14 random SSR markersA total of 168 alleles that were obtained from the polymorphism analysis. The average of polymorphic information content (PIC) value observed was 0.7337 per SSR locus. Based on marker reproducibility rate, PIC value, number of rare alleles, frequency of dominant alleles, and percentage of SSR fragment detected by genetic analyzer, we identified five SSR markers i.e. Satt414, Satt147, Satt308, Satt009, and Satt516 as a SSR marker set to be used for soybean variety identification purposes. This marker set was used to develop the identity (ID) of the 42 Indonesian soybean varieties.

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Gonçalves-Vidigal, Maria Celeste, and Luciana Benchimol Rubiano. "Development and application of microsatellites in plant breeding." Crop Breeding and Applied Biotechnology 11, spe (June 2011): 66–72. http://dx.doi.org/10.1590/s1984-70332011000500010.

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Molecular markers are powerful tools for analyzing genome diversity within a species, and to evaluate genetic relationships between individuals and populations. Among them, microsatellites (SSRs) are one of the most important polymorphic markers that can be used effectively to distinguish germplasm accessions. These markers present high informative content due to their codominant inheritance, multiallelism, mendelian pattern and good genome coverage. The enrichment methodology for microsatellite development has a superior efficiency in plants, especially when performed using biotin-labeled microsatellite oligoprobes and streptavidin-coated magnetic beads. The development of EST-SSR markers has become a fast and relatively inexpensive way but it is limited to species for which this type of database exists. Given the high polymorphism level of microsatellites when compared to other markers, SSRs have been used to study population structure, for genetic diversity analysis, genetic mapping and marker assisted selection.

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Kim, Hyun Jung, Jungsu Jung, Myung-Shin Kim, Je Min Lee, Doil Choi, and Inhwa Yeam. "Molecular marker development and genetic diversity exploration by RNA-seq in Platycodon grandiflorum." Genome 58, no. 10 (October 2015): 441–51. http://dx.doi.org/10.1139/gen-2015-0017.

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Platycodon grandiflorum, generally known as the bellflower or balloon flower, is the only species in the genus Platycodon of the family Campanulaceae. Platycodon plants have been traditionally used as a medicinal crop in East Asia for their antiphlogistic, antitussive, and expectorant properties. Despite these practical uses, marker-assisted selection and molecular breeding in platycodons have lagged due to the lack of genetic information on this genus. In this study, we performed RNA-seq analysis of three platycodon accessions to develop molecular markers and explore genetic diversity. First, genic simple sequence repeats (SSRs) were retrieved and compared; dinucleotide motifs were the most abundant repeats (39%–40%) followed by trinucleotide (25%–31%), tetranucleotide (1.5%–1.9%), and pentanucleotide (0.3%–1.0%) repeats. The result of in silico SSR analysis, three SSR markers were detected and showed possibility to distinguish three platycodon accessions. After several filtering procedures, 180 single nucleotide polymorphisms (SNPs) were used to design 40 cleaved amplified polymorphic sequence (CAPS) markers. Twelve of these PCR-based markers were validated as highly polymorphic and utilized to investigate genetic diversity in 21 platycodon accessions collected from various regions of South Korea. Collectively, the 12 markers yielded 35 alleles, with an average of 3 alleles per locus. Polymorphism information content (PIC) values ranged from 0.087 to 0.693, averaging 0.373 per locus. Since platycodon genetics have not been actively studied, the sequence information and the DNA markers generated from our research have the potential to contribute to further genetic improvements, genomic studies, and gene discovery in this genus.

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Li, J., D. L. Klindworth, F. Shireen, X. Cai, J. Hu, and S. S. Xu. "Molecular characterization and chromosome-specific TRAP-marker development for Langdon durum D-genome disomic substitution lines." Genome 49, no. 12 (December 2006): 1545–54. http://dx.doi.org/10.1139/g06-114.

