To investigate photosynthetic characteristics of the subtending leaf at the 2-3rd and 10-11th fruiting branch (FBN, FB2-3 and FB10-11), and their relationship with cotton yield and quality, field experiments were conducted using two cotton cultivars, Kemian 1 and Sumian 15. The results showed that with FBN increasing, chlorophyll (Chl) components, Pn and non-photochemical quenching (NPQ) in the subtending leaf significantly declined, while soluble sugar, amino acid and their ratio (CSS/CAA) as well as Fv/Fm increased. These results indicated that 1) non-radiative dissipation of excess light energy at FB2-3 was reduced to improve solar energy utilization efficiency to compensate for lower Pn, 2) higher NPQ at FB10-11 played a role in leaf photo-damage avoidance, 3) boll weight was related to the CSS/CAA ratio rather than carbohydrates content alone, 4) with FBN increasing, lint biomass and lint/seed ratio increased significantly, but lint yield decreased due to lower relative amount of bolls, and 5) the decreases in Pn, sucrose content and CSS/CAA in the subtending leaf at FB2-3 resulted in lower boll weight and fiber strength.

Thidiazuron (TDZ) is the main defoliant used in production to promote leaf abscission for machine-picked cotton. Under low temperatures, the defoliation rate of cotton treated with TDZ decreases and the time of defoliation is delayed, but there is little information about this mechanism. In this study, RNA-seq and physiological analysis are performed to reveal the transcriptome profiling and change in endogenous phytohormones upon TDZ treatment in abscission zones (AZs) under different temperatures (daily mean temperatures: 25 °C and 15 °C). Genes differentially expressed in AZs between TDZ treatment and control under different temperatures were subjected to gene ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) analyses to compare the enriched GO terms and KEGG pathways between the two temperature conditions. The results show that, compared with the corresponding control group, TDZ induces many differentially expressed genes (DEGs) in AZs, and the results of the GO and KEGG analyses show that the plant hormone signaling transduction pathway is significantly regulated by TDZ. However, under low temperature, TDZ induced less DEGs, and the enriched GO terms and KEGG pathways were different with those under normal temperature condition. Many genes in the plant hormone signal transduction pathway could not be induced by TDZ under low temperature conditions. In particular, the upregulated ethylene-signaling genes and downregulated auxin-signaling genes in AZs treated with TDZ were significantly affected by low temperatures. Furthermore, the expression of ethylene and auxin synthesis genes and their content in AZs treated with TDZ were also regulated by low temperature conditions. The upregulated cell wall hydrolase genes induced by TDZ were inhibited by low temperatures. However, the inhibition of low temperature on genes in AZs treated with TDZ was relieved with the extension of the treatment time. Together, these results indicate that the responses of ethylene and auxin synthesis and the signaling pathway to TDZ are inhibited by low temperatures, which could not induce the expression of cell wall hydrolase genes, and then inhibit the separation of AZ cells and the abscission of cotton leaves. This result provides new insights into the mechanism of defoliation induced by TDZ under low temperature conditions.