Large‐fragment insertion activates gene GaFZ (Ga08G0121) and is associated with the fuzz and trichome reduction in cotton (Gossypium arboreum)

Abstract

Summary Cotton seeds are typically covered by lint and fuzz fibres. Natural ‘fuzzless’ mutants are an ideal model system for identifying genes that regulate cell initiation and elongation. Here, using a genome‐wide association study (GWAS), we identified a ~ 6.2 kb insertion, larINDELFZ, located at the end of chromosome 8, composed of a ~ 5.0 kb repetitive sequence and a ~ 1.2 kb fragment translocated from chromosome 12 in fuzzless Gossypium arboreum. The presence of larINDELFZ was associated with a fuzzless seed and reduced trichome phenotypes in G. arboreum. This distant insertion was predicted to be an enhancer, located ~ 18 kb upstream of the dominant‐repressor GaFZ (Ga08G0121). Ectopic overexpression of GaFZ in Arabidopsis thaliana and G. hirsutum suggested that GaFZ negatively modulates fuzz and trichome development. Co‐expression and interaction analyses demonstrated that GaFZ might impact fuzz fibre/trichome development by repressing the expression of genes in the very‐long‐chain fatty acid elongation pathway. Thus, we identified a novel regulator of fibre/trichome development while providing insights into the importance of noncoding sequences in cotton.

Genome-wide identification and expression analysis of GL2-interacting-repressor (GIR) genes during cotton fiber and fuzz development

“…The GL2-interacting-repressors (GIRs) negatively regulate root hair development by interacting with GL2 and controlling the interaction network (Wu and Citovsky 2017a, b). Several recent studies indicated that GaFzl, which is annotated as GIR1 in diploid cotton, adversely affects fuzz development (Du et al 2018;Feng et al 2019;Liu et al 2020;Wang et al 2020c). However, the characteristics and underlying mechanisms of the GIRs functions and regulatory network in cotton remain unknown.…”

Genome-Wide Analysis of SRNF Genes in Gossypium hirsutum Reveals the Role of GhSRNF18 in Primary Root Growth

“…Cotton is cross-pollinated, and there were many genetic variations that existed among different cotton cultivars. Although gene sequences of GaFZ and its homologous gene of GhSRNF5/18 are highly conserved, there are divergences in their promoter regions (Feng et al, 2019 ; Wang et al, 2021 ), suggesting that their expression patterns may vary greatly among different cotton cultivars. Consequently, GhSRNF18 probably are involved in root development in some upland cotton cultivars, although the level of GhSRNF18 expression in roots of TM-1 was relatively low ( Figure 6 ).…”

“…In Arabidopsis , GIR1 and GIR2 interact with GL2 and TPL proteins in the nucleus due to the BiFC assays (Wu and Citovsky, 2017a , b ). GhSRNF18 orthologous GaSRNF7 (GaFZ) protein was observed predominantly in the membrane and nucleus (Wang et al, 2021 ). The results of subcellular localization assays in Arabidopsis protoplast showed GhSRNF18 distributed in the nucleus ( Figure 9 ), which implies that GhSRNF18 may control the expression level of several PR-related genes.…”

“…Previous reports had demonstrated that the GIR/SRNF genes play vital roles in root hair development and fiber elongation (Wu and Citovsky, 2017a,b;Feng et al, 2019;Wang et al, 2021). To identify the functions of GhSRNF genes at different developmental stages, the expression levels of GhSRNFs were evaluated from the published transcriptomes from CottonOmics (see footnote 10) during vegetative, reproductive growth stages, and fiber development stages.…”

“…In Arabidopsis , GL2-interacting repressor 1 (GIR1) and GL2-interacting repressor 2 (GIR2) have been identified recently as novel plant-specific proteins, which negatively regulate the root hair development through interaction with GLABRA2 (GL2) (Wu and Citovsky, 2017a ). In Gossypium arboreum, GaFzl , a gene homologous to the GIR1 in Arabidopsis , has been proved to be closely associated with trichome and fuzz development (Feng et al, 2019 ; Wang et al, 2021 ). However, the GIR family proteins have not been defined.…”