Genome-wide analysis of radiation-induced mutations in rice (Oryza sativa L. ssp. indica).
Radiation has been efficiently used for rice germplasm innovation. However, the molecular mechanisms by which radiation induces mutations are still unclear. In this study, we performed whole genome sequencing to reveal the comprehensive mutations in rice treated with radiation. Red-1 (a rice rich in beneficial ingredients for human health) was derived from rice 9311 after γ-radiation. Solexa sequencing technology was applied to uncover the mutations. Compared with the 9311 genome, 9.19% of genome sequences were altered in the Red-1 genome. Among these alterations, there were 381,403 SNPs, 50,116 1-5 bp Indels, 1279 copy number variations, and 10,026 presence/absence variations. These alterations were located in 14,493 genes, the majority of which contained a kinase domain, leucine rich repeats, or Cyt_P450. Point mutations were the main type of variation in the Red-1 genome. Gene ontology clustering revealed that genes that are associated with cell components, binding function, catalytic activity and metabolic processes were susceptible to γ-radiation. It was also predicted that 8 mutated genes were involved in the biosynthetic pathways of beneficial products or pigment accumulation. We conclude that genome-wide analysis of mutations provides novel insights into the mechanisms by which radiation improves the beneficial ingredients in rice Red-1.
Crop Quality Institute, Fujian Agriculture and Forestry University, Fuzhou 350002, China. chengzuxin@163.com linjc2011@126.com lintx69@yahoo.com xmfau@163.com hzwfau@163.com yangzj41@163.com 764900262@qq.com jinguizheng@126.com.
Zuxin
Z
Cheng
Juncheng
J
Lin
Tongxiang
T
Lin
Ming
M
Xu
Zhiwei
Z
Huang
Zhijian
Z
Yang
Xinying
X
Huang
Jingui
J
Zheng
D001483:Base Sequence; D002874:Chromosome Mapping; D056915:DNA Copy Number Variations; D018744:DNA, Plant / Q000235:genetics / Q000528:radiation effects*; D005720:Gamma Rays / Q000009:adverse effects*; D018628:Gene Dosage; D020869:Gene Expression Profiling; D018745:Genome, Plant / Q000528:radiation effects*; D054643:INDEL Mutation; D009154:Mutation / Q000528:radiation effects; D012275:Oryza / Q000235:genetics* / Q000528:radiation effects*; D020641:Polymorphism, Single Nucleotide; D017422:Sequence Analysis, DNA
D018744:DNA, Plant