The Pattern and Distribution of Induced Mutations in J. curcas Using Reduced Representation Sequencing

Frontiers in Plant Science
Fatemeh MaghulyMargit Laimer

Abstract

Mutagenesis in combination with Genotyping by Sequencing (GBS) is a powerful tool for introducing variation, studying gene function and identifying causal mutations underlying phenotypes of interest in crop plant genomes. About 400 million paired-end reads were obtained from 82 ethylmethane sulfonate (EMS) induced mutants and 14 wild-type accessions of Jatropha curcas for the detection of Single Nucleotide Polymorphisms (SNPs) and Insertion/Deletions (InDels) by two different approaches (nGBS and ddGBS) on an Illumina HiSeq 2000 sequencer. Using bioinformatics analyses, 1,452 induced SNPs and InDels were identified in coding regions, which were distributed across 995 genes. The predominantly observed mutations were G/C to A/T transitions (64%), while transversions were observed at a lower frequency (36%). Regarding the effect of mutations on gene function, 18% of the mutations were located in intergenic regions. In fact, mutants with the highest number of heterozygous SNPs were found in samples treated with 0.8% EMS for 3 h. Reconstruction of the metabolic pathways showed that in total 16 SNPs were located in six KEGG pathways by nGBS and two pathways by ddGBS. The most highly represented pathways were ether-lipid metabolism an...Continue Reading

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Citations

Oct 11, 2020·Plant, Cell & Environment·Alexander FeinerDavid Riewe

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Datasets Mentioned

BETA
SRP136238

Methods Mentioned

BETA
chips
genotyping
Restriction-site
PCR
nGBS
electrophoresis
Chip
Illumina sequencing

Software Mentioned

VCFtools
SnpEff
ddGBS
CASAVA
Freebayes
BWA
nGBS
Blast2GO
RADSeq

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