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Achieving Crop Stress Tolerance and Improvement—an Overview of Genomic Techniques. Appl Biochem Biotechnol 2015; 177:1395-408. [DOI: 10.1007/s12010-015-1830-9] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2015] [Accepted: 09/02/2015] [Indexed: 01/09/2023]
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Winter P, Kahl G. Molecular marker technologies for plant improvement. World J Microbiol Biotechnol 2014; 11:438-48. [PMID: 24414752 DOI: 10.1007/bf00364619] [Citation(s) in RCA: 46] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2022]
Abstract
The exploitation of DNA polymorphisms by an ever-increasing number of molecular marker technologies has begun to have an impact on plant genome research and breeding. Restriction fragment length polymorphisms, micro- and mini-satellites and PCR-based approaches are used to determine inter- and intra-specific genetic diversity and construct molecular maps of crops using specially designed mapping populations. Resistance genes and other agronomically important loci are tagged with tightly linked DNA markers and the genes isolated by magabase DNA technology and cloning into yeast artificial chromosomes (YAC). This review discusses some recent developments and results in this field.
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Kuczmog A, Galambos A, Horváth S, Mátai A, Kozma P, Szegedi E, Putnoky P. Mapping of crown gall resistance locus Rcg1 in grapevine. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2012; 125:1565-74. [PMID: 22801874 DOI: 10.1007/s00122-012-1935-2] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/16/2012] [Accepted: 06/28/2012] [Indexed: 05/22/2023]
Abstract
Agrobacteria are efficient plant pathogens. They are able to transform plant cells genetically resulting in abnormal cell proliferation. Cultivars of Vitis vinifera are highly susceptible to many virulent Agrobacterium strains but certain wild Vitis species, including Vitis amurensis have resistant genotypes. Studies of the molecular background of such natural resistance are of special importance, not only for practical benefits in agricultural practice but also for understanding the role of plant genes in the transformation process. Earlier, crown gall resistance from V. amurensis was introgressed into V. vinifera through interspecific breeding and it was shown to be inherited as a single and dominant Mendelian trait. To develop this research further, towards understanding underlying molecular mechanisms, a mapping population was established, and resistance-coupled molecular DNA markers were identified by three different approaches. First, RAPD makers linked to the resistance locus (Rcg1) were identified, and on the basis of their DNA sequences, we developed resistance-coupled SCAR markers. However, localization of these markers in the grapevine genome sequence failed due to their similarity to many repetitive regions. Next, using SSR markers of the grapevine reference linkage map, location of the resistance locus was established on linkage group 15 (LG15). Finally, this position was supported further by developing new chromosome-specific markers and by the construction of the genetic map of the region including nine loci in 29.1 cM. Our results show that the closest marker is located 3.3 cM from the Rcg1 locus that may correspond to 576 kb.
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Affiliation(s)
- Anett Kuczmog
- Faculty of Sciences, Institute of Biology, University of Pécs, Ifjúság u. 6., 7635, Pécs, Hungary
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Aanlysis of short photo-periodic sensitive genic male sterility and molecular mapping of rpms3(t) gene in rice (Oryza sativa L.) using SSR markers. Genes Genomics 2011. [DOI: 10.1007/s13258-010-0074-x] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/16/2022]
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Poompuang S, Hallerman EM. Toward detection of quantitative trait loci and marker‐assisted selection in fish. ACTA ACUST UNITED AC 2008. [DOI: 10.1080/10641269709388600] [Citation(s) in RCA: 27] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022]
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Yoke-Kqueen C, Radu S. Random amplified polymorphic DNA analysis of genetically modified organisms. J Biotechnol 2006; 127:161-6. [PMID: 16860900 DOI: 10.1016/j.jbiotec.2006.06.001] [Citation(s) in RCA: 29] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2006] [Revised: 05/25/2006] [Accepted: 06/06/2006] [Indexed: 11/26/2022]
Abstract
Randomly amplified polymorphic DNA (RAPD) was used to analyzed 78 samples comprises of certified reference materials (soya and maize powder), raw seeds (soybean and maize), processed food and animal feed. Combination assay of two arbitrary primers in the RAPD analysis enable to distinguish genetically modified organism (GMO) reference materials from the samples tested. Dendrogram analysis revealed 13 clusters at 45% similarity from the RAPD. RAPD analysis showed that the maize and soybean samples were clustered differently besides the GMO and non-GMO products.
