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Single-gene resolution of locally adaptive genetic variation in Mexican maize

https://doi.org/10.1101/706739
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What this work says

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

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Updated high‐resolution grids of monthly climatic observations – the CRU TS3 .10 Dataset
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WorldClim 2: new 1‐km spatial resolution climate surfaces for global land areas
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Fertile fruit trees obtained by somatic hybridization: navel orange (Citrus sinensis) and Troyer citrange (C. sinensis x Poncirus trifoliata)
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Quantitative trait loci for plant height in four maize populations and their associations with qualitative genetic loci
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RFLP analysis of the size of chromosomal segments retained around the Tm-2 locus of tomato during backcross breeding
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QTL mapping in three tropical maize populations reveals a set of constitutive and adaptive genomic regions for drought tolerance
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Two different heat shock transcription factors regulate immediate early expression of stress genes in Arabidopsis
inferredcites →https://doi.org/10.1007/s10722-018-0693-7openalex-snapshot
Structure of local adaptation across the landscape: flowering time and fitness in Mexican maize (Zea mays L. subsp. mays) landraces
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Mapping of QTL controlling root hair length in maize (Zea mays L.) under phosphorus deficiency
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Overexpression of a NTR1 in transgenic soybean confers tolerance to water stress
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Diversity in global maize germplasm: Characterization and utilization
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Role of Tocopherol (Vitamin E) in Plants
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Use of CRISPR/Cas9 for Crop Improvement in Maize and Soybean
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Engineering Quantitative Trait Variation for Crop Improvement by Genome Editing
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Can genomics deliver climate-change ready crops?
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Towards a more predictable plant breeding pipeline with CRISPR/Cas-induced allelic series to optimize quantitative and qualitative traits
inferredcites →https://doi.org/10.1016/j.plantsci.2019.02.011openalex-snapshot
Auxin and GA signaling play important roles in the maize response to phosphate deficiency
inferredcites →https://doi.org/10.1016/j.tplants.2018.01.007openalex-snapshot
Fast-Forwarding Genetic Gain
inferredcites →https://doi.org/10.1016/j.tplants.2018.02.003openalex-snapshot
The C/S1 bZIP Network: A Regulatory Hub Orchestrating Plant Energy Homeostasis
inferredcites →https://doi.org/10.1016/s0016-7061(03)00040-5openalex-snapshot
Fertility capability soil classification: a tool to help assess soil quality in the tropics
inferredcites →https://doi.org/10.1016/s0378-4290(96)01005-2openalex-snapshot
Temperature effects on radiation use and biomass partitioning in diverse tropical maize cultivars
inferredcites →https://doi.org/10.1016/s0378-4290(96)01006-4openalex-snapshot
Temperature responses of tropical maize cultivars selected for broad adaptation
inferredcites →https://doi.org/10.1038/hdy.1979.42openalex-snapshot
Glossy mutants of maize
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Influence of extreme weather disasters on global crop production
inferredcites →https://doi.org/10.1038/nature22971openalex-snapshot
Improved maize reference genome with single-molecule technologies
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Near-optimal probabilistic RNA-seq quantification
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A meta-analysis of crop yield under climate change and adaptation
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1.5 °C and climate research after the Paris Agreement
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Exome sequencing of geographically diverse barley landraces and wild relatives gives insights into environmental adaptation
inferredcites →https://doi.org/10.1038/ng.3784openalex-snapshot
A study of allelic diversity underlying flowering-time adaptation in maize landraces
inferredcites →https://doi.org/10.1038/nmeth.4324openalex-snapshot
Differential analysis of RNA-seq incorporating quantification uncertainty
inferredcites →https://doi.org/10.1038/s41477-019-0384-1openalex-snapshot
Nitrate–NRT1.1B–SPX4 cascade integrates nitrogen and phosphorus signalling networks in plants
