Characterization of OsMIK in a rice mutant with reduced phytate content reveals an insertion of a rearranged retrotransposon

• Published in: Theoretical and applied genetics 2013-12, Vol.126 (12), p.3009-3020
• Main Authors: Zhao, Hai-Jun, Cui, Hai-Rui, Xu, Xiu-Hong, Tan, Yuan-Yuan, Fu, Jun-Jie, Liu, Guo-Zhen, Poirier, Yves, Shu, Qing-Yao
• Format: Article
• Language: English
• Subjects: Acids; Agriculture; Biochemistry; Biomedical and Life Sciences; Biosynthesis; Biotechnology; Blotting, Southern; Blotting, Western; breeding; Chromosome Mapping; Chromosomes, Plant - genetics; DNA Methylation; DNA repair; DNA, Plant - genetics; epigenetics; Gene Expression Regulation, Plant; Gene mutations; Gene Rearrangement; Genes; Genetic aspects; Genetic testing; homologous recombination; introns; Kinases; Life Sciences; loci; methylation; Mutagenesis; Mutagenesis, Insertional; mutants; Mutation; Mutation - genetics; Original Paper; Oryza - genetics; Oryza - metabolism; Phenotype; Physiological aspects; phytic acid; Phytic Acid - metabolism; Plant Biochemistry; Plant Breeding/Biotechnology; Plant Genetics and Genomics; Plant Proteins - genetics; promoter regions; Real-Time Polymerase Chain Reaction; recessive genes; Retroelements - genetics; Retrotransposons; Reverse Transcriptase Polymerase Chain Reaction; Rice; RNA, Messenger - genetics; Seeds
• ISSN: 0040-5752; 1432-2242
• DOI: 10.1007/s00122-013-2189-3

The rice low phytic acid (lpa) mutant Os-lpa-XS110-1(XS-lpa) has ~45 % reduction in seed phytic acid (PA) compared with the wild-type cultivar Xiushui 110. Previously, a single recessive gene mutation was shown to be responsible for the lpa phenotype and was mapped to a region of chromosome 3 near OsMIK (LOC_Os03g52760) and OsIPK1 (LOC_Os03g51610), two genes involved in PA biosynthesis. Here, we report the identification of a large insert in the intron of OsMIK in the XS-lpa mutant. Sequencing of fragments amplified through TAIL-PCRs revealed that the insert was a derivative of the LINE retrotransposon gene LOC_Os03g56910. Further analyses revealed the following characteristics of the insert and its impacts: (1) the inserted sequence of LOC_Os03g56910 was split at its third exon and rejoined inversely, with its 5′ and 3′ flanking sequences inward and the split third exon segments outward; (2) the LOC_Os03g56910 remained in its original locus in XS-lpa, and the insertion probably resulted from homologous recombination repair of a DNA double strand break; (3) while the OsMIK transcripts of XS-lpa and Xiushui 110 were identical, substantial reductions of the transcript abundance (~87 %) and the protein level (~60 %) were observed in XS-lpa, probably due to increased methylation in its promoter region. The above findings are discussed in the context of plant mutagenesis, epigenetics and lpa breeding.