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The aneuploid stocks of durum wheat ( Triticum turgidum L. subsp. durum (Desf.) Husnot) and common wheat ( T. aestivum L.) have been developed mainly in ‘Langdon’ (LDN) and ‘Chinese Spring’ (CS) cultivars, respectively. The LDN-CS D-genome chromosome disomic substitution (LDN-DS) lines, where a pair of CS D-genome chromosomes substitute for a corresponding homoeologous A- or B-genome chromosome pair of LDN, have been widely used to determine the chromosomal locations of genes in tetraploid wheat. The LDN-DS lines were originally developed by crossing CS nulli-tetrasomics with LDN, followed by 6 backcrosses with LDN. They have subsequently been improved with 5 additional backcrosses with LDN. The objectives of this study were to characterize a set of the 14 most recent LDN-DS lines and to develop chromosome-specific markers, using the newly developed TRAP (target region amplification polymorphism)-marker technique. A total of 307 polymorphic DNA fragments were amplified from LDN and CS, and 302 of them were assigned to individual chromosomes. Most of the markers (95.5%) were present on a single chromosome as chromosome-specific markers, but 4.5% of the markers mapped to 2 or more chromosomes. The number of markers per chromosome varied, from a low of 10 (chromosomes 1A and 6D) to a high of 24 (chromosome 3A). There was an average of 16.6, 16.6, and 15.9 markers per chromosome assigned to the A-, B-, and D-genome chromosomes, respectively, suggesting that TRAP markers were detected at a nearly equal frequency on the 3 genomes. A comparison of the source of the expressed sequence tags (ESTs), used to derive the fixed primers, with the chromosomal location of markers revealed that 15.5% of the TRAP markers were located on the same chromosomes as the ESTs used to generate the fixed primers. A fixed primer designed from an EST mapped on a chromosome or a homoeologous group amplified at least 1 fragment specific to that chromosome or group, suggesting that the fixed primers might generate markers from target regions. TRAP-marker analysis verified the retention of at least 13 pairs of A- or B-genome chromosomes from LDN and 1 pair of D-genome chromosomes from CS in each of the LDN-DS lines. The chromosome-specific markers developed in this study provide an identity for each of the chromosomes, and they will facilitate molecular and genetic characterization of the individual chromosomes, including genetic mapping and gene identification.

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Shi, Z. X., X. M. Chen, R. F. Line, H. Leung, and C. R. Wellings. "Development of resistance gene analog polymorphism markers for the Yr9 gene resistance to wheat stripe rust." Genome 44, no. 4 (August 1, 2001): 509–16. http://dx.doi.org/10.1139/g01-028.

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The Yr9 gene, which confers resistance to stripe rust caused by Puccinia striiformis f.sp. tritici (P. s. tritici) and originated from rye, is present in many wheat cultivars. To develop molecular markers for Yr9, a Yr9 near-isogenic line, near-isogenic lines with nine other Yr genes, and the recurrent wheat parent 'Avocet Susceptible' were evaluated for resistance in the seedling stage to North American P. s. tritici races under controlled temperature in the greenhouse. The resistance gene analog polymorphism (RGAP) technique was used to identify molecular markers for Yr9. The BC7:F2 and BC7:F3 progeny, which were developed by backcrossing the Yr9 donor wheat cultivar Clement with 'Avocet Susceptible', were evaluated for resistance to stripe rust races. Genomic DNA was extracted from 203 BC7:F2 plants and used for cosegregation analysis. Of 16 RGAP markers confirmed by cosegregation analysis, 4 were coincident with Yr9 and 12 were closely linked to Yr9 with a genetic distance ranging from 1 to 18 cM. Analyses of nulli-tetrasomic 'Chinese Spring' lines with the codominant RGAP marker Xwgp13 confirmed that the markers and Yr9 were located on chromosome 1B. Six wheat cultivars reported to have 1B/1R wheat-rye translocations and, presumably, Yr9, and two rye cultivars were inoculated with four races of P. s. tritici and tested with 9 of the 16 RGAP markers. Results of these tests indicate that 'Clement', 'Aurora', 'Lovrin 10', 'Lovrin 13', and 'Riebesel 47/51' have Yr9 and that 'Weique' does not have Yr9. The genetic information and molecular markers obtained from this study should be useful in cloning Yr9, in identifying germplasm that may have Yr9, and in using marker-assisted selection for combining Yr9 with other stripe rust resistance genes.Key words: molecular markers, Puccinia striiformis f.sp. tritici, resistance gene analog polymorphism, Triticum aestivum.

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Pardo, J., J. A. Fernández, and L. G. Gómez. "DEVELOPMENT OF MOLECULAR MARKERS FOR ORIGIN DETERMINATION IN SAFFRON." Acta Horticulturae, no. 650 (May 2004): 95–98. http://dx.doi.org/10.17660/actahortic.2004.650.9.

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Pelsey, Frederique, Lucie Schehrer, and Didier Merdinoglu. "DEVELOPMENT OF GRAPEVINE RETROTRANSPOSON-BASED MOLECULAR MARKERS (S-SAP)." Acta Horticulturae, no. 603 (April 2003): 83–87. http://dx.doi.org/10.17660/actahortic.2003.603.7.

