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Role of Molecular Breeding Tools in Enhancing the Breeding of Drought-Resilient Cotton Genotypes: An Updated Review

College of Agronomy, Hunan Agricultural University, Changsha 410128, China
College of Agriculture, Fujian Agriculture and Forestry University, Fuzhou 350002, China
Department of Agronomy, University of Agriculture Faisalabad, Faisalabad 38040, Pakistan
Department of Horticulture, Khwaja Fareed University of Engineering and Information Technology, Rahim Yar Khan 64200, Pakistan
Department of Biology, College of Science, King Khalid University, Abha 61413, Saudi Arabia
Botany and Microbiology Department, Faculty of Science, Assiut University, Assiut 71516, Egypt
Research Center on Ecological Sciences, Jiangxi Agricultural University, Nanchang 330045, China
Gansu Provincial Key Lab of Arid Land Crop Science, College of Agronomy, Gansu Agricultural University, Lanzhou 730070, China
Author to whom correspondence should be addressed.
Water 2023, 15(7), 1377;
Submission received: 30 December 2022 / Revised: 7 March 2023 / Accepted: 28 March 2023 / Published: 3 April 2023
(This article belongs to the Section Water, Agriculture and Aquaculture)


Drought stress is an inevitable factor that disturbs the production of plants by altering morphological, physiological, biochemical, and molecular functions. Breeding for drought tolerance requires a complete understanding of the molecular factors controlling stress-responsive pathways. The plant responds to drought stress by adopting four mechanisms: avoidance, escape, tolerance, and recovery. Traditional plant-breeding tools have been employed to increase tolerance in cotton, but the complexity of drought tolerance has limited the use of these breeding methods. The plant adopts several key strategies against drought stress, such as activating the signaling network and activating molecular factors. Cotton breeders have been engaged in elucidating the molecular mechanisms of drought tolerance in cotton using significant molecular tools such as quantitative trait loci (QTL) mapping, transcription factor (TFs) analysis, transcriptome analysis, genome-wide association studies (GWAS), genetic engineering, and CRISPR/Cas9. Breeders have studied the functional description of genes and the interacting pathways accountable for controlling drought tolerance in cotton. Hundreds of genes/QTL have been identified, and many have been cloned for drought tolerance in cotton; however, a complete understanding of these traits still needs more study. This review presents a detailed overview of molecular tools, their application for improving drought tolerance in cotton, and their prospects. This review will help future researchers to conduct further studies to develop drought-tolerant cotton genotypes that can thrive under conditions of water scarcity.

1. Introduction

Climate change and global warming adversely affect crops and food security [1,2]. Abiotic stresses are a significant hazard to crop production, and have led to a 73% reduction in cotton production worldwide [3,4]. Cotton is leading fiber crop in China; cotton currently accounts for more than 40% of textile raw material. Xinjiang is the leading cotton-producing area in China [5,6]. China, the USA, India, and Pakistan are the top cotton producers in the world, and cotton generates huge revenue, especially in Pakistan [5,7,8]. Drought stress is the existence of a low water level for an extended period, and it reduces crop productivity [9,10,11]. The major threats to cotton production in these countries are less availability of irrigated water, variation in rainfall patterns, and heat stress [12,13].
Cotton is vulnerable to environmental changes [14,15], and it is a crop in tropical and subtropical regions; cotton has a moderate level of drought tolerance at the vegetative growth stage, but it is susceptible to drought stress in the reproductive phase [16,17]. Around 20% of the global area faces moderate-to-severe water stress [18]. The severity of water stress is expected to increase and continue to affect the crop in a widespread area [11]. Cotton production will be affected by long water drought spells in the future [7]. To adopt a breeding plan to decrease the harmful consequences of drought, it is important to examine the effects of drought on cotton [19]. Taproot length has increased in drought-treated cotton [20]. Drought stress inhibits cotton growth and development, decreases shoot length and root activity, blocks vascular tissues, and reduces cell elongation [21,22]. Drought stress decreases stomatal conductance, reduces photosynthesis, and reduces leaf water potential and the content of Rubisco binding protein [23,24]. Drought stress reduces seedlings growth (Figure 1) and boll numbers in Gossypium herbaceum during harvest time because of bolls’ shedding and decreased fruit positioning, ultimately affecting the lint yield [25]. Prolonged drought stress hinders the interaction of nitrogen (N) and carbon metabolism in the roots of cotton [26]. Drought stress reduces the content of protein, carotenoids, and starch in cotton genotypes [27].
Drought stress decreases the cotton boll weight and yield [28] (Figure 1). Drought tolerance is the plant’s capability to stand against prolonged water scarcity conditions without compromising growth and production. It is a polygenic trait governed by multiple genes and their signaling pathways. These genes modify several physio-morphological responses [4]. ROS scavenging may be correlated with a plant’s drought tolerance capability [24]. At the morphological level, the plant closes its stomata to prevent water loss and maintain photosynthesis at the physiological level [24]. At the molecular level, the plant changes its gene expression, leading to several variations in protein synthesis. Genes and gene products have been implicated in drought response, but documenting potent genes involved in drought tolerance is still a technical challenge [11,29].
Tolerant cotton genotypes can adopt better root growth, photosynthesis, and proline contents [22]. In the past and current era, many significant breeding techniques have been employed to identify the genes/QTL used for drought-tolerant breeding in cotton. QTL mapping has been employed to identify cotton’s putative QTL under severe drought stress conditions. Decoding of the cotton genome has facilitated the generation of large-scale high-throughput DNA markers and QTL detection, which permits validation of targeted genes and their use in marker-assisted-selection (MAS) [30]. Shukla et al. [31] identified nine significant QTLs for drought tolerance traits in cotton [31]. Developing novel cotton cultivars requires understanding of the molecular functions regulated by gene products [32].
In the same way, GWAS has identified several QTL/genes and single nucleotide polymorphisms (SNPs) linked with drought tolerance in cotton. GWAS has identified several genes/QTL which can be exploited in molecular breeding [33]. TF analysis helps to discover the essential proteins that regulate gene expression under drought stress. TF identification has paved the way to speed up molecular breeding programs in cotton [32]. Cotton researchers have identified several transcriptomes under drought stress which can be used in molecular breeding. Sajjad et al. [34] validated the critical role of TF GhWOX4, which modulated drought tolerance with that of vascular growth in cotton. Comparative RNA sequence analysis revealed that ethylene and abscisic acid (ABA) were remarkably induced. Moreover, heat shock transcription factors (HSFs) were also expressed in control plants compared to GhWOX4-silenced plants. Results suggested that the promotor zone of GhWOX4 was congested with plant growth and stress response-related cis-elements. These findings expanded the context in which we may explore the essential role of GhWOX4 transcription factors (TFs), which enhance drought tolerance [34]. In the same way, CRISPR/Cas9 and genetic engineering have been used to develop drought-tolerant cotton genotypes [13]. These molecular tools have been very effective in genetically improving cotton cultivars that can thrive under low water conditions [13]. Integrating different molecular mechanisms can facilitate the investigation of the functional and genetic basis of superior applicant genes [13]. These studies highlighted the worth of molecular tools in improving drought tolerance in cotton; however, success stories about the functional cloning and applications of drought-tolerant genes are limited. The definite objective of this updated review was to present a complete outline of molecular breeding tools and their applications to breed drought-tolerant cotton varieties. This information can expedite future research studies to develop drought tolerance in cotton that can grow in changing climatic conditions, and will offer data to understand the complex cellular biology of drought tolerance in cotton.

