1 Introduction

Cotton is an important cash crop in many countries, but it is quite "picky" about the environment. For example, it is easy to be "out of shape" when encountering drought, saline-alkali land, large temperature differences, or even high heavy metal content in the soil. These abiotic stresses, to put it bluntly, make it difficult for cotton to grow normally, and eventually reduce production, and even the quality will deteriorate. Many cotton-growing areas around the world are actually facing similar problems, not just a special case in a certain region (Wang et al., 2017; Zafar et al., 2020; Kilwake et al., 2023).

What to do? We can only rely on improving varieties. But it is not simply to increase yields, but more importantly to make cotton itself "stand up". For example, if it can reduce leaf loss during drought and germinate in saline-alkali land, then the problem will be solved. Interestingly, this type of highly stress-resistant variety can not only reduce the use of fertilizers and pesticides, but also provide an extra insurance in today's increasingly unstable climate (Saud and Wang, 2022; Shiraku et al., 2022; Kumar et al., 2023).

Traditional breeding is certainly doing this, but the speed is too slow. At this time, gene editing technology is particularly important. In particular, the CRISPR/Cas system can accurately "start" whether it is to transform functional genes that control drought resistance or to regulate components that respond to salt stress. Moreover, some methods can also do not introduce exogenous DNA, which is a significant advantage for public acceptance and regulatory review (He et al., 2020; Ling et al., 2024).

This study wants to sort out these contents. We will not just make a list, but will make a systematic summary from the identification of key genes, the use of gene editing technology, to how to use these tools to breed more adaptable cotton varieties. I hope this information can be helpful to colleagues in scientific research and breeding, especially you and me who are facing the problem of "difficult to serve" cotton.

2 Overview of Abiotic Stresses in Cotton

Cotton (Gossypium spp.) is widely planted around the world, especially as a source of fiber. Its importance goes without saying. But then again, it is not easy to grow cotton - especially when facing the "face" of the natural environment. When drought comes, the land is dry; saline-alkali land prevents seeds from germinating; not to mention the extreme weather of hot and cold weather, any of which can reduce both yield and quality. Not all cotton-growing areas have the same problems. Some areas have prominent droughts, and some have high soil salinity, but no matter which one, it is not a trivial matter. Once the environment changes, the sensitive physiological reactions in cotton will be disrupted, and key functions such as photosynthesis and nutrient transport will be affected. In the end, not only will there be less cotton, but the fiber quality will not be high. So the focus of the problem now is not "whether there is stress" but "how to make cotton survive." The breeding road must continue, but the goal must be clear: not the higher the yield, the better, but to withstand these environmental tosses (Hassan et al., 2020; Patil et al., 2024).

2.1 Drought stress: physiological effects and crop losses

Drought is one of the most common and most impactful problems for cotton. Insufficient water will cause cotton to grow poorly, and both yield and fiber quality will decrease. Insufficient water will cause many changes, such as reduced water content in the cotton body, poor photosynthesis, and increased protective substances such as proline and soluble sugars. Drought also increases reactive oxygen species (ROS) in the body, causing oxidative damage. If these reactive oxygen species are not removed, they may damage cell structure (Zhang et al., 2021b). The end result is a significant reduction in cotton yield, so drought-tolerant varieties must be bred as soon as possible (Figure 1) (Sadau et al., 2024).

Figure 1 Advances and prospects on using DREB TFs for enhanced abiotic stress tolerance in transgenic cotton plants (Adopted from Sadau et al., 2024)

2.2 Salinity stress: ion imbalance and osmotic challenges

Salt stress is also an important issue affecting cotton cultivation, especially in areas with high irrigation water or severe drought. Too much salt in the soil can cause ion poisoning and osmotic pressure, affecting the normal ion balance and water absorption of cells. This will make it difficult for seeds to germinate, the plants will grow slowly, turn yellow, and the fiber will decrease. Cotton can cope with these problems by regulating ion transport proteins and accumulating some small molecules. However, if it is in a high-salt environment for a long time, these countermeasures will not be enough, and it will eventually lead to serious yield reductions (Wang et al., 2017; Kilwake et al., 2023).

