Drought Stress in Cassava (Manihot esculenta): Management Strategies and Breeding Technologies

Abstract

Drought stress is a major constraint to cassava productivity, especially in drought-prone regions. Although cassava is considered drought-tolerant, prolonged or severe water scarcity significantly reduces tuber yield, carbon assimilation capacity and overall plant growth. The development, selection and deployment of cassava genotypes with enhanced drought tolerance and water use efficiency (WUE) will help to achieve food security. The ability of cassava genotypes to maintain productivity under drought stress is enhanced by drought-responsive genes that regulate stress-related proteins and metabolites, contributing to stomatal closure, osmotic adjustment, antioxidant defense, and efficient carbon assimilation. Therefore, this comprehensive review aimed to document: (i) the effects of drought stress on cassava’s physiological, biochemical and agronomic traits, and (ii) the mitigation strategies and breeding technologies that can improve cassava yield production, drought tolerance and WUE. The key traits discussed include stomatal regulation, chlorophyll degradation, source–sink imbalance, root system architecture and carbon allocation dynamics. In addition, the review presents advances in genomic, proteomic and metabolomic tools, and emphasizes the role of early bulking genotypes, drought tolerance indices, and multi-trait selection in developing cassava cultivars with enhanced drought tolerance, drought escape and drought avoidance mechanism. Therefore, the integration of these strategies will accelerate the development, selection and deployment of improved cassava varieties, which contribute to sustainable productivity and global food security under climate change.

1. Introduction

Cassava (Manihot esculenta Crantz, Euphorbiaceae, 2n = 36) is one of the most important tuber crops, serving as a major source of food for over 800 million people globally [1]. This crop is gaining popularity because it provides over 60% of the daily energy needs for millions of people living in tropical America, Africa, and Asia [2]. Global cassava production has consistently increased from approximately 279.11 million tons in 2013 to 333.68 million tons in 2023 [3]. Africa remains the leading producer of cassava, contributing nearly 56% to global production [4]. Despite Africa’s dominance in production, cassava yield per hectare on the continent remains below the global average [5,6], due to suboptimal soil fertility, inadequate field management and erratic rainfall. This forces the countries (including South Africa) to rely on importing cassava to meet local demands for food and industrial purposes [7].

Although cassava is widely recognized for its drought tolerance [8], the development of climate-resilient varieties with enhanced tolerance to severe drought remains a key priority. This is because severe or prolonged drought events are more frequent and intense due to climate change, threatening yield stability and cassava yield and quality [9,10]. The persistent and huge yield gap between Africa and the global average [11], demonstrates the underutilization of cassava’s genetic potential under water-limited conditions. Moreover, as climate variability increases, many regions are experiencing droughts that exceed the natural resilience of existing cassava cultivars. Therefore, this puts more pressure on breeding programs to prioritize the development of superior varieties focusing on target traits that contribute to maintaining yield stability and ensuring food security for millions who depend on cassava as a staple food crop [12].

Plant adaptation to drought stressed conditions involves distinct yet complementary mechanisms classified as drought tolerance, drought avoidance and drought escape [13]. Drought tolerance refers to the ability of a plant to endure low tissue water status while maintaining metabolic function through mechanisms such as osmotic adjustment and cellular protection. On the other hand, drought avoidance, encompasses strategies that maintain favorable plant water status despite soil water limitation, primarily via reductions in transpiration and enhancement of water uptake through deep or extensive root systems. These mechanisms delay or minimize plant dehydration and maintain metabolic activity during periods of drought stress. Drought escape refers to the ability of a plant to complete its life cycle or reach critical developmental stages before severe water deficits occur [13]. Each mechanism addresses drought stress at different temporal and physiological scales, and their integration supports cassava plant survival in drought-prone environments.

Furthermore, cassava possesses several unique physiological traits that contribute to its adaptability under drought stress, which are often overlooked in drought-related reviews. It has a C₃–C₄ intermediate photosynthetic system [14], enabling more efficient carbon fixation under low CO₂ and water-limited conditions. Unlike many other crops, cassava has amphistomatous leaves with stomata on both leaf surfaces to allow flexible regulation of gas exchange based on environmental conditions. Its highly plastic growth habit enables dynamic adjustment of canopy size, root development and assimilate allocation in response to environmental stress. In addition, cassava stores starch reserves in roots and stems, providing a physiological buffer that supports survival during drought and facilitate rapid recovery post-stress [15]. These traits are rarely found in combination with other food crops and form the foundation of cassava’s drought tolerance and drought avoidance mechanisms.

Drought poses a major threat to human livelihood and food security [16]. According to Ayanlade et al. [17] drought is likely to drive agrarian crises in many sub-Saharan African (SSA) countries due to high temperatures and lower rainfall. For example, in the first quarter of 2024, countries in the SSA region, such as Zimbabwe, Malawi and Zambia, declared drought a national disaster [18]. This is due to unpredictable rainfall patterns that caused drought stress in drylands across the SSA region [19]. These conditions disrupt soil moisture regimes and crop water availability, which severely impact cassava by inducing drought stress that limits growth and storage root formation [20].

In response to drought stress, cassava activates a series of physiological mechanisms to conserve water and maintain cellular function [21]. One of the earliest responses is stomatal closure mediated by abscisic acid (ABA) [22], which reduces transpiration but also restricts CO₂ uptake, compromising C assimilation and biomass allocation. Simultaneously, drought reduces turgor pressure, disrupting cell division and expansion necessary for root growth and tuber development [23]. Moreover, the oxidative stress that arises from excessive reactive oxygen species (ROS) during drought damages the membranes, proteins and nucleic acids [24]. In response, plants activate enzymatic antioxidant defence systems, including superoxide dismutase and catalase, to maintain cellular redox homeostasis [25]. Furthermore, under water-deficit conditions, cassava also exhibits physiological responses such as decreased chlorophyll content and reduced photosynthetic efficiency. These are often accompanied by oxidative stress due to the overaccumulation of reactive oxygen species (ROS). While ROS are traditionally viewed as damaging, recent studies highlight their role as signaling molecules, mediating stress perception and triggering protective responses including antioxidant pathways and stress-responsive gene expression [26,27]. These mechanisms influence key processes such as chlorophyll retention, phloem loading, and assimilate transport, ultimately affecting the source–sink balance and root development [28,29]. Therefore, screening of available germplasm, selection and deployment of cassava genotypes with improved water use efficiency (WUE) will assist in reducing the negative effects of drought stress.

WUE refers to the amount of biomass and yield produced per unit of water used by the crop [30]. Genotypes with high WUE are tolerant to drought [31], making this trait crucial for improving tuber yields in water-limited conditions [32]. The WUE of cassava is influenced by both genetic and environmental factors, including genotype-specific traits (such as reduced stomatal conductance and enhanced root depth). The WUE of tuber crops varies under different moisture levels [33,34], emphasizing the need for tailored cultivation strategies. Improved WUE in cassava is linked to physiological traits that help the plants to conserve water. For instance, reduced stomatal conductance and lower transpiration rates enable cassava to retain soil moisture during dry periods [35]. In addition, genotypes with deeper root systems access water from deeper soil layers, enhancing water uptake and buffering the plant against drought stress [36]. The osmotic adjustment through the upregulation of specific metabolites helps to maintain cell turgor and enzyme function during drought stress [12]. High-WUE genotypes often exhibit increased antioxidant enzyme activity, which mitigates oxidative damage caused by drought-induced reactive oxygen species. In addition, the agronomic practices such as mulching and supplemental irrigation have been widely adopted to enhance both WUE and tuber yield [33,37,38,39]. These interventions help conserve soil moisture, reduce evaporative losses and support plant productivity.