2. Molecular Basis for Drought Tolerance

Numerous genes and their interacting networks which control drought tolerance have been detected in cotton [4]. These genetic factors include genes, QTL, and their interactions at several points. These genomic regions regulate stress tolerance in cotton. Drought tolerance is a polygenic trait. Although conventional breeding methods have made significant progress in developing drought-tolerant lines/genotypes, they are time-consuming, and take years to breed a new variety. At the same time, they are very costly and pose several limitations [35]. Molecular breeding methods can replace these traditional breeding methods [11]. Different loci with minor effects control drought tolerance in cotton; these genetic loci represent the genetic architecture of numerous morphological and physiological responses of plants, and describe the joint influence of hundreds of genes. Different QTL linkage maps have been developed. Various molecular markers have been employed to create the linkage map for documentation of QTL governing yield and other characters under stress circumstances in cotton [4]. In future studies, expanding the use of potential molecular markers such as single nucleotide polymorphisms (SNPs) would facilitate the building of linkage maps and increase genetic variety for drought tolerance in cotton.

3. Signaling Pathways for Drought Tolerance in Cotton

Several signaling pathways regulate plant reactions to abiotic stresses [11]; however, these pathways have not been fully elucidated in cotton. Plants use numerous adaptations against environmental stresses, such as signaling and expression of stress-responsive genes. One of the most critical factors is MAPK cascade, which regulates stress responses by transducing signals to outer stimuli. Cell division, hormonal response, apoptosis, and developmental programs are governed by MAPK pathways. The diverse classes of proteins MAPK, and MAPKK are called cascades, and their activity requires sequential phosphorylation [36,37]. MAPKK phosphorylates, targets and regulates the activity of phospholipids and several TFs, facilitating several responses [38] (Figure 2). MAPK signaling pathways are triggered by environmental stresses. A new cotton MAPM3K gene GhMAP3K449 was detected, induced by ABA and ROS [39]. Different MAPK genes have been documented in cotton and are involved in response to various environmental stresses, including drought and heat [40]. Further inquiries into MAPK cascades will give deeper insight into their role in stress responses. Calcium (Ca2+) is a significant regulator of morphological and physiological processes. Ca2+ governs many physiological developments in cotton. ABA and drought stress are responsible for change in the concentration of Ca2+ [41]. Drought and ABA treatments induce GhCIPK6, thereby enhancing drought tolerance [42].
Among different plant hormones, ABA signaling has been extensively studied in crops under abiotic stress (Figure 2) [11,43,44]. ABA is a significant regulator of plant growth and development. It is crucial in seed dormancy and germination under abiotic stress conditions [45,46]. ABA facilitates a series of processes in growth and development, water use efficiency (WUE), gene expression during seed growth, and environmental stress [47]. ABA regulates about 10% of signaling genes in Arabidopsis [48]. ABA is accountable for stress-responsive genes in the ABA-dependent pathway. Earlier, it was reported that TF, GhirNAC2 modulated ABA biosynthesis and stomatal closure under drought stress conditions in cotton. Hence, it indicated the role of ABA in drought tolerance in cotton [49]. The interaction between ABA and MAPK pathways needs further studies to understand the basis of drought tolerance. These signaling networks control different plant responses under drought stress. Their genes and proteins could be useful for molecular breeding to improve the genetic mechanism of drought tolerance.