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Affiliation(s)
- Cheah Yoke-Kqueen
- Department of Biomedical Science, Faculty of Medicine and Health Sciences, Universiti Putra Malaysia, 43400 UPM Serdang, Selangor, Malaysia.
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Linde-Laursen I, Bothmer R. Nucleolar Organization in Three Asiatic Species of Hordeum Section Stenostachys (Poaceae). Hereditas 2004. [DOI: 10.1111/j.1601-5223.1995.00177.x] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022] Open
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Colormapping: a non-mathematical procedure for genetic mapping. ACTA BIOLOGICA HUNGARICA 1998. [DOI: 10.1007/bf03542985] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
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Caetano-Anollés G. Scanning of nucleic acids by in vitro amplification: new developments and applications. Nat Biotechnol 1996; 14:1668-74. [PMID: 9634849 DOI: 10.1038/nbt1296-1668] [Citation(s) in RCA: 24] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
Nucleic acids can be characterized using a variety of "fingerprinting" techniques usually based on nucleic acid hybridization or enzymatic amplification. The scanning of nucleic acids by amplification with arbitrary oligonucleotide primers has become popular because it can generate simple-to-complex patterns from anonymous DNA or RNA templates without requiring prior knowledge of nucleic acid sequence or cloned or characterized probes. Discrete loci are amplified within genomic DNA, DNA complementary to mRNA populations (cDNA), cloned DNA fragments, and even PCR products. The potential and limitations of the various genome scanning techniques, novel improvements, and their recent use in comparative and experimental biology applications, including the analysis of plant and bacterial genomes are discussed.
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Affiliation(s)
- G Caetano-Anollés
- Department of Ornamental Horticulture and Landscape Design, University of Tennessee, Knoxville 37901-1071, USA
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Cho YG, Blair MW, Panaud O, McCouch SR. Cloning and mapping of variety-specific rice genomic DNA sequences: amplified fragment length polymorphisms (AFLP) from silver-stained polyacrylamide gels. Genome 1996; 39:373-8. [PMID: 8984005 DOI: 10.1139/g96-048] [Citation(s) in RCA: 69] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/03/2023]
Abstract
An efficient technique for cloning DNA from silver-stained denaturing polyacrylamide gels was developed to allow the isolation of specific bands obtained from selective restriction fragment amplification (SRFA). This method proved as reliable as cloning radioactively labelled SRFA bands from the same gels. Rice DNA was used as a template, both with and without [32P]dCTP, using the same PCR profiles. Amplified products were separated using denaturing polyacryamide gel electrophoresis and visualized either by silver staining of gels or by autoradiography of 32P-labelled products. We cloned specific polymorphic SRFA bands directly from the denaturing polyacrylamide gels with one round of PCR amplification and confirmed that the sequences of the bands from silver-stained gels were identical to the corresponding 32P-labelled bands. The bands that were chosen represented amplified fragment length polymorphisms (AFLPs) between japonica and indica rice varieties. We studied the ability of two cloned AFLP bands to serve as heritable genetic markers by mapping them as RFLPs in an interspecific rice population and found that they represented single-copy DNA at unique loci in the rice genome.
