Recognizing the enormous potential of DNA markers in plant breeding, many agricultural research centers and plant breeding institutes have adopted the capacity for marker development and marker-assisted selection (MAS). However, due to rapid developments in marker technology, statistical methodology for identifying quantitative trait loci (QTLs) and the jargon used by molecular biologists, the utility of DNA markers in plant breeding may not be clearly understood by non-molecular biologists. This review provides an introduction to DNA markers and the concept of polymorphism, linkage analysis and map construction, the principles of QTL analysis and how markers may be applied in breeding programs using MAS. This review has been specifically written for readers who have only a basic knowledge of molecular biology and/or plant genetics. Its format is therefore ideal for conventional plant breeders, physiologists, pathologists, other plant scientists and students.

/pdf/an-introduction-to-markers-quantitative-trait-loci-qtl-35ykqmequ8.pdf

An introduction to markers, quantitative trait loci (QTL) mapping and marker-assisted selection for crop improvement: The basic concepts

In order to assess the feasibility of using microsatellites as markers in plant genetics, a survey of published DNA sequence data for presence, abundance and ubiquity in higher plants of all types of dinucleotide and trinucleotide repeats with a minimum number of 10 and 7 units, respectively, was conducted. This search revealed that such microsatellites are frequent and widely distributed; they were uncovered in 34 species, with a frequency of one every 50 kb. AT repeats were by far the most frequently observed class of dinucleotide microsatellites, whereas AC/TG repeats, which are common in animals, were observed only once. TAT repeats prevailed among trinucleotides. Polymerase chain reaction amplification of (AT)n and (TAT)n microsatellites in soybean (Glycine max (L.) Merr.) revealed that they are highly polymorphic, as a consequence of length variation, somatically stable and inherited in a co-dominant Mendelian manner. The abundance and amount of information derived from such markers, together with the ease by which they can be identified, make them ideal markers for plant genetic linkage and physical mapping, population studies and varietal identification.

https://onlinelibrary.wiley.com/doi/pdf/10.1046/j.1365-313X.1993.t01-9-00999.x

PCR-amplified microsatellites as markers in plant genetics.

NAC transcription factors are one of the largest families of transcriptional regulators in plants, and members of the NAC gene family have been suggested to play important roles in the regulation of the transcriptional reprogramming associated with plant stress responses. A phylogenetic analysis of NAC genes, with a focus on rice and Arabidopsis, was performed. Herein, we present an overview of the regulation of the stress responsive NAC SNAC/(IX) group of genes that are implicated in the resistance to different stresses. SNAC factors have important roles for the control of biotic and abiotic stresses tolerance and that their overexpression can improve stress tolerance via biotechnological approaches. We also review the recent progress in elucidating the roles of NAC transcription factors in plant biotic and abiotic stresses. Modification of the expression pattern of transcription factor genes and/or changes in their activity contribute to the elaboration of various signaling pathways and regulatory networks. However, a single NAC gene often responds to several stress factors, and their protein products may participate in the regulation of several seemingly disparate processes as negative or positive regulators. Additionally, the NAC proteins function via auto-regulation or cross-regulation is extensively found among NAC genes. These observations assist in the understanding of the complex mechanisms of signaling and transcriptional reprogramming controlled by NAC proteins.

/pdf/roles-of-nac-transcription-factors-in-the-regulation-of-52iqess6kd.pdf

Roles of NAC transcription factors in the regulation of biotic and abiotic stress responses in plants

