Limited haplotype diversity underlies polygenic trait architecture across 70 years of wheat breeding
Year: 2021
Type: article
Abstract: BACKGROUND: Selection 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. RESULTS: We 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. CONCLUSIONS: Our 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.
Source: Genome biology
Institutions: University of East Anglia, Norwich Research Park, University College London, National Institute of Agricultural Botany, Centro Internacional de Mejoramiento de Maíz Y Trigo, International Maize and Wheat Improvement Center, Earlham Institute, Aberystwyth University, Institute of Biological, Environmental and Rural Sciences, Scotland's Rural College
Language: English
Subfield: Plant Science
Domain: Life Sciences
SDG: Zero hunger
Open Access status: gold
Estimated APC paid: $4,890
Awards: 15-IWYP Using Next Generation Genetic Approaches to Exploit Phenotypic Variation in Photosynthetic Efficiency to Increase Wheat Yield, G1366862294, Supporting EI’s ISPs and the UK Community with Genomics and Single Cell Analysis, Improvement of Barley, Rice and Chickpea by Population Sequencing, Enhancing diversity in UK wheat through a public sector prebreeding programme, SEQUENCING THE GENIC PORTION OF SEEDS OF DISCOVERY ADVANCE PRE- BREEDING GERMPLASM TO UNCOVER THE GENETIC VARIATION, National Plant Phenomics Centre, G3202646069, G338365092, G3593750065, BBSRC Core Strategic Programme in Resilient Crops: Oats, G3921636091, G469817495, BBSRC-NCG in Plant Phenotyping, The wheat DIVERSE MAGIC: Community Access to Resources, Protocols and Tools, G5347142819, Signatures of Domestication and Adaptation, G5627136915, G5948631762, G7341187767, The wheat Diverse MAGIC platform: Community Access to Resources, Protocols and Tools, G8094012365, G8204187466, G8357017033, Development of multi-parent advanced intercoss populations for fine mapping QTL in wheat
OpenAlex ID: W3158317536