4. QTL Mapping for Drought Tolerance in Cotton

QTL mapping is a powerful technique to identify the potential genomic regions controlling drought tolerance in cotton [50,51]. The QTL mapping technique uses linked gene loci to analyze the phenotypic characters related to polygenic inheritance. QTL mapping analysis and use of different markers to understand the genetic basis of drought tolerance has been a very successful technique [4,52,53]. Identifying genomic regions helps improve marker-assisted selection (MAS) for developing tolerant cultivars [31]. Shukla et al. [31] identified nineteen QTL for drought tolerance traits in cotton. For the chlorophyll stability index, two QTL, qCSI01 and qCSI02, could play a key role in physiologically based drought tolerance in cotton [31] (Table 1). Evaluating the cotton population under drought stress conditions is critical to identify the QTL responsible for drought tolerance. Two QTL for relative water content (RWC) were mapped on chromosomes 12 and 23. qRWC12 and qRWC23 significantly contributed to drought tolerance in cotton. Another QTL, qELWL23, was recognized for excised leaf water loss (ELWL). These QTL have revealed the genetic basis of drought tolerance, so cotton breeders must exploit these QTL to engineer drought-tolerant cultivars. These QTL could enhance be used in breeding programs [54].
Earlier studies revealed that QTL identification under water-limited conditions could be a significant step toward developing drought-tolerant cotton genotypes. Two QTL, qtlOA-1 and qtlPH-1, were detected under water-limited conditions and opened up ways to enhance the MAS in cotton [55]. Zheng et al. [56] identified the drought-tolerant QTL in the 188 F2:3 mapping population of cotton, and revealed the genetic architecture of drought tolerance. Some 67 and 35 QTL were identified under water-limited and well-watered conditions. Most of these QTL exhibited partial or over-dominant genetic effects for increasing trait values. The study identified four consistent QTL under water-limited situations on chromosomes 5, 8, 9, and 16; no consistent QTL were found under well-watered conditions. Besides these, 13 QTL clusters were detected on chromosomes 2, 3, 5, 6, 9, 14, 15, 16, and 21. qBla-Chr5-1 was identified under water-limited conditions. These findings could help to elucidate the genetic basis of drought tolerance in cotton [56]. Magwanga et al. [57] evaluated 200 BC2F2 populations to detect the QTL controlling drought tolerance in cotton. Thirty stable QTL were detected under drought stress conditions [57]. A total of 181 RILs of cotton were evaluated under drought stress conditions. Some 53 QTL controlling plant height (PH) and boll number (BN) were detected under water-limited and irrigated circumstances. One QTL, qNSB22, controlled the number of sympodial branches under water-limited conditions [58]. In another study, a total of 165 QTL were mapped for drought and salt tolerance in cotton. These QTL were detected under field and greenhouse situations. qFTD1 was detected for field drought tolerance in cotton, significantly contributing to cotton drought breeding [59]. QTL regions controlling fiber quality traits under drought stress conditions are potential breeding targets. 23 QTL were noticed under water shortage and well water conditions.
Moreover, 19 QTL were stable under both water regimes. QTL detected under water-limited conditions could be used to develop drought-tolerant cultivars of cotton [60]. These studies indicated that QTL mapping is significant in identifying potential genomic regions for drought tolerance in cotton genotypes. These identified QTL should be cloned and transferred to develop tolerant cultivars. Further studies would be highly useful to identify and use more potential genomic areas for drought tolerance. The validation and cloning of detected QTL are critical to enhancing the success of molecular breeding for developing drought-tolerant cotton cultivars. Genome sequencing of wild relatives of cotton would be a practical step to map the tolerant regions as potential treasure troves.
Table 1. QTL identified for drought tolerance in cotton.
Table 1. QTL identified for drought tolerance in cotton.
181 RILqNSB2222[58]
RILqCSI01, qCSI021, 2[31]
97 RILqFTD11[59]
99 upland cotton genotypesqPH99[60]
188 F:2:3 mappingqBla-Chr5-15[56]
F2 populationqRWC12, qRWC2312, 13[54]
F2 populationqtlOA-1, and qtlPH-11[55]

