title: Lack of Genotype and Phenotype Correlation in a Rice T-DNA Tagged Line Is Likely Caused by Introgression in the Seed Source.
abstract: Rice (Oryza sativa) is one of the most important crops in the world. Several rice insertional mutant libraries are publicly available for systematic analysis of gene functions. However, the tagging efficiency of these mutant resources-the relationship between genotype and phenotype-is very low. We used whole-genome sequencing to analyze a T-DNA-tagged transformant from the Taiwan Rice Insertional Mutants (TRIM) resource. The phenomics records for M0028590, one of the TRIM lines, revealed three phenotypes-wild type, large grains, and tillering dwarf-in the 12 T1 plants. Using the sequencing data for 7 plants from three generations of this specific line, we demonstrate that introgression from an indica rice variety might occur in one generation before the seed was used for callus generation and transformation of this line. In addition, the large-grain trait came from the GS3 gene of the introgressed region and the tillering dwarf phenotype came from a single nucleotide change in the D17 gene that occurred during the callus induction to regeneration of the transformant. As well, another regenerant showed completely heterozygous single-nucleotide polymorphisms across the whole genome. In addition to the known sequence changes such as T-DNA integration, single nucleotide polymorphism, insertion, deletion, chromosome rearrangement and doubling, spontaneous outcrossing occurred in the rice field may also explain some mutated traits in a tagged mutant population. Thus, the co-segregation of an integration event and the phenotype should be checked when using these mutant populations.
authors.affiliation: Institute of Plant and Microbial Biology, Academia Sinica, Taipei, Taiwan.|Department of Agronomy, National Taiwan University, Taipei, Taiwan.
authors.forename: Fu-Jin
authors.initials: FJ
authors.lastname: Wei
authors.affiliation: Institute of Plant and Microbial Biology, Academia Sinica, Taipei, Taiwan.
authors.forename: Yuan-Ching
authors.initials: YC
authors.lastname: Tsai
authors.affiliation: Institute of Plant and Microbial Biology, Academia Sinica, Taipei, Taiwan.
authors.forename: Yu-Ming
authors.initials: YM
authors.lastname: Hsu
authors.affiliation: Department of Agronomy, National Taiwan University, Taipei, Taiwan.
authors.forename: Yu-An
authors.initials: YA
authors.lastname: Chen
authors.affiliation: Department of Agronomy, National Taiwan University, Taipei, Taiwan.
authors.forename: Ching-Ting
authors.initials: CT
authors.lastname: Huang
authors.affiliation: Institute of Plant and Microbial Biology, Academia Sinica, Taipei, Taiwan.
authors.forename: Hshin-Ping
authors.initials: HP
authors.lastname: Wu
authors.affiliation: Institute of Plant and Microbial Biology, Academia Sinica, Taipei, Taiwan.
authors.forename: Lin-Tzu
authors.initials: LT
authors.lastname: Huang
authors.affiliation: Crop Science Division, Taiwan Agriculture Research Institute, Taichung, Taiwan.
authors.forename: Ming-Hsin
authors.initials: MH
authors.lastname: Lai
authors.affiliation: Transgenic Plant Core Facility, Academia Sinica, Taipei, Taiwan.
authors.forename: Lin-Yun
authors.initials: LY
authors.lastname: Kuang
authors.affiliation: Institute of Molecular Biology, Academia Sinica, Taipei, Taiwan.
authors.forename: Shuen-Fang
authors.initials: SF
authors.lastname: Lo
authors.affiliation: Institute of Molecular Biology, Academia Sinica, Taipei, Taiwan.
authors.forename: Su-May
authors.initials: SM
authors.lastname: Yu
authors.affiliation: Department of Agronomy, National Taiwan University, Taipei, Taiwan.
authors.forename: Yann-Rong
authors.initials: YR
authors.lastname: Lin
authors.affiliation: Institute of Plant and Microbial Biology, Academia Sinica, Taipei, Taiwan.|Department of Agronomy, National Taiwan University, Taipei, Taiwan.
authors.forename: Yue-Ie Caroline
authors.initials: YI
authors.lastname: Hsing
mesh_terms: D004269:DNA, Bacterial; D018744:DNA, Plant; D022761:Gene Transfer, Horizontal; D018745:Genome, Plant; D005838:Genotype; D009154:Mutation; D012275:Oryza / Q000235:genetics*; D010641:Phenotype; D020641:Polymorphism, Single Nucleotide; D011995:Recombination, Genetic; D012639:Seeds / Q000235:genetics*; D017422:Sequence Analysis, DNA
chemical_list: D004269:DNA, Bacterial; D018744:DNA, Plant; C036483:T-DNA