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Whole-genome sequencing of diverse wheat accessions uncovers genetic changes during modern breeding in China and the United States

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What this work says

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

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Identification of regions under selection and loci controlling agronomic traits in a soft red winter wheat population

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Genome-wide variation patterns between landraces and cultivars uncover divergent selection during modern wheat breeding

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Identification of a candidate gene for a QTL for spikelet number per spike on wheat chromosome arm 7AL by high-resolution genetic mapping

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Structural variation in the 5′ upstream region of photoperiod-insensitive alleles Ppd-A1a and Ppd-B1a identified in hexaploid wheat (Triticum aestivum L.), and their effect on heading time

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Tiller formation in rice is altered by overexpression of OsIAGLU gene encoding an IAA-conjugating enzyme or exogenous treatment of free IAA

inferredcites →https://doi.org/10.1016/j.ajhg.2010.11.011openalex-snapshot

GCTA: A Tool for Genome-wide Complex Trait Analysis

inferredcites →https://doi.org/10.1016/j.cj.2019.12.005openalex-snapshot

Fine mapping and characterization of the awn inhibitor B1 locus in common wheat (Triticum aestivum L.)

inferredcites →https://doi.org/10.1016/j.cj.2020.12.007openalex-snapshot

Wheat MADS-box gene TaSEP3-D1 negatively regulates heading date

inferredcites →https://doi.org/10.1016/j.molp.2020.07.008openalex-snapshot

High-Resolution Genome-wide Association Study Identifies Genomic Regions and Candidate Genes for Important Agronomic Traits in Wheat

inferredcites →https://doi.org/10.1016/j.molp.2020.09.001openalex-snapshot

Resequencing of 145 Landmark Cultivars Reveals Asymmetric Sub-genome Selection and Strong Founder Genotype Effects on Wheat Breeding in China

inferredcites →https://doi.org/10.1016/j.molp.2022.01.004openalex-snapshot

Wheat breeding history reveals synergistic selection of pleiotropic genomic sites for plant architecture and grain yield

inferredcites →https://doi.org/10.1016/j.molp.2022.01.014openalex-snapshot

Cloning and functional characterization of Rht8, a “Green Revolution” replacement gene in wheat

inferredcites →https://doi.org/10.1016/j.nbt.2011.04.006openalex-snapshot

An atypical HLH protein OsLF in rice regulates flowering time and interacts with OsPIL13 and OsPIL15

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Landraces: A review of definitions and classifications

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‘Green revolution’ genes encode mutant gibberellin response modulators

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Feeding the future

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Non-canonical regulation of SPL transcription factors by a human OTUB1-like deubiquitinase defines a new plant type rice associated with higher grain yield

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Reconstructing Indian population history

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Resequencing 302 wild and cultivated accessions identifies genes related to domestication and improvement in soybean

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Erratum: Resequencing 302 wild and cultivated accessions identifies genes related to domestication and improvement in soybean

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Genomic analyses in cotton identify signatures of selection and loci associated with fiber quality and yield traits

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Crop genomics: advances and applications

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GS9 acts as a transcriptional activator to regulate rice grain shape and appearance quality

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Diversity analysis of 80,000 wheat accessions reveals consequences and opportunities of selection footprints

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Origin and adaptation to high altitude of Tibetan semi-wild wheat

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O-linked N-acetylglucosamine transferase is involved in fine regulation of flowering time in winter wheat

inferredcites →https://doi.org/10.1038/s41467-022-31581-0openalex-snapshot

Dispersed emergence and protracted domestication of polyploid wheat uncovered by mosaic ancestral haploblock inference

inferredcites →https://doi.org/10.1038/s41477-023-01367-3openalex-snapshot

Population genomics unravels the Holocene history of bread wheat and its relatives