5. GWAS Analysis for Drought Tolerance in Cotton

GWAS helps to determine trait markers’ association and identification of potential genes/QTL underlying drought tolerance in cotton. GWAS is an efficient technique for dissecting complex traits. GWAS investigates single nucleotide polymorphisms (SNPs) of a specific trait using whole genome sequences. The excavation of drought-tolerant genes and their use in breeding programs poses many challenges. A multi-parent advanced generation inter-cross (MAGIC) population of 550 RIL was evaluated to identify the QTL linked with drought tolerance at the seedling stage. GWAS identified the 20 QTL for drought tolerance, including 13 and seven QTL for plant height (PH) and dry shoot weight (DSW), respectively. These QTL could be used for MAS selection [33]. The drought tolerance of 316 cotton accessions was studied using GWAS. A total of seven QTL were identified and linked with different tolerance traits. The candidate gene WRKY70 was involved in response to abscisic acid (ABA) under drought stress conditions [61]. The gap between genomics and phenomics must be covered [62]. An automatic phenotypic platform (APP) was applied to examine the 119 image-based digital traits (i-traits) during drought stress at the seedling stage of 200 cotton genotypes. Three hundred ninety genetic loci (Table 2) were detected using phenomics data for 65 morphological and three i-traits. GhRD2 was identified as a candidate gene for drought tolerance [62].
GWAS with genetic diversity analysis helps identify genes with diverse functions against abiotic stresses. GWAS was performed on a panel of 99 upland cotton genotypes using 177 simple sequence repeats (SSR). 23 potential SSR were identified and associated with drought tolerance in cotton. Most of these loci were newly identified regions for drought tolerance [63]. A set of 376 upland cotton genotypes was evaluated to determine the QTL associated with drought tolerance at the seedling stage. Based on GWAS analysis, 53 QTL were detected for drought tolerance, and eleven QTL were common with salt tolerance. These QTL provided important information about the genetic basis of drought tolerance in cotton [64]. In another study, Abdelraheem [65] used an association mapping panel of 376 upland cotton accessions and identified drought-tolerant QTL based on GWAS analysis [65].
Guo et al. [66] used 188 cotton accessions to conduct GWAS to identify QTL related to drought tolerance. Thirty-six SNPs were identified based on GWAS analysis. Eight and 28 SNPs were distributed in the A and D subgenomes. Among the identified SNPs, TM73079 was located on chromosome D10 and linked with fresh and dry leaf weight. Moreover, 520 genes were identified based on GWAS analysis, which showed different expression patterns. Gh_D08G2462 and Gh_A03G0043 may be the candidate genes for drought tolerance [66]. Genome-wide identification of 89 KNOX genes in cotton genotypes revealed the detailed genetic mechanism of drought tolerance in cotton. GhKNOX4-A and GhKNOX22-D significantly contributed to drought tolerance in cotton by regulating stomata opening and oxidative stress [67]. Identifying differently expressed genes in cotton under water-limited conditions helped to elucidate the genetic mechanism of drought tolerance in cotton. A total of 519 differently expressed transcript-derived fragments were identified in cotton. These transcripts showed a naturally occurring response in the cotton genome to environmental stresses such as drought stress. These genes can be used to manipulate the water-use characteristics of cotton cultivars [68]. These GWAS reports indicated the role of different SNP/QTL in cotton’s drought tolerance. Further research should be conducted to identify the QTL/SNPs related to physiologically based drought tolerance in cotton.
Table 2. GWAS-based identified QTL/SNPs for drought tolerance in cotton.
Table 2. GWAS-based identified QTL/SNPs for drought tolerance in cotton.
Cotton genotypes89 KNOX genesRegulates stomata opening[67]
188 cotton accessionsGh_D08G2462, and Gh_A03G0043Potential candidate genes for drought tolerance[66]
MAGIC (550 RIL)20 QTLRegulates PH and DSW[33]
376 upland cotton genotypes53 QTLRegulates drought tolerance[64]
200 cotton genotypes390 genetic loci/GhRD2Candidate gene for drought tolerance[62]
316 cotton accessionsSeven QTL/WRKY70Responds to abscisic acid[61]
cv. Siokra L-23519 genesDrought tolerance[68]