Furthermore, advancements in high-throughput phenotyping and omics technologies are transforming cassava breeding for drought tolerance and WUE. The tools such as liquid chromatography-mass spectrometry-based metabolomic and proteomic profiling, assist in identifying drought-responsive biomarkers, including metabolites and protein expression signatures [20,40]. These biomarkers of stress response accelerate screening for drought tolerance and WUE, shortening breeding cycles and enhancing genetic gains and ultimately contribute to food security in the face of climate change.

In the last two decades, the need to develop drought-tolerant and water-use-efficient crop cultivars has increased due to population growth and climate change. The approaches including utilization of drought indices and multiple traits selection have enhanced the efficiency of identifying superior cassava genotypes under drought stress. Drought indices improve the selection of high-yielding cassava genotypes, while multiple trait selection enables breeders to target key physiological traits, proteins, and metabolites associated with drought tolerance and WUE. For example, selection for traits such as lower stomatal conductance, low canopy temperature, high leaf relative water content and high root-to-shoot ratio are useful for selecting drought-resilient and water-efficient genotypes in cassava. Despite these advances, there is limited information on how physio-biochemical traits interact to confer drought tolerance, and their translation into heritable, selection-ready traits is not well established. Furthermore, genetic and molecular studies on WUE and drought tolerance are relatively sparse compared to other staple crops, and the application of high-throughput phenotyping and omics tools has not yet been fully integrated into cassava breeding programs. Addressing these gaps is essential to accelerate the development of superior genotypes that combine drought tolerance with high tuber yield and WUE. In light of the above, the objectives of this review were to document: (i) the effects of drought stress on cassava’s physiological, biochemical and agronomic traits, and (ii) the mitigation strategies and breeding technologies that can improve cassava tuber yield production, drought tolerance and WUE.

2. Effects of Drought Stress on Cassava Performance

Drought stress poses a major challenge to cassava production [41], by disrupting physiological, biochemical, and agronomic processes (Figure 1) essential for growth and development. A deeper understanding of the effects of drought stress on cassava is crucial for developing effective management and breeding strategies to enhance its drought tolerance. This section provides detailed information on the effects of drought stress on cassava performance, highlighting the crop’s adaptive mechanisms.

2.1. Effects of Drought Stress on Physiological Traits

Cassava exhibits a series of physiological disruptions when exposed to drought stress, leading to poor root development [42]. Drought stress reduces soil water availability, limiting nutrient diffusion and mass flow towards the root surface, which decreases nutrient uptake and assimilation efficiency [43]. Moreover, drought-induced oxidative stress leads to lipid peroxidation that impairs cell membrane integrity and permeability, thereby disrupting nutrient transport and ion homeostasis within cells [44]. As water absorption diminishes during drought, the plant experiences reduced turgor pressure [45], resulting in reduced cell elongation, inhibited root growth and smaller tuber size (Figure 1) [45]. Furthermore, drought stress slows down the electron transport chain in photosystem II and reduces relative water content in leaves, resulting in chlorophyll degradation and impaired light harvesting [46]. Studies have shown that chlorophyll content in cassava can decline by over 20% under drought, directly reducing photosynthetic efficiency [47]. This reduction, partly due to ROS accumulation, compromises biomass production and leaf function [46]. The reduction in turgor pressure affects growth and limits the plant’s ability to maintain adequate photosynthetic activity. The interplay between these physiological factors creates a challenging environment for cassava under drought stress. Moreover, studies indicate that cassava cultivars exhibit varying degrees of tolerance to drought stress through different adaptive strategies [12]. For example, some cultivars may prioritize root growth and nutrient uptake efficiency under water-limited conditions, while others might enhance their antioxidant mechanisms to mitigate oxidative damage caused by ROS [48]. In addition, its capacity to store starch provides a physiological buffer during extended drought, helping sustain growth and enabling rapid post-drought recovery. These adaptations highlight the importance of identifying trait-specific responses when screening for drought tolerance and WUE.

2.2. Effects of Drought Stress on Biochemical Traits

Cassava responds to water-deficit conditions with a range of biochemical changes aimed at mitigating oxidative and osmotic stress. One primary response to drought is the suppression of photosynthetic enzyme activity, particularly ribulose-1,5-bisphosphate carboxylase/oxygenase (RuBisCO), due to reduced CO₂ availability and enzymatic degradation [49]. This contributes to declines in carbon assimilation and overall energy production. In addition, under drought conditions, cassava relies on key enzymatic antioxidants (such as superoxide dismutase and catalase). These enzymes neutralize ROS and protect cellular membranes and proteins [25]. For instance, a study conducted by Zhu et al. [46] showed that genotypes, RS01 and SC124 maintained higher relative water content and chlorophyll levels due to the upregulation of antioxidants (such as ascorbate and glutathione) compared to drought-sensitive varieties such as SC205 and GR4. Drought stress alters osmotic potential, leading to the accumulation of osmolytes such as proline and soluble sugars [49,50]. These solutes promote osmotic adjustment, preserve the integrity of proteins, enzymes, and membranes to maintain cell water balance even under environmental stress [51]. The osmotic adjustment capacity varies by genotype, and identifying genotypes with strong osmolyte production is key to breeding programs.

Moreover, the phytohormone ABA plays a central role in cassava’s biochemical drought response [48]. The ABA accumulation mediates stomatal closure and activates stress-responsive gene expression, including those encoding antioxidant enzymes and osmolyte biosynthesis pathway [52,53]. This hormone interacts with secondary messengers (e.g., Ca²⁺, H₂O₂) and transcription factors to regulate drought adaptation pathways [54]. Despite significant advancements, further exploration is needed regarding the molecular pathways involved in osmolyte accumulation and antioxidant enzyme expression. In addition, the role of plant–microbe interactions in the rhizosphere in enhancing drought tolerance through biochemical mechanisms warrants thorough investigation. Therefore, addressing these gaps is essential for developing strategies to improve cassava’s drought tolerance through targeted breeding programs and agronomic practices.

2.3. Effects of Drought Stress on Agronomic Traits

Drought stress induces a complex interplay of physiological and biochemical changes that negatively affect agronomic traits in cassava. It reduces cell expansion and division, resulting in stunted growth and reduced plant height in cassava [41]. This restricts the photosynthetic surface area, compounding reductions in biomass production in cassava genotypes. The shoot biomass reduction can be attributed to the reduction in dry matter production [55]. Moreover, drought shifts assimilate allocation from shoot to root, as cassava prioritizes water uptake over aboveground growth [56,57,58]. This results in reduced shoot biomass and increased root-to-shoot ratios under stress [55]. However, tuber yield may still decline due to impaired photosynthesis and assimilate loading, leading to reduced carbohydrate storage in tubers and higher fibrous root content [59,60]. Root system architecture changes under drought. Shallow, lateral root development may increase to capture surface moisture, but this comes at the expense of deep-rooted structures that support long-term resilience [61]. Collectively, these changes lead to reduced harvest index and lower marketable tuber yield. That is consistent with the results from other studies presented in Table 1, indicating the tuber yield reduction ranging from 18% to 87%, depending on the cultivar and drought severity. This highlights the urgent need for drought-resilient cultivars with stable agronomic traits. Therefore, understanding the interconnected effects of drought on plant height, shoot and root biomass, dry matter allocation and harvest index is crucial for developing effective breeding strategies to enhance cassava’s drought tolerance. These insights guide future research directions that focus on improving cassava’s adaptability to increasingly challenging environmental conditions.

Table 1. Reports on the effect of drought stress on cassava tuber yield.

