ArticleGenome biology2021
Limited haplotype diversity underlies polygenic trait architecture across 70 years of wheat breeding.
Article in Genome biology, 2021. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 55 papers.
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Who cites it
55 citing papers in PubMed, 77 citations in OpenAlex.
- Multi-metric evaluation and parametric optimization of stochastic gradient boosting machines for genomic prediction and selection in wheat (Triticum aestivum) breeding.G3 (Bethesda, Md.) · 2026Article
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- Wheat's war against stripe rust: Integrating host immunity, genomics and breeding for durable resistance.The plant genome · 2026Review
- Discovery and characterization of gene-by-environment and epistatic genetic effects in a vertebrate model.Cell genomics · 2026Article
- Beyond Data: Artificial intelligence, knowledge graphs, and the next revolution in wheat breeding.Plant communications · 2026Review
- Association mapping of hybrid seed set and heterosis in a central European multi-parental wheat population.TAG. Theoretical and applied genetics. Theoretische und angewandte Genetik · 2026Article
- pyRootHair: Machine learning accelerated software for high-throughput phenotyping of plant root hair traits.GigaScience · 2026Article
- MAGIC populations: a next-generation framework for dissecting complex quantitative traits and accelerating molecular breeding in crops.Frontiers in plant science · 2026Review
- Normalized cumulative gain as an alternative evaluation measure for genomic selection models.Genetics, selection, evolution : GSE · 2025Article
- Historic insights and future potential in wheat elaborated using a diverse cultivars collection and extended phenotyping.Scientific reports · 2025Article
- The Genetics of Plant-Plant Interactions and Their Cascading Effects on Agroecosystems-from Model Plants to Applications.Plant & cell physiology · 2025Review
- Advances in multi-trait genomic prediction approaches: classification, comparative analysis, and perspectives.Briefings in bioinformatics · 2025Review
- Recombination and structural variation in a large 8-founder wheat MAGIC population.G3 (Bethesda, Md.) · 2025Article
- Using feedback in pooled experiments augmented with imputation for high genotyping accuracy at reduced cost.G3 (Bethesda, Md.) · 2025Article
- Identification and validation of a major QTL, QFhb-6AL, for Fusarium head blight resistance on chromosome 6AL in wheat.TAG. Theoretical and applied genetics. Theoretische und angewandte Genetik · 2025Article
- MRI-Seed-Wizard: combining deep learning algorithms with magnetic resonance imaging enables advanced seed phenotyping.Journal of experimental botany · 2025Article
- Multispectral imaging and automated analysis for quantifying grain quality to reveal known and potential novel alleles affecting grain traits in wheat.Frontiers in plant science · 2025Article
- FlexLMM: a Nextflow linear mixed model framework for GWAS.Bioinformatics (Oxford, England) · 2024Article
- An eight-founder wheat MAGIC population allows fine-mapping of flowering time loci and provides novel insights into the genetic control of flowering time.TAG. Theoretical and applied genetics. Theoretische und angewandte Genetik · 2024Article
- lcQTH: Rapid quantitative trait mapping by tracing parental haplotypes with ultra-low-coverage sequencing.Plant communications · 2024Article
Corrections and comments
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Authors and funding
12 authors at 5 institutions in 3 countries.
Funding
Abstract
backgroundSelection has dramatically shaped genetic and phenotypic variation in bread wheat. We can assess the genomic basis of historical phenotypic changes, and the potential for future improvement, using experimental populations that attempt to undo selection through the randomizing effects of recombination.
resultsWe bred the NIAB Diverse MAGIC multi-parent population comprising over 500 recombinant inbred lines, descended from sixteen historical UK bread wheat varieties released between 1935 and 2004. We sequence the founders' genes and promoters by capture, and the MAGIC population by low-coverage whole-genome sequencing. We impute 1.1 M high-quality SNPs that are over 99% concordant with array genotypes. Imputation accuracy only marginally improves when including the founders' genomes as a haplotype reference panel. Despite capturing 73% of global wheat genetic polymorphism, 83% of genes cluster into no more than three haplotypes. We phenotype 47 agronomic traits over 2 years and map 136 genome-wide significant associations, concentrated at 42 genetic loci with large and often pleiotropic effects. Around half of these overlap known quantitative trait loci. Most traits exhibit extensive polygenicity, as revealed by multi-locus shrinkage modelling.
conclusionsOur results are consistent with a gene pool of low haplotypic diversity, containing few novel loci of large effect. Most past, and projected future, phenotypic changes arising from existing variation involve fine-scale shuffling of a few haplotypes to recombine dozens of polygenic alleles of small effect. Moreover, extensive pleiotropy means selection on one trait will have unintended consequences, exemplified by the negative trade-off between yield and protein content, unless selection and recombination can break unfavorable trait-trait associations.
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Registered trials
Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.