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Genebank genomics highlights the diversity of a global barley collection

inferredcites →https://doi.org/10.1038/s41588-019-0382-2openalex-snapshot

Exome sequencing highlights the role of wild-relative introgression in shaping the adaptive landscape of the wheat genome

inferredcites →https://doi.org/10.1038/s41588-019-0393-zopenalex-snapshot

Tracing the ancestry of modern bread wheats

inferredcites →https://doi.org/10.1038/s41588-020-00722-wopenalex-snapshot

Triticum population sequencing provides insights into wheat adaptation

inferredcites →https://doi.org/10.1038/s41588-020-0616-3openalex-snapshot

Genome-wide selection and genetic improvement during modern maize breeding

inferredcites →https://doi.org/10.1038/s41588-022-01189-7openalex-snapshot

Genomics-informed prebreeding unlocks the diversity in genebanks for wheat improvement

inferredcites →https://doi.org/10.1038/s41598-019-38570-2openalex-snapshot

Genome-wide association study revealed that the TaGW8 gene was associated with kernel size in Chinese bread wheat

inferredcites →https://doi.org/10.1038/s41598-019-50331-9openalex-snapshot

TaAPO-A1, an ortholog of rice ABERRANT PANICLE ORGANIZATION 1, is associated with total spikelet number per spike in elite European hexaploid winter wheat (Triticum aestivum L.) varieties

inferredcites →https://doi.org/10.1073/pnas.0607142103openalex-snapshot

The wheat and barley vernalization gene VRN3 is an orthologue of FT

inferredcites →https://doi.org/10.1073/pnas.1217133110openalex-snapshot

Genome-wide comparative diversity uncovers multiple targets of selection for improvement in hexaploid wheat landraces and cultivars

inferredcites →https://doi.org/10.1073/pnas.1515919112openalex-snapshot

Breeding signatures of rice improvement revealed by a genomic variation map from a large germplasm collection

inferredcites →https://doi.org/10.1086/519795openalex-snapshot

PLINK: A Tool Set for Whole-Genome Association and Population-Based Linkage Analyses

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CLUMPP: a cluster matching and permutation program for dealing with label switching and multimodality in analysis of population structure

inferredcites →https://doi.org/10.1093/bioinformatics/btp324openalex-snapshot

Fast and accurate short read alignment with Burrows–Wheeler transform

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/bty875openalex-snapshot

PopLDdecay: a fast and effective tool for linkage disequilibrium decay analysis based on variant call format files

inferredcites →https://doi.org/10.1093/jxb/erv122openalex-snapshot

Exploiting genetic diversity from landraces in wheat breeding for adaptation to climate change

inferredcites →https://doi.org/10.1093/pcp/pcaa152openalex-snapshot

De Novo Genome Assembly of the Japanese Wheat Cultivar Norin 61 Highlights Functional Variation in Flowering Time andFusarium-Resistant Genes in East Asian Genotypes

inferredcites →https://doi.org/10.1101/gr.094052.109openalex-snapshot

Fast model-based estimation of ancestry in unrelated individuals

inferredcites →https://doi.org/10.1101/gr.100545.109openalex-snapshot

Population differentiation as a test for selective sweeps

inferredcites →https://doi.org/10.1101/gr.107524.110openalex-snapshot

The Genome Analysis Toolkit: A MapReduce framework for analyzing next-generation DNA sequencing data

inferredcites →https://doi.org/10.1104/pp.18.00023openalex-snapshot

Rht18 Semidwarfism in Wheat Is Due to Increased GA 2-oxidaseA9 Expression and Reduced GA Content

inferredcites →https://doi.org/10.1104/pp.20.00279openalex-snapshot

Mitochondria-Associated Pyruvate Kinase Complexes Regulate Grain Filling in Rice

inferredcites →https://doi.org/10.1111/j.1365-313x.2012.05001.xopenalex-snapshot

Rice RNA‐dependent RNA polymerase 6 acts in small RNA biogenesis and spikelet development

inferredcites →https://doi.org/10.1111/nph.16152openalex-snapshot

Sequence‐based mapping identifies a candidate transcription repressor underlying awn suppression at the B1 locus in wheat

inferredcites →https://doi.org/10.1111/nph.16154openalex-snapshot

Dominant inhibition of awn development by a putative zinc‐finger transcriptional repressor expressed at the B1 locus in wheat

inferredcites →https://doi.org/10.1111/nph.17388openalex-snapshot

FRIZZY PANICLE defines a regulatory hub for simultaneously controlling spikelet formation and awn elongation in bread wheat