Country	Genotype Names	Number of Cultivars	Yield Reduction	Reference
Kenya	98/0002, TME-419, 95/0306, 95/0166, 14-2-1425, 96/1569, 98/2101, 98/0505, I91/02322, 98/2132, I91B/00462, I96/1439, M98/0068, 990/183, I92/0067, 92/0342, 94/0039, 97/4779, 99/0204, 96/0409, 98/0196, 94/0020, 01/0014, I91/02324, 92/0427, 95/0289, I92/0057, I92/0326, I92B/00061, 96/2132, I30/572, 98/0406, 96/2226, 94/0026, I91/02312, I91/02327, PYT, Ex-Mariakani	37	59%	[21]
Brazil	IAC 576–70	1	45.7%	[50]
Brazil	9624-09, BGM0089, BGM0096, BGM0116, BGM0163, BGM0279, BGM0331, BGM0360, BGM0541, BGM0598, BGM0785, BGM0815, BGM0818, BGM0856, BGM0876, BGM0908, BGM1171, BGM1195, BGM1482, BGM2020, Branquinha, BRS Amansa Burro, BRS Dourada, BRS Formosa, BRS Gema de Ovo, BRS Kiriris, Cacau, Cachimbo, Do Céu, Engana Ladrão, Eucalipto, GCP-001, GCP-009, GCP-014, GCP-020, GCP-025, GCP-043, GCP-046, GCP-095, GCP-128, GCP-179, GCP-190, GCP-194, GCP-227, GCP-374, Mani Branca, NG310, Paulo Rosa, Sacai	49	73%	[61]
Nigeria	(30572, 96/0326, 91/02324, 95/0211, 96/0016, 96/0304, 96/0529, 96/0565 and 96/1632)	9	87%	[62]
Uganda	Akena, AladoAlado, Bao, Buganda, Bukalasa, Ditu, Icilecili, Egabu, Guaranda, Kabwa, Kidimo, Kwatamumpare, Luderudu, Lugbara, Maburu, Magana, Mercury, MH96/0686, MH97/2961, MufumbaChai, Musita, Namukoni, Namulalu, NASE1, NASE11, NASE12, NASE2, NASE3, NASE9, Njule, Nyakakwa, Nyalanda, Nyamutukura, Nyapamitu, Nyaraboke, Nyarare, Omongole, Pilipili, Rugogoma, Rwaburaru, Ryahorore, TME14, TME204, Tongolo, Tongolo2 Yellow	46	37%	[63]
Ghana	00/0203, 96/1708, 96/409, ATR 002, ATR 007, Biabasse, CTSIA 110, CTSIA 112, CTSIA 230, CTSIA 45, CTSIA 48, CTSIA 65, CTSIA 72, I91934, MM 96/1751, NWA 004, Ponstisange, TME 419, TME 435, UCC 2001/449	20	39%	[64]
Nigeria	IBA120008, I098510, I010040, I070539, TMEB419, TMEB693, I011368, I980581, I070593, I920326	10	37%	[65]
Kenya	110(07/0621HS), 128(05/0099HS), 169(98/002HS), 183907/0751HS), 197(01/1797HS), 212(07/576HS), 29(06/1475HS), 29B29, 89(06/1475HS), 93(07/0756HS), 94(05/0741HS), 99(07/1313HS), CH05-203, CK9, COLICANANA, D31, Ex-Ndolo, EYOPE, F10-30R2, F19, FUMBA CHAI, I92/0427, I95/034095-N, KALAWE, KALESO, Karembo, KBH2002/066-3, KBH2006-026, KIBANDAMENO, KIZIMBANI, KME 1, LML/2008/363, M96/7151, MAGANA, MATUJA, MH95/0183, MIGYERA, MKUMBA-1, MKUMBA-2, MM06/0013, MM06/0046, MM06/0074, MM06/0082, MM06/0083, MM06/0138, MM06/0139, MM06/0143, MM08/2206, MM96/0669, MM96/0686, MM96/1871, MM96/1956, MM96/2480, MM96/3868, MM96/4684, MM96/5280, MM96/6966A, MM96/6966B, MM96/9308, MM97/0293, MM97/1744, MM98/1642, MM98/1669, MM98/2270, MM98/3567, Mucericer, NASE 14, NASE 18, NASE 3, ORERA, PWANI, SANGOJA, SAUTI, SERERE, TAJIRIKA, TME 14, TZ-130, UNKNOWN 4, YIZASO	79	18%	[66]

Table 1. Reports on the effect of drought stress on cassava tuber yield.

Country	Genotype Names	Number of Cultivars	Yield Reduction	Reference
Kenya	98/0002, TME-419, 95/0306, 95/0166, 14-2-1425, 96/1569, 98/2101, 98/0505, I91/02322, 98/2132, I91B/00462, I96/1439, M98/0068, 990/183, I92/0067, 92/0342, 94/0039, 97/4779, 99/0204, 96/0409, 98/0196, 94/0020, 01/0014, I91/02324, 92/0427, 95/0289, I92/0057, I92/0326, I92B/00061, 96/2132, I30/572, 98/0406, 96/2226, 94/0026, I91/02312, I91/02327, PYT, Ex-Mariakani	37	59%	[21]
Brazil	IAC 576–70	1	45.7%	[50]
Brazil	9624-09, BGM0089, BGM0096, BGM0116, BGM0163, BGM0279, BGM0331, BGM0360, BGM0541, BGM0598, BGM0785, BGM0815, BGM0818, BGM0856, BGM0876, BGM0908, BGM1171, BGM1195, BGM1482, BGM2020, Branquinha, BRS Amansa Burro, BRS Dourada, BRS Formosa, BRS Gema de Ovo, BRS Kiriris, Cacau, Cachimbo, Do Céu, Engana Ladrão, Eucalipto, GCP-001, GCP-009, GCP-014, GCP-020, GCP-025, GCP-043, GCP-046, GCP-095, GCP-128, GCP-179, GCP-190, GCP-194, GCP-227, GCP-374, Mani Branca, NG310, Paulo Rosa, Sacai	49	73%	[61]
Nigeria	(30572, 96/0326, 91/02324, 95/0211, 96/0016, 96/0304, 96/0529, 96/0565 and 96/1632)	9	87%	[62]
Uganda	Akena, AladoAlado, Bao, Buganda, Bukalasa, Ditu, Icilecili, Egabu, Guaranda, Kabwa, Kidimo, Kwatamumpare, Luderudu, Lugbara, Maburu, Magana, Mercury, MH96/0686, MH97/2961, MufumbaChai, Musita, Namukoni, Namulalu, NASE1, NASE11, NASE12, NASE2, NASE3, NASE9, Njule, Nyakakwa, Nyalanda, Nyamutukura, Nyapamitu, Nyaraboke, Nyarare, Omongole, Pilipili, Rugogoma, Rwaburaru, Ryahorore, TME14, TME204, Tongolo, Tongolo2 Yellow	46	37%	[63]
Ghana	00/0203, 96/1708, 96/409, ATR 002, ATR 007, Biabasse, CTSIA 110, CTSIA 112, CTSIA 230, CTSIA 45, CTSIA 48, CTSIA 65, CTSIA 72, I91934, MM 96/1751, NWA 004, Ponstisange, TME 419, TME 435, UCC 2001/449	20	39%	[64]
Nigeria	IBA120008, I098510, I010040, I070539, TMEB419, TMEB693, I011368, I980581, I070593, I920326	10	37%	[65]
Kenya	110(07/0621HS), 128(05/0099HS), 169(98/002HS), 183907/0751HS), 197(01/1797HS), 212(07/576HS), 29(06/1475HS), 29B29, 89(06/1475HS), 93(07/0756HS), 94(05/0741HS), 99(07/1313HS), CH05-203, CK9, COLICANANA, D31, Ex-Ndolo, EYOPE, F10-30R2, F19, FUMBA CHAI, I92/0427, I95/034095-N, KALAWE, KALESO, Karembo, KBH2002/066-3, KBH2006-026, KIBANDAMENO, KIZIMBANI, KME 1, LML/2008/363, M96/7151, MAGANA, MATUJA, MH95/0183, MIGYERA, MKUMBA-1, MKUMBA-2, MM06/0013, MM06/0046, MM06/0074, MM06/0082, MM06/0083, MM06/0138, MM06/0139, MM06/0143, MM08/2206, MM96/0669, MM96/0686, MM96/1871, MM96/1956, MM96/2480, MM96/3868, MM96/4684, MM96/5280, MM96/6966A, MM96/6966B, MM96/9308, MM97/0293, MM97/1744, MM98/1642, MM98/1669, MM98/2270, MM98/3567, Mucericer, NASE 14, NASE 18, NASE 3, ORERA, PWANI, SANGOJA, SAUTI, SERERE, TAJIRIKA, TME 14, TZ-130, UNKNOWN 4, YIZASO	79	18%	[66]

