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Genomic and phenotypic evidence for an incomplete domestication of South American grain amaranth ( Amaranthus caudatus )

https://doi.org/10.1101/025866
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What this work says

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

inferredcites →https://doi.org/10.1002/9780470650172.ch7openalex-snapshot
Genetic Resources and Breeding ofAmaranthus
inferredcites →https://doi.org/10.1007/978-94-007-6401-9_12openalex-snapshot
Molecular Genetic Basis of the Domestication Syndrome in Cereals
inferredcites →https://doi.org/10.1007/s00122-005-0045-9openalex-snapshot
A genome-wide analysis of differentiation between wild and domesticated Phaseolus vulgaris from Mesoamerica
inferredcites →https://doi.org/10.1007/s00122-011-1619-3openalex-snapshot
Genetic diversity and population structure in cultivated sunflower and a comparison to its wild progenitor, Helianthus annuus L
inferredcites →https://doi.org/10.1016/j.cell.2006.12.006openalex-snapshot
The Molecular Genetics of Crop Domestication
inferredcites →https://doi.org/10.1016/j.pbi.2014.02.001openalex-snapshot
The contribution of genetic and genomic approaches to plant domestication studies
inferredcites →https://doi.org/10.1016/j.quaint.2013.02.035openalex-snapshot
Amaranthus hybridus L. ssp. hybridus in an archaeological site from the initial mid-Holocene in the Southern Argentinian Puna
inferredcites →https://doi.org/10.1016/j.tplants.2013.08.007openalex-snapshot
Molecular mechanisms involved in convergent crop domestication
inferredcites →https://doi.org/10.1016/j.tplants.2013.12.002openalex-snapshot
Plant domestication versus crop evolution: a conceptual framework for cereals and grain legumes
inferredcites →https://doi.org/10.1038/npre.2012.6956.1openalex-snapshot
Inference of population splits and mixtures from genome-wide allele frequency data
inferredcites →https://doi.org/10.1038/sj.hdy.6800563openalex-snapshot
Amaranthus hybridus can be pollinated frequently by A. tuberculatus under field conditions
inferredcites →https://doi.org/10.1073/pnas.0603152103openalex-snapshot
Phylogeography of Asian wild rice, Oryza rufipogon , reveals multiple independent domestications of cultivated rice, Oryza sativa
inferredcites →https://doi.org/10.1073/pnas.1215985110openalex-snapshot
Population genomic and genome-wide association studies of agroclimatic traits in sorghum
inferredcites →https://doi.org/10.1073/pnas.81.24.8014openalex-snapshot
Ribosomal DNA spacer-length polymorphisms in barley: mendelian inheritance, chromosomal location, and population dynamics.
inferredcites →https://doi.org/10.1093/bioinformatics/btg412openalex-snapshot
APE: Analyses of Phylogenetics and Evolution in R language
inferredcites →https://doi.org/10.1093/bioinformatics/btr330openalex-snapshot
The variant call format and VCFtools
inferredcites →https://doi.org/10.1093/bioinformatics/btr521openalex-snapshot
adegenet 1.3-1 : new tools for the analysis of genome-wide SNP data
inferredcites →https://doi.org/10.1093/molbev/msh018openalex-snapshot
Neighbor-Net: An Agglomerative Method for the Construction of Phylogenetic Networks
inferredcites →https://doi.org/10.1093/molbev/msj030openalex-snapshot
Application of Phylogenetic Networks in Evolutionary Studies
inferredcites →https://doi.org/10.1093/molbev/msu063openalex-snapshot
Empirical Assessment of RAD Sequencing for Interspecific Phylogeny
inferredcites →https://doi.org/10.1093/oxfordjournals.jhered.a109580openalex-snapshot
Outcrossing rate in grain amaranths
inferredcites →https://doi.org/10.1101/085472openalex-snapshot
Analysis of phylogenetic relationships and genome size evolution of the Amaranthus genus using GBS indicates the ancestors of an ancient crop
inferredcites →https://doi.org/10.1101/gr.094052.109openalex-snapshot
Fast model-based estimation of ancestry in unrelated individuals
inferredcites →https://doi.org/10.1111/1755-0998.12291openalex-snapshot
Restriction site‐associated DNA sequencing, genotyping error estimation and de novo assembly optimization for population genetic inference
inferredcites →https://doi.org/10.1111/j.1399-3054.1992.tb04764.xopenalex-snapshot
Comparison of three DNA fluorochromes for flow cytometric estimation of nuclear DNA content in plants
inferredcites →https://doi.org/10.1111/j.1469-8137.2012.04253.xopenalex-snapshot
Patterns and processes in crop domestication: an historical review and quantitative analysis of 203 global food crops
inferredcites →https://doi.org/10.1111/j.1558-5646.1984.tb05657.xopenalex-snapshot
ESTIMATING F -STATISTICS FOR THE ANALYSIS OF POPULATION STRUCTURE
inferredcites →https://doi.org/10.1111/mec.12276openalex-snapshot
RAD seq underestimates diversity and introduces genealogical biases due to nonrandom haplotype sampling
inferredcites →https://doi.org/10.1111/mec.12354openalex-snapshot
Stacks: an analysis tool set for population genomics
inferredcites →https://doi.org/10.1111/mec.12738openalex-snapshot
Transcriptome population genomics reveals severe bottleneck and domestication cost in the A frican rice ( O ryza glaberrima)
inferredcites →https://doi.org/10.1111/nph.13518openalex-snapshot
Single vs multiple independent olive domestications: the jury is (still) out
inferredcites →https://doi.org/10.1111/pbr.12027openalex-snapshot
Genetic diversity and population structure of the selected core set in A maranthus using SSR markers
inferredcites →https://doi.org/10.1146/annurev-arplant-050312-120048openalex-snapshot
A Bountiful Harvest: Genomic Insights into Crop Domestication Phenotypes
inferredcites →https://doi.org/10.1186/1471-2156-11-94openalex-snapshot
Discriminant analysis of principal components: a new method for the analysis of genetically structured populations
inferredcites →https://doi.org/10.1186/s13059-015-0712-3openalex-snapshot
Barley landraces are characterized by geographically heterogeneous genomic origins
inferredcites →https://doi.org/10.1371/journal.pbio.0050310openalex-snapshot
Population Genomics: Whole-Genome Analysis of Polymorphism and Divergence in Drosophila simulans
inferredcites →https://doi.org/10.1371/journal.pgen.1002703openalex-snapshot
New Insight into the History of Domesticated Apple: Secondary Contribution of the European Wild Apple to the Genome of Cultivated Varieties
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.0032253openalex-snapshot
Development of High-Density Genetic Maps for Barley and Wheat Using a Novel Two-Enzyme Genotyping-by-Sequencing Approach
inferredcites →https://doi.org/10.1371/journal.pone.0039563openalex-snapshot
Genetic Patterns of Domestication in Pigeonpea (Cajanus cajan (L.) Millsp.) and Wild Cajanus Relatives
inferredcites →https://doi.org/10.1371/journal.pone.0102448openalex-snapshot
Using Genotyping-By-Sequencing (GBS) for Genomic Discovery in Cultivated Oat
inferredcites →https://doi.org/10.1534/g3.111.000240openalex-snapshot
Stacks: Building and Genotyping Loci De Novo From Short-Read Sequences
inferredcites →https://doi.org/10.1600/036364415x688376openalex-snapshot
Morphologic and Taxonomic Analysis of the Weedy and Cultivated Amaranthus hybridus Species Complex
inferredcites →https://doi.org/10.2135/cropsci2005.0163openalex-snapshot
Genome Size Analysis of Weedy Amaranthus Species
inferredcites →https://doi.org/10.2135/cropsci2007.08.0457openalex-snapshot
Development and Characterization of Microsatellite Markers for the Grain Amaranths
inferredcites →https://doi.org/10.2135/cropsci2012.07.0413openalex-snapshot
Assessment of Genetic Diversity in Peruvian Amaranth (Amaranthus caudatus and A. hybridus) Germplasm using Single Nucleotide Polymorphism Markers
inferredcites →https://doi.org/10.2135/cropsci2013.03.0173openalex-snapshot
Relationships between the Weedy Amaranthus hybridus (Amaranthaceae) and the Grain Amaranths
inferredcites →https://doi.org/10.2307/2394998openalex-snapshot
The Grain Amaranths and Their Relatives: A Revised Taxonomic and Geographic Survey
inferredcites →https://doi.org/10.2307/3088717openalex-snapshot
Stem Morphology and Anatomy in Amaranthus L. (Amaranthaceae), Taxonomic Significance
inferredcites →https://doi.org/10.3389/fpls.2016.00816openalex-snapshot
Crossing Methods and Cultivation Conditions for Rapid Production of Segregating Populations in Three Grain Amaranth Species
inferredcites →https://doi.org/10.3835/plantgenome2009.08.0022openalex-snapshot
SNP Discovery via Genomic Reduction, Barcoding, and 454‐Pyrosequencing in Amaranth
inferredcites →https://doi.org/10.7554/elife.06633openalex-snapshot
Ventromedial hypothalamic neurons control a defensive emotion state

