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Published (Version of record)CC BY V4.0, Open Access
Published (Version of record)CC BY V4.0, Open
Journal article
Structural variants in 3000 rice genomes
Genome research, Vol.29(5), pp.870-880
05/2019
PMCID: PMC6499320
PMID: 30992303
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Source: InCites
Abstract
Investigation of large structural variants (SVs) is a challenging yet important task in understanding trait differences in highly repetitive genomes. Combining different bioinformatic approaches for SV detection, we analyzed whole-genome sequencing data from 3000 rice genomes and identified 63 million individual SV calls that grouped into 1.5 million allelic variants. We found enrichment of long SVs in promoters and an excess of shorter variants in 5' UTRs. Across the rice genomes, we identified regions of high SV frequency enriched in stress response genes. We demonstrated how SVs may help in finding causative variants in genome-wide association analysis. These new insights into rice genome biology are valuable for understanding the effects SVs have on gene function, with the prospect of identifying novel agronomically important alleles that can be utilized to improve cultivated rice.
Details
- Title
- Structural variants in 3000 rice genomes
- Creators
- Roven Rommel Fuentes - International Rice Research InstituteDmytro Chebotarov - International Rice Research InstituteJorge Duitama - Universidad de Los AndesSean Smith - Rutgers, The State University of New JerseyJuan Fernando De la Hoz - International Center for Tropical AgricultureMarghoob Mohiyuddin - Roche Sequencing Solutions, Belmont, California 94002, USA.Rod A Wing - University of ArizonaKenneth L McNally - International Rice Research InstituteTatiana Tatarinova - University of La VerneAndrey Grigoriev - Rutgers, The State University of New JerseyRamil Mauleon - International Rice Research InstituteNickolai Alexandrov - International Rice Research Institute (Phillipines)
- Publication Details
- Genome research, Vol.29(5), pp.870-880
- Publisher
- Cold Spring Harbor Laboratory Press
- Grant note
- R15 CA220059 / NCI NIH HHS
- Identifiers
- 991013099200102368
- Copyright
- © 2019 Fuentes et al. This article, published in Genome Research, is available under a Creative Commons License (Attribution 4.0 International), as described at http://creativecommons.org/licenses/by/4.0/.
- Academic Unit
- Faculty of Science and Engineering
- Language
- English
- Resource Type
- Journal article