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Grover, Atul, and P. C. Sharma. "Development and use of molecular markers: past and present." Critical Reviews in Biotechnology 36, no. 2 (November 28, 2014): 290–302. http://dx.doi.org/10.3109/07388551.2014.959891.

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Gupta, Pushpendra K., Harindra S. Balyan, Rajeev K. Varshney, and Kulvinder S. Gill. "Development and use of molecular markers for crop improvement." Plant Breeding 132, no. 5 (October 2013): 431–32. http://dx.doi.org/10.1111/pbr.12110.

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Ulrich, Detlef, and Frank Dunemann. "Towards the development of molecular markers for apple volatiles." Flavour and Fragrance Journal 27, no. 4 (May 28, 2012): 286–89. http://dx.doi.org/10.1002/ffj.3097.

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Hue, Isabelle. "Determinant molecular markers for peri-gastrulating bovine embryo development." Reproduction, Fertility and Development 28, no. 2 (2016): 51. http://dx.doi.org/10.1071/rd15355.

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Peri-gastrulation defines the time frame between blastocyst formation and implantation that also corresponds in cattle to elongation, pregnancy recognition and uterine secretion. Optimally, this developmental window prepares the conceptus for implantation, placenta formation and fetal development. However, this is a highly sensitive period, as evidenced by the incidence of embryo loss or early post-implantation mortality after AI, embryo transfer or somatic cell nuclear transfer. Elongation markers have often been used within this time frame to assess developmental defects or delays, originating either from the embryo, the uterus or the dam. Comparatively, gastrulation markers have not received great attention, although elongation and gastrulation are linked by reciprocal interactions at the molecular and cellular levels. To make this clearer, this peri-gastrulating period is described herein with a focus on its main developmental landmarks, and the resilience of the landmarks in the face of biotechnologies is questioned.

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Fry, Lucia C., Klaus Mönkemüller, and Peter Malfertheiner. "Molecular markers of pancreatic cancer: development and clinical relevance." Langenbeck's Archives of Surgery 393, no. 6 (February 12, 2008): 883–90. http://dx.doi.org/10.1007/s00423-007-0276-0.

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Islam, M. Thoihidul, Mohammad Rashid Arif, and Arif Hasan Khan Robin. "Characterization of blast resistance related protein domains in wheat for molecular marker development." Journal of the Bangladesh Agricultural University 17, no. 2 (June 28, 2019): 161–71. http://dx.doi.org/10.3329/jbau.v17i2.41939.

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Wheat blast is a devastating disease which is baffling scientists from its inception. This study characterized the blast resistance related protein domains with a view to develop molecular markers to identify resistant wheat genotypes against Blast fungus Magnaporthe oryzae. A genome browse analysis detected that the candidate resistance gene against blast could be located in several different chromosomes. An in silico analysis was collected with fifty nucleotide-binding site leucine-rich repeat (NBS-LRR), leucine-rich repeat (LRR), pathogenesis and resistance protein-encoding accessions on the basis of the previous resistance report. The phylogenetic tree of those putative resistance accessions, bearing resistance related protein-encoding domains, showed that an NBS-LRR accession JP957107.1 has 67% similarity with the disease resistance protein domain encoding accession of Brazilian resistant cultivar Thatcher. By contrast, the rice blast resistance Pita gene has 72% similarity with 18 pathogenesis protein domain encoding accessions. Among putative protein domains, disease resistance protein of Thatcher has 78% similarity with two NBS-LRR protein domains AAZ99757.1 and AAZ99757.1. Eighteen microsatellite markers were designed from eighteen putative NBS-LRR protein encoding accessions along with Piz3 marker. The 19 markers were unable to separate resistant and susceptible genotypes. Diffused versus conspicuous bands indicated either presence of insertion/deletion (InDel) or single nucleotide polymorphism (SNP) among wheat genotypes. Detection of InDel or SNP markers is a subject of further investigation. Additional markers are needed to be designed using new NBS-LRR, pathogenesis, coiled-coil (CC), translocated intimin receptor (TIR) resistance protein encoding accessions to find out markers specific for blast resistance. J. Bangladesh Agril. Univ. 17(2): 161–171, June 2019

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Abebe, Alebel Mekuriaw, Jinwoo Choi, Youngjun Kim, Chang-Sik Oh, Inhwa Yeam, Ill-Sup Nou, and Je Min Lee. "Development of diagnostic molecular markers for marker-assisted breeding against bacterial wilt in tomato." Breeding Science 70, no. 4 (2020): 462–73. http://dx.doi.org/10.1270/jsbbs.20027.

