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

https://doi.org/10.1101/714907
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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/s10681-009-9898-3openalex-snapshot
Genetic loci responding to two cycles of divergent selection for grain yield under drought stress in a rice breeding population
inferredcites →https://doi.org/10.1007/s11295-018-1296-3openalex-snapshot
Molecular signatures of divergence and selection in closely related pine taxa
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Identification of transcriptome SNPs between Xiphophorus lines and species for assessing allele specific gene expression within F1 interspecies hybrids
inferredcites →https://doi.org/10.1016/j.cj.2015.01.001openalex-snapshot
QTL IciMapping: Integrated software for genetic linkage map construction and quantitative trait locus mapping in biparental populations
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/10.1038/nature02698openalex-snapshot
Evolutionary changes in cis and trans gene regulation
inferredcites →https://doi.org/10.1038/nature03235openalex-snapshot
Chance caught on the wing: cis-regulatory evolution and the origin of pigment patterns in Drosophila
inferredcites →https://doi.org/10.1038/ncomms1954openalex-snapshot
Cis- and trans-regulatory divergence between progenitor species determines gene-expression novelty in Arabidopsis allopolyploids
inferredcites →https://doi.org/10.1038/ng.3162openalex-snapshot
Gene-gene and gene-environment interactions detected by transcriptome sequence analysis in twins
inferredcites →https://doi.org/10.1038/ng.77openalex-snapshot
Regulatory changes underlying expression differences within and between Drosophila species
inferredcites →https://doi.org/10.1038/ng992openalex-snapshot
Detection of regulatory variation in mouse genes
inferredcites →https://doi.org/10.1038/nmeth.1923openalex-snapshot
Fast gapped-read alignment with Bowtie 2
inferredcites →https://doi.org/10.1038/nmeth.2251openalex-snapshot
Streaming fragment assignment for real-time analysis of sequencing experiments
inferredcites →https://doi.org/10.1038/srep14799openalex-snapshot
Drought susceptibility of modern rice varieties: an effect of linkage of drought tolerance with undesirable traits
inferredcites →https://doi.org/10.1038/srep15183openalex-snapshot
Action of multiple intra-QTL genes concerted around a co-localized transcription factor underpins a large effect QTL
inferredcites →https://doi.org/10.1071/pp9860329openalex-snapshot
Influence of Soil Water Supply on the Plant Water Balance of Four Tropical Grain Legumes
inferredcites →https://doi.org/10.1073/pnas.1530509100openalex-snapshot
Statistical significance for genomewide studies
inferredcites →https://doi.org/10.1093/bib/bbs046openalex-snapshot
A comprehensive evaluation of normalization methods for Illumina high-throughput RNA sequencing data analysis
inferredcites →https://doi.org/10.1093/bioinformatics/btp352openalex-snapshot
The Sequence Alignment/Map format and SAMtools
inferredcites →https://doi.org/10.1093/bioinformatics/btp579openalex-snapshot
Effect of read-mapping biases on detecting allele-specific expression from RNA-sequencing data
inferredcites →https://doi.org/10.1093/gbe/evt072openalex-snapshot
RNA-Seq Analysis of Allele-Specific Expression, Hybrid Effects, and Regulatory Divergence in Hybrids Compared with Their Parents from Natural Populations
inferredcites →https://doi.org/10.1093/gbe/evv057openalex-snapshot
Regulatory Divergence between Parental Alleles Determines Gene Expression Patterns in Hybrids
inferredcites →https://doi.org/10.1093/gbe/evx035openalex-snapshot
Evolutionary Dynamics of Regulatory Changes Underlying Gene Expression Divergence among Saccharomyces Species
inferredcites →https://doi.org/10.1093/jxb/err315openalex-snapshot
Light-harvesting chlorophyll a/b-binding proteins are required for stomatal response to abscisic acid in Arabidopsis
