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The genetic basis of cis-regulatory divergence between the subspecies of cultivated rice ( Oryza sativa )

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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/bf00290078openalex-snapshot

Isozymes and classification of Asian rice varieties

inferredcites →https://doi.org/10.1007/s00425-008-0742-0openalex-snapshot

OsCO3, a CONSTANS-LIKE gene, controls flowering by negatively regulating the expression of FT-like genes under SD conditions in rice

inferredcites →https://doi.org/10.1007/s11103-006-9112-0openalex-snapshot

Genome-wide transcriptional analysis of salinity stressed japonica and indica rice genotypes during panicle initiation stage

inferredcites →https://doi.org/10.1007/s11103-016-0474-7openalex-snapshot

OsPhyA modulates rice flowering time mainly through OsGI under short days and Ghd7 under long days in the absence of phytochrome B

inferredcites →https://doi.org/10.1016/j.cpb.2016.12.003openalex-snapshot

SNP-Seek II: A resource for allele mining and analysis of big genomic data in Oryza sativa

inferredcites →https://doi.org/10.1016/j.csda.2007.10.022openalex-snapshot

Size and power of tests for a zero random effect variance or polynomial regression in additive and linear mixed models

inferredcites →https://doi.org/10.1023/b:plan.0000038261.21060.47openalex-snapshot

A Rice Semi-Dwarf Gene, Tan-Ginbozu (D35), Encodes the Gibberellin Biosynthesis Enzyme, ent-Kaurene Oxidase

inferredcites →https://doi.org/10.1038/nature11532openalex-snapshot

A map of rice genome variation reveals the origin of cultivated rice

inferredcites →https://doi.org/10.1038/ncomms10532openalex-snapshot

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.2394openalex-snapshot

Mapping cis- and trans-regulatory effects across multiple tissues in twins

inferredcites →https://doi.org/10.1038/ng.3624openalex-snapshot

Tensor decomposition for multiple-tissue gene expression experiments

inferredcites →https://doi.org/10.1038/ng.695openalex-snapshot

Genome-wide association studies of 14 agronomic traits in rice landraces

inferredcites →https://doi.org/10.1038/s41586-018-0063-9openalex-snapshot

Genomic variation in 3,010 diverse accessions of Asian cultivated rice

inferredcites →https://doi.org/10.1038/s41588-018-0040-0openalex-snapshot

Genomes of 13 domesticated and wild rice relatives highlight genetic conservation, turnover and innovation across the genus Oryza

inferredcites →https://doi.org/10.1073/pnas.1003124107openalex-snapshot

Rice pollen hybrid incompatibility caused by reciprocal gene loss of duplicated genes

inferredcites →https://doi.org/10.1073/pnas.141239398openalex-snapshot

Cloning and functional analysis of two gibberellin 3β-hydroxylase genes that are differently expressed during the growth of rice

inferredcites →https://doi.org/10.1073/pnas.1711656115openalex-snapshot

Lineage-specific gene acquisition or loss is involved in interspecific hybrid sterility in rice

inferredcites →https://doi.org/10.1093/bioinformatics/btp120openalex-snapshot

TopHat: discovering splice junctions with RNA-Seq

inferredcites →https://doi.org/10.1093/bioinformatics/btr330openalex-snapshot

The variant call format and VCFtools

inferredcites →https://doi.org/10.1093/bioinformatics/btu170openalex-snapshot

Trimmomatic: a flexible trimmer for Illumina sequence data

inferredcites →https://doi.org/10.1093/bioinformatics/btu638openalex-snapshot

HTSeq—a Python framework to work with high-throughput sequencing data

inferredcites →https://doi.org/10.1093/genetics/155.2.945openalex-snapshot

Inference of Population Structure Using Multilocus Genotype Data

inferredcites →https://doi.org/10.1093/nar/gku1039openalex-snapshot

SNP-Seek database of SNPs derived from 3000 rice genomes

inferredcites →https://doi.org/10.1093/nar/gkw1135openalex-snapshot

Rice SNP-seek database update: new SNPs, indels, and queries

inferredcites →https://doi.org/10.1101/gr.106120.110openalex-snapshot

Function annotation of the rice transcriptome at single-nucleotide resolution by RNA-seq

inferredcites →https://doi.org/10.1101/gr.2479404openalex-snapshot

An SNP Resource for Rice Genetics and Breeding Based on SubspeciesIndicaandJaponicaGenome Alignments

inferredcites →https://doi.org/10.1104/pp.107.110304openalex-snapshot

Characteristic and Expression Analysis of a Metallothionein Gene, OsMT2b, Down-Regulated by Cytokinin Suggests Functions in Root Development and Seed Embryo Germination of Rice

inferredcites →https://doi.org/10.1104/pp.108.121491openalex-snapshot

Genome-Wide Analysis of Transposon Insertion Polymorphisms Reveals Intraspecific Variation in Cultivated Rice

inferredcites →https://doi.org/10.1105/tpc.105.035899openalex-snapshot

Distinct and Cooperative Functions of Phytochromes A, B, and C in the Control of Deetiolation and Flowering in Rice

inferredcites →https://doi.org/10.1111/j.1365-313x.2012.04915.xopenalex-snapshot

Footprints of natural and artificial selection for photoperiod pathway genes in Oryza

inferredcites →https://doi.org/10.1111/j.1471-8286.2005.01155.xopenalex-snapshot

genalex 6: genetic analysis in Excel. Population genetic software for teaching and research

inferredcites →https://doi.org/10.1111/j.1558-5646.1975.tb00851.xopenalex-snapshot