2.3 Temperature extremes: heat and cold sensitivity in cotton

Cotton is afraid of both heat and cold, and climate change is making such extreme weather more and more common. Too hot weather will damage photosynthesis, cause rapid evaporation of water, and accelerate the production of reactive oxygen species (ROS), causing cell damage and reduced yields. Too cold weather will affect membrane stability, enzyme activity and other metabolic processes, thereby affecting the normal growth of plants. When faced with these temperature changes, cotton will activate some specific gene expressions and metabolic adjustments to protect itself, but if the time is too long or the degree is too severe, the plant may suffer irreparable damage, ultimately leading to a significant reduction in yield (Guo et al., 2022).

3 Gene Editing Technologies Applicable to Cotton Improvement

After all, traditional breeding is sometimes too slow, but the environmental problems facing cotton cannot wait. In recent years, gene editing technology has become more and more practical, and many researchers have begun to use it to "hands-on" adjust the genes of cotton. It's not for the pursuit of some cool new methods, but because it can really help solve real problems. It is difficult to improve resistance to environmental stresses such as drought and salinity by conventional means. But now, with these editing tools, target genes can be adjusted more accurately. Interestingly, this technology can not only improve stress resistance, but sometimes also increase yields, and can even fine-tune the specific traits of cotton according to the agricultural needs of different regions (Thangaraj et al., 2024).

3.1 CRISPR/Cas systems: advancements and specific tools

The CRISPR/Cas system, especially CRISPR/Cas9, has become the main method for editing cotton genes because of its simple operation, high efficiency and strong adaptability. It can not only accurately modify the target gene, but also modify multiple genes at a time, and even find similar homologous genes in the complex tetraploid cotton genome for manipulation (Gao et al., 2017). There are now updated versions of CRISPR/Cas12a (also called Cpf1) and CRISPR/Cas13, which can recognize more target sequences and are more specific and less likely to accidentally damage genes (Li et al., 2019). Scientists have also improved the design method of guide RNA and promoter selection, which can increase the success rate of editing (Long et al., 2018). This system has been used to improve many important traits of cotton, such as stress resistance, fiber quality and yield.

3.2 TALENs and ZFNs: earlier platforms and their limitations

Transcription activator-like effector nucleases (TALENs) and zinc finger nucleases (ZFNs) are the earliest tools used for genetic modification of plants (including cotton). These two tools can indeed achieve site-specific gene modification, but because the operation requires complex protein design, low efficiency and high cost, they are now used less and less (Khan et al., 2023). These problems have led researchers to choose CRISPR systems more for cotton improvement (Kumar et al., 2024).

3.3 Base editing and prime editing: precision in nucleotide modification

If conventional CRISPR is like "cutting" the gene, then base editing and Prime editing are much more meticulous. They do not need to cut the DNA, but can directly make "micro-modifications" to the nucleotides in situ. These two methods are actually upgraded versions of CRISPR technology, but they are played in different ways. Sometimes you just want to replace one base with another, and don't want to make a big fuss - then use base editing. Prime editing has more "means", not only can it replace, but also can add, delete, and even accurately change a specific sequence. However, having said that, although these technologies are new, they have already shown their advantages in many crop studies. For cotton, many key traits, such as drought resistance and salt resistance, are often controlled by several core sites. Using these high-precision tools to "adjust parameters" is not only less prone to errors, but also reduces the interference of irrelevant mutations (Saleem et al., 2024). Therefore, they are indeed a more suitable choice for gene fine-tuning.

4 Molecular Targets for Abiotic Stress Resistance

4.1 Transcription factors (e.g., DREB, NAC, WRKY)

Whether cotton can "handle things" sometimes depends on how the genes are arranged, especially those transcription factors that play a commanding role. DREB is one of the more famous examples. It can bind to dehydration-related sequences, thereby driving a group of stress resistance genes to "go online". This method makes cotton less likely to "break down" when it is short of water, high salt, low temperature or even high temperature (Sadau et al., 2024). Of course, DREB is not the only one that can do it. Some MYB-type transcription factors, such as GhMYB36, have shown good drought and disease resistance. Its method is to increase the expression level of defense genes such as PR1 (Liu et al., 2021). Another example is the BRX family. This category is also very "resistant". They can regulate the activities of some stress marker genes and enhance the performance of antioxidant enzymes. They are quite good at dealing with salinity and low temperature. Overall, there may not be many transcription factors, but they are really useful at critical times-editing the right site can increase resistance.

