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

Vaughn, Justin N, Korani, Walid, Stein, Joshua C, Edwards, Jeremy D, Peterson, Daniel G, Simpson, Sheron A, Youngblood, Ramey C, Grimwood, Jane, Chougule, Kapeel, Ware, Doreen H, McClung, Anna M, Scheffler, Brian E (March 2021) Gene disruption by structural mutations drives selection in US rice breeding over the last century. PLoS Genetics, 17 (3). e1009389. ISSN 1553-7404

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Abstract

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.

Item Type:	Paper
Subjects:	bioinformatics bioinformatics > genomics and proteomics > genetics & nucleic acid processing > DNA, RNA structure, function, modification > DNA expression bioinformatics > genomics and proteomics > genetics & nucleic acid processing > DNA, RNA structure, function, modification bioinformatics > genomics and proteomics > genetics & nucleic acid processing bioinformatics > genomics and proteomics organism description > plant > Oryza bioinformatics > genomics and proteomics > genetics & nucleic acid processing > DNA, RNA structure, function, modification > mutations organism description > plant > rice bioinformatics > genomics and proteomics > genetics & nucleic acid processing > DNA, RNA structure, function, modification > DNA expression > transposable elements
CSHL Authors:	Stein, Joshua C. Chougule, Kapeel Ware, Doreen H.
Communities:	CSHL labs > Ware lab
SWORD Depositor:	CSHL Elements
Depositing User:	CSHL Elements
Date:	March 2021
Date Deposited:	05 May 2021 13:57
Last Modified:	25 Jan 2024 20:33
PMCID:	PMC7971508
Related URLs:	Publisher
URI:	https://repository.cshl.edu/id/eprint/39988

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