Gene disruption by structural mutations drives selection in US rice breeding over the last century

Autoři: Justin N. Vaughn aff001;  Walid Korani aff002;  Joshua C. Stein aff003;  Jeremy D. Edwards aff004;  Daniel G. Peterson aff005;  Sheron A. Simpson aff001;  Ramey C. Youngblood aff005;  Jane Grimwood aff006;  Kapeel Chougule aff003;  Doreen H. Ware aff003;  Anna M. McClung aff004;  Brian E. Scheffler aff001
Působiště autorů: USDA-ARS, Genomics and Bioinformatics Research Unit, Stoneville, Mississippi, United States of America aff001;  University of Georgia, Athens, Institute of Plant Breeding, Genetics, and Genomics, Athens, Georgia, United States of America aff002;  Cold Spring Harbor Laboratory, Cold Springs Harbor, New York, United States of America aff003;  USDA-ARS, Dale Bumpers National Rice Research Center, Stuttgart, Arkansas, United States of America aff004;  Mississippi State University, Institute for Genomics, Biocomputing & Biotechnology, Starkville, Mississippi, United States of America aff005;  Hudson-Alpha Institute for Biotechnology, Huntsville, Alabama, United States of America aff006;  USDA-ARS, Robert W. Holley Center for Agriculture and Health, Ithaca, New York, United States of America aff007
Vyšlo v časopise: Gene disruption by structural mutations drives selection in US rice breeding over the last century. PLoS Genet 17(3): e1009389. doi:10.1371/journal.pgen.1009389
Kategorie: Research Article


The genetic basis of general plant vigor is of major interest to food producers, yet the trait is recalcitrant to genetic mapping because of the number of loci involved, their small effects, and linkage. Observations of heterosis in many crops suggests that recessive, malfunctioning versions of genes are a major cause of poor performance, yet we have little information on the mutational spectrum underlying these disruptions. To address this question, we generated a long-read assembly of a tropical japonica rice (Oryza sativa) variety, Carolina Gold, which allowed us to identify structural mutations (>50 bp) and orient them with respect to their ancestral state using the outgroup, Oryza glaberrima. Supporting prior work, we find substantial genome expansion in the sativa branch. While transposable elements (TEs) account for the largest share of size variation, the majority of events are not directly TE-mediated. Tandem duplications are the most common source of insertions and are highly enriched among 50-200bp mutations. To explore the relative impact of various mutational classes on crop fitness, we then track these structural events over the last century of US rice improvement using 101 resequenced varieties. Within this material, a pattern of temporary hybridization between medium and long-grain varieties was followed by recent divergence. During this long-term selection, structural mutations that impact gene exons have been removed at a greater rate than intronic indels and single-nucleotide mutations. These results support the use of ab initio estimates of mutational burden, based on structural data, as an orthogonal predictor in genomic selection.

Klíčová slova:

Alleles – Genetic loci – Genomics – Haplotypes – Mutation – Rice – Sequence alignment – Single nucleotide polymorphisms


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