Whole-genome sequence analysis of mutations in rice plants regenerated from zygotes, mature embryos, and immature embryos

Abstract

Somaclonal variation was studied by whole-genome sequencing in rice plants (Oryza sativa L., ‘Nipponbare’) regenerated from the zygotes, mature embryos, and immature embryos of a single mother plant. The mother plant and its seed-propagated progeny were also sequenced. A total of 338 variants of the mother plant sequence were detected in the progeny, and mean values ranged from 9.0 of the seed-propagated plants to 37.4 of regenerants from mature embryos. The ratio of single nucleotide variants among the variants was 74.3%, and the natural mutation rate calculated using the variants in the seed-propagated plants was 1.2 × 10−8. The percentage and the mutation rate were consistent with the values reported previously. Plants regenerated from mature embryos had significantly more variants than different progeny types. Therefore, using zygotes and immature embryos can reduce somaclonal variation during the genetic manipulation of rice.

Low mutation rate of spontaneous mutants enables detection of causative genes by comparing whole genome sequences

“…The fixed homozygous mutations per generation are estimated to be one-quarter of the heterozygous mutations in the previous generation, i.e., N/2, according to Mendel's laws. Based on the reports of spontaneous mutation rate in rice (Yang et al, 2015;Ichikawa et al, 2023), the number of fixed mutations per generation is estimated to be 1.38-2.25, and when 50 generations have passed, the number of mutations is estimated to be 69.0-112.5 in the whole genome, and 10.4-16.9 in the coding region based on Itoh et al (2007) (Figure 1). Furthermore, by eliminating mutations that are not involved in changes in gene function, including non-synonymous substitutions, the number of candidate causative polymorphisms can be reduced to ~10.…”

“…The fixed homozygous mutations per generation are estimated to be one-quarter of the heterozygous mutations in the previous generation, i.e., N/2. Based on the reports of spontaneous mutation rate in rice (Yang et al, 2015;Ichikawa et al, 2023), the number of fixed mutations per generation is estimated to be 1.38-2.25, and when 50 generations have passed, the mutations are estimated 69.0-112.5 in the whole genome, and 10.4-16.9 in the coding region. Suganami et al 10.3389/fpls.2024.1366413 (Supplementary Figures 4, 5).…”