4.2 Genes regulating osmolyte biosynthesis and ion transport (e.g., P5CS, NHX1)

Sometimes, whether a cell is stable or not does not entirely depend on the external environment, but on whether it can adjust itself internally. For example, when faced with drought or salt stress, the expression of genes such as GhSAMS2 will increase rapidly. It participates in anti-oxidation and protects cell membranes, and is a "first aid" player (Kilwake et al., 2023). Look at NHX1, this type of ion transporter is mainly responsible for sodium-potassium balance. Without them, cotton is basically difficult to survive in saline-alkali land. Other related genes cannot be ignored, such as GhSOS1 and GhCIPK6. Although they do not directly transport ions, they can indirectly help by regulating signal pathways. As for GbPLA1-32, it is related to lipid signals and stress responses. Once this gene is "turned off", cotton's tolerance to salt will be significantly reduced (Zhang et al., 2021a). From these examples, it can be seen that not all regulation is in the foreground, and some are also critical in the "backstage".

4.3 Stress-responsive signaling components

It’s not that cotton doesn’t react, but it needs a “signal” to be transmitted first. When the external environment changes, the first to “sens” is a class of signal transduction molecules. For example, the calcium sensor GhCBL10 can interact with GhSAMS2 to activate the salt resistance mechanism. This linkage relationship may not be obvious, but neither can be missing. In addition, kinases such as GhSnRK2.6 and GhCIPK6 are generally activated at the beginning of stress. They are not directly resistant to stress, but trigger a series of protective reactions (Wei et al., 2024). There are also antioxidant enzymes such as SikCuZnSOD3, whose function is to maintain the balance of reactive oxygen species (ROS) and prevent cell damage (Zhang et al., 2021b). In short, as long as these “first response” mechanisms can be understood and they can be “tuned” through editing methods, cotton’s ability to cope with environmental stress can indeed be greatly improved.

5 Case Study: Application of CRISPR/Cas9 in Enhancing Drought Resistance

5.1 Targeting GhDREB2 for improved drought tolerance in field trials

Not all drought-resistant traits can be selected through breeding, especially in crops with complex genomes such as cotton. Therefore, the researchers simply "made changes" and turned their attention to the key transcription factor GhDREB2. This gene is usually responsible for helping plants cope with drought, with fast response and obvious effects, so it seems natural to use it to "start". The use of CRISPR/Cas9 technology here is not complicated, and the goal is clear-to transform GhDREB2 so that cotton can activate its self-protection mechanism in time when it is short of water. In this way, the field performance is more stable, and the yield will not fluctuate greatly due to drought (Erdoğan et al., 2023). Of course, some people may ask, what is the essential difference between this and traditional breeding? In fact, the biggest difference is speed. The traditional method of selecting from generation to generation is so slow that it makes people worry; and this fixed-point editing technology is efficient and accurate in direction. In a few years, a batch of new cotton varieties that are truly "drought-resistant" can be screened out.

5.2 Knockout of negative regulators like GhABI1 enhances water-use efficiency

In addition to enhancing positive regulatory genes, CRISPR/Cas9 can also be used to knock out negative regulatory genes such as GhABI1. These genes hinder cotton's ability to cope with drought. After knocking them out, cotton can more easily close stomata and reduce water loss, which can improve water use efficiency (Shinwari et al., 2020). This method allows cotton to grow normally and maintain a certain yield even in an environment with little water. This shows that CRISPR/Cas9 can regulate multiple links and is a good tool for dealing with complex stress responses.