What points at this work

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

inferred← citeshttps://doi.org/10.1007/978-981-10-1469-7_5openalex-snapshot
Taxonomy and Phylogeny of Grain Amaranths
inferred← citeshttps://doi.org/10.1016/j.plantsci.2018.01.018openalex-snapshot
Review: Shaping a sustainable food future by rediscovering long-forgotten ancient grains
inferred← citeshttps://doi.org/10.1101/085472openalex-snapshot
Analysis of phylogenetic relationships and genome size evolution of the Amaranthus genus using GBS indicates the ancestors of an ancient crop
inferred← citeshttps://doi.org/10.14522/darwiniana.2019.71.824openalex-snapshot
EVIDENCIAS ARQUEOBOTANICAS TEMPRANAS EN EL OASIS DE CALAMA, EL CEMENTERIO TOPATER 1 (FORMATIVO MEDIO, 500 AC-100 DC, DESIERTO DE ATACAMA, NORTE DE CHILE)
inferred← citeshttps://doi.org/10.3389/fpls.2016.00816openalex-snapshot
Crossing Methods and Cultivation Conditions for Rapid Production of Segregating Populations in Three Grain Amaranth Species
inferred← citeshttps://doi.org/10.3389/fpls.2023.1329377openalex-snapshot
Editorial: Amaranthus: naturally stress-resistant resources for improved agriculture and human health, volume II
inferred← citeshttps://doi.org/10.3389/fpls.2026.1716624openalex-snapshot
Amaranth, the ancient pseudocereal: a promising crop for climate-resilient agriculture and healthy diets
inferred← citeshttps://doi.org/10.3390/app9020253openalex-snapshot
Genome Size Unaffected by Variation in Morphological Traits, Temperature, and Precipitation in Turnip
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