inferredcites →https://doi.org/10.1093/molbev/msv196openalex-snapshot
Widespread and Adaptive Alterations in Genome-Wide Gene Expression Associated with Ecological Divergence of TwoOryzaSpecies
inferredcites →https://doi.org/10.1093/molbev/msw011openalex-snapshot
Contrasting Frequencies and Effects ofcis- andtrans-Regulatory Mutations Affecting Gene Expression
inferredcites →https://doi.org/10.1093/molbev/msw096openalex-snapshot
The Footprint of Polygenic Adaptation on Stress-ResponsiveCis-Regulatory Divergence in theArabidopsis Genus
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/gkw492openalex-snapshot
Mechanisms of transcription factor evolution in Metazoa
inferredcites →https://doi.org/10.1093/nar/gkx382openalex-snapshot
agriGO v2.0: a GO analysis toolkit for the agricultural community, 2017 update
inferredcites →https://doi.org/10.1101/511550openalex-snapshot
The genetic basis of cis-regulatory divergence between the subspecies of cultivated rice ( Oryza sativa )
inferredcites →https://doi.org/10.1101/gr.102491.109openalex-snapshot
Regulatory divergence in Drosophila revealed by mRNA-seq
inferredcites →https://doi.org/10.1101/gr.4252305openalex-snapshot
Genomic scans for selective sweeps using SNP data
inferredcites →https://doi.org/10.1105/tpc.114.130310openalex-snapshot
Extensive cis -Regulatory Variation Robust to Environmental Perturbation in Arabidopsis
inferredcites →https://doi.org/10.1111/evo.12875openalex-snapshot
Genome-wide patterns of regulatory divergence revealed by introgression lines
inferredcites →https://doi.org/10.1111/j.1558-5646.2008.00450.xopenalex-snapshot
THE LOCI OF EVOLUTION: HOW PREDICTABLE IS GENETIC EVOLUTION?
inferredcites →https://doi.org/10.1126/science.1140247openalex-snapshot
Genetic Properties Influencing the Evolvability of Gene Expression
inferredcites →https://doi.org/10.1126/science.1169766openalex-snapshot
A Yeast Hybrid Provides Insight into the Evolution of Gene Expression Regulation
inferredcites →https://doi.org/10.1186/1471-2156-12-89openalex-snapshot
qDTY 1.1 , a major QTL for rice grain yield under reproductive-stage drought stress with a consistent effect in multiple elite genetic backgrounds
inferredcites →https://doi.org/10.1186/gb-2010-11-3-r25openalex-snapshot
A scaling normalization method for differential expression analysis of RNA-seq 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/s12284-016-0123-4openalex-snapshot
Analysis of Allelic Imbalance in Rice Hybrids Under Water Stress and Association of Asymmetrically Expressed Genes with Drought-Response QTLs
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/10.1371/journal.pone.0054537openalex-snapshot
Transcriptome Profiling of Leaf Elongation Zone under Drought in Contrasting Rice Cultivars
inferredcites →https://doi.org/10.1534/genetics.117.201459openalex-snapshot
Cis- and Trans-regulatory Effects on Gene Expression in a Natural Population of Drosophila melanogaster
inferredcites →https://doi.org/10.3389/fpls.2019.00228openalex-snapshot
AP2/ERF Transcription Factor Regulatory Networks in Hormone and Abiotic Stress Responses in Arabidopsis
inferredcites →https://doi.org/10.3389/fpls.2020.00115openalex-snapshot
C2H2 Zinc Finger Proteins: Master Regulators of Abiotic Stress Responses in Plants
inferredcites →https://doi.org/10.3390/agronomy10050621openalex-snapshot
RNA-seq Reveals Differentially Expressed Genes between Two indica Inbred Rice Genotypes Associated with Drought-Yield QTLs
inferredcites →https://doi.org/10.7554/elife.43785openalex-snapshot
Predominance of cis-regulatory changes in parallel expression divergence of sticklebacks

What points at this work

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

inferred← citeshttps://doi.org/10.3390/agronomy10050621openalex-snapshot
RNA-seq Reveals Differentially Expressed Genes between Two indica Inbred Rice Genotypes Associated with Drought-Yield QTLs
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