RT Journal Article
SR Electronic
T1 Exome sequencing of ion-beam-induced mutants facilitates the detection of candidate genes responsible for phenotypes of mutants in rice
JF bioRxiv
FD Cold Spring Harbor Laboratory
SP 666677
DO 10.1101/666677
A1 Yutaka Oono
A1 Hiroyuki Ichida
A1 Ryouhei Morita
A1 Shigeki Nozawa
A1 Katsuya Satoh
A1 Akemi Shimizu
A1 Tomoko Abe
A1 Hiroshi Kato
A1 Yoshihiro Hase
YR 2019
UL http://biorxiv.org/content/early/2019/06/10/666677.abstract
AB Ion beams are physical mutagens and used for plant and microbe breeding. They are thought to cause mutations via a distinct mechanism from chemical mutagens or gamma rays. Characteristics of ion-beam-induced mutations have been analyzed using marker genes; however, little is known about the extent of the mutations induced by ion beams at a genomic level. To understand the properties of ion beam-induced mutations at a genomic level, we conducted whole-exome sequencing of rice DNA. DNA extracted from carbon-ion-beam-induced rice mutants were fragmented and captured with a custom probe library covering 66.3 M bases of all exons and miRNAs. A total of 56 mutations, including 24 single nucleotide variations, 23 deletions, and 5 insertions, were detected in 5 mutant rice lines (2 dwarf and 3 early-heading-date mutants). The mutations were distributed among all 12 chromosomes, and the average mutation frequency in the M1 generation was estimated to be 2.6 × 10−7 per base. Many single base insertions and deletions were associated with homopolymeric repeats, whereas larger deletions up to 7 base pairs were more linked to polynucleotide repeats in the DNA sequences of the mutation sites. Among 56 mutations, 6 (1.2 mutations per line on average) were classified as high-impact mutations that caused a frame shift or loss of exons. A gene that was functionally related to the phenotype of the mutant was disrupted by a high-impact mutation in 4 of the 5 lines, suggesting that whole-exome sequencing of an ion-beam-irradiated mutant could facilitate detection of a candidate gene responsible for the mutant phenotype.