Staff Publications

Staff Publications

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    'Staff publications' is the digital repository of Wageningen University & Research

    'Staff publications' contains references to publications authored by Wageningen University staff from 1976 onward.

    Publications authored by the staff of the Research Institutes are available from 1995 onwards.

    Full text documents are added when available. The database is updated daily and currently holds about 240,000 items, of which 72,000 in open access.

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Record number 550885
Title Structural variants in 3000 rice genomes
Author(s) Fuentes, Roven Rommel; Chebotarov, Dmytro; Duitama, Jorge; Smith, Sean; Hoz, Juan Fernando De la; Mohiyuddin, Marghoob; Wing, Rod A.; McNally, Kenneth L.; Tatarinova, Tatiana; Grigoriev, Andrey; Mauleon, Ramil; Alexandrov, Nickolai
Source Genome Research 29 (2019)5. - ISSN 1088-9051 - p. 870 - 880.
DOI https://doi.org/10.1101/gr.241240.118
Department(s) Bioinformatics
Publication type Refereed Article in a scientific journal
Publication year 2019
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.

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