生活習慣病とgenome-wide association study

Contents Summary 523 I. Introduction 523 II. Sensing salt stress 524 III. Ion homeostasis regulation 524 IV. Metabolite and cell activity responses to salt stress 527 V. Conclusions and perspectives 532 Acknowledgements 533 References 533 SUMMARY: Excess soluble salts in soil (saline soils) are harmful to most plants. Salt imposes osmotic, ionic, and secondary stresses on plants. Over the past two decades, many determinants of salt tolerance and their regulatory mechanisms have been identified and characterized using molecular genetics and genomics approaches. This review describes recent progress in deciphering the mechanisms controlling ion homeostasis, cell activity responses, and epigenetic regulation in plants under salt stress. Finally, we highlight research areas that require further research to reveal new determinants of salt tolerance in plants.

https://nph.onlinelibrary.wiley.com/doi/epdf/10.1111/nph.14920

Elucidating the molecular mechanisms mediating plant salt-stress responses

Fears about global food security led to a spike in food prices in 2008, social unrest and pushed a further 100 million people into poverty. Prices remain high and volatile. In this paper we take a closer look at rice, a crop that feeds billions of people in the world, and focus in particular on Asia and Africa. On both continents, rice is grown in a wide range of climatic conditions, from river deltas to mountainous regions. Irrigated systems dominate in Asia and rainfed systems in Africa. Predicted demands for rice remain strong. An additional 116 million tons of rice will be needed by 2035 to feed growing populations. In Africa, where rice is the most rapidly growing food source, about 30 million tons more rice will be needed by 2035, representing an increase of 130% in rice consumption from 2010. About one-third of this extra rice will be needed in Nigeria alone. In Asia, per capita consumption of rice may go down in some mid- and high-income countries. Rice farming will need to produce about 8–10 million tons more paddy per year over the next decade. Without area expansion this will require an annual yield increase of about 1.2–1.5%, equivalent to an average yield increase of 0.6 t ha−1 world-wide. Improving global food security will, therefore, necessitate concerted efforts to increase the productivity of rice per unit of land, water and/or labor in Asia and Africa, and the development of new land and water resources in a responsible and equitable manner to counteract losses due to urbanization and industrialization. During 2007–2011, productivity increases in Africa have been leading the way, with paddy rice production levels increasing by 9.5% per year, compared to 1.6% in Asia. Priorities for rice sector development include (i) continued and increased research efforts to close yield gaps and raise yield ceilings across rice growing environments through varietal development and improved rice production methods, and coping with climate change in both continents and (ii) strengthened and equitable public-private sector partnerships and conducive policy environments in Africa, with special emphasis on mechanization of rice farming from land preparation to harvest and rice processing practices.

Crops that feed the world 7: Rice

The development and use of 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. No molecular markers are available yet that fulfill all requirements needed by researchers. According to the kind of study to be undertaken, one can choose among the variety of molecular techniques, each of which combines at least some desirable properties. This article provides detail review for 11 different molecular marker methods: restriction fragment length polymorphism (RFLP), random amplified polymorphic DNA (RAPD), amplified fragment length polymorphism (AFLP), inter-simple sequence repeats (ISSRs), sequence characterized regions (SCARs), sequence tag sites (STSs), cleaved amplified polymorphic sequences (CAPS), microsatellites or simple sequence repeats (SSRs), expressed sequence tags (ESTs), single nucleotide polymorphisms (SNPs), and diversity arrays technology (DArT).

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An overview of molecular marker methods for plants

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

Summary Inter simple sequence repeat (ISSR)-PCR is a technique, which involves the use of microsatellite sequences as primers in a polymerase chain reaction to generate multilocus markers. It is a simple and quick method that combines most of the advantages of microsatellites (SSRs) and amplified fragment length polymorphism (AFLP) to the universality of random amplified polymorphic DNA (RAPD). ISSR markers are highly polymorphic and are useful in studies on genetic diversity, phylogeny, gene tagging, genome mapping and evolutionary biology. This review provides an overview of the details of the technique and its application in genetics and plant breeding in a wide range of crop plants.

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Inter simple sequence repeat (ISSR) polymorphism and its application in plant breeding

Cultivated rice (Oryza sativa L.) is endowed with a rich genetic variability. In spite of such a great diversity, the modern rice cultivars have narrow genetic base for most of the agronomically important traits. To sustain the demand of an ever increasing population, new avenues have to be explored to increase the yield of rice. Wild progenitor species present potential donor sources for complex traits such as yield and would help to realize the dream of sustained food security. Advanced backcross method was used to introgress and map new quantitative trait loci (QTLs) relating to yield and its components from an Indian accession of Oryza rufipogon. An interspecific BC2 testcross progeny (IR58025A/O. rufipogon//IR580325B///IR58025B////KMR3) was evaluated for 13 agronomic traits pertaining to yield and its components. Transgressive segregants were obtained for all the traits. Thirty nine QTLs were identified using interval mapping and composite interval mapping. In spite of it's inferiority for most of the traits studied, O. rufipogon alleles contributed positively to 74% of the QTLs. Thirty QTLs had corresponding occurrences with the QTLs reported earlier, indicating that these QTLs are stable across genetic backgrounds. Nine QTLs are novel and reported for the first time. The study confirms that the progenitor species constitute a prominent source of still unfolded variability for traits of complex inheritance like yield. With the availability of the complete genome sequence of rice and the developments in the field of genomics, it is now possible to identify the genes underlying the QTLs. The identification of the genes constituting QTLs would help us to understand the molecular mechanisms behind the action of QTLs.

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Identification and mapping of yield and yield related QTLs from an Indian accession of Oryza rufipogon.

African rice Oryza glaberrima (2n = 24, AA) has many unique traits such as weed competitiveness, drought tolerance and the ability to grow under low input conditions. These traits have been recently combined with high yield of Oryza sativa to develop NERICA (NEw Rice for AfriCA). The new rice varieties are high-yielding, drought- and pest-resistant and are uniquely adapted to the growing conditions of West Africa. The major problems in combining useful traits of both cultivated Oryza species are sexual incompatibility and hybrid sterility. Reproductive barriers between the two species have been studied and genetic models based on sporogametophytic interactions proposed. The availability of a molecular linkage map of 0. glaberrima and molecular markers linked to sterility loci would aid in the introgression of desirable traits and elimination of sterility loci quickly. The use of 0. glaberrima in rice breeding is challenging, but promising. The genetic base of Asian rice 0. sativa can be widened for obtaining higher yields under adverse conditions and using non-transgenic approaches.

Neelamraju Sarla

Papers

Inter simple sequence repeat (ISSR) polymorphism and its application in plant breeding

Identification and mapping of yield and yield related QTLs from an Indian accession of Oryza rufipogon.

Oryza glaberrima : A source for the improvement of Oryza sativa

Mapping QTLs and candidate genes for iron and zinc concentrations in unpolished rice of Madhukar × Swarna RILs

Yield-enhancing quantitative trait loci (QTLs) from wild species.