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Iakovlev, A. A., A. Volkov, G. Tarasova, and A. Zubova. "P039 New molecular markers of the development of ulcerative colitis." Journal of Crohn's and Colitis 15, Supplement_1 (May 1, 2021): S151. http://dx.doi.org/10.1093/ecco-jcc/jjab076.168.

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Abstract Background The mechanisms of ulcerative colitis (UC) progression require detailed study. Modern achievements of proteomic methods of analysis are ideal for research that is free from hypotheses and allows us to define molecular characteristics of inflammation in colon mucosa of UC patients. Methods The study was comparative cohort with parallel design and included 88 patients (range from 22 to 35 years, 37 men and 51 women): 53 (60.2%) pancolitis and 35 (39.8%) left-sided UC, mild and moderate activity. The control group included 30 healthy individuals. Biosamples of colon mucosa in patients with UC in the active stage and in healthy persons were received by ileocolonoscopy with colon mucosa biopsy. The separation of individual proteins of colon mucosa was based on technologies of IEF, SDS-PAGE, 2DPAGE, by standard sets (MB-HIC C8 Kit, MB-IMAC Cu, MB-Wax Kit, «Bruker», USA). Automated mass spectrometry imaging was performed by MALDI-TOF-MS/MS, Ultraflex II, «Bruker», USA). The data of the molecular interactions and functional features of proteins were received with STRING 10.0 database. Results We identified following functional groups of peptides and proteins in molecular patterns of colon mucosa in UC patients: SMAD family member 2 (SMAD2) activates the transcription of TFG1β, that leads to specific regulation of the CCN2 gene in cells and the development of fibrosis in colon submucosa in UC patients; the stimulation of the expression of apoС-III in affected colon mucosa in UC is associated with the activation of the FOXO1 signaling pathway that supports inflammatory processes in colon mucosa; the second small heat shock protein (HSP2) controls the apoptosis of colonocytes, is also responsible for the mucosa resistance to therapeutic strategies; caspase 8 protects colonocytes from TNFα-induced cell death through a necroptosis mechanism via the blockade of the RIP3 expression; the expression of prohibitin maintains optimal activity of the electronic transport chain through the activity of transcription factor STAT3 and the decrease in the TNFα expression; significant decrease of the PPARγ expression promotes the activation of STAT and AP-1 signaling pathways, which promotes the activity of immune and inflamation processes in colon mucosa and a significant increase in the NF-kB expression in colon mucosa is associated with the activation of TNFα and IL-1, which promotes the increase of immune processes in colon mucosa. Conclusion Bioinformatics analysis revealed the presence of molecules that are the participants in the universal pathways of UC in the active stage, and the molecular interactions involved. This information may provide new avenues for the development of novel diagnostic tests for UC.

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Kole, Pravas Ranjan, Rajeev Singh Rana, and Kangila Venkataramana Bhat. "Optimization of the choice of molecular markers for identification of commercially used rice varieties in India using rapid DNA extraction protocol." Journal of Applied and Natural Science 8, no. 2 (June 1, 2016): 1028–34. http://dx.doi.org/10.31018/jans.v8i2.916.

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The present investigating aimed at the development of molecular marker for cultivar identification and genetic purity assessment. A total of four SSR markers and six SRAP primer were developed for the identification of sixteen different commercial varieties of rice. Traditional practice like grow-out-test based on morphological traits is time consuming and sometimes environmentally influenced. After development of molecular marker, it is using as an alternative to grow â€“out â€“test because of its rapid, accurate detection. We have assessed the potential of simple sequence repeat and sequence-related amplified polymorphism markers in distinguishing rice varieties and four simple sequence repeat markers namely CT-14, CT-25 CT XY-1 and ATC-3 and six sequence-related amplified polymorphism markers primers could be clearly distinguished sixteen commercially cultivar rice varieties. In addition to single markers, itâ€™s better to try with marker combinations, which were amenable for PCR and capable of distinguishing the varieties. Larger differences for each crop were found between cultivers from different seed companies than within the same company. These DNA markers can provide an easier and faster reliable genetic identification of rice cultivars.

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Cheon, Kyeong-Seong, Young-Min Jeong, Hyoja Oh, Jun Oh, Do-Yu Kang, Nyunhee Kim, Eungyeong Lee, et al. "Development of 454 New Kompetitive Allele-Specific PCR (KASP) Markers for Temperate japonica Rice Varieties." Plants 9, no. 11 (November 10, 2020): 1531. http://dx.doi.org/10.3390/plants9111531.

