Characterization of γ-Radiation-Induced DNA Polymorphisms in the M1 Population of the Japonica Rice Variety Gaogengnuo by Whole-Genome Resequencing

Abstract

Radiation has been widely used for rice germplasm innovation. The molecular mechanisms by which radiation induces mutations at the genome level require further investigation. To determine the pattern of DNA polymorphisms induced by radiation in the M1 population, we performed whole-genome sequencing of the rice cultivar Gaogengnuo, which was subjected to two 60Co γ-radiation doses, generating the 300 Gy group and the 400 Gy group (11.2 Gy min–1). A total of 356,314 and 588.414 single nucleotide polymorphisms (SNPs), 73,495 and 95,807 insertion/deletion polymorphisms (InDels), 9075 and 8852 structural variations and 5100 and 4252 copy number variations were identified in the 300 Gy group and 400 Gy group, respectively, based on the Nipponbare genome. Through an integrative analysis of resequencing data, we identified 609,209 SNPs and 67,885 InDels that differed between the 300 Gy and Gaogengnuo groups and 632,745 SNPs and 69,899 InDels that differed between the 400 Gy and Gaogengnuo groups. We also detected 2682 homozygous SNPs and 2988 homozygous InDels that were present in the Gaogengnuo, 300 Gy and 400 Gy groups. Gene Ontology clustering showed that the mutated genes in the 300 Gy and 400 Gy groups were classified into two main categories, molecular function and biological process, suggesting that genes associated with molecular functions and biological processes were susceptible to γ-radiation.