Abstract
BackgroundArtificial mutagenesis not only provides a new approach to increase the diversity of desirable traits for breeding new varieties but are also beneficial for characterizing the genetic basis of functional genes. In recent decades, many mutation genes have been identified which are responsible for phenotype changes in mutants in various species including Arabidopsis and rice. However, the mutation feature in induced mutants and the underlying mechanisms of various types of artificial mutagenesis remain unclear.ResultsIn this study, we adopted a transcriptome sequencing strategy to characterize mutations in coding regions in a barley dwarf mutant induced by gamma-ray radiation. We detected 1193 genetic mutations in gene transcription regions introduced by gamma-ray radiation. Interestingly, up to 97% of the gamma irradiation mutations were concentrated in certain regions in chromosome 5H and chromosome 7H. Of the 26,745 expressed genes, 140 were affected by gamma-ray radiation; their biological functions included cellular and metabolic processes.ConclusionOur results indicate that mutations induced by gamma-ray radiation are not evenly distributed across the whole genome but located in several concentrated regions. Our study provides an overview of the feature of genetic mutations and the genes affected by gamma-ray radiation, which should contribute to a deeper understanding of the mechanisms of radiation mutation and their application in gene function analysis.
Highlights
Artificial mutagenesis provides a new approach to increase the diversity of desirable traits for breeding new varieties but are beneficial for characterizing the genetic basis of functional genes
Whole-transcriptome analysis with total RNA sequencing (RNA-Seq) reveal all coding genes and multiple forms of noncoding RNAs, offering a cost-effective alternative to the whole-genome sequencing for investigating genetic variants in coding regions, in which mutations are likely to lead to the change of phenotype
single-nucleotide polymorphism (SNP) and insertion or deletion of bases (InDel) screening through transcriptome sequencing To understand the feature of genetic mutations induced by gamma-ray radiation, RNA-Seq was performed to investigate the mutations in a gamma-ray radiation mutant (Vla-MT) with dwarf phenotype (Fig. 1a)
Summary
Artificial mutagenesis provides a new approach to increase the diversity of desirable traits for breeding new varieties but are beneficial for characterizing the genetic basis of functional genes. Thousands of new crop varieties have been bred from induced mutants and cultivated worldwide [1] These varieties have played an important role in offering desirable agronomic traits including higher yield, improved quality and abiotic stress tolerance. A study on six rice mutants induced by gamma-ray radiation using whole-genome resequencing found that the mutations were more or less evenly distributed across each chromosome [20, 21]. Direct genome sequencing and comparative analysis have been used to identify causal genes in individual mutants [24] or to characterize all mutations in a large mutant library [22, 23]. Whole-transcriptome analysis with total RNA sequencing (RNA-Seq) reveal all coding genes and multiple forms of noncoding RNAs, offering a cost-effective alternative to the whole-genome sequencing for investigating genetic variants in coding regions, in which mutations are likely to lead to the change of phenotype
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