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Temperate japonica rice varieties exhibit wide variation in the phenotypes of several important agronomic traits, including disease resistance, pre-harvest sprouting resistance, plant architecture, and grain quality, indicating the presence of genes contributing to favorable agronomic traits. However, gene mapping and molecular breeding has been hampered as a result of the low genetic diversity among cultivars and scarcity of polymorphic DNA markers. Single nucleotide polymorphism (SNP)-based kompetitive allele-specific PCR (KASP) markers allow high-throughput genotyping for marker-assisted selection and quantitative trait loci (QTL) mapping within closely related populations. Previously, we identified 740,566 SNPs and developed 771 KASP markers for Korean temperate japonica rice varieties. However, additional markers were needed to provide sufficient genome coverage to support breeding programs. In this study, the 740,566 SNPs were categorized according to their predicted impacts on gene function. The high-impact, moderate-impact, modifier, and low-impact groups contained 703 (0.1%), 20,179 (2.7%), 699,866 (94.5%), and 19,818 (2.7%) SNPs, respectively. A subset of 357 SNPs from the high-impact group was selected for initial KASP marker development, resulting in 283 polymorphic KASP markers. After incorporation of the 283 markers with the 771 existing markers in a physical map, additional markers were developed to fill genomic regions with large gaps between markers, and 171 polymorphic KASP markers were successfully developed from 284 SNPs. Overall, a set of 1225 KASP markers was produced. The markers were evenly distributed across the rice genome, with average marker density of 3.3 KASP markers per Mbp. The 1225 KASP markers will facilitate QTL/gene mapping and marker-assisted selection in temperate japonica rice breeding programs.

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Saftic-Pankovic, Dejana. "Application of molecular markers in sunflower breeding." Genetika 39, no. 1 (2007): 1–11. http://dx.doi.org/10.2298/gensr0701001s.

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The results of the application of molecular markers in sunflower breeding obtained in the Institute of Field and Vegetable Crops in the last decade are reviewed. Our results on genetic distance (GD=7-75%) between sunflower inbred lines obtained with RAPD and SSR markers, indicate large variability and provide important information for the selection of parental lines for future crosses. Interspecific hybridization is often used in sunflower breeding. As only some populations of H. giganteus and H. maximiliani are resistant to sunflower diseases, the investigation of genetic variability in/between two species is of interest. The results obtained with SSR markers are presented. The successful hybridization between H. rigidus and H. annuus was confirmed with RAPD markers, and the variability between F1 and BC1F1 plants is discussed. Desirable alleles and haplotypes can be detected with molecular markers both in early phases of plant development and in early phases of the production of improved lines, which reduces or completely eliminates the large number of testing cycles for desirable phenotypes. CAPS markers for resistance to downy mildew, that can be used in marker assisted selection are presented. .

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Lippe, S., M.-S. Roy, C. Perchet, and M. Lassonde. "Electrophysiological Markers of Visuocortical Development." Cerebral Cortex 17, no. 1 (February 1, 2006): 100–107. http://dx.doi.org/10.1093/cercor/bhj130.

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Loxdale, H. D., and G. Lushai. "Molecular markers in entomology." Bulletin of Entomological Research 88, no. 6 (December 1998): 577–600. http://dx.doi.org/10.1017/s0007485300054250.

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AbstractA diverse range of novel molecular (DNA) markers are now available for entomological investigations. Both DNA and protein markers have revolutionized the biological sciences and have enhanced many fields of study, especially ecology. Relative to DNA markers, allozymes are cheap, often much quicker to isolate and develop, even from minute insects (aphids, thrips, parasitic wasps, etc.), and subsequently easy to use. They display single or multi-locus banding patterns of a generally easily interpretable Mendelian nature, and the statistics for their analysis are well established. DNA markers are also suitable for use with small amounts of insect material and can be used with stored, dry or old samples. They have an expanding range of applications, many involving intra- and interspecific discriminations. Like allozymes, they can be single or multilocus, whilst methods for their statistical analysis have recently been published. However, they can be considerably more expensive than allozymes, require more complex preparatory protocols, expensive equipment, may involve lengthy development procedures (e.g. isolating cloned oligonucleotides to develop primers to detect microsatellite regions) and some have complex multi-locus banding patterns which may be of a non-Mendelian nature (e.g. RAPDs, randomly amplified polymorphic DNA), and are in some cases, not easily repeatable. In this review, we hope to inform the general reader about the methodology and scope of the main molecular markers commonly in use, along with brief details of some other techniques which show great promise for entomological studies. Thereafter, we discuss their applications including suitability for particular studies, the methods used to load and run samples, subsequent band detection, band scoring and interpretation, the reliability of particular techniques, the issues of safety involved, cost effectiveness and the statistical analyses utilized.