2.4. Effects of Drought Stress on WUE

Among the multiple traits affected by limited water availability, WUE stands out as a key indicator of drought tolerance in cassava because it links drought tolerance with productivity. The genotypes with lower WUE are associated with drought susceptibility and lower tuber yield [60]. Drought reduces WUE in cassava by disrupting the balance between transpiration and photosynthesis. The stomatal closure limits CO₂ assimilation while reducing water loss [67,68], leading to decreased intrinsic and instantaneous WUE (Figure 2). In addition, drought stress compromises stomatal conductance, transpiration rate and net photosynthetic rate, which collectively contribute to lower WUE [69]. During drought-stress conditions, cassava plants tend to reduce shoot biomass accumulation while increasing root biomass to enhance water uptake capacity [70]. This plasticity results in higher root biomass WUE but reduced shoot productivity [71], indicating that drought affects cassava’s water use capabilities and highlights the complexity of its physiological, biochemical and agronomic responses. The genotypes with greater WUE tend to maintain higher photosynthetic efficiency and better osmotic adjustment under stress [32,72]. Improving WUE requires integrating genetic and agronomic strategies. Precision irrigation, mulching, and soil water retention practices enhance yield productivity and WUE [73], while selection of traits including stomatal conductance, leaf temperature, and canopy dynamics informs breeding. Therefore, research into the genetic basis of drought tolerance and the molecular pathways involved in osmotic adjustment and antioxidant responses is essential for identifying traits that improve WUE.

2.5. Effects of Drought Stress on Carbon Assimilation Capacity

Carbon assimilation capacity is a fundamental trait that enhances the process of capturing atmospheric carbon dioxide (CO₂) and storing it within the plants. Cassava plants assimilate CO₂ through photosynthesis, converting it into carbohydrates that serve as energy sources for growth and development [74]. However, drought stress disrupts source-sink interactions by decreasing stomatal conductance, which limits CO₂ uptake and carbon fixation (Figure 2) [20]. In addition, reduced turgor and increased phloem resistance hinder assimilate translocation to storage tissues [75]. During drought, storage organs may reverse their roles, becoming sources of carbohydrates to support growing tissues, which depletes stored carbohydrates and reduces overall biomass [76]. Furthermore, cassava’s stems serve as intermediate carbohydrate storage organs, a common feature that supports sink tissues under drought by remobilizing starch [28]. However, extended stress leads to carbohydrate depletion and reduced biomass accumulation [73]. The oxidative damage to chloroplasts and RuBisCO inhibition during drought lowers assimilation efficiency [77]. These responses reduce the plant’s capacity to maintain a positive carbon balance under drought stress. Despite this understanding, the transcriptional regulation of key carbon assimilation genes under drought is still not well characterized in cassava. Therefore, research is needed to map the signaling networks involved in source–sink regulation, enzyme stability and remobilization during stress. Such knowledge is vital for improving carbon assimilation and drought adaptation through breeding and metabolic engineering.

3. Drought Response and Tolerance

3.1. Physiological and Morphological Mechanisms

Cassava exhibits a remarkable ability to withstand drought, making it a staple crop of strategic importance in SSA, where rainfall patterns are increasingly erratic due to climate change [78]. Compared to other major staples, cassava shows greater yield stability under prolonged dry spells [79], making it an ideal candidate for cultivation in semi-arid and marginal environments. This drought tolerance mechanism arises from a complex interplay of physiological, morphological and molecular adaptations (Table 2), that allow cassava to maintain metabolic function and growth under water-limited conditions (Figure 2) [21]. These mechanisms work across scales from whole-plant architecture to gene regulation, enabling cassava to survive and continue allocating resources under drought stress. One key adaptation is cassava’s deep and extensive root system, which accesses moisture from deeper soil layers and buffers against short-term droughts [9]. Drought-resilient cultivars exhibit significantly deeper root penetration, which correlates with improved yield stability and resource-use efficiency during dry periods. Another important trait is dynamic stomatal regulation (Figure 2), where cassava behaves largely as an isohydric species, rapidly closing stomata under drought stress to conserve water while maintaining a minimal conductance that allows limited CO₂ uptake. Furthermore, cassava adjusts its canopy morphology, through partial leaf shedding, which reduces the surface area for water loss while preserving the photosynthetic capacity of remaining leaves [80]. This leaf area modulation helps balance carbon assimilation and water conservation during severe drought events. At the cellular level, osmotic adjustment plays a pivotal role in cassava’s drought tolerance. The accumulation of compatible solutes such as proline, soluble sugars, and proteins maintains turgor pressure and protects macromolecules from dehydration (Figure 2) [67,81,82]. These osmolytes act as molecular chaperones, stabilizing proteins and membranes under osmotic stress.

Table 2. Some of the major adaptive strategies that help cassava plants to withstand drought stress.

Adaptive Trait	Type	Mechanism	Effect on Tuber Yield	References
Proline and soluble sugars	Molecular/metabolites	Osmotic adjustment	Maintains turgor, protects proteins/membranes	[50]
Stay green	Morphological	Allow continued photosynthesis	Improved tuber yield	[67]
MeALDH	Molecular	Detoxifies reactive aldehydes	Maintains membrane stability	[67]
MeZFP	Molecular	Regulates antioxidant genes	Maintains redox homeostasis	[67]
MeRAV5	Molecular	The transcription Factor regulating H2O2 homeostasis and lignin biosynthesis	Strengthens cell walls, reduces damage	[83]
Reduced stomatal conductance	Physiological	Isohydric closure, limited CO2 uptake	Conserves water, maintains minimal assimilation	[84]
Leaf area modulation	Morphological	Reducing leaf area growth	Reduces water loss, maintains photosynthesis	[69]

Table 2. Some of the major adaptive strategies that help cassava plants to withstand drought stress.

Adaptive Trait	Type	Mechanism	Effect on Tuber Yield	References
Proline and soluble sugars	Molecular/metabolites	Osmotic adjustment	Maintains turgor, protects proteins/membranes	[50]
Stay green	Morphological	Allow continued photosynthesis	Improved tuber yield	[67]
MeALDH	Molecular	Detoxifies reactive aldehydes	Maintains membrane stability	[67]
MeZFP	Molecular	Regulates antioxidant genes	Maintains redox homeostasis	[67]
MeRAV5	Molecular	The transcription Factor regulating H2O2 homeostasis and lignin biosynthesis	Strengthens cell walls, reduces damage	[83]
Reduced stomatal conductance	Physiological	Isohydric closure, limited CO2 uptake	Conserves water, maintains minimal assimilation	[84]
Leaf area modulation	Morphological	Reducing leaf area growth	Reduces water loss, maintains photosynthesis	[69]

3.2. Molecular and Genetic Mechanisms

Cassava’s drought response is further reinforced by a robust antioxidant defence system. Upon drought-induced oxidative stress, cassava activates key enzymes such as superoxide dismutase, catalase and peroxidases, which scavenge ROS [27,46]. Importantly, ROS such as hydrogen peroxide (H₂O₂) also function as signaling molecules, triggering downstream protective responses including gene activation and metabolic reprogramming [82]. At the molecular level, cassava’s drought tolerance is governed by a network of stress-responsive genes, particularly those associated with ABA signaling in the roots (Figure 2), antioxidant defense, and structural reinforcement. Recent advances have identified several transcription factors and regulatory proteins as central components in this response. For instance, MeRAV5, a key transcription factor, enhances drought tolerance by regulating H₂O₂ homeostasis and activating lignin biosynthesis pathways [83]. Increased lignin deposition strengthens cell walls and mitigates structural damage during dehydration. MeRAV5 exemplifies the integration of ROS signaling and structural defense, giving emphasis to the dual role of ROS as both damaging and adaptive signaling molecules. These molecular regulators interact with metabolic pathways and hormonal pathways. This integration supports physiological responses such as osmotic adjustment, ROS signaling and water conservation (Figure 2).

