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Genetic structure of Photosystem II functionality in rice unraveled by GWAS analysis

https://doi.org/10.1101/2020.09.28.317479
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What this work says

Outgoing claims: the papers this work cites, builds on, or argues with.

inferredcites →https://doi.org/10.1007/bf00989140openalex-snapshot
Breaking the yield frontier of rice
inferredcites →https://doi.org/10.1007/s10681-012-0697-xopenalex-snapshot
Genome-wide association analysis detecting significant single nucleotide polymorphisms for chlorophyll and chlorophyll fluorescence parameters in soybean (Glycine max) landraces
inferredcites →https://doi.org/10.1007/s10709-016-9932-zopenalex-snapshot
Genome wide association study (GWAS) for grain yield in rice cultivated under water deficit
inferredcites →https://doi.org/10.1007/s11099-018-0770-3openalex-snapshot
Chlorophyll a fluorescence induction: Can just a one-second measurement be used to quantify abiotic stress responses?
inferredcites →https://doi.org/10.1007/s11103-017-0652-2openalex-snapshot
Mapping and comparative proteomic analysis of the starch biosynthetic pathway in rice by 2D PAGE/MS
inferredcites →https://doi.org/10.1007/s11120-015-0151-8openalex-snapshot
Photochemical properties in flag leaves of a super-high-yielding hybrid rice and a traditional hybrid rice (Oryza sativa L.) probed by chlorophyll a fluorescence transient
inferredcites →https://doi.org/10.1007/s11738-015-1865-0openalex-snapshot
Chlorophyll fluorescence and lipid peroxidation changes in rice somaclonal lines subjected to salt stress
inferredcites →https://doi.org/10.1016/j.jphotobiol.2010.12.010openalex-snapshot
On the relation between the Kautsky effect (chlorophyll a fluorescence induction) and Photosystem II: Basics and applications of the OJIP fluorescence transient
inferredcites →https://doi.org/10.1016/j.plantsci.2016.07.012openalex-snapshot
GL2-type homeobox gene Roc4 in rice promotes flowering time preferentially under long days by repressing Ghd7
inferredcites →https://doi.org/10.1016/j.plaphy.2014.06.005openalex-snapshot
Photosynthetic changes of flag leaves during senescence stage in super high-yield hybrid rice LYPJ grown in field condition
inferredcites →https://doi.org/10.1016/s0254-6299(15)30246-5openalex-snapshot
Phenotyping of dark and light adapted barley plants by the fast chlorophyll a fluorescence rise OJIP
inferredcites →https://doi.org/10.1016/s0269-7491(01)00091-4openalex-snapshot
Multiple effects of chromate on the photosynthetic apparatus of Spirodela polyrhiza as probed by OJIP chlorophyll a fluorescence measurements
inferredcites →https://doi.org/10.1016/s0981-9428(02)01425-0openalex-snapshot
Regulation of photosynthesis and antioxidant metabolism in maize leaves at optimal and chilling temperatures: review
inferredcites →https://doi.org/10.1023/a:1007199408689openalex-snapshot
Greening of Peas: Parallel Measurements of 77 K Emission Spectra, OJIP Chlorophyll a Fluorescence Transient, Period Four Oscillation of the Initial Fluorescence Level, Delayed Light Emission, and P700
inferredcites →https://doi.org/10.1023/b:phot.0000046153.08935.4copenalex-snapshot
Effects of Nitrogen Deficiency on Gas Exchange, Chlorophyll Fluorescence, and Antioxidant Enzymes in Leaves of Rice Plants
inferredcites →https://doi.org/10.1038/nature03895openalex-snapshot
The map-based sequence of the rice genome
inferredcites →https://doi.org/10.1038/ncomms10527openalex-snapshot
Genome-wide association and high-resolution phenotyping link Oryza sativa panicle traits to numerous trait-specific QTL clusters
inferredcites →https://doi.org/10.1038/ncomms10532openalex-snapshot
Open access resources for genome-wide association mapping in rice
inferredcites →https://doi.org/10.1038/ncomms11346openalex-snapshot
Correction: Corrigendum: Open access resources for genome-wide association mapping in rice
inferredcites →https://doi.org/10.1038/ncomms1467openalex-snapshot
Genome-wide association mapping reveals a rich genetic architecture of complex traits in Oryza sativa
inferredcites →https://doi.org/10.1038/ng.1018openalex-snapshot
Genome-wide association study of flowering time and grain yield traits in a worldwide collection of rice germplasm
inferredcites →https://doi.org/10.1038/ng.548openalex-snapshot
Variance component model to account for sample structure in genome-wide association studies
inferredcites →https://doi.org/10.1038/s41467-017-01576-3openalex-snapshot
Natural variation of YELLOW SEEDLING1 affects photosynthetic acclimation of Arabidopsis thaliana
inferredcites →https://doi.org/10.1073/pnas.1515919112openalex-snapshot
