Cold stress strongly hinders plant growth and development. However, the molecular and physiological adaptive mechanisms of cold stress tolerance in plants are not well understood. Plants adopt several morpho-physiological changes to withstand cold stress. Plants have evolved various strategies to cope with cold stress. These strategies included changes in cellular membranes and chloroplast structure, regulating cold signals related to phytohormones and plant growth regulators (ABA, JA, GA, IAA, SA, BR, ET, CTK, and MET), reactive oxygen species (ROS), protein kinases, and inorganic ions. This review summarizes the mechanisms of how plants respond to cold stress, covering four main signal transduction pathways, including the abscisic acid (ABA) signal transduction pathway, Ca²⁺ signal transduction pathway, ROS signal transduction pathway, and mitogen-activated protein kinase (MAPK/MPK) cascade pathway. Some transcription factors, such as AP2/ERF, MYB, WRKY, NAC, and bZIP, not only act as calmodulin-binding proteins during cold perception but can also play important roles in the downstream chilling-signaling pathway. This review also highlights the analysis of those transcription factors such as bHLH, especially bHLH-type transcription factors ICE, and discusses their functions as phytohormone-responsive elements binding proteins in the promoter region under cold stress. In addition, a theoretical framework outlining plant responses to cold stress tolerance has been proposed. This theory aims to guide future research directions and inform agricultural production practices, ultimately enhancing crop resilience to cold stress.

Proteome analysis of grafted cotton exposed to low-temperature stress can provide insights into the molecular mechanistic of chilling tolerance in plants. In this study, grafted and non-grafted cotton plants were exposed to chilling stress (10 °C/5 °C) for 7 d. After the stress, rootstock and scion samples were labeled by 8-plex iTRAQ (isobaric Tags for Relative and Absolute Quantification), followed by two-dimensional liquid chromatography separation and tandem mass spectrometry identification. In total, 68 differential proteins were identified that were induced by low-temperature stress and grafting, and these proteins regulate physiological functioning. Under low-temperature stress, in the cotton seedlings, the proteins responded to the MAPK signaling pathway and calcium signaling pathway enhanced, the metabolisms of carbohydrate, lipid, nucleotide, and amino acid had a tendency to intensify, the proteins related to protein folding and degradation were activated, along with the system of antioxidant enzymes to offset cellular oxidative damage. In contrast, chilling stress reduced oxidative phosphorylation, photosynthesis, and carbon fixation. These data indicated that the physiological changes in cotton seedlings comprise a complex biological process, and the ability of plants to resist this stress can be improved after grafting onto a vigorous rootstock, although this was not obvious in the young plants. Further studies of low-temperature stress and/or graft-related differences in proteins could lead to the identification of new genes associated with chilling tolerance in plants. These data provide the basis for further studies on the molecular mechanism of chilling tolerance and the relationship of grafting and chilling tolerance in cotton.

Ratoon is the stub or root of a perennial plant that is commonly retained after harvest to produce a following crop. This paper presents a review of ratoon cotton in relation to a broader framework that has been examining perennialization of agriculture for the benefit of ecology and economy. Cotton is botanically indeterminate, but has been treated as an annual after domestication, yet the habit of perenniality is retained and the plants begin to resprout after the first harvest. In some cropping systems, this tendency is exploited using the “ratooning” practice (i.e. growing one or more crops on the rootstock of the first). Ratooning has declined for various reasons such as an increase in the prevalence of pests and diseases and overwintering risk. However, ratooning has many benefits such as no annual tillage before sowing, a well-established root system, and high yield. The three methods of ratooning offer flexibility to balance the environmental and economic benefits in agriculture. The greatest environmental benefits arise from perennial ratoon cropping of semi-wild cotton, and the greatest economic benefit is obtained from biannually cropping modern annual cultivars. However, an optimum solution would be provided by perennial cropping annual cultivars. To realize both environmental and economic benefits, research is needed in the following main areas: preventing the buildup of pests and diseases, breeding the most suitable cotton cultivars for ratooning, and developing light and simplified cultivation (LSC) systems for ratoon cultivation.

Ratoon cropping systems have gained increasing attention for their potential to mitigate greenhouse gas (GHG) emissions, including carbon dioxide (CO₂), methane (CH₄), and nitrous oxide (N₂O). Building on the well-established root system of the previous crop, ratoon crops require no land preparation, sowing, or transplanting and need less fertilizer, water, and pesticides than annual crops while achieving earlier harvests, thereby reducing GHG emission intensity (GHGI) by 7.9–17.3% and N₂O emissions by 40.4–78.1%. Reduced fertilization, efficient water management, and integrated pest management can further curtail GHG emissions, while improved soil fertility, sustainable land management, and cover crop integration enhance soil carbon sequestration. Genetic improvement of ratoon crops can additionally enhance stress tolerance and resource use efficiency, reducing fertilizer requirements and ultimately lowering GHG emissions. This review also addresses ratoon cropping in dryland systems, including sugarcane, sorghum, cotton, and pigeon pea, highlighting their distinct GHG emission profiles and mitigation potential. Its innovative contribution is an integrated framework—synthesizing crop physiology, soil carbon processes, agronomic management, and genetic improvement—that evaluates GHG mitigation opportunities across both ratoon rice and dryland ratoon crops while explicitly addressing trade-offs, context-dependency, and evidence gaps.