Other key genes include MeALDH, which encodes an aldehyde dehydrogenase that detoxifies reactive aldehydes generated during oxidative stress, thus preserving membrane stability and osmotic balance [67]. MeZFP, a zinc finger protein, regulates downstream genes involved in antioxidant responses and contributes to the maintenance of redox homeostasis under drought stress [67]. These molecular components function as adaptive switches, coordinating metabolic, hormonal, and structural responses under limited water availability and linking molecular regulation directly to physiological adaptations such as root depth, stomatal control, and osmotic adjustment. Therefore, understanding these interactions provides practical breeding targets, as genotypes with active MeRAV5, MeALDH, and MeZFP expression may exhibit deeper roots, efficient stomatal regulation, robust osmotic adjustment and strong antioxidant defense to enhance yield stability and WUE (Figure 2). These traits directly contribute to food security in drought-prone regions.

4. Mitigation Strategies of Drought Stress in Cassava Production

4.1. Mulching

Mulching plays a significant role in reducing the effects of drought stress on cassava plants by improving soil moisture retention and maintaining soil temperature which leads to improved yield and WUE [85]. It also enhances water infiltration during rainstorms, thereby reducing runoff and improving water availability in the root zone [86]. In Sri Lanka, mulching with rice straw, grass leaves, and legume leaves increased cassava yield by 43.15%, 40.43%, and 28.66%, respectively [37]. Under water-deficit conditions, mulching improved tuber yield by more than 31% compared to non-mulched plants [39]. These improvements are attributable to enhanced soil moisture availability, facilitating better root growth and nutrient uptake, leading to improved biomass accumulation and carbohydrate storage in tubers. Therefore, integrating mulching with physiologically adaptive genotypes, such as deep-rooted and high water use efficient cassava varieties, can further enhance drought tolerance and yield stability in semi-arid and marginal environments. However, the lack of awareness is reducing the adoption of mulching practices in tuber crops by smallholder farmers. Notable efforts have been made to educate smallholder farmers in Ethiopia and Zambia through the Sustainable Land Management Project [87], Zambia through the Sasakawa-Global 2000 program [88] and in Zimbabwe through the Pfumvudza program [89].

4.2. Irrigation

The application of water through irrigation improves plant growth and development and tuber yield. Therefore, applying water in cassava plants through precision irrigation techniques (such as drip irrigation) offers a targeted water management strategy that mitigates drought stress while conserving water [33,73]. These systems optimize water by delivering water directly to the root zone of cassava plants based on real-time data and crop water requirements essential for sustaining C assimilation and biomass accumulation. In the 2006/2007 growing season, Odubanjo et al. [38] reported that irrigation increased cassava tuber yield by 84% and water use efficiency (WUE) by 67% compared to rainfed conditions. Similarly, irrigating soil to 60% water availability increased cassava tuber yield and WUE by 58% and 17%, respectively [33]. Additional studies confirm that increased irrigation levels significantly enhance cassava tuber yield and WUE [73]. When combined with drought-resilient genotypes characterized by deep roots and other adaptive traits, precision irrigation can maximize yield gains and WUE. Furthermore, integrating rapid phenotyping approaches enables the identification of superior germplasm for drought-prone environments, enhancing the efficiency of breeding programs and agronomic interventions. Despite the importance, the progress in adopting the use of drip irrigation in cassava farms is very slow in SSA [90] because of high installation and maintenance costs, limited access to irrigation equipment, as well as water scarcity. Consequently, most smallholder farmers rely on more affordable but less efficient methods such as flood or furrow irrigation, leading to lower WUE in plants.

4.3. The Use of Genotypes with Drought-Adaptive Traits

Drought adaptation in cassava is a critical survival strategy that enables certain genotypes to cope with water scarcity by modulating physiological, morphological and biochemical traits [91]. These adaptations are vital in cassava, which is often grown in regions susceptible to drought [92]. The drought-adaptive genotypes exhibit enhanced osmotic adjustment, allowing cells to maintain turgor pressure under low water potential by upregulating metabolites which protect cellular structures [93]. Genotypes with effective water-conservation mechanisms can maintain a higher internal water status during drought by reducing transpiration through early stomatal closure [35]. This stomatal regulation is mediated by ABA signaling that develops in the roots as response to declining water supply, which travels through the xylem to the leaves and triggers stomatal guard cells to close to minimize water loss [94,95]. In addition, one of the key morphological traits associated with drought tolerance in cassava is its extensive root system, which enables the plant to access deeper soil moisture reserves [9]. In optimal soil environments, cassava roots can grow rapidly, potentially reaching depths of up to 2.5 m, which is crucial for accessing water during prolonged dry periods [21]. This deep-rooting ability contributes to improved harvest index and yield, making it a vital trait for cassava cultivation under drought-stressed conditions. Additionally, partial leaf shedding under prolonged drought reduces canopy size and transpiration demand, conserving water and minimizing exposure to excessive evaporative loss.

Cassava genotypes with drought-adaptive traits have been identified across several studies. For instance, Rayong 9, Huay Bong 60 and Rayong 11 from Thailand have long and deeper root systems that can enhance drought tolerance [41]. Similarly, I980581 from Nigeria showed enhanced water-use efficiency and stable yield under drought conditions [65]. These genotypes often exhibit traits such as delayed leaf senescence, efficient osmotic adjustment and strong antioxidant responses. Their inclusion in breeding programs can facilitate the development of cultivars with durable drought tolerance. Some genotypes also exhibit early stomatal closure as a protective response to declining soil moisture, limiting water loss and extending soil moisture availability [96]. This phenological adjustment reduces photosynthetic capacity but is essential to avoid irreversible damage from prolonged drought stress. Therefore, these adaptive strategies enhance cassava’s ability to cope with drought conditions. However, it is important to note that no cassava genotype has been developed with absolute drought tolerance [15]. Breeders have focused on selecting genotypes with traits such as higher stomatal conductance and a deep root system as useful proxy traits for identifying drought-tolerant and water-use-efficient cassava genotypes [21,51,96]. Extended periods of drought in cassava can result in substantial tuber yield losses. When drought begins early, it prompts the activation of drought-adaptive strategies in crop cultivars that cannot finish their life cycles before harsh drought conditions occur. As such, it is necessary to breed and select drought-tolerant, as well as water-use-efficient characteristics in cassava to maintain food security in drought-prone areas.