We report the sequences of 17 primer pairs of microsatellite loci, which we have cloned and sequenced from two genomic libraries of peach [Prunus persica (L) Batsch] ‘Redhaven’, enriched for AC/GT and AG/CT repeats respectively. For ten of these microsatellite loci we were able to demonstrate Mendelian inheritance in a segregating back-cross population; the remainder did not segregate. The polymorphism of the microsatellites was evaluated in a panel of ten peach genotypes, including true-to-type peaches, nectarines and one canning-peach. Fifteen microsatellites (88%) were polymorphic showing 2–4 alleles each. The mean heterozygosity, averaged over all loci, was 0.32 and significantly higher than that reported in the literature for isozymes and molecular markers, such as RFLPs and RAPDs. We have also assayed the cross-species transportability and found that ten microsatellite (59%) gave apparently correct amplification in all Prunus species surveyed, namely P. domestica (European plum), P. salicina (Japanese plum), P. armeniaca (apricot), P. dulcis (almond), P. persica var. vulgaris (peach), P. persica var. laevis (nectarine), P. avium (sweet cherry) and P. cerasus (sour cherry), with three of them also being amplified in Malus (apple). The remaining microsatellites gave less-extensive amplification. Because of their appreciable polymorphism and wide cross-species transportability, most of these new markers can be integrated into the linkage maps which are currently being constructed in peach, as well as in other stone fruit crops, such as almond, apricot, cherry and plum.

AC/GT and AG/CT microsatellite repeats in peach [Prunus persica (L) Batsch]: isolation, characterisation and cross-species amplification in Prunus.