5.3 Phenotypic and transcriptomic validation of edited lines

It is not enough to just assume that the edited cotton has been "trained". Whether it is "trained" or not, we still have to see the actual performance. The researchers went to the fields to see that under drought conditions, these cottons did live longer, grew stronger, and the yield did not drop significantly. At least from the phenotype, the difference is quite obvious. But it is not enough to just look at the appearance. Whether the genes behind it move with it, there must be data to speak. The results of transcriptome analysis showed that these edited cottons did activate more gene pathways related to stress resistance (Rai et al., 2023). In other words, not only "live well", but also the mechanism level is right (Figure 2). It is worth mentioning that these genetic changes did not cause confusion in other important traits, and the main traits such as yield and plant type were not significantly affected (Kumar et al., 2023). This is very critical, otherwise the changes will "hurt the vitality". In the final analysis, comparing the field measurements and molecular verification, CRISPR/Cas9 is indeed reliable in improving the drought resistance of cotton. We have already obtained many good results in the experiments, and it is worth looking forward to whether it can be popularized and applied in the future.

Figure 2 Schematic representation of genome editing mediated abiotic stress (drought, salinity, heat, cold, heavy metals) tolerance in plants. The model shows the stress-induced expression of the abiotic stress-responsive gene that leads to reduced plant biomass; photosynthetic rate; SOD, CAT, GPX, and PAL activities; and chlorophyll content and increased reactive oxygen species (ROS), flower and pod abortion, transpiration rate, ion leakage, and lipid peroxidation. Genome-edited knock-out/knock-in of stress-responsive genes resulted in broken/modified protein that modulates biochemical and physiological characteristics in plants and provides abiotic stress tolerance. SOD, superoxide dismutase; CAT, catalase; GPX, guaiacol peroxidase; PAL, phenylalanine ammonia-lyase; MDA, malondialdehyde; RWC, relative water content; EL, electrolytic leakage, As, Arsenic (Adopted from Kumar et al., 2023)

6 Challenges in Implementing Gene Editing for Abiotic Stress Tolerance

6.1 Off-target effects and genome instability concerns

Things don’t always go as planned. Gene editing is said to be “precise”, but it can also “go off-target” sometimes - this is what we often refer to as off-target effects. The target is one, but the editing tool changes something else. It’s not intentional, but the consequences can be troublesome, such as genome disruption and even unexpected trait problems. The cotton genome is large and complex, making this risk of “accidental damage” even more difficult to fully control (Erdoğan et al., 2023). Of course, researchers are not sitting back and watching. The current common approach is to optimize the design of the guide RNA and switch to smarter CRISPR tools to reduce bias - but to be honest, it is still technically difficult to achieve zero off-target effects. In this case, the accuracy of the editing is not only important for the scientific research itself, but also has a direct impact on whether it can pass regulatory approval (Khan et al., 2023). In other words, if you can’t ensure that the right place is changed and other areas are not disturbed, many subsequent links may be stuck.

6.2 Regulatory hurdles and public perception of gene-edited crops

Currently, gene-edited crops have to pass the supervision of many countries, and each country has different definitions and approval rules for such crops. Some CRISPR technologies do not require the addition of foreign DNA, so they are not classified as genetically modified, which has eased the regulatory pressure to a certain extent. However, many people are still worried about its safety, environmental impact and ethical issues, and public acceptance is not high (Rahman et al., 2022). If gene-edited cotton is to be promoted, the public must be informed of the real situation, and there must also be a clear safety testing process and clear regulatory rules.

6.3 Limitations in cotton transformation and tissue regeneration efficiency

Cotton is a relatively difficult crop to transform, and its tissue culture and regeneration processes are inefficient, which has become a major problem in the application of gene editing. Methods such as Agrobacterium-mediated transformation have a low success rate in cotton, which makes it difficult to breed stable edited varieties in large quantities (Ahmed et al., 2024). In order for gene editing technology to be truly used in cotton breeding, it is necessary to improve transformation and regeneration methods. Only by solving these practical problems can the huge potential of gene editing in breeding stress-resistant varieties be truly realized.