4.4. The Use of Early Bulking Genotypes

Tuber crop genotypes use early bulking as a mechanism for drought escape, enabling some cultivars to complete the growing cycle before drought stress occurs [97]. This characteristic is crucial, especially in regions with unpredictable water supply, as it allows early maturing cassava to minimize the effects of drought stress [97]. Crop genotypes that mature early possess several important traits (including a shorter vegetative phase) that help them withstand drought conditions [98]. Early bulking cassava genotypes are capable of accumulating significant root biomass within a short period, making them ideal for regions with unpredictable rainfall. For example, genotype 96/1708 in Ghana and the genotypes (W940006, NR090146, TMS982123, TMS13F1060P0014, and NR010161) in Nigeria have been identified as early bulking [63]. These varieties efficiently partition carbon to storage roots early in development, ensuring harvestable yield even under terminal drought conditions. The early bulking genotypes accelerate C partitioning towards storage roots, facilitated by enhanced sink strength and mobilization of photosynthates. This combination leads to reduced evapotranspiration and enhanced gas exchange rates, allowing the plants to improve net photosynthesis while maintaining WUE. These physiological adaptations are critical for maximizing growth and yield under water-limited environments. Several studies have shown a positive correlation between early bulking and tuber yield, indicating that early-maturing genotypes can better withstand drought conditions in regions with short rainfall periods [64,98,99,100]. However, early bulking triggers earlier senescence and reduced duration of photosynthetic activity, which limit biomass and yield production if not properly managed. Therefore, the trade-off between early maturity and tuber yield requires careful selection of cassava cultivars that balance these traits effectively because shorter days of photosynthetic activity may lead to reduced tuber yield. In addition, early bulking genotypes increase the activity of sucrose synthase and starch phosphorylase to support efficient starch accumulation in the storage roots under drought conditions. Therefore, continued breeding efforts are essential to develop early-maturing cassava cultivars that produce optimum yields across varying moisture conditions to achieve food security in the face of climate change.

4.5. The Use of Drought-Tolerant and Water-Use-Efficient Germplasm

The projected increase in drought occurrence and water scarcity by 2030 poses a major threat to cassava productivity, especially in the rainfed farming systems of SSA. The deployment of drought-tolerant and water-use-efficient cassava genotypes is critical for ensuring yield stability and long-term food security under climate stress. These traits offer a sustainable pathway to improve productivity in marginal environments where conventional varieties often fail. However, improving drought tolerance and WUE of cassava genotypes is complex due to their polygenic nature and is affected by genotype-by-environmental interactions. These traits are governed by interconnected mechanisms including stomatal regulation, deep rooting and antioxidant defense activation [101]. These mechanisms enhance a plant’s ability to maintain cellular homeostasis under drought stress. Nonetheless, understanding the genetic and molecular responses of cassava plants to drought stress requires deep knowledge, which indicates the need for collaboration in breeding water-use-efficient cultivars.

In addition, the stored starch in cassava provides an internal reserve to buffer against temporary drought stress. These adaptations are rarely found together in other staple crops and should be leveraged more directly in breeding programs. Despite these advantages, progress in breeding for drought tolerance has been uneven, partly due to insufficient integration of physiological, biochemical and genetic data. Nonetheless, considerable progress has been made in characterizing drought-tolerant germplasm across various countries, leading to the identification of promising cultivars for breeding (Table 3). For instance, the characterization of existing cassava germplasm was conducted in Sierra Leone [102], Indonesia [103] and Kenya [104], which has helped uncover genotypes with superior WUE and tuber yield under drought conditions. Moreover, large germplasm collections maintained by institutions such as the International Institute of Tropical Agriculture and the International Centre for Tropical Agriculture house over 8000 cassava accessions [5,15]. These collections offer a vast and largely untapped genetic reservoir for improving drought tolerance, especially when paired with high-throughput phenotyping and genomic selection platforms.

Table 3. Drought-tolerant cassava varieties reported in different countries.

Variety Name	Country	Reference
BRS Formosa	Brazil	[61]
MH96/0686 and Magana	Uganda	[63]
I980581	Nigeria	[65]
MM06/0013	Kenya	[66]
M98/0068, 94/0039, 95/0306, 98/0002 and I92/0067	Switzerland	[103]
Guajira, Guajira 3, Guajira 4, Concha Rosada, and MeVen 77-1	Venezuela	[104]
OMM 1207-22	Indonesia	[105]
MLG 10361 and MLG 10362	Indonesia	[106]
8S501	India	[107]

Table 3. Drought-tolerant cassava varieties reported in different countries.

Variety Name	Country	Reference
BRS Formosa	Brazil	[61]
MH96/0686 and Magana	Uganda	[63]
I980581	Nigeria	[65]
MM06/0013	Kenya	[66]
M98/0068, 94/0039, 95/0306, 98/0002 and I92/0067	Switzerland	[103]
Guajira, Guajira 3, Guajira 4, Concha Rosada, and MeVen 77-1	Venezuela	[104]
OMM 1207-22	Indonesia	[105]
MLG 10361 and MLG 10362	Indonesia	[106]
8S501	India	[107]

4.6. The Use of Genotypes with Enhanced Carbon Assimilation Capacity

Carbon assimilation capacity plays a key role in cassava’s drought adaptation because it directly influences biomass production, tuber yield and drought tolerance. Cassava can sustain growth even when water availability is limited by maintaining C uptake and converting it into carbohydrates. This trait is critical for yield maintenance under drought and supports long-term carbon sequestration goals in climate-resilient agriculture [108,109,110]. Cassava’s ability to accumulate and remobilize non-structural carbohydrates gives it a physiological buffer that is common in other crops. During drought, these stored carbohydrates support metabolic activity, which contribute to osmotic balance [111]. In addition, the genotypes with enhanced photosynthetic efficiency are characterized by improved RuBisCO activity and optimized Photosystem II function maintain higher rates of carbon fixation under drought stress. These genotypes often exhibit improved stomatal control, allowing them to balance C intake with reduced water loss, which contributes to higher intrinsic WUE. This trade-off is vital for breeding programs targeting resilience and productivity in limited water environments. In addition, greater leaf area and chlorophyll content are linked to improved mesophyll conductance, allowing cassava genotypes to capture more light and maintain high photosynthetic capacity [112]. When coupled with deeper root systems, these traits enable the plant to optimize source–sink relationships and enhance dry matter accumulation even under stress [113].

The root system architecture is linked to water capture and carbon deposition. Genotypes with deeper and more fibrous roots contribute to long-term soil organic carbon pools, offering dual benefits of increased drought tolerance and enhanced climate change mitigation through soil carbon sequestration [114,115]. The breeding programs should prioritize the integration of physiological screening with omics-based approaches to accelerate genetic gains. The use of metabolomic and proteomic markers can help identify key regulators of carbon assimilation under stress. High-throughput phenotyping tools, such as chlorophyll fluorescence imaging, leaf gas exchange systems and hyperspectral reflectance can be used to evaluate photosynthetic performance of large populations under drought-stressed conditions. Therefore, selecting genotypes with high carbon assimilation capacity and efficient water use will contribute to yield stability and to the development of climate-resilient cassava systems that support sustainable production.

5. Breeding Technologies for Cassava Drought Tolerance and WUE

5.1. Genes Associated with Drought Tolerance and WUE

Drought tolerance and WUE in cassava are quantitative and polygenic traits, shaped by complex molecular interactions that govern the plant’s capacity to adapt to drought conditions. Recent advances in genomics have enabled the identification of key genes involved in stress perception, signal transduction, osmotic regulation and tuber yield development (Table 4). Each of these genes contribute to the plant’s ability to withstand drought stress, providing valuable targets for breeding programs aimed at improving drought tolerance and productivity. Among the most critical pathways involved is ABA-mediated signaling, which regulates stomatal behaviour, gene expression, and metabolic responses during drought. A notable example is the MeABF gene family, encoding ABA-responsive element-binding transcription factors [116]. These MeABF genes regulate downstream drought-responsive genes, including MeBADH1, which encodes betaine aldehyde dehydrogenase involved in glycine betaine biosynthesis. The glycine betaine functions as an osmoprotectant, stabilizing proteins and membranes and maintaining cellular turgor under dehydration stress. Its accumulation is essential for sustaining photosynthetic efficiency and protecting enzyme function during drought stress.