Breeding signatures of rice improvement revealed by a genomic variation map from a large germplasm collection
inferredcites →https://doi.org/10.1073/pnas.201394398openalex-snapshot
Structure of linkage disequilibrium and phenotypic associations in the maize genome
inferredcites →https://doi.org/10.1086/519795openalex-snapshot
PLINK: A Tool Set for Whole-Genome Association and Population-Based Linkage Analyses
inferredcites →https://doi.org/10.1093/bioinformatics/btm108openalex-snapshot
GenABEL: an R library for genome-wide association analysis
inferredcites →https://doi.org/10.1093/dnares/dsu046openalex-snapshot
Genome-wide association mapping of salinity tolerance in rice (Oryza sativa)
inferredcites →https://doi.org/10.1093/jexbot/50.338.1533openalex-snapshot
Chlorophyll fluorescence as a selection tool for cold tolerance of photosynthesis in maize (Zea mays L.)
inferredcites →https://doi.org/10.1093/jxb/erv258openalex-snapshot
Phenotypic and genetic dissection of component traits for early vigour in rice using plant growth modelling, sugar content analyses and association mapping
inferredcites →https://doi.org/10.1093/jxb/erx276openalex-snapshot
Genetic architecture of photosynthesis in Sorghum bicolor under non-stress and cold stress conditions
inferredcites →https://doi.org/10.1093/jxb/ery186openalex-snapshot
Genome-wide association reveals novel genomic loci controlling rice grain yield and its component traits under water-deficit stress during the reproductive stage
inferredcites →https://doi.org/10.1104/pp.114.238626openalex-snapshot
High-Resolution Inflorescence Phenotyping Using a Novel Image-Analysis Pipeline, PANorama
inferredcites →https://doi.org/10.1104/pp.125.4.1558openalex-snapshot
Non-Photochemical Quenching. A Response to Excess Light Energy
inferredcites →https://doi.org/10.1104/pp.16.01585openalex-snapshot
Diurnal Solar Energy Conversion and Photoprotection in Rice Canopies
inferredcites →https://doi.org/10.1104/pp.17.00332openalex-snapshot
Leaf Photosynthetic Parameters Related to Biomass Accumulation in a Global Rice Diversity Survey
inferredcites →https://doi.org/10.1105/tpc.18.00063openalex-snapshot
A Core Regulatory Pathway Controlling Rice Tiller Angle Mediated by the LAZY1-Dependent Asymmetric Distribution of Auxin
inferredcites →https://doi.org/10.1105/tpc.18.00375openalex-snapshot
Genome-Wide Association Studies Reveal the Genetic Basis of Ionomic Variation in Rice
inferredcites →https://doi.org/10.1111/j.1365-313x.2004.02082.xopenalex-snapshot
Functional analyses of the flowering time gene OsMADS50 , the putative SUPPRESSOR OF OVEREXPRESSION OF CO 1 / AGAMOUS‐LIKE 20 ( SOC1/AGL20 ) ortholog in rice
inferredcites →https://doi.org/10.1111/j.1365-313x.2010.04238.xopenalex-snapshot
Brittle Culm 12, a dual‐targeting kinesin‐4 protein, controls cell‐cycle progression and wall properties in rice
inferredcites →https://doi.org/10.1111/jipb.12179openalex-snapshot
Quantitative genetic analysis of chlorophyll a fluorescence parameters in maize in the field environments
inferredcites →https://doi.org/10.1111/jipb.12186openalex-snapshot
Performance index: An expeditious tool to screen for improved drought resistance in the Lathyrus genus
inferredcites →https://doi.org/10.1111/mpp.12340openalex-snapshot
Dissection of the genetic architecture of rice resistance to the blast fungus Magnaporthe oryzae
inferredcites →https://doi.org/10.1111/pbr.12394openalex-snapshot
Cold tolerance during juvenile development in sorghum: a comparative analysis by genomewide association and linkage mapping
inferredcites →https://doi.org/10.1111/pbr.12425openalex-snapshot
Genome‐wide association analysis reveals flowering‐related genes regulating rachis length in rice
inferredcites →https://doi.org/10.1111/pce.12096openalex-snapshot
Association mapping for chilling tolerance in elite flint and dent maize inbred lines evaluated in growth chamber and field experiments
inferredcites →https://doi.org/10.1186/1471-2164-8-242openalex-snapshot
MADS-box gene family in rice: genome-wide identification, organization and expression profiling during reproductive development and stress
inferredcites →https://doi.org/10.1186/2047-217x-3-8openalex-snapshot
The 3,000 rice genomes project: new opportunities and challenges for future rice research
inferredcites →https://doi.org/10.1186/s12284-015-0065-2openalex-snapshot
Photoprotection as a Trait for Rice Yield Improvement: Status and Prospects
inferredcites →https://doi.org/10.1186/s12870-017-1044-0openalex-snapshot
Genome-wide association study of salt tolerance at the seed germination stage in rice
inferredcites →https://doi.org/10.1186/s13742-015-0047-8openalex-snapshot
Second-generation PLINK: rising to the challenge of larger and richer datasets
