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Title: Evolving best practices for transcriptome-wide association studies accelerate discovery of gene-phenotype links

Journal Article · · Current Opinion in Plant Biology

Not Available

Sponsoring Organization:
USDOE Advanced Research Projects Agency - Energy (ARPA-E)
Grant/Contract Number:
AR0001064; AR0001367; SC0020355
OSTI ID:
2479384
Journal Information:
Current Opinion in Plant Biology, Journal Name: Current Opinion in Plant Biology Journal Issue: C Vol. 83; ISSN 1369-5266
Publisher:
ElsevierCopyright Statement
Country of Publication:
United Kingdom
Language:
English

References (63)

Status and prospects of genome‐wide association studies in plants journal January 2021
Transcriptome‐wide association and prediction for carotenoids and tocochromanols in fresh sweet corn kernels journal March 2022
A cis-regulatory atlas in maize at single-cell resolution journal May 2021
Integration of eQTL and machine learning to dissect causal genes with pleiotropic effects in genetic regulation networks of seed cotton yield journal September 2023
Genome- and transcriptome-wide association studies provide insights into the genetic basis of natural variation of seed oil content in Brassica napus journal March 2021
Dysregulation of expression correlates with rare-allele burden and fitness loss in maize journal March 2018
A gene-based association method for mapping traits using reference transcriptome data journal August 2015
Integrative approaches for large-scale transcriptome-wide association studies journal February 2016
Identification of a functional transposon insertion in the maize domestication gene tb1 journal September 2011
Using probabilistic estimation of expression residuals (PEER) to obtain increased power and interpretability of gene expression analyses journal February 2012
Benchmarking of cell type deconvolution pipelines for transcriptomics data journal November 2020
PH13 improves soybean shade traits and enhances yield for high-density planting at high latitudes journal October 2023
Transcriptome-wide association analyses reveal the impact of regulatory variants on rice panicle architecture and causal gene regulatory networks journal November 2023
A pan-grass transcriptome reveals patterns of cellular divergence in crops journal May 2023
Genomic innovation and regulatory rewiring during evolution of the cotton genus Gossypium journal December 2022
2D association and integrative omics analysis in rice provides systems biology view in trait analysis journal September 2018
Recombinant inbred lines for mapping RFLP and phenotypic markers in Arabidopsis thaliana journal October 1993
Conserved noncoding genomic sequences associated with a flowering-time quantitative trait locus in maize journal June 2007
The yl Gene of Maize Codes for Phytoene Synthase journal May 1996
Genome-wide mediation analysis: an empirical study to connect phenotype with genotype via intermediate transcriptomic data in maize journal April 2022
Combining GWAS and TWAS to identify candidate causal genes for tocochromanol levels in maize grain journal June 2022
Association mapping across a multitude of traits collected in diverse environments in maize journal August 2022
BLINK: a package for the next level of genome-wide association studies with both individuals and markers in the millions journal December 2018
Transcriptome-wide association study coupled with eQTL analysis reveals the genetic connection between gene expression and flowering time in Arabidopsis journal July 2023
GWAS Atlas: an updated knowledgebase integrating more curated associations in plants and animals journal October 2022
Integrative omics analysis elucidates the genetic basis underlying seed weight and oil content in soybean journal February 2024
TWAS results are complementary to and less affected by linkage disequilibrium than GWAS journal April 2021
Machine learning-enabled phenotyping for GWAS and TWAS of WUE traits in 869 field-grown sorghum accessions journal July 2021
Phenotyping stomatal closure by thermal imaging for GWAS and TWAS of water use efficiency-related genes journal August 2021
Integrating GWAS and TWAS to elucidate the genetic architecture of maize leaf cuticular conductance journal May 2022
The 2020 derecho revealed limited overlap between maize genes associated with root lodging and root system architecture journal March 2023
Quantitative Resistance Loci to Southern Rust Mapped in a Temperate Maize Diversity Panel journal March 2022
Involvement of the MADS-Box GeneZMM4in Floral Induction and Inflorescence Development in Maize     journal June 2008
Shared Genetic Control of Root System Architecture between Zea mays and Sorghum bicolor journal November 2019
The FT -Like ZCN8 Gene Functions as a Floral Activator and Is Involved in Photoperiod Sensitivity in Maize journal March 2011
Insights into the Maize Pan-Genome and Pan-Transcriptome journal January 2014
Transcriptome-Based Prediction of Complex Traits in Maize journal October 2019
Combined GWAS and eQTL analysis uncovers a genetic regulatory network orchestrating the initiation of secondary cell wall development in cotton journal February 2020
A combination of genome‐wide and transcriptome‐wide association studies reveals genetic elements leading to male sterility during high temperature stress in cotton journal May 2021
Genetic control of photoprotection and photosystem II operating efficiency in plants journal May 2023
Integrating a genome‐wide association study with a large‐scale transcriptome analysis to predict genetic regions influencing the glycaemic index and texture in rice journal January 2019
Genome‐ and transcriptome‐wide association studies reveal the genetic basis and the breeding history of seed glucosinolate content in Brassica napus journal October 2021
eQTLs play critical roles in regulating gene expression and identifying key regulators in rice journal September 2022
Validation of an updated Associative Transcriptomics platform for the polyploid crop species Brassica napus by dissection of the genetic architecture of erucic acid and tocopherol isoform variation in seeds journal December 2017
A common resequencing‐based genetic marker data set for global maize diversity journal February 2023
Population‐level gene expression can repeatedly link genes to functions in maize journal May 2024
A First-Generation Haplotype Map of Maize journal November 2009
Interspecific analysis of diurnal gene regulation in panicoid grasses identifies known and novel regulatory motifs journal June 2020
Substantial contribution of genetic variation in the expression of transcription factors to phenotypic variation revealed by eRD-GWAS journal October 2017
Mapping regulatory variants controlling gene expression in drought response and tolerance in maize journal July 2020
Multi-omics analysis dissects the genetic architecture of seed coat content in Brassica napus journal March 2022
PCA outperforms popular hidden variable inference methods for molecular QTL mapping journal October 2022
Comprehensive transcriptional variability analysis reveals gene networks regulating seed oil content of Brassica napus journal November 2022
A role for heritable transcriptomic variation in maize adaptation to temperate environments journal March 2023
A Morning-Specific Phytohormone Gene Expression Program underlying Rhythmic Plant Growth journal September 2008
Large-scale investigation of the reasons why potentially important genes are ignored journal September 2018
Association Mapping across Numerous Traits Reveals Patterns of Functional Variation in Maize journal December 2014
Iterative Usage of Fixed and Random Effect Models for Powerful and Efficient Genome-Wide Association Studies journal February 2016
Expression reflects population structure journal December 2018
Haplotype associated RNA expression (HARE) improves prediction of complex traits in maize journal October 2021
Global Profiling of Rice and Poplar Transcriptomes Highlights Key Conserved Circadian-Controlled Pathways and cis-Regulatory Modules journal June 2011
The Genomes of Recombinant Inbred Lines journal February 2005
Genetic Mapping of Agronomic Traits Using Recombinant Inbred Lines of Soybean journal September 1996