inferredcites →https://doi.org/10.1111/nph.17733openalex-snapshot

Crop genetic erosion: understanding and responding to loss of crop diversity

inferredcites →https://doi.org/10.1111/pbi.12770openalex-snapshot

Uncovering the dispersion history, adaptive evolution and selection of wheat in China

inferredcites →https://doi.org/10.1111/pbi.13361openalex-snapshot

The Wheat 660K SNP array demonstrates great potential for marker‐assisted selection in polyploid wheat

inferredcites →https://doi.org/10.1111/pce.14101openalex-snapshot

Rice shaker potassium channel OsAKT2 positively regulates salt tolerance and grain yield by mediating K + redistribution

inferredcites →https://doi.org/10.1111/tpj.13613openalex-snapshot

WIDE AND THICK GRAIN 1 , which encodes an otubain‐like protease with deubiquitination activity, influences grain size and shape in rice

inferredcites →https://doi.org/10.1111/tpj.14168openalex-snapshot

A wheat dominant dwarfing line with Rht12 , which reduces stem cell length and affects gibberellic acid synthesis, is a 5AL terminal deletion line

inferredcites →https://doi.org/10.1111/tpj.14575openalex-snapshot

Natural variations in the promoter of Awn Length Inhibitor 1 ( ALI‐1 ) are associated with awn elongation and grain length in common wheat

inferredcites →https://doi.org/10.1126/sciadv.aav0536openalex-snapshot

Worldwide phylogeography and history of wheat genetic diversity

inferredcites →https://doi.org/10.1126/science.1094305openalex-snapshot

The Wheat VRN2 Gene Is a Flowering Repressor Down-Regulated by Vernalization

inferredcites →https://doi.org/10.1126/science.1117619openalex-snapshot

The Pseudo-Response Regulator Ppd-H1 Provides Adaptation to Photoperiod in Barley

inferredcites →https://doi.org/10.1126/science.1250092openalex-snapshot

Ancient hybridizations among the ancestral genomes of bread wheat

inferredcites →https://doi.org/10.1126/science.aar7191openalex-snapshot

Shifting the limits in wheat research and breeding using a fully annotated reference genome

inferredcites →https://doi.org/10.1186/s12864-018-4969-2openalex-snapshot

Unlocking the novel genetic diversity and population structure of synthetic Hexaploid wheat

inferredcites →https://doi.org/10.1186/s12870-020-02473-6openalex-snapshot

Identification of a novel ERF gene, TaERF8, associated with plant height and yield in wheat

inferredcites →https://doi.org/10.1186/s13059-015-0606-4openalex-snapshot

A haplotype map of allohexaploid wheat reveals distinct patterns of selection on homoeologous genomes

inferredcites →https://doi.org/10.1186/s13059-019-1744-xopenalex-snapshot

Frequent intra- and inter-species introgression shapes the landscape of genetic variation in bread wheat

inferredcites →https://doi.org/10.1371/journal.pgen.1002967openalex-snapshot

Inference of Population Splits and Mixtures from Genome-Wide Allele Frequency Data

inferredcites →https://doi.org/10.1371/journal.pone.0066428openalex-snapshot

Yield Trends Are Insufficient to Double Global Crop Production by 2050

What points at this work

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

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Genetic and transcriptomic identification of WPG1 controlling nitrogen allocation-related leaf chlorisis and premature senescence in wheat

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AcRR1 of Agropyron cristatum boosts wheat yield by regulating grain number per spike and heading date

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inferred← citeshttps://doi.org/10.6084/m9.figshare.26143682openalex-snapshot

Additional file 1 of Tagging large CNV blocks in wheat boosts digitalization of germplasm resources by ultra-low-coverage sequencing

inferred← citeshttps://doi.org/10.6084/m9.figshare.26143796openalex-snapshot

Additional file 2 of Tagging large CNV blocks in wheat boosts digitalization of germplasm resources by ultra-low-coverage sequencing

inferred← citeshttps://doi.org/10.6084/m9.figshare.26741195openalex-snapshot

Additional file 3 of Tagging large CNV blocks in wheat boosts digitalization of germplasm resources by ultra-low-coverage sequencing

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