THE GENETIC BASIS OF EVOLUTIONARY CHANGE

inferredcites →https://doi.org/10.1111/j.2517-6161.1995.tb02031.xopenalex-snapshot

Controlling the False Discovery Rate: A Practical and Powerful Approach to Multiple Testing

inferredcites →https://doi.org/10.1126/science.1068037openalex-snapshot

A Draft Sequence of the Rice Genome ( Oryza sativa L. ssp. indica )

inferredcites →https://doi.org/10.1126/science.1068275openalex-snapshot

A Draft Sequence of the Rice Genome ( Oryza sativa L. ssp. japonica )

inferredcites →https://doi.org/10.1146/annurev-arplant-043014-115555openalex-snapshot

Photoperiodic Flowering: Time Measurement Mechanisms in Leaves

inferredcites →https://doi.org/10.1186/1471-2164-15-101openalex-snapshot

Diversity of floral regulatory genes of japonica rice cultivated at northern latitudes

inferredcites →https://doi.org/10.1186/1471-2164-8-154openalex-snapshot

Highly asymmetric rice genomes

inferredcites →https://doi.org/10.1186/1939-8433-6-19openalex-snapshot

Genome-wide identification and analysis of Japonica and Indica cultivar-preferred transcripts in rice using 983 Affymetrix array data

inferredcites →https://doi.org/10.1186/preaccept-2784872521277375openalex-snapshot

Whole genome de novo assemblies of three divergent strains of rice, Oryza sativa , document novel gene space of aus and indica

inferredcites →https://doi.org/10.1186/s13059-014-0550-8openalex-snapshot

Moderated estimation of fold change and dispersion for RNA-seq data with DESeq2

inferredcites →https://doi.org/10.1266/jjg.15.10openalex-snapshot

Some considerations on the classification of Oryza sativa L. into two subspecies, so-called 'Japonica' and 'Indica'

inferredcites →https://doi.org/10.1270/jsbbs1951.31.402openalex-snapshot

Phylogenetic Differentiation of Cultivated Rice, XXII. Numerical Evaluation of the Indica-Japonica Differentiation

inferredcites →https://doi.org/10.1371/journal.pgen.0030163openalex-snapshot

Genome-Wide Patterns of Nucleotide Polymorphism in Domesticated Rice

inferredcites →https://doi.org/10.1371/journal.pgen.1001317openalex-snapshot

Single-Tissue and Cross-Tissue Heritability of Gene Expression Via Identity-by-Descent in Related or Unrelated Individuals

inferredcites →https://doi.org/10.1371/journal.pgen.1002221openalex-snapshot

Genetic Architecture of Aluminum Tolerance in Rice (Oryza sativa) Determined through Genome-Wide Association Analysis and QTL Mapping

inferredcites →https://doi.org/10.1371/journal.pgen.1003486openalex-snapshot

A Statistical Framework for Joint eQTL Analysis in Multiple Tissues

inferredcites →https://doi.org/10.1534/genetics.104.035642openalex-snapshot

Genetic Structure and Diversity in Oryza sativa L.

inferredcites →https://doi.org/10.1534/genetics.107.079616openalex-snapshot

The Extent of Linkage Disequilibrium in Rice ( Oryza sativa L.)

inferredcites →https://doi.org/10.1534/genetics.113.159970openalex-snapshot

Global Genomic Diversity of Oryza sativa Varieties Revealed by Comparative Physical Mapping

inferredcites →https://doi.org/10.18637/jss.v067.i01openalex-snapshot

Fitting Linear Mixed-Effects Models Using lme4

inferredcites →https://doi.org/10.3168/jds.2007-0980openalex-snapshot

Efficient Methods to Compute Genomic Predictions

inferredcites →https://doi.org/10.3198/jpr2013.03.0013crmpopenalex-snapshot

Registration of the Rice Diversity Panel 1 for Genomewide Association Studies

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/10.1101/690479openalex-snapshot

Leveraging genome-enabled growth models to study shoot growth responses to water deficit in rice

inferred← citeshttps://doi.org/10.1101/714907openalex-snapshot

cis dominantly explains regulatory divergence between two indica rice genotypes; drought further enhances regulatory differences

inferred← citeshttps://doi.org/10.3390/genes13081396openalex-snapshot

Assessing Loss of Regulatory Divergence, Genome–Transcriptome Incongruence, and Preferential Expression Switching in Abaca × Banana Backcrosses

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