6. Transcription Factors Analysis for Drought Tolerance in Cotton

Identifying TFs is one of most powerful ways to develop drought tolerance in cotton (Figure 3). TFs are protein families that regulate gene expression, and their expression is induced by drought stress. Due to the inherent complexity of drought tolerance, genetic improvement of water deficit tolerance in crops has been largely unsuccessful because of slow growth and delayed reproduction. Dehydration-responsive element binding (DREB) is critical in regulating cotton’s response to drought stress. StDREB2 TF was isolated and overexpressed in cotton. Plants with overexpression of StDREB2 showed enhanced activity of protein content, proline content, boll number, expression of stress-related genes, and gas exchange parameter [69]. The NAC family is one of the most prominent families of TFs, which regulates several reactions under drought stress; however, their functions still need to be uncovered. Shang et al. [49] studied the molecular function of GhirNAC2, a NAC TF, under drought stress in cotton. The overexpression of GhirNAC2 significantly enhanced seed germination, root growth, and plant survival under drought stress [49] (Table 3). The CaHB12 gene encodes a TF of the HD-Zip I subfamily involved in drought tolerance in cotton. CaHB12 in cotton transgenic lines improved tolerance to water deficit by increasing the photosynthesis rate and water usage efficiency [32].
The MYB family of TFs also regulates plants’ response to drought stress. An MYB TF, GbMYB5, conferred drought tolerance in cotton by improving the survival rate and reducing water loss in cotton and tobacco (Table 3). These findings suggest that GbMYB5 positively regulated drought tolerance in cotton [70]. Another study revealed that transgenic cotton with overexpression of AtABI5 TF showed improved tolerance to drought stress in field and greenhouse conditions. Transgenic plants showed improved photosynthesis and water usage efficiency. Transgenic plants also showed enhanced photo-assimilation and root and shoot sink strengths [47]. bZIP is one of the most prominent families of TFs and plays a crucial role in abiotic stress tolerance in plants. An earlier study revealed that bZIP is an essential regulator of cotton’s abscisic acid-mediated stress signaling pathways. The cloning and characterization of bZIP TF GhABF2 improved drought stress tolerance in cotton. Transcriptome analysis revealed that GhABF2 increased drought tolerance by regulating genes linked with ABA and drought. Transgenic plants showed high proline content and increased activity of superoxide dismutase (SOD) and catalase (CAT) when compared to wild plants under drought stress [71].
The co-expression pattern of the gene network linked with drought stress was examined using transcriptome profiles. Gh_D01G0514 (GhNAC072) was in the nucleus and cytoplasm. A Y2H assay showed that Gh_D01G0514 has the potential of auto-activation, which was highly upregulated in both tissues. Its validation was completed using a virus-induced gene silencing (VIGS) experiment, the results of which showed that VIGS plants have higher excised water loss and ion leakage than wild-type plants. This candidate gene might be responsible for drought tolerance in cotton [72]. Wang, et al. [73] studied the function of a bZIP TF, ABP9 in drought tolerance in cotton. This gene was transformed to cotton using Agrobacterium-mediated transformation. Transgenic lines showed a higher survival rate, relative water content (RWC), proline content, and soluble sugar content. ABP9 also significantly upregulated the transcription level of stress-related genes GhDBP2 and GhNCED2 [73].
Another WRKY TF, GhWRKY21, regulates the intensity of drought-induced ABA signaling pathways by governing the expression of GhHAB in cotton. The mechanism that regulates ABA signals is not fully uncovered. The silencing of GhWRKY21 dramatically increased drought tolerance in cotton. These findings indicated the mechanism of ABA-mediated drought tolerance in cotton [74]. The NAC TF, GhJUB1L1 was expressed in the stem, and its expression was induced by drought stress. GhJUB1L1 acted as a positive regulator of drought tolerance in cotton. These findings laid the foundation for transgenic cotton cultivars’ development [75]. Ectopic expression of the bZIP TF ABF2D improved drought tolerance in cotton. ABF2D improved drought tolerance through stomatal regulation and photosynthetic productivity [76]. TCP TFs play a crucial role in plant growth and development; however, their role in drought tolerance in sea island cotton is mainly unknown. GbTCP4, a TCP TF involved in drought tolerance in cotton and its expression, was induced by drought stress. GbTCP4 activated the transcription of GbUVR8 and GbbHLH130 genes to increase drought tolerance [77]. Yu, et al. [78] reported that the transgene AtHDG11 could change a plant’s tolerance to drought. Transgenic cotton lines showed drought tolerance with an improved root system and improved leaf and epidermal size [78]. Some 120 NAC genes were involved in response to multiple stresses, including drought in cotton. These genes could be used for molecular breeding programs [79].
The trehelix TF has been studied for its role in drought tolerance in cotton. Gh_A05G2067 was upregulated under drought stress in cotton, and its expression increased drought tolerance by lowering the hydrogen peroxide (H2O2) content and enhancing the activity of antioxidant enzymes. Stress-responsive genes SOS1 and ABF4 were highly upregulated in transgenic lines compared to wild plants [80]. Recently, a bZIP TF, GhABF3, was cloned and characterized for its role in drought tolerance in cotton. Exogenous expression of GhABF3 resulted in improved drought tolerance in cotton [81]. The NAC gene, SNAC1, improved drought tolerance in cotton via root development and reduced transpiration rates [82]. The overexpression of the NAC TF GhNAC79 enhanced drought tolerance in cotton, as studied by Guo, et al. [83]. GhNAC79 responded to ethylene treatment and was identified as the best candidate gene for stress studies in cotton [83]. These findings indicated the detailed mechanism of drought tolerance in cotton regulated by different TFs. Different TF families such as MYB and DREB need further studies, because their role is not yet fully uncovered. These findings offer an excellent opportunity to accelerate molecular breeding programs to develop drought-tolerant cotton cultivars.
Table 3. Detailed analysis of different TFs and their role in drought tolerance in cotton.
Table 3. Detailed analysis of different TFs and their role in drought tolerance in cotton.
TF FamilyTFsRoleReferences
bZIPGhABF3Increased drought tolerance[81]
TCPGbTCP4Increased the transcription of stress-related genes[77]
NACGhJUB1L1Acted as a positive regulator of drought tolerance[75]
WRKYGhWRKY21Regulated the GhHAB expression[74]
GhNAC072Gh_D01G0514Might be responsible for drought tolerance[72]
HD-Zip ICaHB12Increased photosynthesis and activity of GhPP2C and GhSnRK2[32]
NACGhirNAC2Increased seed germination, and root growth[49]
DREBStDREB2Increased proline and protein content[69]
TrehelixGh_A05G2067Increased the activity of antioxidant enzymes[80]
bZIPGhABF2Increased the activity of antioxidant enzymes[71]
HOMEODOMAIN-GLABROUS11AtHDG11Increased cotton yield[78]
bZIPABF2DStomatal regulation[76]
bZIPABP9, GhDBP2 and GhNCED2Increased survival rate and relative water content[73]
NACGhNAC79Improved drought tolerance[83]
MYBGbMYB5Increased survival rate[70]
bZIPsAtABI5Increased water usage efficiency[47]