The overexpression of MeBADH1, under the control of MeABF transcriptional activation, enhances osmotic adjustment and contributes to improved stomatal regulation, enabling cassava to balance water conservation with carbon dioxide uptake. This is valuable given cassava’s amphistomatous leaf architecture, which allows stomatal conductance to be finely tuned across both leaf surfaces. Such regulation is a key contributor to cassava’s relatively high intrinsic WUE and its ability to maintain photosynthesis under drought. Other transcription factors, such as those in the WRKY family, have been shown to mediate root development. For instance, Orek [48] demonstrated that WRKY overexpression in cassava improves lateral root proliferation and root length under drought stress. These traits enable plants to access deeper soil moisture, reinforcing drought tolerance. In drought-resilient cassava cultivars have deep root architecture is closely linked to enhanced water uptake and sustained carbohydrate accumulation—traits crucial for tuber development and yield stability under stress.

In addition, several structural and enzymatic genes have been implicated in drought response. Genes encoding aldehyde dehydrogenases detoxify reactive aldehydes formed during oxidative stress, preserving membrane integrity and supporting cellular homeostasis [67]. Meanwhile, zinc finger proteins (e.g., MeZFP) regulate drought-responsive gene expression, enhancing antioxidant capacity and conferring tolerance across diverse environments. These genes contribute to cassava’s multifaceted drought adaptation strategy, encompassing osmotic adjustment, ROS detoxification, and optimized source–sink dynamics. Importantly, these molecular mechanisms align with cassava’s inherent physiological advantages such as stem starch storage and plastic growth patterns, which allow it to survive prolonged drought and rapidly recover once water becomes available. These insights offer tangible targets for enhancing drought tolerance and WUE. Moreover, transgenic and CRISPR-based gene editing tools provide opportunities to fine-tune gene expression and regulatory networks in elite backgrounds, offering precision breeding solutions tailored to diverse agroecological zones. Recent advances in speed breeding and genomic selection have accelerated the development of drought-tolerant cassava. Speed breeding shortens generation times and allows multiple breeding cycles per year by accelerating the genetic gain via phenome- and genome-assisted trait introgression, re-domestication and plant variety registration [117]. Genomic selection leverages genome-wide markers to predict breeding values and genotype performance [118], enabling the identification of superior genotypes for drought tolerance and WUE before extensive field testing. Therefore, integrating these approaches with molecular knowledge, physiological screening, and precision phenotyping allows breeders to combine deep rooting, high WUE, and stress-responsive gene expression into elite cultivars in a short period of time.

Table 4. Genes reported for improving drought tolerance in cassava genotypes.

Genes	Coded Proteins	Function	References
WRKY	WRKY transcription factor family	Regulatory pathways for drought tolerance Drought stress responses. Water uptake from the soil.	[48]
MeALDH MeZFP MeMSD MeRD28	Aldehyde dehydrogenase Zinc Finger Protein Manganese Superoxide Dismutase Responsive to Dehydration 28	Drought stress tolerance Regulating metabolic pathways	[67]
MeABF, MeBADH1	ABA-binding factor; betaine aldehyde dehydrogenase	Drought tolerance Water use efficiency	[116]
IPT	Isopentenyl transferase	Involved in cytokinin biosynthesis, affecting plant growth and drought stress responses.	[119]
MeERF	Ethylene-responsive factor	It coordinates ethylene signaling with drought-responsive pathways by modulating stomatal closure and leaf senescence.	[120]
MeKUP	Potassium transporter	Upregulation of metabolites that contribute to drought tolerance.	[121]
AREB1	ABA-responsive element binding protein	Involved in drought response	[122]
ALDH7B4	Aldehyde dehydrogenase	Drought tolerance	[123]
MeRSZ21b	Serine/arginine-rich splicing factor	Improved drought tolerance Modulating ABA-dependent signaling.	[124]
MeAMY MeBAM	α- and β-amylases	Drought tolerance	[125]

Table 4. Genes reported for improving drought tolerance in cassava genotypes.

Genes	Coded Proteins	Function	References
WRKY	WRKY transcription factor family	Regulatory pathways for drought tolerance Drought stress responses. Water uptake from the soil.	[48]
MeALDH MeZFP MeMSD MeRD28	Aldehyde dehydrogenase Zinc Finger Protein Manganese Superoxide Dismutase Responsive to Dehydration 28	Drought stress tolerance Regulating metabolic pathways	[67]
MeABF, MeBADH1	ABA-binding factor; betaine aldehyde dehydrogenase	Drought tolerance Water use efficiency	[116]
IPT	Isopentenyl transferase	Involved in cytokinin biosynthesis, affecting plant growth and drought stress responses.	[119]
MeERF	Ethylene-responsive factor	It coordinates ethylene signaling with drought-responsive pathways by modulating stomatal closure and leaf senescence.	[120]
MeKUP	Potassium transporter	Upregulation of metabolites that contribute to drought tolerance.	[121]
AREB1	ABA-responsive element binding protein	Involved in drought response	[122]
ALDH7B4	Aldehyde dehydrogenase	Drought tolerance	[123]
MeRSZ21b	Serine/arginine-rich splicing factor	Improved drought tolerance Modulating ABA-dependent signaling.	[124]
MeAMY MeBAM	α- and β-amylases	Drought tolerance	[125]

5.2. Quantitative Trait Loci (QTL) Associated with Drought Tolerance and WUE

Drought tolerance and WUE are critical adaptive traits which influence cassava production. As climate change exacerbates water scarcity, the development of cassava varieties that can endure drought conditions becomes increasingly essential. Exploring genetic loci in cassava where alleles influence variation in quantitative traits is vital, as these traits are shaped by both genetic and environmental factors [126]. Identifying quantitative trait loci (QTL) provides valuable insights into the genetic mechanisms that enable cassava to withstand drought stress. The QTL mapping integrates phenotypic variation with molecular marker data to identify genomic regions associated with drought-adaptive traits. In cassava, QTLs have been associated with stomatal conductance, osmotic adjustment, and carbon assimilation, which are key processes that maintain cellular hydration and metabolic activity under drought conditions [127,128]. These QTLs regulate physiological responses that help sustain photosynthesis and biomass accumulation during drought.

In addition, QTLs have also been linked to root system traits such as root length, density, and depth, which enhance access to subsoil moisture [15]. Deep-rooted genotypes exhibit improved water uptake, higher transpiration efficiency, and better yield stability under drought conditions. Such traits contribute to increased hydraulic conductivity and sustained gas exchange, reinforcing both drought tolerance and WUE. The integration of QTL data into marker-assisted selection (MAS) enables breeders to screen large populations for favourable alleles, accelerating the development of stress-resilient genotypes. Furthermore, CRISPR-Cas9 genome editing offers a precise tool to manipulate key QTL regions, fine-tuning gene expression to improve drought-responsive traits such as stomatal behaviour, antioxidant enzyme regulation, and carbon partitioning. Despite this progress, challenges remain in the fine mapping of QTLs and the identification of underlying causal genes. Therefore, advances in transcriptomics and multi-omics integration will be crucial to unravel regulatory networks and signaling cascades that control drought responses at the molecular level [129]. These efforts will support the development of high-resolution markers for use in cassava breeding programs aimed at improving drought tolerance and WUE.

5.3. Proteins Associated with Drought Tolerance and WUE

Drought stress triggers the expression of specific genes that influence protein synthesis to reduce cellular damage. Therefore, proteomic analysis can significantly assist breeders in identifying drought-responsive proteins that enhance tolerance by stabilizing cellular functions and optimizing physiological responses [130]. A key focus in proteomic analysis is the identification of abscisic acid (ABA) receptors, especially the PYR1 protein (Figure 3), which acts as a molecular sensor of drought-induced ABA accumulation. When ABA binds to PYR1, it inhibits protein phosphatase 2C (PP2C) proteins that typically suppress the drought response pathway. This inhibition activates downstream kinases and transcription factors, leading to the expression of drought-responsive genes and promoting water conservation [131,132]. The PYR/PYL/RCAR receptor family is highly conserved across different plant species, making it a significant target for improving stress responses in crops through genetic manipulation. These processes are visually summarized in Figure 3. This mechanism is crucial for developing cassava varieties that can endure drought conditions more effectively [20].