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Affiliation(s)
- Y G Cho
- Department of Plant Breeding, Cornell University, Ithaca, NY 14853, U.S.A
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Cifarelli RA, Gallitelli M, Cellini F. Random amplified hybridization microsatellites (RAHM): isolation of a new class of microsatellite-containing DNA clones. Nucleic Acids Res 1995; 23:3802-3. [PMID: 7479019 PMCID: PMC307288 DOI: 10.1093/nar/23.18.3802] [Citation(s) in RCA: 60] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/25/2023] Open
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Caetano-Anollés G, Callahan LM, Williams PE, Weaver KR, Gresshoff PM. DNA amplification fingerprinting analysis of bermudagrass (Cynodon): genetic relationships between species and interspecific crosses. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 1995; 91:228-35. [PMID: 24169768 DOI: 10.1007/bf00220882] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/08/1994] [Accepted: 02/03/1995] [Indexed: 05/17/2023]
Abstract
We have used DNA amplification fingerprinting (DAF) to study the genetic variation of bermudagrass (Cynodon) species and cultivars of interspecific crosses that exhibit leaf-blade textural characteristics ranging from coarse to fine. Arbitrary octamer primers produced complex and reproducible amplification profiles with high levels of polymorphic DNA. Phylogenetic analysis using parsimony (PAUP) and unweighted pair group cluster analysis using arithmetic means (UPGMA) grouped 13 bermudagrass cultivars into several clusters, including one containing the African-type bermudagrasses (C. transvaalensis) and another containing the common-type bermudagrasses (C. dactylon). The latter group included C. magennissii ('Sunturf') and a interspecific C. transvaalensisxC. dactylon cross ('Midiron'), 2 cultivars that exhibited leaf textural characteristics closer to the common-types. All other C. transvaalensisxC. dactylon crosses grouped between the African and common types. An extended screen of 81 octamer primers was needed to separate cultivar 'Tifway' from the irradiation-induced mutant 'Tifway II'. The use of either template endonuclease digestion prior to amplification or arbitrary mini-hairpin primers increased detection of polymorphic DNA and simplified the task of distinguishing these closely related cultivars. Alternatively, the use of capillary electrophoresis (CE) resolved fingerprints adequately and detected products with high sensitivity, thereby promising to increase throughput and the detection of polymorphic DNA. When used to fingerprint samples from commercial sources, DAF identified bermudagrass plant material on the basis of unique reference profiles generated with selected primers. DAF represents an excellent technique for bermudagrass cultivar verification, seed certification, varietal protection, and for the identification of mistakes in plantings, mislabeled plant materials, and contamination or substitutions of sod fields.
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Affiliation(s)
- G Caetano-Anollés
- Plant Molecular Genetics, Institute of Agriculture and Center for Legume Research, The University of Tennessee, 37901-1071, Knoxville, TN, USA
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Mohan D, Rao KB, Dixit A, Ali S. Assessment of amplicons in the DNA from boiled tissue by PCR and AP-PCR amplification. GENETIC ANALYSIS : BIOMOLECULAR ENGINEERING 1995; 12:57-62. [PMID: 7648472 DOI: 10.1016/1050-3862(95)00103-4] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/26/2023]
Abstract
Polymerase chain reaction (PCR) is a technique sensitive enough to amplify small DNA fragments a billion-fold. The generation of amplicons either by PCR with a set of oligo primers or by arbitrarily primed AP-PCR with a single oligonucleotide primer is based on the availability of intact template and priming sites. With these approaches, it is possible to generate specific and random amplicons to assess the extent of damage to DNA caused by any of the physical, chemical, or environmental factors. We report the amplification of sex chromosome and autosome specific loci in the buffalo (Bubalus bubalis) genome by symmetrical and AP-PCR performed on DNA samples isolated from the muscle tissues that were boiled (treated) for different lengths of time. No difference was noticed in the amplification profile of DNA cooked for various lengths of time. However, after HinfI treatment, AP-PCR amplification of these DNAs revealed more bands on agarose gel than unrestricted samples. The successful amplification of the DNA samples isolated from the boiled tissues is attributed to the intactness of the amplicons. This suggests that despite storage for more than a year and subsequent heat treatment to the muscle tissues, the DNA remains a good substrate for PCR and AP-PCR amplification. Relevance of this work in the context of DNA probe technology is discussed.