PREFACE REPETITIVE DNA: AN IMPORTANT SOURCE OF VARIATION IN EUKARYOTIC GENOMES Categories of DNA Sequence Mutations Tandem-Repetitive DNA: The Biology of Mini- and Microsatellites Minisatellites Microsatellites Transposable Elements Class I Transposons Class II Transposons Unclassified Transposons Transposons and Genome Evolution Transposons as Molecular Markers DETECTING DNA VARIATION BY MOLECULAR MARKERS Properties of Molecular Markers Traditional Marker Systems Protein Markers and Allozymes DNA Sequencing Restriction Fragment Length Polymorphism (RFLP) Analysis The PCR Generation: Molecular Markers Based on In Vitro DNA Amplification Principle of the PCR Cleaved Amplified Polymorphic Sequences PCR with Arbitrary Primers: RAPD and Its Variants Microsatellites Inter-Repeat PCR DNA Profiling of Genic Regions: Resistance Gene Analog Polymorphism, Sequence-Related Amplified Polymorphism, and Target Region Amplification Polymorphism Hybridization of Microsatellites to RAPD and MP-PCR Products AFLP Analysis and Its Variants Single-Strand Conformation Polymorphism Analysis and Related Techniques Miscellaneous Techniques LABORATORY EQUIPMENT METHODOLOGY Safety Precautions Isolation, Purification, and Quantitation of Plant DNA Collection and Preservation of Plant Tissue in the Field Plant DNA Extraction: General Considerations CTAB Protocol I CTAB Protocol II SDS-Potassium Acetate Protocol DNA Preparation via Nuclei Quantitation of DNA Basic Molecular Techniques Restriction of DNA Polymerase Chain Reaction DNA Sequencing Agarose Gel Electrophoresis PAA Gel Electrophoresis Detection of DNA in Gels Gel Drying Southern Blotting Generation of Radiolabeled Probes, Primers, and PCR Products Blot Hybridization Signal Detection PCR with Arbitrary Primers Standard RAPD Protocol Influence of Reaction Conditions and Components Modifications Microsatellite-Primed PCR Standard Protocol of Microsatellite-Primed PCR Influence of Reaction Conditions and Components Modifications PCR and Hybridization: Combinatory Techniques Assessing the Genomic Copy Number of PCR Amplicons Testing the Homology of Comigrating Bands Random Amplified Polymorphic Microsatellites Amplified Fragment Length Polymorphism Standard AFLP Protocol Using Radioisotopes AFLP Protocol Using Fluorescence-Labeled Primers Selective Amplification of Microsatellite Polymorphic Loci and Microsatellite AFLP Protocols Technical Aspects and Modifications Robustness and Reproducibility Generation and Analysis of Microsatellite Markers Microsatellite Analysis Using Radioisotopes Microsatellite Analysis Using Fluorochromes Technical Aspects and Modifications Generating Microsatellite Markers Without Cloning Microsatellite Cloning CAPS Analysis of cpDNA and mtDNA Standard CAPS Protocol Choice of CAPS Primers EVALUATION OF MOLECULAR MARKER DATA Robustness and Reproducibility Reliability Band Homology Band Linkage and Neutrality Fragment Sizing and Matching General Precautions Equipment Multilocus vs. Single-Locus Approaches Multilocus Markers Single-Locus Markers and Polyploids Band Sharing and Genetic Distances Coefficients of Similarity Dissimilarity Coefficients and Genetic Distances Identity and Uniqueness Clonal Structure Ordination, Clustering, and Dendrograms Ordination Techniques Construction of Dendrograms Population Genetic Analysis Measures of Variation Genetic Differentiation between Populations Genetic Distances between Populations Inbreeding Coefficient and Mating Systems Estimation of Relatedness and Paternity Testing Migration and Hybridization Gene Flow, Isolation-by-Distance, and Spatial Structure Phylogeography and Nested Clade Analysis Statistical Testing of Hypotheses: Analytical and Computational Methods APPLICATIONS OF DNA FINGERPRINTING IN PLANT SCIENCES A Brief History of DNA Fingerprinting Minisatellite and Oligonucleotide DNA Probes Detect Genetic Variation PCR-Based Methods Enter the Stage Microsatellite DNA Analyses Yield Codominant Markers Universal Organellar DNA Primers Produce Uniparental Markers Genotype Identification Individual-Specific DNA Fingerprints Cultivar Identification In Vitro-Propagated Plant Material and Somaclonal Variation Sports and Other Mutants Genetic Diversity Variation and Relatedness among Cultivars Analysis of Population Genetic Diversity and Its Distribution Hybridization and Introgression Plant Conservation Germplasm Characterization and Preservation Plant Taxonomy and Systematics Taxonomic Relationships Revealed by Multilocus DNA Methods Microsatellite Markers in Taxonomic Studies Taxonomic Consequences from DNA Profiling Data Phylogeography Phylogeography Based on cpDNA Phylogeography Based on Nuclear Genes LINKAGE ANALYSIS AND GENETIC MAPS Generating High-Density Genetic Maps Selection of Parent Plants Mapping Population Linkage Analysis The Genetic Map Cytogenetic Maps Genetic vs. Physical Maps Synteny: The Comparative Analysis of Genomes Marker-Assisted Selection Molecular Markers and Positional Cloning WHICH MARKER FOR WHAT PURPOSE: A COMPARISON Morphological Characters and Allozymes vs. DNA Markers Different Kinds of DNA Markers Discriminatory Power Genetic Distances Within- and Among-Population Variation Gene Tagging and Genetic Linkage Mapping Costs Conclusions FUTURE PROSPECTS: SNIPS AND CHIPS FOR DNA AND RNA PROFILING Single-Nucleotide Polymorphisms What Is a SNiP SNP Discovery DNA Microarrays Expression Profiling and Expression Markers APPENDIX 1: PLANT DNA ISOLATION PROTOCOLS APPENDIX 2: SUPPLIERS AND SELLERS OF REAGENTS AND EQUIPMENT APPENDIX 3: COMPUTER PROGRAMS DEALING WITH THE EVALUATION OF DNA SEQUENCE VARIATION AND MOLECULAR MARKER DATA APPENDIX 4: WEB PAGES OF INTEREST REFERENCES INDEX

DNA fingerprinting in plants: principles, methods, and applications

The poor definition of variation in the ascochyta blight fungus (Ascochyta rabiei) has historically hindered breeding for resistance to the chickpea (Cicer arietinum L.) blight disease in West Asia and North Africa. We have employed 14 RAPD markers and an oligonucleotide probe complementary to the microsatellite sequence (GATA)4 to construct a genotype-specific DNA fragment profile from periodically sampled Syrian field isolates of this fungus. By using conventional pathogenicity tests and genome analysis with RAPD and microsatellite markers, we demonstrated that the DNA markers distinguish variability within and among the major pathotypes of A. rabiei and resolved each pathotypes into several genotypes. The genetic diversity estimate based on DNA marker analysis within pathotypes was highest for the least-aggressive pathotype (pathotype I), followed by the aggressive (pathotype II) and the most-aggressive pathotype (pathotype III). The pair-wise genetic distance estimated for all the isolates varied from 0.00 to 0.39, indicating a range from a clonal to a diverse relationship. On the basis of genome analysis, and information on the spatial and temporal distribution of the pathogen, a general picture of A. rabiei evolution in Syria is proposed.