inferredcites →https://doi.org/10.1038/s41477-019-0420-1openalex-snapshot
Author Correction: Nitrate–NRT1.1B–SPX4 cascade integrates nitrogen and phosphorus signalling networks in plants
inferredcites →https://doi.org/10.1038/s41598-017-17342-wopenalex-snapshot
Dissecting the Genetic Basis of Local Adaptation in Soybean
inferredcites →https://doi.org/10.1038/srep02479openalex-snapshot
The maize leaf lipidome shows multilevel genetic control and high predictive value for agronomic traits
inferredcites →https://doi.org/10.1073/pnas.0503927102openalex-snapshot
microRNA172 down-regulates glossy15 to promote vegetative phase change in maize
inferredcites →https://doi.org/10.1073/pnas.1203189109openalex-snapshot
ZmCCT and the genetic basis of day-length adaptation underlying the postdomestication spread of maize
inferredcites →https://doi.org/10.1073/pnas.1222463110openalex-snapshot
Assessing agricultural risks of climate change in the 21st century in a global gridded crop model intercomparison
inferredcites →https://doi.org/10.1074/jbc.m205375200openalex-snapshot
Profiling Membrane Lipids in Plant Stress Responses
inferredcites →https://doi.org/10.1093/bfgp/ely014openalex-snapshot
Role of genomics in promoting the utilization of plant genetic resources in genebanks
inferredcites →https://doi.org/10.1093/bioinformatics/btt730openalex-snapshot
CrossMap: a versatile tool for coordinate conversion between genome assemblies
inferredcites →https://doi.org/10.1093/jxb/erv453openalex-snapshot
Extensive tissue-specific transcriptomic plasticity in maize primary roots upon water deficit
inferredcites →https://doi.org/10.1093/jxb/ery110openalex-snapshot
Distinct gene networks modulate floral induction of autonomous maize and photoperiod-dependent teosinte
inferredcites →https://doi.org/10.1093/jxb/erz131openalex-snapshot
Maize glossy6 is involved in cuticular wax deposition and drought tolerance
inferredcites →https://doi.org/10.1098/rspb.2018.1049openalex-snapshot
Evolutionary and food supply implications of ongoing maize domestication by Mexicancampesinos
inferredcites →https://doi.org/10.1101/373902openalex-snapshot
Fast and flexible linear mixed models for genome-wide genetics
inferredcites →https://doi.org/10.1101/gad.10.23.3018openalex-snapshot
Glossy15, an APETALA2-like gene from maize that regulates leaf epidermal cell identity.
inferredcites →https://doi.org/10.1101/gad.228802openalex-snapshot
In the complex family of heat stress transcription factors, HsfA1 has a unique role as master regulator of thermotolerance in tomato
inferredcites →https://doi.org/10.1104/pp.112.200444openalex-snapshot
Effects of Drought on Gene Expression in Maize Reproductive and Leaf Meristem Tissue Revealed by RNA-Seq
inferredcites →https://doi.org/10.1104/pp.114.248930openalex-snapshot
Lipid Biosynthesis and Protein Concentration Respond Uniquely to Phosphate Supply during Leaf Development in Highly Phosphorus-Efficient Hakea prostrata
inferredcites →https://doi.org/10.1104/pp.117.4.1135openalex-snapshot
Regulation of the Heat-Shock Response
inferredcites →https://doi.org/10.1105/tpc.6.10.1343openalex-snapshot
Glossy15 Controls the Epidermal Juvenile-to-Adult Phase Transition in Maize
inferredcites →https://doi.org/10.1111/j.1752-4571.2008.00038.xopenalex-snapshot
Asymmetrical local adaptation of maize landraces along an altitudinal gradient
inferredcites →https://doi.org/10.1111/tpj.12007openalex-snapshot
Differential remodeling of the lipidome during cold acclimation in natural accessions of Arabidopsis thaliana
inferredcites →https://doi.org/10.1111/tpj.13414openalex-snapshot
Natural variation for gene expression responses to abiotic stress in maize
inferredcites →https://doi.org/10.1126/sciadv.1400218openalex-snapshot
Genome-environment associations in sorghum landraces predict adaptive traits
inferredcites →https://doi.org/10.1126/science.1209244openalex-snapshot
Adaptation to Climate Across the Arabidopsis thaliana Genome
inferredcites →https://doi.org/10.1126/science.aam9425openalex-snapshot
Genomic estimation of complex traits reveals ancient maize adaptation to temperate North America
inferredcites →https://doi.org/10.1186/s12711-015-0105-9openalex-snapshot
Defining window-boundaries for genomic analyses using smoothing spline techniques
inferredcites →https://doi.org/10.1186/s12870-016-0930-1openalex-snapshot
Dual functions of the ZmCCT-associated quantitative trait locus in flowering and stress responses under long-day conditions
inferredcites →https://doi.org/10.1371/journal.pbio.0020347openalex-snapshot
Diversifying Selection in Plant Breeding
inferredcites →https://doi.org/10.1371/journal.pcbi.1003118openalex-snapshot
Software for Computing and Annotating Genomic Ranges
inferredcites →https://doi.org/10.1371/journal.pgen.1003477openalex-snapshot
The Genomic Signature of Crop-Wild Introgression in Maize
inferredcites →https://doi.org/10.1371/journal.pone.0019379openalex-snapshot
A Robust, Simple Genotyping-by-Sequencing (GBS) Approach for High Diversity Species
