Heavy-ion beam, a type of ionizing radiation, has been applied to plant breeding as a powerful mutagen and is also a promising tool for inducing large deletions and chromosomal rearrangements. The effectiveness of heavy-ion irradiation can be explained by linear energy transfer (LET; keV µm-1). Heavy-ion beams with different LET values induce different types and sizes of mutations. Comparing mutations induced by heavy-ion beams from 30 keV μm-1, which has a high mutation rate, to 290 keV μm-1, which has a high lethality rate, we found that deletion size increases with increasing LET value, and the chromosomal rearrangements become more complex. In this study, we mapped heavy-ion beam induced deletions detected in Arabidopsis mutants to its genome. We revealed that deletion sizes were similar between different LETs (100 to 290 keV μm-1). However, the sizes of deletions that were only inherited heterozygously because of homozygous lethality tended to be larger than those that were homozygously inherited showing mendelian inheritance. The upper limit of homozygously inherited deletions was affected by the distribution of essential genes. Furthermore, the detected chromosomal rearrangements avoid disrupting the essential genes. We also focused on tandemly arrayed genes (TAGs), where two or more homologous genes are adjacent to one another in the genome. Our results suggested that 100 keV µm-1 of LET is enough to disrupt TAGs and that the distribution of essential genes strongly affects the heritability of mutations overlapping them. Our results provide a new insight for large deletion inductions in the Arabidopsis genome.