The endogenous transposable element Tgm9 is suitable for generating knockout mutants for functional analyses of soybean genes and genetic improvement in soybean

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 of the anthocyanin pigment biosynthetic pathway. DFR2 was mapped to the W4 locus, where the allele containing Tgm9 was termed w4-m. In this study we have demonstrated that previously identified morphological mutants (three chlorophyll deficient mutants, one male sterile-female fertile mutant, and three partial female sterile mutants) were caused by insertion of Tgm9 following its excision from DFR2. Analyses of Tgm9 insertion sites among 105 independent mutants demonstrated that Tgm9 hops to all 20 soybean chromosomes from its original location on Chromosome 17. Some genomic regions are prone to increased Tgm9-insertions. Tgm9 transposed over 25% of the time into exon or intron sequences. Tgm9 is therefore suitable for generating an indexed insertional mutant collection for functional analyses of most soybean genes. Furthermore, desirable Tgm9-induced stable knockout mutants can be utilized in generating improved traits for commercial soybean cultivars.

Single nucleotide polymorphisms facilitate distinctness‐uniformity‐stability testing of soybean cultivars for plant variety protection

“…For example, residual variation within soybean cultivars Benning, Cook, and Haskell, each of which appeared uniform when grown according to common agronomic practice, was sufficient to allow up to seven new morphologically and agronomically distinct cultivars to be selected from individual plants when planting densities were much reduced (Fasoula & Boerma, 2005; 2007; Fasoula et al., 2007a; 2007b; 2007c; Haun et al., 2011; Varala, Swaminathan, Li, & Hudson, 2011; Yates, Boerma, & Fasoula, 2012). Genetic heterogeneity can also result from mutation, intragenic recombination, unequal crossing over, DNA methylation, excision or insertion of transposable elements, and gene duplication (Cullis, 1990; Kidwell & Lisch, 2002; Morgante et al., 2005; Rasmusson & Phillips, 1997; Sandhu et al., 2017).…”

Mutation of YL Results in a Yellow Leaf with Chloroplast RNA Editing Defect in Soybean

“…Of these genes, six lethal yellow mutant genes, including Y11, Y18/Y18_1, Y18_2, YL_PR350, PsbP, and CD-5, were mapped to chromosomes 13, 14, 17, 15, 3 and 15, respectively [5][6][7][8][9]. The other nine viable yellow mutant genes, including Y9, Y10, Y12, Y13, Y17, Y20, Y23, Tic110, and Cd1, were mapped to chromosomes 15, 3, 6, 13, 15, 12, 13, 2, and 10, respectively [8,[10][11][12][13][14][15][16]. However, only the function of Y11 and Y9 genes in yellow foliage was validated by complementary analysis [6,9].…”