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Affiliation(s)
- D Mohan
- National Institute of Immunology, Aruna Asaf Ali Marg, New Delhi, India
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Caetano-Anollés G. MAAP: a versatile and universal tool for genome analysis. PLANT MOLECULAR BIOLOGY 1994; 25:1011-1026. [PMID: 7919212 DOI: 10.1007/bf00014674] [Citation(s) in RCA: 22] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/22/2023]
Abstract
Multiple arbitrary amplicon profiling (MAAP) uses one or more oligonucleotide primers (> or = 5 nt) of arbitrary sequence to initiate DNA amplification and generate characteristic fingerprints from anonymous genomes or DNA templates. MAAP markers can be used in general fingerprinting as well as in mapping applications, either directly or as sequence-characterized amplified regions (SCARs). MAAP profiles can be tailored in the number of monomorphic and/or polymorphic products. For example, multiple endonuclease digestion of template DNA or the use of mini-hairpin primers can enhance detection of polymorphic DNA. Comparison of the expected and actual number of amplification products produced with primers differing in length, sequence and GC content from templates of varying complexity reveal severe departures from theoretical formulations with interesting implications in primer-template interaction. Extensive primer-template mismatching can occur when using templates of low complexity or long primers. Primer annealing and extension appears directed by an 8 nt 3'-terminal primer domain, requires sites with perfect homology to the first 5-6 nt fom the 3' terminus, and involves direct physical interaction between amplicon annealing sites.
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Affiliation(s)
- G Caetano-Anollés
- Institute of Agriculture, University of Tennessee, Knoxville 37901-1071
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Caetano-Anollés G, Gresshoff PM. DNA amplification fingerprinting using arbitrary mini-hairpin oligonucleotide primers. BIO/TECHNOLOGY (NATURE PUBLISHING COMPANY) 1994; 12:619-23. [PMID: 7764952 DOI: 10.1038/nbt0694-619] [Citation(s) in RCA: 25] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/27/2023]
Abstract
The enzymatic amplification of DNA directed by very short oligonucleotides of arbitrary sequence produces complex DNA profiles useful for genome analysis and identity testing. Mini-hairpins harboring a "core" arbitrary sequence at the 3' terminus primed the amplification of a wide range of templates ranging from plasmid DNA to plant and animal genomes. Primer core regions of only 3 nucleotides produced complex fingerprints, but the hairpin sequence also influenced the amplification reaction. Oligonucleotide substitution with degenerate bases tailored the complexity of fingerprint patterns. Simulation studies of the amplification of plasmids pUC18 and pBR322 using primers with short arbitrary cores allowed assignment of amplification products to expected regions and revealed physical interaction between annealing sites during amplification of first-round products. Mini-hairpin primers can increase detection of polymorphic DNA, and be used to study subgenomic fragments like yeast artificial chromosomes (YACs), cloned DNA and PCR products.
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Affiliation(s)
- G Caetano-Anollés
- Institute of Agriculture, University of Tennessee, Knoxville 37901-1071
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DNA amplification fingerprinting: A general tool with applications in breeding, identification and phylogenetic analysis of plants. ACTA ACUST UNITED AC 1994. [DOI: 10.1007/978-3-0348-7527-1_2] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register]
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17
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Caetano-Anollés G. Amplifying DNA with arbitrary oligonucleotide primers. PCR METHODS AND APPLICATIONS 1993; 3:85-94. [PMID: 8268791 DOI: 10.1101/gr.3.2.85] [Citation(s) in RCA: 215] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/29/2023]
Affiliation(s)
- G Caetano-Anollés
- Institute of Agriculture, University of Tennessee, Knoxville 37901-1071
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