Functional Characterization of Candidate Genes, <i>Gohir.D05G103700</i> and <i>Gohir.D12G153600</i>, Identified through Expression QTL Analysis Using Virus-Induced Gene Silencing in Upland Cotton (<i>Gossypium hirsutum</i> L.)

Cotton (<i>Gossypium</i> spp.) is a major source of natural fiber and an important cash crop. The cotton growth habit and architecture determine its productivity and influence management strategies for commercial production. The GATA transcription factors (TFs) control various developmental processes in plants, such as flower, bract and embryo development, and petal differentiation. As stable transformation is still a bottleneck in many plant species, TRV-VIGS was used to manipulate gene expression in different plants, including <i>Gossypium hirsutum</i> L. In this study, we undertook the TRV-based VIGS to functionally characterize two candidate genes, <i>Gohir.D05G103700</i> and <i>Gohir.D12G153600</i>, identified through expression QTL analysis for five floral induction and meristem identity genes using the upland cotton mini-core collection. Virus-induced silencing of the <i>Gohir.D05G103700</i> gene resulted in up to a 1.4-fold reduction in the transcript level in two inoculated plants, G3 and G4, and <i>Gohir.D12G153600</i> gene resulted in up to a 2.3-fold reduction in transcript level in a single inoculated plant P05 relative to the mock-treated plant. The TRV2-<i>Gohir.D05G103700</i>-inoculated plants G3 and G4 also exhibited loss of the supernumerary (fourth) floral bract in the squares, whereas the TRV2-<i>Gohir.D12G153600</i>-inoculated plants did not show any observable phenotypic change relative to the mock-treated plants. Altogether, this study suggested that TRV-VIGS can be used to characterize genes in cotton relatively rapidly, and the cotton <i>Gohir.D05G103700</i> gene is a positive regulator of the indeterminate growth habit in cotton, which could be manipulated to obtain a cotton plant with architecture best suited for the cultivation area.