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ARS Home » Research » Publications at this Location » Publication #341433
Title: Transposon-based functional characterization of soybean genes

Author
item Sandhu, Devinder
item BHATTACHARYYA, MADAN - Iowa State University

Submitted to: Book Chapter
Publication Type: Book / Chapter
Publication Acceptance Date: 10/12/2017
Publication Date: 10/13/2017
Citation: Sandhu, D., Bhattacharyya, M.K. 2017. Transposon-based functional characterization of soybean genes. In: Nguyen, H.T., Bhattacharyya, M.K., editors. The Soybean Genome. Cham, Switzerland: Springer International Publishing. p. 183-192. https://doi.org/10.1007/978-3-319-64198-0.
DOI: https://doi.org/10.1007/978-3-319-64198-0

Interpretive Summary: Transposable elements jump from place to place in a genome that can cause mutations in the genes they land into, hence are great tool for functional characterization of genes. Due to the lack of an active transposable element in soybean, several elements from other species have been successfully applied in soybean, that include Ac/Ds from maize, mPing from rice, and Tnt1 from tobacco. However, due to reduced efficiency of transposable elements from other species and the expense associated with genetic modification, the quest for native transposable elements continues in soybean. Recently, we have identified a highly active native transposable element from a pigment gene (DFR2) in soybean. Plants with the intact DFR2 gene have purple flowers; in the mutant where transposon is interrupting the gene, flowers are variegated. Early excision of the Tgm9 element from DFR2 results in purple flower. Sequence analysis of the line (T322) containing the transposable element revealed that there is single active copy of Tgm9 in the genome. Several known mutants identified in the progeny of T322 were characterized and the corresponding genes were isolated. In addition, 105 independent Tgm9-induced mutants were generated and characterized. The analysis revealed that Tgm9 transposes to all 20 soybean chromosomes from its original location on Chromosome 17. Among the mutants characterized, ~26 % times Tgm9 transposed into genes. Our analysis showed that Tgm9 is a suitable tool for functional characterization of soybean genes and development of desirable mutants that can be utilized by soybean breeders in their breeding programs. This work may help in expediting basic and applied research in soybean.

Technical Abstract: Type II transposable elements that use cut and paste mechanism for jumping from one genomic region to another is ideal in tagging and cloning genes. Precise excision from an insertion site in a mutant gene leads to regaining the wild-type function. Thus, function of a gene can be established based on the mutant phenotype and regaining of the wild-type phenotype following precise excision of the element. Heterologous type II transposable elements including Ac/Ds system from maize, miniature inverted repeat system, mPing from rice, and Tnt1 retrotransposon from tobacco have been successfully applied in functional analyses of soybean genes. Although several endogenous transposable elements have been identified in soybean, evidence of an active type II transposable element in soybean was largely lacking. Earlier we have isolated the type II soybean transposon Tgm9 from intron II of the dihyroflavonol-4-reductase 2 (DFR2) gene of the W4 locus. Tgm9 is an active element and produces variegated flowers through somatic excision. Excision of the Tgm9 element from the progenitor cells of flower buds results in genotypes with purple flowers that are known as germinal revetants. The element was discovered from a commercial soybean cultivar and the line carrying the element was termed T322. The T322 genome contains only one active Tgm9 copy in the W4 locus. In a recent study the utility of Tgm9 was assed by studying a set of random germinal revertants. The new mutations created following excision of Tgm9 from DFR2 were evaluated by performing a transposon display assay. This study revealed that Tgm9 transposes to all 20 soybean chromosomes from its original site in the DFR2 gene. Although Tgm9 exhibited preferential transposition to a few genomic regions, among 25.7 % of the mutants Tgm9 was detected in exon or intron sequences. Thus, Tgm9 is a suitable endogenous type II transposon to generate an indexed insertional mutant collection for functional characterization of most of the soybean genes.