Microsoft Excel 2007
AuthorsFuentes, Roven Rommel
De la Hoz, Juan Fernando
Wing, Rod Anthony
McNally, Kenneth L.
Online Publication Date2019-04-16
Print Publication Date2019-05
Permanent link to this recordhttp://hdl.handle.net/10754/652911
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AbstractInvestigation 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.
CitationFuentes RR, Chebotarov D, Duitama J, Smith S, De la Hoz JF, et al. (2019) Structural variants in 3000 rice genomes. Genome Research 29: 870–880. Available: http://dx.doi.org/10.1101/gr.241240.118.
SponsorsWork in the Grigoriev laboratory is supported by awards from the National Science Foundation (DBI-1458202, ACI-1548562), National Institute of Health (R15CA220059), and New Jersey Health Foundation (PC77-17). We thank XSEDE (MCB150014), PRAGMA, Universidad de los Andes, and the Department of Science and Technology, Advanced Science and Technology Institute of the Philippines for computing resources. We thank the Bill and Melinda Gates Foundation for support to the 3K RG via the GSR Phase 2 award OPPGD1393.
PublisherCold Spring Harbor Laboratory
Except where otherwise noted, this item's license is described as 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/.