7. Transcriptome Analysis of Drought Tolerance in Cotton

Transcriptomes play a crucial role in drought tolerance in cotton. Earlier studies identified many transcriptomes involved in drought tolerance in cotton [67]. Investigating cotton cultivars’ gene expression profiles helps identify the potential genetic factors regulating drought tolerance. Hasan et al. [84] identified 6968 differentially expressed genes (DEGs) in cotton genotypes under drought stress. Several TFs associated with ethylene-responsive genes were involved in acclimatizing under drought stress. Drought stress changed the expression of different ABA-related genes such as NCED, and PYL [84]. Han et al. [85] completed a transcriptome and metabolic profiling of cotton genotypes to elucidate the molecular mechanism of drought tolerance. Heat shock protein (HSP) genes and different ATP-binding cassette genes revealed that genes play a crucial role in cotton drought tolerance. VIGS and ATP-binding cassette (ABC) transporter genes revealed that those genes play a key role in cotton drought tolerance [85]. The crosstalk of other stress-responsive genes has been studied in cotton. In a previous study, 5608 genes were identified under drought stress conditions in cotton. These genes were involved in drought tolerance in cotton and opened up new ways for molecular mechanisms to accelerate the drought breeding program. These genes could be highly useful for functional study under diverse stresses [86]. In another study, 110 drought-responsive genes were identified in cotton, and their expression was induced by drought stress. These genes were ideal candidates for developing molecular markers associated with drought tolerance in cotton. This was the first study of integration of transcriptome analysis to develop molecular markers which were linked with drought tolerance in cotton [87].
Phosphatidylinositol signaling plays a key role in response to drought stress in cotton. In order to investigate the phosphatidylinositol signaling response to drought stress, a transcriptome analysis of cotton samples was performed under drought stress conditions [88]. Gene ontology analysis revealed that most differentially expressed genes (DEGs) were mainly involved in protein modification and phosphatidylinositol. Gohir.A07G058200 was involved in drought tolerance by regulating auxin signaling in the early stages of drought stress. Hence, auxin and phosphatidylinositol signaling can be improved to increase drought tolerance in cotton [88] (Table 4). Identifying genes for fiber quality and yield under drought stress is one of the critical objectives of transcriptome analysis. GhADF1 gene expression was induced by drought stress. Cotton lines with overexpression of GhADF1 had a higher proline content and activity of antioxidant enzymes. Transcriptome analysis has identified 124 genes in leaves of GhADF1-RNi lines under drought stress. The results indicated that GhADF1 could be used in breeding programs to develop high-yielding and drought-tolerant cotton cultivars [89]. Cotton GhDRP1 is involved in drought tolerance and involves stress signal transduction. Cotton plants with overexpression of GhDRP1 showed high proline content, stomatal closure, and increased activity of antioxidant enzymes. These findings suggested that GhDRP1 regulates drought tolerance through ABA signaling and biosynthesis of flavonoids. Hence, we can alter the ABA signaling and metabolites’ biosynthesis to enhance drought tolerance in cotton [90]. Plant hormones improve drought tolerance in cotton, as shown by the transcriptome findings. Auxin plays a crucial role in plant growth and development. Detailed characterization of the YUC gene family has not been completed in cotton. Transcriptome analysis indicated that GhYUCs is involved in drought tolerance in cotton. The GhYUC22 gene was responsive to ABA and identified via virus-induced gene silencing (VIGS). GhYUC22 increased drought tolerance by modulating the ABA signaling pathway. Hence, auxin and ABA homeostasis can regulate drought tolerance in cotton [91].
A batch of drought-tolerant genes was identified using whole transcriptome sequencing. Gohir.A07G220600 was upregulated under drought stress and involved in drought tolerance. Gohir.A07G220600 was involved in plant antioxidant reactions. This gene may be a potential candidate for drought tolerance in cotton. These findings suggested that the gene expression network can quickly screen the drought-tolerant genes in cotton [92]. The GhDAN1-silenced cotton plants showed drought tolerance that can thrive under water shortage conditions. The suppression of GhDAN1 family regulates genes with AAAG motifs in auxin response pathways which are associated with regulation of drought stress [93]. These results suggested the role of different transcriptomes in drought tolerance in cotton. More studies should be conducted to identify the genes related to chlorophyll content under drought stress in cotton. The identified genes should be used in molecular breeding programs to develop drought-tolerant cotton cultivars. We strongly suggest using wild relatives of cotton cultivars as they are a rich source of tolerant genes and can be used to accelerate drought breeding in cotton.
Table 4. List of different transcriptomes identified for drought tolerance in cotton.
Table 4. List of different transcriptomes identified for drought tolerance in cotton.
Gohir.A07G058200Regulates auxin signaling[88]
124 DEGsIncreased proline content[89]
GhYUC22This gene modulated ABA and the auxin signaling pathway[91]
Gohir.A07G220600Involved in antioxidant reactions[92]
GhDRP1This gene increased proline content and altered flavonoid biosynthesis[90]
6968 genesAcclimatizing under drought stress[84]
5608 genesImproved drought tolerance[86]
110 genesImproved drought tolerance[87]

