Screening populations for copy number variation using genotyping-by-sequencing: a proof of concept using soybean fast neutron mutants

BMC Genomics
Marc-André LemayFrançois Belzile

Abstract

The effective use of mutant populations for reverse genetic screens relies on the population-wide characterization of the induced mutations. Genome- and population-wide characterization of the mutations found in fast neutron populations has been hindered, however, by the wide range of mutations generated and the lack of affordable technologies to detect DNA sequence changes. In this study, we therefore aimed to test whether genotyping-by-sequencing (GBS) technology could be used to characterize copy number variation (CNV) induced by fast neutrons in a soybean mutant population. We called CNVs from GBS data in 79 soybean mutants and assessed the sensitivity and precision of this approach by validating our results against array comparative genomic hybridization (aCGH) data for 19 of these mutants as well as targeted PCR and ddPCR assays for a representative subset of the smallest events detected by GBS. Our GBS pipeline detected 55 of the 96 events found by aCGH, with approximate detection thresholds of 60 kb, 500 kb and 1 Mb for homozygous deletions, hemizygous deletions and duplications, respectively. Among the whole set of 79 mutants, the GBS data revealed 105 homozygous deletions, 32 hemizygous deletions and 19 duplications. ...Continue Reading

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Citations

Oct 15, 2019·Frontiers in Plant Science·Jens KeilwagenDragan Perovic

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Datasets Mentioned

BETA
GPL22907

Methods Mentioned

BETA
genotyping
PCR
chips
chip
fast neutron irradiation

Software Mentioned

Sabre
BWA
GenomicAlignments
R
R package robseg
Cutadapt
Fast
Bioconductor
delgbs
Rsamtools

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