inferredcites →https://doi.org/10.1371/journal.pone.0047659openalex-snapshot
Inferences from the Historical Distribution of Wild and Domesticated Maize Provide Ecological and Evolutionary Insight
inferredcites →https://doi.org/10.1371/journal.pone.0071377openalex-snapshot
Adaptation of Maize to Temperate Climates: Mid-Density Genome-Wide Association Genetics and Diversity Patterns Reveal Key Genomic Regions, with a Major Contribution of the Vgt2 (ZCN8) Locus
inferredcites →https://doi.org/10.1371/journal.pone.0090346openalex-snapshot
TASSEL-GBS: A High Capacity Genotyping by Sequencing Analysis Pipeline
inferredcites →https://doi.org/10.1534/g3.116.026914openalex-snapshot
Environmental Association Analyses Identify Candidates for Abiotic Stress Tolerance inGlycine soja, the Wild Progenitor of Cultivated Soybeans
inferredcites →https://doi.org/10.1534/g3.119.400549openalex-snapshot
Transcriptome-Wide Association Supplements Genome-Wide Association in Zea mays
inferredcites →https://doi.org/10.1534/genetics.108.097238openalex-snapshot
Historical Divergence and Gene Flow in the Genus Zea
inferredcites →https://doi.org/10.1534/genetics.113.159319openalex-snapshot
Genomic Signature of Adaptation to Climate in Medicago truncatula
inferredcites →https://doi.org/10.1534/genetics.115.178327openalex-snapshot
Independent Molecular Basis of Convergent Highland Adaptation in Maize
inferredcites →https://doi.org/10.2135/cropsci1994.0011183x003400010002xopenalex-snapshot
Highland Maize from Central Mexico—Its Origin, Characteristics, and Use in Breeding Programs
inferredcites →https://doi.org/10.2135/cropsci1995.0011183x003500020009xopenalex-snapshot
In Situ Conservation of Landraces in Centers of Crop Diversity
inferredcites →https://doi.org/10.2135/cropsci2012.09.0545openalex-snapshot
Identification of Drought, Heat, and Combined Drought and Heat Tolerant Donors in Maize
inferredcites →https://doi.org/10.31274/rtd-180813-12789openalex-snapshot
Identification of quantitative trait loci associated with flowering, vegetative traits and photoperiod response in maize (Zea mays L)
inferredcites →https://doi.org/10.3389/fpls.2017.00937openalex-snapshot
Manipulation of Metabolic Pathways to Develop Vitamin-Enriched Crops for Human Health
inferredcites →https://doi.org/10.3389/fpls.2018.01919openalex-snapshot
Genome-Wide Association Mapping and Genomic Prediction Analyses Reveal the Genetic Architecture of Grain Yield and Flowering Time Under Drought and Heat Stress Conditions in Maize
inferredcites →https://doi.org/10.3390/plants5040041openalex-snapshot
Synthesis and Functions of Jasmonates in Maize
inferredcites →https://doi.org/10.3835/plantgenome2015.07.0053openalex-snapshot
Expanding Maize Genetic Resources with Predomestication Alleles: Maize–Teosinte Introgression Populations
inferredcites →https://doi.org/10.7554/elife.05861openalex-snapshot
Genetic, evolutionary and plant breeding insights from the domestication of maize
inferredcites →https://doi.org/10.7554/elife.32077openalex-snapshot
LPCAT1 controls phosphate homeostasis in a zinc-dependent manner

What points at this work

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

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Achieving High‐Density and Stress‐Resilient Maize Breeding Via Germplasm Innovation
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The impact of Pleistocene glaciations and environmental gradients on the genetic structure of Embothrium coccineum
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Extensive haplotypes are associated with population differentiation and environmental adaptability in Upland cotton (Gossypium hirsutum)
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Comparative Transcriptome Analysis Reveals Divergent Gene Expression Dynamics During Anther Maturation in Maize and Its Wild Progenitor Teosinte
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GGE analysis and stability of traits in tomato cultivars grown under organic farming conditions: A two-year study
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Bringing more players into play: Leveraging stress in genome wide association studies
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Crop adaptation to climate change: An evolutionary perspective
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Redesigning crop varieties to win the race between climate change and food security
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The arches and spandrels of maize domestication, adaptation, and improvement
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Environmental genome-wide association studies across precipitation regimes reveal that the E3 ubiquitin ligase MBR1 regulates plant adaptation to rainy environments
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Diversity analysis of 80,000 wheat accessions reveals consequences and opportunities of selection footprints
