Genome-Wide and Exome-Capturing Sequencing of a Gamma-Ray-Induced Mutant Reveals Biased Variations in Common Wheat.

Yuting Li,Jiazi Zhang,Jiayu Gu,Luxiang Liu,Zhengwu Fang,Shirong Zhao,Yuping Ding,Huijun Guo,Chunyun Zhou,Linshu Zhao,Hongchun Xiong,Yongdun Xie

doi:10.3389/fpls.2021.793496

Abstract

Induced mutagenesis is a powerful approach for the creation of novel germplasm and the improvement of agronomic traits. The evaluation of mutagenic effects and functional variations in crops is needed for breeding mutant strains. To investigate the mutagenic effects of gamma-ray irradiation in wheat, this study characterized genomic variations of wheat early heading mutant (eh1) as compared to wild-type (WT) Zhongyuan 9 (ZY9). Whole-genome resequencing of eh1 and ZY9 produced 737.7 Gb sequencing data and identified a total of 23,537,117 homozygous single nucleotide polymorphism (SNP) and 1,608,468 Indel. Analysis of SNP distribution across the chromosome suggests that mutation hotspots existed in certain chromosomal regions. Among the three subgenomes, the variation frequency in subgenome D was significantly lower than in subgenomes A and B. A total of 27.8 Gb data were obtained by exome-capturing sequencing, while 217,948 SNP and 13,554 Indel were identified. Variation annotation in the gene-coding sequences demonstrated that 5.0% of the SNP and 5.3% of the Indel were functionally important. Characterization of exomic variations in 12 additional gamma-ray-induced mutant lines further provided additional insights into the mutagenic effects of this approach. Gene ontology (GO) and Kyoto Encyclopedia of Genes and Genome (KEGG) analysis suggested that genes with functional variations were enriched in several metabolic pathways, including plant–pathogen interactions and ADP binding. Kompetitive allele-specific PCR (KASP) genotyping with selected SNP within functional genes indicated that 85.7% of the SNPs were polymorphic between the eh1 and wild type. This study provides a basic understanding of the mechanism behind gamma-ray irradiation in hexaploid wheat.

Highlights

Induced mutagenesis is an effective method of generating novel genetic resources and improving important agronomic traits
Transcriptome sequencing with mutants induced by EMS, gamma-ray, and ion beams identified regions with a high frequency of mutations at specific locations of certain chromosomes (Xiong et al, 2020a,b), indicating that the sensitivity of some chromosome segments to mutagenesis in wheat varies greatly
This study presented a genome-wide analysis of single nucleotide polymorphism (SNP) in the gamma-ray-induced wheat mutant and showed that the frequency of transition was significantly higher than that of a transversion and that during transitions, there was no significant difference in the number of SNPs from pyrimidine to pyrimidine or purine to purine (Figure 2A)

Summary

Introduction

Induced mutagenesis is an effective method of generating novel genetic resources and improving important agronomic traits. The gamma-ray, one of the traditional physical mutagens, has been widely utilized in crop breeding and improvement of ornamental plants. Numerous valuable agronomic traits, including yield (Kato et al, 2020), plant height (Andrew et al, 2021), and abiotic stress (Abdelnour-Esquivel et al, 2020), have been identified in gamma-ray-induced mutants. This technique contributed to the creation of novel genetic resources and increased genetic diversity for wheat breeding (Hussain et al, 2021). In addition to its application in cereal corps, gamma-ray irradiation can effectively diversify morphological variations in ornamental plants such as Ruscus (Kutsher et al, 2020), Gypsophila paniculate (Li F. et al, 2020), and Tuberose (Kutty et al, 2019)

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