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ARS Home » Pacific West Area » Riverside, California » U.S. Salinity Laboratory » Water Reuse and Remediation Research » Research » Publications at this Location » Publication #324343

Research Project: Crop Genetic Improvement and Crop Management in Irrigated Areas Affected by Salinity and Toxic Ions

Location: Water Reuse and Remediation Research

Title: The endogenous transposable element Tgm9 is suitable for functional analyses of soybean genes and generating novel mutants for genetic improvement of soybean

Author
item Sandhu, Devinder
item Ghosh, Jayadri - Iowa State Hygienic Laboratory
item Johnson, Callie - Iowa State University
item Baumbach, Jordan - Iowa State University
item Baumert, Eric - University Of Wisconsin
item Cina, Tyler - University Of Wisconsin
item Grant, David
item Palmer, Reid
item Bhattacharyya, Madan - Iowa State University

Submitted to: PLoS One
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 6/20/2017
Publication Date: 8/10/2017
Citation: Sandhu, D., Ghosh, J., Johnson, C., Baumbach, J., Baumert, E., Cina, T., Grant, D.M., Palmer, R.G., Bhattacharyya, M.K. 2017. The endogenous transposable element Tgm9 is suitable for functional analyses of soybean genes and generating novel mutants for genetic improvement of soybean. PLoS One. 12(8):1-14. doi: 10.1371/journal.pone.0180732.

Interpretive Summary: Soybean genome has been sequenced but assigning functions to different genes is still very difficult. The main goal of this investigation was to explore applicability of an active jumping gene known as Tgm9 in the functional characterization of soybean genes. In a previous study we used Tgm9 to isolate a gene involved in soybean fertility. Here we extend these findings to assign functions to a large number of soybean genes. The disruption caused by the insertion of the jumping gene leads to the loss of function of the gene it lands into. We studied 138 mutants generated due to insertion of Tgm9. Our results showed that Tgm9 jumps to all 20 chromosomes and the majority of the insertion sites was present in genes, signifying feasibility of Tgm9 in studying genes on all soybean chromosomes. Additionally, this study shows suitability of Tgm9 in generating desirable mutants for soybean breeding programs, which may expedite basic and applied research in this economically important crop. Findings of this work will be used by soybean breeders and geneticists in developing enhanced quality and high yielding soybean varieties.

Technical Abstract: In soybean, variegated flowers can be caused by somatic excision of the CACTA-type transposable element Tgm9 from intron 2 of the DFR2 gene encoding dihydroflavonol-4-reductase in the anthocyanin pigment biosynthetic pathway. DFR2 has been mapped to the W4 locus where the allele containing the element is termed w4-m. In this study we have demonstrated that morphological mutants previously identified by screening Tgm9 germinal revertants were caused by reinsertion of Tgm9 following its excision from DFR2. We also report that Tgm9 transposes to all 20 soybean chromosomes. In certain areas, the element tends to insert more frequently. The element also shows a preference for transposing into genic regions with approximately 30 % of the mutants expected to be knockout mutants. Physical mapping of 107 Tgm9-insertion sites among the mutants established that the active endogenous transposable element is suitable for generating an indexed insertional mutant collection for most soybean genes suitable for reverse genetics studies. An unlimited number of Tgm9-induced mutants can be generated without the limitations often encountered when generating mutants using a heterologous transposable element introduced through genetic transformation.