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Evolutionary and functional genomics of DNA methylation in maize domestication and improvement
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Maladaptation in cereal crop landraces following a soot-producing climate catastrophe
inferred← citeshttps://doi.org/10.1038/s41477-024-01654-7openalex-snapshot
Heritable microbiome variation is correlated with source environment in locally adapted maize varieties
inferred← citeshttps://doi.org/10.1038/s41588-024-01761-3openalex-snapshot
Seedling root system adaptation to water availability during maize domestication and global expansion
inferred← citeshttps://doi.org/10.1071/9781486314935.bk08025_part3openalex-snapshot
Adaptation and change
inferred← citeshttps://doi.org/10.1073/pnas.2100036119openalex-snapshot
An adaptive teosinte mexicana introgression modulates phosphatidylcholine levels and is associated with maize flowering time
inferred← citeshttps://doi.org/10.1073/pnas.2205769120openalex-snapshot
The next era of crop domestication starts now
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A B73×Palomero Toluqueño mapping population reveals local adaptation in Mexican highland maize
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Analysis of genotype-by-environment interactions in a maize mapping population
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Molecular Parallelism Underlies Convergent Highland Adaptation of Maize Landraces
inferred← citeshttps://doi.org/10.1101/2020.09.30.321018openalex-snapshot
Genome-wide SNP genotyping of DNA pools identifies untapped landraces and genomic regions that could enrich the maize breeding pool
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Not so local: the population genetics of convergent adaptation in maize and teosinte
inferred← citeshttps://doi.org/10.1101/2024.02.02.578655openalex-snapshot
Genome-wide diversity in lowland and highland maize landraces from southern South America: population genetics insights to assist conservation
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Genotype-environment association across precipitation regimens reveals the mechanism of plant adaptation to rainy environments
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The utility of environmental data from traditional varieties for climate-adaptive maize breeding
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RDAforest: Identifying Environmental Drivers of Polygenic Adaptation
inferred← citeshttps://doi.org/10.1111/eva.13372openalex-snapshot
Demonstration of local adaptation in maize landraces by reciprocal transplantation
inferred← citeshttps://doi.org/10.1111/eva.13673openalex-snapshot
Evidence that variation in root anatomy contributes to local adaptation in Mexican native maize
inferred← citeshttps://doi.org/10.1111/eva.70047openalex-snapshot
Genome‐Wide Diversity in Lowland and Highland Maize Landraces From Southern South America: Population Genetics Insights to Assist Conservation
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Identification of Genetic Variation Associated With Heat Tolerance in Cowpea ( Vigna unguiculata L. Walp.)
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Genotyping of DNA pools identifies untapped landraces and genomic regions to develop next‐generation varieties
inferred← citeshttps://doi.org/10.1126/science.adg8940openalex-snapshot
Two teosintes made modern maize
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Göte Turesson’s research legacy to Hereditas: from the ecotype concept in plants to the analysis of landraces’ diversity in crops
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Diamonds in the not-so-rough: Wild relative diversity hidden in crop genomes
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Gene regulatory effects of a large chromosomal inversion in highland maize
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Environmental data provide marginal benefit for predicting climate adaptation
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Selective Loss of Diversity in Doubled-Haploid Lines from European Maize Landraces
inferred← citeshttps://doi.org/10.3389/fpls.2021.674036openalex-snapshot
Opportunities and Challenges of Predictive Approaches for Harnessing the Potential of Genetic Resources
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Multivariate Interaction Analysis of Zea mays L. Genotypes Growth Productivity in Different Environmental Conditions
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Uncoupling the Effects of Highland Maize Chromosomal Inversion Inv4m from Leaf Phosphorus Deficiency Responses
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The population genetics of convergent adaptation in maize and teosinte is not locally restricted
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Not so local: the population genetics of convergent adaptation in maize and teosinte
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