7 Future Directions in Gene Editing for Cotton Improvement

7.1 Integration of multi-omics data for target gene discovery

Now, scientists are combining different research methods such as genomics, transcriptomics, proteomics and metabolomics to find important genes related to cotton drought resistance, salt resistance, etc. more quickly. These genes may also control cotton fiber quality and yield. With the continuous progress of cotton whole genome sequencing, researchers can more accurately locate target genes that can be edited, thereby providing better ideas and strategies for improving cotton traits (Peng et al., 2020). Through these omics data, people can discover new editing targets and verify whether they are indeed related to stress resistance or yield (Huang et al., 2021).

7.2 Use of AI and machine learning to optimize guide RNA design

How to design guide RNA (gRNA) has always been an unavoidable problem in CRISPR editing. In the early days, it mainly relied on manual experience, but now it is different. Artificial intelligence (AI) and machine learning have also begun to intervene in this field and have done a good job. These algorithms are not omnipotent, but they are very practical in one respect - they can predict in advance which places may be "off-target" and help select the most suitable target sites. Especially when facing a "complex player" like cotton with many genes and many repetitive sequences, it is really not easy to manually design gRNA (Kumar et al., 2024). Of course, this type of AI tool is not without a threshold to use, but once it runs through, the editing process can indeed become more convenient. Not only is the accuracy improved, but the failure rate can also be reduced. For the entire breeding process, it is equivalent to adding an "accelerator".

7.3 Development of transgene-free editing techniques for regulatory acceptance

The goal of non-GMO editing technology is to make the final cotton variety free of foreign DNA. Such methods are more likely to pass regulatory approval and be more acceptable to consumers. For example, transient expression of CRISPR/Cas or direct delivery of protein complexes into cells will not leave the GMO fragments in the plant (Mubarik et al., 2021). This will not only reduce concerns about GMOs, but also increase people's trust in gene-edited cotton (Khan et al., 2023). In the future, gene editing research in cotton is likely to rely more and more on the integration of multi-omics methods, the help of artificial intelligence, and non-GMO editing methods to enhance cotton's stress resistance while meeting strict regulatory requirements.

8 Concluding Remarks

Now, gene editing, especially CRISPR/Cas9 technology, has become an important tool for improving cotton's drought resistance, salt resistance, heat resistance, cold resistance and other abilities. It can directly modify regulatory genes and functional genes, making the improvement faster and more targeted. This method breaks through the limitations of traditional breeding and transgenic methods. Moreover, it can also breed cotton varieties without foreign genes, which makes it more acceptable and more likely to pass regulation.

The next research should focus more on combining different omics data, such as genomes and transcriptomes. This will find new key genes and regulatory networks, and give a clearer understanding of how cotton responds to stress. Artificial intelligence and machine learning are also useful. They can help optimize the design of guide RNAs, improve the success rate of editing, and minimize off-target situations. In addition, if gene editing is to be widely used in cotton breeding, it is also necessary to improve the transformation efficiency and the success rate of tissue regeneration. Researchers, breeders and government departments should communicate more and work together to solve regulatory problems and make more people understand and accept gene-edited crops.

Although the goals of stress resistance, stable yield, and high-quality fiber sound ideal, it is becoming increasingly difficult to achieve them using conventional methods. At present, gene editing technology is constantly advancing, and many traits that were originally difficult to deal with can now be accurately "cut". It's not to say that the problem has been solved all at once, but at least the direction is clearer. The tools have been updated, the data has been integrated, and the algorithms are smarter - these new means together make cotton planting less passive in responding to climate change. After all, it's not just as simple as increasing yields. For future food and fiber security, this technical path may be one of the few that still has hope. If the cotton industry wants to be stable, it can't just rely on the old methods. These current advances may be the key to moving forward.

Acknowledgments

I extend my sincere thanks to two anonymous peer reviewers for their invaluable feedback on the initial draft of this paper, whose evaluations and suggestions have contributed to the improvement of my manuscript.

Conflict of Interest Disclosure

The author affirms that this research was conducted without any commercial or financial relationships that could be construed as a potential conflict of interest.

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