Genotyping with RAPD and microsatellite markers resolves pathotype diversity in the ascochyta blight pathogen of chickpea

A set of 12 randomly selected (TAA)n microsatellite loci of the cultivated chickpea (Cicer arietinum L.) were screened in a worldwide sample comprising 72 landraces, four improved cultivars and two wild species of the primary gene pool (C. reticulatum and C. echinosperum) to determine the level and pattern of polymorphism in these populations. A single fragment was amplified from all the accessions with each of 12 sequence-tagged microsatellite site markers, except for one locus where no fragment was obtained from either of the two wild species. There was a high degree of intraspecific polymorphism at these microsatellite loci, although isozymes, conventional RFLPs and RAPDs show very little or no polymorphism. Overall, the repeat number at a locus (excluding null alleles) ranged from 7 to 42. The average number of alleles per locus was 14.1 and the average genetic diversity was 0.86. Based on the estimates obtained, 11 out of the 12 frequency distributions of alleles at the loci tested can be considered to be non-normal. A significant positive correlation between the average number of repeats (size of the locus) and the amount of variation was observed, indicating that replication slippage may be the molecular mechanism involved in generation of variability at the loci. A comparison between the infinite allele and stepwise mutation models revealed that for 11 out of the 12 loci the number of alleles observed fell in between the values predicted by the two models. Phylogenetic analysis of microsatellite polymorphism in C. arietinum showed no relationship between accession and geographic origin, which is compatible with the recent expansion of this crop throughout the world.

Allelic variation at (TAA)n microsatellite loci in a world collection of chickpea (Cicer arietinum L.) germplasm.

Polymorphic simple GATA/GACA repeats in plant genomes.

Synthetic oligonucleotides complementary to simple repetitive DNA sequences were used to detect inter- and intra-specific polymorphisms in a leguminous crop plant (chickpea, Cicer arietinum) and its wild relatives. All the investigated repetitive motifs [(GACA)4, (GATA)4, (GTG)5, (CA)8, (TCC)5, (GGAT)4, and (AGTTT)4] were abundantly present and polymorphic in the chickpea genome. Different probes revealed different levels of variability. Whereas species-specific banding patterns were obtained with the (GTG)5 probe, other probes revealed differences between accessions, or even individuals. The somatic multilocus patterns were stable for all probes.Key words: genetic polymorphism, simple repetitive sequences, DNA fingerprinting, synthetic oligonucleotide probes.

Oligonucleotide fingerprinting reveals various probe-dependent levels of informativeness in chickpea (Cicer arietinum)

The abundance and polymorphism of 38 different simple-sequence repeat motifs was studied in four accessions of cultivated chickpea (Cicer arietinum L.) by in-gel hybridization of synthetic oligonucleotides to genomic DNA digested with 14 different restriction enzymes. Among 38 probes tested, 35 yielded detectable hybridization signals. The abundance and level of polymorphism of the target sequences varied considerably. The probes fell into three broad categories: (1) probes yielding distinct, polymorphic banding patterns; (2) probes yielding distinct, monomorphic banding patterns, and (3) probes yielding blurred patterns, or diffused bands superimposed on a high in lane background. No obvious correlation existed between abundance, fingerprint quality, and the sequence characteristics of a particular motif. Digestion with methyl-sensitive enzymes revealed that simple-sequence motifs are enriched in highly methylated genomic regions. The high level of intraspecific polymorphism detected by oligonucleotide fingerprinting suggests the suitability of simple-sequence repeat probes as molecular markers for genome mapping.

Abundance and polymorphism of di-, tri-and tetra-nucleotide tandem repeats in chickpea (Cicer arietinum L.)

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