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Link, C. D., C. W. Ehrenfels, and W. B. Wood. "Mutant expression of male copulatory bursa surface markers in Caenorhabditis elegans." Development 103, no. 3 (July 1, 1988): 485–95. http://dx.doi.org/10.1242/dev.103.3.485.

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In a search for molecular markers of male tail morphogenesis in C. elegans, we have detected two surface markers that are specifically observed in the copulatory bursa of adult males and the vulva of adult hermaphrodites. These markers are defined by binding of a monoclonal antibody (Ab117) and the lectin wheat germ agglutinin (WGA) to live intact animals. Expression of these markers is dependent on sex, stage and anterior-posterior position in the animal. Four of ten mutants with specific defects in bursal development show altered expression of one or both markers. Because the WGA marker can be expressed in intersexual animals with very little bursal development, posterior surface expression of this marker can serve as an indication of subtle masculinization of hermaphrodites. The timing of expression of these markers is not affected by heterochronic mutations that cause larval animals to express adult cuticles or adult animals to express larval cuticles, indicating that marker expression can be uncoupled from general cuticle development. Mutant lin-22 males, which have an anterior-to-posterior transformation of cell fates in the lateral hypodermis, ectopically express both markers in a manner consistent with a ‘posteriorization’ of positional information in these animals. These markers should be useful for the isolation and characterization of mutants defective in bursal and vulval development, sex determination and expression of anterior-posterior positional information.

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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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Striem, M. J., G. Ben-Hayyim, and P. Spiegel-Roy. "Identifying Molecular Genetic Markers Associated with Seedlessness in Grape." Journal of the American Society for Horticultural Science 121, no. 5 (September 1996): 758–63. http://dx.doi.org/10.21273/jashs.121.5.758.

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Excluding seeded offspring at an early stage could be of great value to the breeder concerned with the development of seedless grapes (Vitis vinifera L.). We used the random amplified polymorphic DNA (RAPD) technique to identify molecular genetic markers, analyzing 82 individuals of a progeny resulting from a cross between `Early Muscat' (seeded) and `Flame Seedless'. Seven variables representing the traits of seedlessness were analyzed: mean fresh weight of one seed, total fresh weight of seeds per berry, perception of seed content, seed size categories evaluated visually, degree of hardness of the seed coat, degree of development of the endosperm, and degree of development of the embryo. Among 160 10mer primers, 110 gave distinct band patterns. Twelve markers yielded significant correlations with several subtraits of seedlessness, mainly with the mean fresh weight of one seed and the total fresh weight of seeds per berry. Multiple linear regression analysis resulted in high coefficients, such as R = 0.779 for fresh weight of seeds per berry, when the seven markers were included as independent variables in the model. Most of the seeded individuals, about 44% of the progeny, could be excluded using a two-step process of marker assisted selection.

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Buzás, György Miklós. "History of the development of tumor markers of the digestive tract cancers." Orvosi Hetilap 154, no. 21 (May 2013): 810–19. http://dx.doi.org/10.1556/oh.2013.29611.

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Tumor markers are gene products which signal the occurrence of tumors in different organs as well as their response to surgery and chemotherapy. The discovery of tumor markers occurred after the demonstration of tumor-specific transplantation antigens in chemically or virally induced tumors in syngenic rodents. The history of currently used tumor markers began in the 1940s, the first discovered being alpha-fetoprotein in 1956, followed by that of carcinoembryonic antigen in 1965. Since then the range of tumor markers has widened continously. Their chemical structure and genetics is now well known. Some may play part in tumor growth and development of metastases. The potential uses of tumor markers are general or high risk population screening, adjunct in diagnosis of cancer, preoperative indicator of tumor burden, indicator of therapeutic success, evidence of postoperative recurrences and use in tumor localization. However, there is no ideal tumor marker fulfilling all the criteria. Isotope-labeled anti-carcinoembryonic antigen antibodies and small molecular E-selectin inhibitors could play a role in the molecular radio- and chemotherapy of colon and pancreatic carcinomas. Orv. Hetil., 2013, 154, 810–819.

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Qi, X., and P. Lindhout. "Development of AFLP markers in barley." Molecular and General Genetics MGG 254, no. 3 (April 1997): 330–36. http://dx.doi.org/10.1007/s004380050423.

