Cotton architecture is determined by the differentiation fate transition of axillary meristem (AM), and influences cotton yield and the efficiency of mechanized harvesting. We observed that the initiation of flowering primordium was earlier in early-maturing than that in late-maturing cultivars during the differentiation and development of AM. The RNA-Seq and expression level analyses showed that genes FLAVIN BINDING, KELCH REPEAT, F-BOX1 (GhFKF1), and GIGANTEA (GhGI) were in response to circadian rhythms, and involved in the regulation of cotton flowering. The gene structure, predicted protein structure, and motif content analyses showed that in Arabidopsis, cotton, rapseed, and soybean, proteins GhFKF1 and GhGI were functionally conserved and share evolutionary origins. Compared to the wild type, in GhFKF1 mutants that were created by the CRISPR/Cas9 system, the initiation of branch primordium was inhibited. Conversely, the knocking out of GhGI increased the number of AM differentiating into flower primordium, and there were much more lateral branch differentiation and development. Besides, we investigated that proteins GhFKF1 and GhGI can interact with each other. These results suggest that GhFKF1 and GhGI are key regulators of cotton architecture development, and may collaborate to regulate the differentiation fate transition of AM, ultimately influencing plant architecture. We describe a strategy for using the CRISPR/Cas9 system to increase cotton adaptation and productivity by optimizing plant architecture.

Cotton fiber is the most important natural raw material for the textile industry, and fiber length (FL) is one of the most important traits in cotton. Quantitative trait locus (QTL) mapping based on high-density genetic maps is an efficient approach to identify genetic regions for FL. In our study, two backcrossed inbred lines (BILs) were chosen as parents to construct a high-density genetic map in F₂ which was used to fine map FL QTL in F_2:3 population. The genetic map had a total size of 3462.8 cM, containing 9182 single-nucleotide polymorphisms (SNPs) based on genotyping-by-sequencing. Two FL related stable QTL were identified on two chromosomes (qFL-A08–1 on A08 and qFL-D03–1 on D03), and qFL-A08–1 was confirmed by a meta-analysis. Utilizing previously obtained RNA-seq data for the two BILs and qRT-PCR analysis, two candidate genes annotated as cytochrome b5 (CB5, Gh_A08G1729) and microtubule end-binding 1C (EB1C, Gh_D03G0232) that may regulate FL during the fiber elongation stage were identified. In addition, nine recombination hotspots in this population were found. The results of this study will provide an important foundation for further studies on the molecular and genetic regulation of fiber elongation.

The cotton fiber is the most important raw material for the textile industry and an ideal model system for studying cell elongation. However, the genetic variation of fiber elongation in relation to miRNA is poorly understood. A high-throughput comparative RNA-seq of two lines differing in fiber length (FL) from a backcross inbred line (BIL) population of G. hirsutum × G. barbadense revealed differentially expressed (DE) miRNAs and their targets in rapidly elongating fibers. A real-time quantitative PCR analysis was further performed to validate the results. A total of 463 (including 47 DE) miRNAs were identified, and seven DE miRNAs were co-localized with seven FL quantitative trait loci (QTL) identified in the G. hirsutum × G. barbadense population. Of 82 (including 21 DE) targets identified, nine (including one DE) were also co-localized with the seven FL QTL. The relationship between the allopolyploid and its diploid ancestral species with respect to miRNAs and their targets was also characterized. These results will facilitate the understanding of the molecular genetic mechanism of fiber elongation with regards to miRNAs in cotton.