Cotton Genomics and Genetics 2025, Vol.16, No.4, 173-183 http://cropscipublisher.com/index.php/cgg 175 2.3 Climate change feedbacks and the urgency for carbon reduction Climate change has already brought many challenges to cotton cultivation, such as affecting yields and water use. Sometimes, more carbon dioxide in the air may lead to higher cotton yields and less water use. But if temperatures continue to rise and climate fluctuations increase, these benefits may be offset, especially in cotton fields that are not irrigated and rely solely on rain (Jans et al., 2021). Carbon emissions from cotton production will in turn exacerbate climate change, and climate change will affect cotton yields. This "interaction" situation makes people more aware that low-carbon measures must be taken now. If traditional high-emission planting methods are not changed immediately, future climate problems will become more and more serious, and cotton yields and the ecological environment will be threatened (Huang et al., 2022). 3 Genomic Insights into Cotton Physiology and Environmental Adaptation 3.1 Identification of genes linked to carbon use efficiency (CUE) Recent studies have found many key genes and related pathways that control carbon metabolism and resource utilization efficiency through genomic analysis of cotton. With the development of genome sequencing and population genetics research, researchers have discovered many genetic differences, such as some haplotypes and gene loci related to environmental adaptation, as well as traits related to carbon utilization efficiency (Yang et al., 2022). For example, through genome-wide association analysis (GWAS), researchers have located regions on certain chromosomes that are related to environmental adaptability. The genes contained in these regions can be used to breed cotton varieties with higher carbon efficiency (Wang et al., 2017; Dai et al., 2020). 3.2 Functional genomics of drought, heat, and nitrogen-use traits Scientists now use functional genomics methods, such as transcriptome analysis and gene expression mapping, to find many genes related to drought, high temperature and nitrogen use efficiency. These genes show obvious changes when facing adverse environments. Many pathways involved in stress response are related to secondary metabolite synthesis, plant hormone transmission and defense mechanisms (Dev et al., 2024). Some important transcription factor families, such as ERF, NAC and bZIP, and some key regulatory genes are also considered to play a core role in adapting to stress (Tahmasebi et al., 2019). Through QTL positioning and GWAS methods, scientists have also found gene regions that can improve cotton yield and quality under drought or high temperature environments. These findings will help breed cotton varieties that are both stress-resistant and resource-saving (Saranga et al., 2001). 3.3 Omics-based modeling of growth-carbon allocation dynamics Studying how cotton grows and how carbon is divided is not as simple as just looking at one gene. Now, scientists no longer work alone, but analyze the genome, transcriptome, and proteome data together to try to piece together a "dynamic panorama" of cotton in various environments. Interestingly, some key genes do not only work alone, but "group" with other genes. Using the method of systems biology, researchers found gene modules that appear together in the expression map when plants are under stress or undergoing cell wall development. These modules are like "operating teams" to respond to environmental changes, and also provide us with a new perspective to understand how carbon is used and how plants grow (Wen et al., 2023). However, the structure of genes is not a monolithic entity. Sometimes, it is not the function of a gene that changes, but its structure-such as the deletion or insertion of a gene segment, or some epigenetic modifications. These differences may not be conspicuous, but they may be the key to cotton's ability to adapt to complex environments and use carbon more efficiently. High-quality genome assembly and alignment allow these subtle but important variations to be found one by one (Lu et al., 2022). 4 Breeding Low-Carbon Cotton Cultivars 4.1 Marker-assisted and genomic selection for carbon-efficient traits In the past, cotton variety selection relied on some experience of "looking at seedlings to identify seeds". But now it is different. Molecular marker-assisted selection (MAS) and genomic selection are increasingly used in breeding, especially in the matter of improving carbon efficiency. Whether photosynthesis is strong, whether nitrogen fertilizer is used sparingly, whether it can withstand drought-these characteristics can now be judged at the genetic
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