inferredcites →https://doi.org/10.1201/9780203022030-8openalex-snapshot
Physiological Basis of Yield and Environmental Adaptation in Rice
inferredcites →https://doi.org/10.1201/9780203022030.ch3openalex-snapshot
Physiological Basis of Yield and Environmental Adaptation in Rice
inferredcites →https://doi.org/10.1201/9781482268010openalex-snapshot
Probing Photosynthesis
inferredcites →https://doi.org/10.1371/journal.pgen.1004982openalex-snapshot
Genomic Selection and Association Mapping in Rice (Oryza sativa): Effect of Trait Genetic Architecture, Training Population Composition, Marker Number and Statistical Model on Accuracy of Rice Genomic Selection in Elite, Tropical Rice Breeding Lines
inferredcites →https://doi.org/10.1371/journal.pgen.1006889openalex-snapshot
Genetic control of the root system in rice under normal and drought stress conditions by genome-wide association study
inferredcites →https://doi.org/10.1371/journal.pone.0119873openalex-snapshot
Genome-Wide Association Mapping for Yield and Other Agronomic Traits in an Elite Breeding Population of Tropical Rice (Oryza sativa)
inferredcites →https://doi.org/10.1371/journal.pone.0155425openalex-snapshot
Genome-Wide Association Study for Traits Related to Plant and Grain Morphology, and Root Architecture in Temperate Rice Accessions
inferredcites →https://doi.org/10.1371/journal.pone.0171254openalex-snapshot
Genome-wide association analysis for heat tolerance at flowering detected a large set of genes involved in adaptation to thermal and other stresses
inferredcites →https://doi.org/10.1371/journal.pone.0172133openalex-snapshot
Genetic architecture of cold tolerance in rice (Oryza sativa) determined through high resolution genome-wide analysis
inferredcites →https://doi.org/10.1371/journal.pone.0196690openalex-snapshot
Identification of candidate genes for gelatinization temperature, gel consistency and pericarp color by GWAS in rice based on SLAF-sequencing
inferredcites →https://doi.org/10.1371/journal.pone.0198012openalex-snapshot
Diversity analysis and genome-wide association studies of grain shape and eating quality traits in rice (Oryza sativa L.) using DArT markers
inferredcites →https://doi.org/10.1534/g3.116.028837openalex-snapshot
Homeobox Is Pivotal for OsWUS Controlling Tiller Development and Female Fertility in Rice
inferredcites →https://doi.org/10.1534/genetics.104.035642openalex-snapshot
Genetic Structure and Diversity in Oryza sativa L.
inferredcites →https://doi.org/10.18637/jss.v067.i01openalex-snapshot
Fitting Linear Mixed-Effects Models Using lme4
inferredcites →https://doi.org/10.3389/fpls.2016.01270openalex-snapshot
Genome-Wide Association Studies Reveal that Diverse Heading Date Genes Respond to Short and Long Day Lengths between Indica and Japonica Rice
inferredcites →https://doi.org/10.3389/fpls.2016.01801openalex-snapshot
Genome-Wide Association Study for Plant Height and Grain Yield in Rice under Contrasting Moisture Regimes
inferredcites →https://doi.org/10.3835/plantgenome2015.08.0072openalex-snapshot
Identification of Genomic Loci Associated with the Photochemical Reflectance Index by Genome‐Wide Association Study in Soybean
inferredcites →https://doi.org/10.3835/plantgenome2015.08.0074openalex-snapshot
Population Structure in the Model Grass Brachypodium distachyon Is Highly Correlated with Flowering Differences across Broad Geographic Areas
inferredcites →https://doi.org/10.3835/plantgenome2017.08.0076openalex-snapshot
Genome‐Wide Association Study Using Historical Breeding Populations Discovers Genomic Regions Involved in High‐Quality Rice
inferredcites →https://doi.org/10.3929/ethz-b-000105397openalex-snapshot
Fitting Linear Mixed-Effects Models Using lme4

What points at this work

Incoming claims: where this work appears in other papers’ reference lists and arguments.

inferred← citeshttps://doi.org/10.1016/j.plaphy.2023.107897openalex-snapshot
Field and genetic evidence support the photosynthetic performance index (PIABS) as an indicator of rice grain yield
inferred← citeshttps://doi.org/10.1101/2023.02.08.527700openalex-snapshot
Rice plants alter their yield component parameters based on their tolerance to low temperatures determined by a non-invasive method during the vegetative stage
inferred← citeshttps://doi.org/10.1111/jac.12670openalex-snapshot
Determination of low‐temperature stress during the vegetative stage as a tool to predict plant yield in rice genotypes with contrasting tolerance levels
inferred← citeshttps://doi.org/10.3390/agronomy12010152openalex-snapshot
Genome-Wide Association Study of Leaf Chlorophyll Content Using High-Density SNP Array in Peanuts (Arachis hypogaea L.)
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