8. Development of Transgenic Cotton Cultivars

Genetic engineering is the most powerful technique to improve crop drought tolerance [11]. Transgenic crops resist increasing drought stress to thrive under low water levels. This common approach has been used to develop transgenic cotton cultivars using Agrobacterium-mediated genetic transformation. In a recent experiment, transgenic cotton plants were produced using the Agrobacterium-mediated genetic transformation method. Results showed that the chlorophyll and leaf relative water content were higher in pGP1 transgenic plants than in non-transgenic plants. Transgenic plants exhibited better root growth under drought stress [94].
In the same way, the transgenic plants with overexpression of AREB/ABF showed drought stress tolerance by stomatal regulation and a higher rate of photosynthesis [76]. Zhang, et al. [95] analyzed the expression of GhEXLB2 against drought stress in cotton. Gene expression was increased under drought stress. GhEXLB2 was cloned and transformed into cotton, increasing drought tolerance at the flowering and seedling stages. In transgenic plants, water usage efficiency (WUE) and soluble sugar content were also high [95]. The TaMnSOD gene increased drought tolerance in transgenic cotton lines. The gene was transformed into cotton lines by an Agrobacterium tumefaciens-mediated transformation method. The physiological and biochemical traits of transgenic and control plants were compared. Transgenic cotton lines showed a higher proline and sugar content than non-transgenic plants [96]. The AtLOS5 gene encodes a molybdenum co-factor and is essential for activating aldehyde oxidase, which is accountable for the biosynthesis of ABA. AtLOS5, was transformed into a cotton cultivar (Zhongmiansuo35) using an Agrobacterium tumefaciens-mediated transformation method. Shoots of transgenic plants showed a slower loss of transpirational water compared to control plants. Moreover, transgenic plants showed a 13% increase in fresh weight [97].
Kuppu, et al. [98] developed transgenic cotton lines to evaluate under drought stress. IPT encodes a rate-limiting enzyme in cytokinin synthesis. IPT was introduced into cotton cultivars, and transgenic lines produced more flowers and a higher photosynthesis rate under a limited water supply than control plants [98]. Targeting the molecular mechanism associated with drought tolerance without decreasing production is a major challenge for cotton breeders. AtDREB2A-CA transgenic cotton showed better shoot growth and root growth. Overexpression of the AtDREB2A-CA gene in transgenic lines showed better morphology without compromising yield under drought stress [99]. An Arabidopsis gene, HUB2 was involved in drought tolerance in cotton. AtHUB2 was introduced into the cotton genome using the cauliflower mosaic virus (CaMV), which significantly improved agricultural traits such as survival rate and sugar content of transgenic cotton under drought stress conditions [100]. Previous studies showed that K2-NhaD in transgenic cotton significantly improved the plant phenotype under drought stress. K2-NhaD was transformed into cotton using an Agrobacterium tumefaciens-mediated transformation method. Transgenic lines (K9, and K17) were identified by polymerase chain reaction (PCR). Overexpression of K2-NhaD in transgenic lines improved the sugar content and activity of antioxidant enzymes [101]. Several members of the TFs families have been engineered to develop drought-tolerant cotton genotypes. Overexpression of GhNAC2 increased root growth in cotton transgenic lines.
Reduced transpiration and stomatal control were observed in cotton transgenic lines [102]. GbWRKY1, a gene of the WRKY TF family, played a significant part in plant growth and responses to stress. GbWRKY1 overexpression in cotton lines enhanced drought tolerance [103]. The AmDUF1517a gene (Table 5) was isolated from a highly tolerant shrub (Ammopiptanthus mongolicus) and improved stress tolerance when introduced into Arabidopsis. AmDUF1517a was inserted into the cotton genome to examine its role in drought tolerance. AmDUF1517a transgenic cotton lines showed higher action of antioxidant enzymes such as peroxidase (POD) and catalase (CAT) [104]. The use of wild relatives to introduce the transgene will be highly useful in developing transgenic lines, because wild relatives are a potential source of stress-tolerant genes.
Table 5. Role of genetic engineering in the improvement of drought tolerance in cotton.
Table 5. Role of genetic engineering in the improvement of drought tolerance in cotton.
GhEXLB2Improved drought tolerance during the seedling stage[95]
pGP1Improved root growth, and leaf relative water content[94]
K2-NhaDIncreased the action of antioxidant enzymes[101]
GbWRKY1Increased drought tolerance[103]
AtHUB2Increased sugar content and survival rate[100]
AmDUF1517aImproved the action of antioxidant enzymes[104]
AtDREB2A-CAImproved shoot and root growth[99]
GhNAC2Reduced transpiration rate[102]
TaMnSODEnhanced proline and sugar contents[96]
IPTIncreased flowering rate and photosynthesis[98]
AtLOS5Enhanced 13% fresh weight of transgenic cultivars[97]

9. CRISPR/Cas9-Mediated Genome Editing for Drought Tolerance

Genome editing is a novel gene editing tool which is being used for genetic improvement of crops [105]. The new expansion of CRISPR/Cas9 using single-guided RNA (sgRNA) to edit double-stranded DNA precisely can transform agriculture [106]. Using labor-intensive and lengthy transformation methods is increasing the cost of varietal development. Therefore, it is necessary to reduce the danger of using ineffective sgRNA that can produce mutants without any desired mutations. The targeted editing and functional validity of genes have been checked in many crops [106]. CRISPR/Cas9 has two parts: sgRNA and Cas9 protein. sgRNA aligns the Cas9 with the targeted gene, and Cas9 cuts the gene to produce targeted mutations. Non-homologous end joining (NHEJ) and homology direct repair (HDR) are used to repair the mismatch sequences before cloning [107,108]. The founders of CRISPR/Cas9 won the 2020 Nobel Prize in chemistry [109]. Conventional breeding methods have been extensively used to develop drought-tolerant cultivars, but they are costly and cannot fix the complex issues of polygenic traits. Plant breeders are now using genome editing techniques to improve agronomically essential traits. CRISPR/Cas9 has been widely accepted due to its simplicity, ease of use, robust nature, and wider applications without any biological barriers. CRISPR/Cas9 is a highly specific and robust tool of various sequence-specific nucleases which has led to the development of novel climate-resistant crops [110].
CRISPR/Cas9-based gene manipulation has been used in cotton for multiple traits and biotic and abiotic stresses [111]. Recently, CRISPR/Cas9 has been used to develop non-transgenic lines of cotton with improved quality traits [112] and resistance to cotton leaf curl virus [113]. Unfortunately, applications of CRISPR/Cas9 to develop drought-tolerant cotton genotypes are limited, and require further studies to understand the functional genomics of stress tolerance. Newly developed editing systems such as base editing (BE) and prime editing (PE) could be used to edit large segments of the cotton genome to achieve targeted results against drought stress.