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Wang, Aoxue, Fanjuan Meng, Xiangyang Xu, Yong Wang, and Jingfu Li. "Development of Molecular Markers Linked to Cladosporium fulvum Resistant Gene Cf-6 in Tomato by RAPD and SSR Methods." HortScience 42, no. 1 (February 2007): 11–15. http://dx.doi.org/10.21273/hortsci.42.1.11.

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Leaf mold, caused by the fungus Cladosporium fulvum, is a serious disease of tomato. In the current study, the main physiological races of C. fulvum collected from three northeastern provinces of China were identified using a set of identification hosts. The results showed that the prevalent pathogenic physiological races were 1.2.3, 1.3, 3, 1.2.3.4, and 1.2.4. F1, F2, and BC1 tomato plants were obtained by crossing C. fulvum-resistant cultivar 03748 carrying the Cf-6 gene and susceptible cultivar 03036. Three 10-mer oligonucleotide random amplified polymorphic DNA (RAPD) primers and two simple sequence repeat (SSR) primers were selected for the further molecular marking analysis after 210 RAPD primers and 50 SSR primers were screened using the bulked segregate analysis method. The polymorphic DNA bands were amplified among parents, 10 F1 plants, 184 F2 plants including 145 resistant plants and 39 sensitive plants using three RAPD primers and two SSR primers so that three RAPD molecular markers and two SSR molecular markers linked to the Cf-6 loci were identified. Three RAPD markers were linked to the Cf-6 resistant locus separated with 8.7 cM, 20.3 cM, and 33.4 cM. Also, one RAPD codominant marker S374619/559 was found. The locations of the two SSR markers were 12.6 cM and 9.7 cM away from the Cf-6 locus. After cloning and sequencing two specific DNA fragments closely connected to the Cf-6 resistant and susceptible alleles respectively, in the RAPD codominant marker S374619/559 and one codominant sequence characterized amplified region marker S674619/559 was converted from RAPD marker S374619/559. In the RAPD marker S374619/559, the length difference of two specific fragments, 619-bp fragment and 559-bp fragment, is the result of one insertion (60 bp) in the 619-bp fragment. These markers will facilitate the selection of resistant tomato germplasm containing the Cf-6 gene and cloning of Cf-6 to breed new C. fulvum resistant tomato cultivars.

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Saal, B., and Günter Wricke. "Development of simple sequence repeat markers in rye (Secale cereale L.)." Genome 42, no. 5 (October 1, 1999): 964–72. http://dx.doi.org/10.1139/g99-052.

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Simple sequence repeats (SSRs), also referred to as microsatellites, represent a PCR-based marker system that has been described in mammalian and plant genomes in recent years. In self-pollinating crop plants they have been shown to be superior to other DNA markers with respect to their level of polymorphism. The technical advantages compared with RFLP markers should also facilitate marker analysis in outcrossing crops like rye. In order to determine the usefulness of SSR markers in rye genetics and breeding, several genomic libraries were screened for (CT/GA)n and (GT/CA)n dinucleotide repeats. It was estimated that these motifs occur at a frequency of one per 268-519 kb. Seventy four out of 182 positive clones were sequenced, and the majority (56.8%) revealed perfect repeats, predominantly of the type (GT/CA)n (61.9%). Fifty seven primer pairs were designed and 27 (47.4%) resulted in specific SSR markers, of which 20 were genetically mapped or assigned to chromosomes or chromosome arms, respectively. The level of polymorphism of four SSR and three RFLP markers was assessed in two open-pollinated rye cultivars. On average, the SSR markers showed larger values of expected heterozygosity (0.62 vs. 0.43) and allele number (5.9 vs. 3.4) than RFLP markers in both cultivars.Key words: simple sequence repeats, microsatellites, mapping, rye, Secale cereale.

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Nuroniah, H. S., O. Gailing, and R. Finkeldey. "Development of SCAR Markers for Species Identification in the Genus Shorea (Dipterocarpaceae)." Silvae Genetica 59, no. 1-6 (December 1, 2010): 249–57. http://dx.doi.org/10.1515/sg-2010-0035.