10. Conclusions and Future Prospective

Cotton plays a vital role in the economy. Cotton fiber is used in the textile industry to make valuable products. Abiotic stresses significantly reduce cotton growth and yield worldwide. Drought stress is the most devastating abiotic factor that reduces cotton growth, yield, and fiber quality. Cotton breeders have been trying hard to develop drought-tolerant cotton genotypes for decades. Still, due to the complexity of the trait and some limitations in the cotton genome, the success of breeding methods has been limited. The complete genome sequencing of the cotton genome has opened up ways to profoundly investigate the molecular factors underlying the essential traits of commercial interest. Using molecular breeding tools such as QTL and GWAS has increased our knowledge of molecular control of drought tolerance in cotton. Many studies have identified the potential genomic regions controlling drought tolerance in cotton. Many QTL have been used in QTL pyramiding, using the MAS breeding scheme. GWAS has identified many genomic areas/QTL and SNP associated with drought tolerance in cotton.
These QTL/genes are a vital genetic resource for a breeding program. Despite this, QTL for physiologically based drought tolerance are limited and need further studies. Genetic engineering is critical in developing drought-tolerant transgenic lines that thrive under water-limited conditions. However, studies should be expanded on the genetic analysis of drought-tolerant transgenic lines so that they can be used as valuable breeding material in future. Transcription factor analysis (TFs) has identified many genes/protein families contributing significantly toward cotton’s drought tolerance. As shown in the above data, complete genetic analysis of all TF families has not been covered and needs further studies. Transcriptome analysis of drought tolerance in cotton has been briefly investigated, and different genes and their expression have been shown in previous studies. Evaluating cotton genotypes under various drought stress levels and conducting transcriptome analysis of the roots/shoots would be better for studying differential gene expression. CRISPR/Cas9, a novel gene-editing technique, promises a bright future by targeting the editing of genes without any biological barrier. The targeted editing of drought-tolerant genes may enhance drought tolerance and help to develop tolerant mutants in future studies. Wild relatives of cotton would be an excellent source of novel genes to accelerate molecular breeding programs. Future studies should focus on the improvement of methods of genetic transformation to develop drought-tolerant cotton genotypes. This review provides a detailed overview of molecular tools and their use in cotton breeding against drought stress for use in future studies.

Author Contributions

A.R. (Adnan Rasheed) conceptualized and prepared the manuscript. L.Z., H.X., A.R. (Ali Raza), A.M., H.S., F.M.A., M.H. and X.L. participated in literature search. A.R. (Ali Raza), M.U.H. and S.F.A.G. reviewed and edited the manuscript. Y.J. supervised the study. All authors have read and agreed to the published version of the manuscript.


This study was financially supported by the National Natural Science Foundation of China (32071940), China National Key R&D Program (2019YFD1002205-3 & 2017FY100604-02), Foundation for the Construction of Innovative Hunan (2020NK2028).

Institutional Review Board Statement

Not applicable.

Data Availability Statement

Not applicable.


The authors are thankful to Muhammad Aamer for his valuable suggestions to improve quality of work. The authors extend their appreciation to the Deanship of Scientific Research, King Khalid University for supporting this work through research groups program under grant number R.G.P. 2/205/44.

Conflicts of Interest

The authors declare no conflict of interest.


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Figure 1. Drought stress affects cotton seed germination, reduces seedling growth, reduces yield, induces ROS, and decreases antioxidant activity and fiber quality. This figure was made with
Figure 1. Drought stress affects cotton seed germination, reduces seedling growth, reduces yield, induces ROS, and decreases antioxidant activity and fiber quality. This figure was made with
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Figure 2. Drought tolerance is regulated by numerous genes and their interacting networks. MAPK, Ca2+, and ABA signaling play an essential part in drought tolerance in cotton. This figure was made with
Figure 2. Drought tolerance is regulated by numerous genes and their interacting networks. MAPK, Ca2+, and ABA signaling play an essential part in drought tolerance in cotton. This figure was made with
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Figure 3. Drought-tolerant cotton genotypes can be developed using different breeding methods such as genetic engineering and CRISPR/Cas9. Identifying tolerant genes from wild relatives can help accelerate the drought breeding program. This figure was made with
Figure 3. Drought-tolerant cotton genotypes can be developed using different breeding methods such as genetic engineering and CRISPR/Cas9. Identifying tolerant genes from wild relatives can help accelerate the drought breeding program. This figure was made with
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Rasheed, A.; Zhao, L.; Raza, A.; Mahmood, A.; Xing, H.; Lv, X.; Saeed, H.; Alqahtani, F.M.; Hashem, M.; Hassan, M.U.; et al. Role of Molecular Breeding Tools in Enhancing the Breeding of Drought-Resilient Cotton Genotypes: An Updated Review. Water 2023, 15, 1377.

AMA Style

Rasheed A, Zhao L, Raza A, Mahmood A, Xing H, Lv X, Saeed H, Alqahtani FM, Hashem M, Hassan MU, et al. Role of Molecular Breeding Tools in Enhancing the Breeding of Drought-Resilient Cotton Genotypes: An Updated Review. Water. 2023; 15(7):1377.

Chicago/Turabian Style

Rasheed, Adnan, Long Zhao, Ali Raza, Athar Mahmood, Hucheng Xing, Xueying Lv, Hamza Saeed, Fatmah M. Alqahtani, Mohamed Hashem, Muhammad Umair Hassan, and et al. 2023. "Role of Molecular Breeding Tools in Enhancing the Breeding of Drought-Resilient Cotton Genotypes: An Updated Review" Water 15, no. 7: 1377.

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