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AbstractThe development of molecular markers unambiguously distinguishing groups at different taxonomic levels has numerous forensic applications. The identification of tropical timber is of particular interest in this context. We describe the development of SCAR (Sequence Characterized Amplified Region) markers for forensic applications taking the example of two closely related species of the tropical tree family Shorea (Dipterocarpaceae). Two AFLP (Amplified Fragment Length Polymorphism) fragments have been described earlier showing strong differentiation between S. leprosula and S. parvifolia. The AFLP markers were isolated from a gel, re-amplified, cloned and sequenced. Primer sets were designed from these sequences and AFLP fragments were converted into SCAR markers. The SCAR markers and PCR-RFLP markers of the chloroplast region trnLF digested with HinfI were used to screen in total 557 samples of S. parvifolia and S. leprosula from nineteen widely separated populations in Indonesia. Complete genetic differentiation between species was observed based on the putatively nuclear SCAR marker and the PCR-RFLP of the cpDNA region. We found a good agreement between leaf morphological variation and species identification based on both marker types and no indication for interspecific hybridization.

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Majeed, Uzma, Essam Darwish, Shoaib Ur Rehman, and Xueyong Zhang. "Kompetitive Allele Specific PCR (KASP): A Singleplex Genotyping Platform and Its Application." Journal of Agricultural Science 11, no. 1 (December 15, 2018): 11. http://dx.doi.org/10.5539/jas.v11n1p11.

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Single nucleotide polymorphism (SNP) can be detected by mining sequence databases or by using different singleplex or multiplex SNP genotyping platforms. Development of high-throughput genotyping molecular markers can be instrumental towards maximizing genetic gain. In this review we provide an overview of Kompetitive Allele Specific PCR (KASP) genotyping platform requirements and its application that might be helpful in KASP marker development. This literature further illustrates the possibilities to design KASP primers. Several research institutes routinely using KASP platform, producing in excess of humungous data points yearly for breeding cultivars and as well as for medical and commercial purposes. KASP genotyping technology offers cost effectiveness and high throughput molecular marker development platform. Conventional molecular markers can be converted into more robust and high throughput KASP markers. More than 2000 published references clearly show the popularity of KASP technology among the researchers.

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Khan, Muhammad A., Charles-Eric Durel, Brion Duffy, Damien Drouet, Markus Kellerhals, Cesare Gessler, and Andrea Patocchi. "Development of molecular markers linked to the ‘Fiesta’ linkage group 7 major QTL for fire blight resistance and their application for marker-assisted selection." Genome 50, no. 6 (June 2007): 568–77. http://dx.doi.org/10.1139/g07-033.

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A fire blight resistance QTL explaining 34.3%–46.6% of the phenotypic variation was recently identified on linkage group 7 of apple cultivar ‘Fiesta’ (F7). However, markers flanking this QTL were AFLP and RAPD markers unsuitable for marker-assisted selection (MAS). Two RAPD markers bracketing the QTL have been transformed into SCAR (sequence-characterized amplified region) markers, and an SSR marker specific for the region was developed. Pedigree analysis of ‘Fiesta’ with these markers enabled tracking of the F7 QTL allele back to ‘Cox’s Orange Pippin’. Stability of the effect of this QTL allele in different backgrounds was analyzed by inoculating progeny plants of a cross between ‘Milwa’, a susceptible cultivar, and ‘1217’, a moderately resistant cultivar, and a set of cultivars that carry or lack the allele conferring increased fire blight resistance. Progenies and cultivars that carried both markers were significantly more resistant than those that did not carry both markers, indicating high stability of the F7 QTL allele in different backgrounds. This stability and the availability of reproducible markers bracketing the QTL make this locus promising for use in MAS.

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Kawchuk, L. M., J. Hachey, and D. R. Lynch. "Development of sequence characterized DNA markers linked to a dominant verticillium wilt resistance gene in tomato." Genome 41, no. 1 (February 1, 1998): 91–95. http://dx.doi.org/10.1139/g97-111.

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Sequences were determined for codominant RAPD markers closely linked to the Ve locus, a dominant verticillium wilt resistance gene in tomato. Analysis of the sequences linked to Ve and ve revealed a perfectly homologous sequence with a central polymorphic region comprising 79 nucleotide substitutions, insertions, and deletions. Codominant and allele-specific SCARs were developed using conserved and polymorphic sequences linked to the Ve locus. High resolution linkage analysis using F2 progeny segregating for resistance and marker-assisted selection indicated that linkage between the genetic markers and the Ve locus is less than 0.67 ± 0.49 cM. Sequences were useful in determining the molecular structure of a polymorphic genomic region closely linked to the Ve locus and in developing genetic markers that facilitated marker-assisted selection of the resistant, susceptible, heterozygous, and homozygous genotypes.

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Journal articles on the topic 'Development molecular markers'

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