Proteins such as late embryogenesis abundant (LEA) proteins and heat shock proteins (HSPs) act as molecular chaperones, stabilizing cellular macromolecules and membranes during dehydration. Their upregulation preserves enzyme activity and structural integrity under osmotic stress [133]. In parallel, antioxidant enzymes—notably superoxide dismutase, catalase, and glutathione-S-transferases neutralize reactive oxygen species (ROS), mitigating oxidative damage and safeguarding metabolic processes [134]. Proteins associated with photosynthesis also contribute to drought tolerance. The RuBisCO activase enhances carbon fixation under stress, while chlorophyll-binding proteins ensure efficient light harvesting despite reduced water availability [135]. These proteins maintain photosynthetic efficiency and support sustained biomass accumulation. In addition, phytohormone signaling proteins modulate crosstalk between ABA and other stress hormones (e.g., ethylene, salicylic acid), coordinating transcriptional responses and optimizing WUE. The identification and manipulation of such proteins through molecular breeding, gene editing, or transgenic approaches hold promise for developing cassava cultivars with enhanced drought tolerance and high WUE. Therefore, understanding the synergistic action of these protein classes and their regulatory networks is crucial for enhancing drought adaptation in cassava.

5.4. Metabolites Associated with Drought Tolerance and WUE

Under drought stress, cassava cultivars trigger specific genes [136], leading to notable changes in the metabolism of key metabolites to mitigate cellular dehydration, preserve energy and sustain physiological processes. The accumulation of compatible solutes, including proline, soluble sugars (e.g., sucrose, glucose, fructose) and sugars plays a vital role in osmotic adjustment [137]. The accumulation of these metabolites helps maintain cell turgor, stabilize proteins and membranes, and scavenge ROS under drought conditions, allowing cassava plants to endure prolonged periods with limited soil moisture. In addition, cassava upregulates metabolites such as salicylic acid and malate, which modulate stomatal behaviour and support photosynthetic activity under drought stress [138]. These metabolites fine-tune C assimilation vs. transpiration trade-offs, helping optimize WUE during limited water environments. Furthermore, drought also alters central metabolic pathways such as glycolysis and the tricarboxylic acid (TCA) cycle, leading to a shift toward energy-efficient processes that conserve ATP and minimize respiratory losses [139]. These adjustments ensure continued metabolic function even under drought conditions. Recent metabolomics studies have shown that drought-tolerant genotypes accumulate higher levels of protective metabolites [140], suggesting a strong correlation between metabolite profiles and stress resilience. These metabolic signatures can serve as biochemical markers for selection and breeding of drought-tolerant varieties. Furthermore, the accumulation of non-structural carbohydrates in stems and roots contributes to carbon storage and remobilization, supporting energy supply and osmotic regulation during drought recovery. These reserves are important in cassava due to its ability to remobilize starch from stems, a trait that buffers yield loss under lower water availability. Therefore, breeding programs aiming to improve drought tolerance and WUE in cassava should incorporate metabolite profiling into their selection strategies. This will enable the identification of cultivars with superior metabolic plasticity and enhanced capacity to withstand environmental stress.

5.5. Utilization of Drought Tolerance Indices

The breeding of cassava genotypes to enhance drought tolerance and tuber yield is a crucial step towards achieving global food security. Therefore, a critical aspect of this process involves the identification of reliable and efficient selection criteria to evaluate genotype performance under both drought-stressed and well-watered conditions. The tuber yield is a key trait for selection, but high productivity under optimal moisture conditions does not always correlate with performance under drought stress. Some cultivars may achieve high yields when water is abundant but fail to maintain productivity during water deficits [140], due to a lack of inherent drought tolerance mechanisms. This discrepancy highlights the need for selection strategies that account for yield stability across contrasting environments. The researchers have developed and adopted various drought tolerance indices that integrate yield data from both stressed and non-stressed conditions. These indices enhance the efficiency and accuracy of genotype selection by quantifying genotypic responses to drought. Studies by Araneda-Cabrera et al. [141], Muiruri et al. [9], and More et al. [12] emphasize the value of using these indices for identifying cassava genotypes that combine high yield potential with drought tolerance. Those drought tolerance indices include stress tolerance index (STI), mean productivity (MP), geometric mean productivity (GMP), tolerance index (TOL), and drought susceptibility index (DSI), which offer different perspectives on genotype performance [140]. For instance, STI and GMP favour genotypes that perform well in both environments, whereas TOL and DSI highlight the sensitivity of a genotype to stress by comparing yield reductions. Table 5 summarizes key indices used in cassava breeding programs. Therefore, understanding the utilization of these drought indices is crucial for selecting drought-tolerant cassava genotypes.

Table 5. Drought indices utilized in crop improvement programs.

Indices	Description	Formula	Reference
Drought susceptibility index	Measures the sensitivity of a genotype to drought based on tuber yield performance	${\displaystyle \frac{\mathrm{Y}\mathrm{s}-\mathrm{Y}\mathrm{p}}{\mathrm{Y}\mathrm{p}}}$	[142]
Stress susceptibility index	Evaluates the relative susceptibility of a genotype to drought.	${\displaystyle \frac{1-\frac{\mathrm{Y}\mathrm{s}}{\mathrm{Y}\mathrm{p}}}{1-\frac{\overline{\mathrm{Y}}\mathrm{s}}{\overline{\mathrm{Y}}\mathrm{p}}}}$	[142]
Tolerance index	Measures the genotype’s drought tolerance based on tuber yield differences.	Yp − Ys	[143]
Yield stability index	Assesses stability by comparing tuber yields under stress to non-stress conditions	${\displaystyle \frac{\mathrm{Y}\mathrm{s}}{\mathrm{Y}\mathrm{p}}}$	[144]
Stress tolerance index	Quantify tuber yield performance and drought tolerance of cassava cultivars.	${\displaystyle \frac{\mathrm{Y}\mathrm{p}\times \mathrm{Y}\mathrm{s}}{{\overline{\mathrm{Y}}}_{\mathrm{p}}^2}}$	[145]
Yield index	Compares each genotype’s performance relative to the average of all the evaluated genotypes	${\displaystyle \frac{\mathrm{Y}\mathrm{s}}{{\overline{\mathrm{Y}}}_{\mathrm{s}}}}$	[146]
Mean productivity	Calculates the average tuber yield of a genotype.	${\displaystyle \frac{\mathrm{Y}\mathrm{p}+\mathrm{Y}\mathrm{s}}{2}}$	[147]
Geometric mean productivity	It accounts for variability in tuber yield performance across environments (drought stress and non-stress).	${(Yp\times Ys) }^{{\displaystyle \frac{1}{2}}}$	[147]
Harmonic mean	Measures cultivar performance based on mean yield response	${\displaystyle \frac{2(Ys\times Yp)}{Yp+Ys}}$	[148]

Y_s = tuber yield under drought stress; Y_p = tuber yield under non-stressed conditions.

Table 5. Drought indices utilized in crop improvement programs.

Indices	Description	Formula	Reference
Drought susceptibility index	Measures the sensitivity of a genotype to drought based on tuber yield performance	${\displaystyle \frac{\mathrm{Y}\mathrm{s}-\mathrm{Y}\mathrm{p}}{\mathrm{Y}\mathrm{p}}}$	[142]
Stress susceptibility index	Evaluates the relative susceptibility of a genotype to drought.	${\displaystyle \frac{1-\frac{\mathrm{Y}\mathrm{s}}{\mathrm{Y}\mathrm{p}}}{1-\frac{\overline{\mathrm{Y}}\mathrm{s}}{\overline{\mathrm{Y}}\mathrm{p}}}}$	[142]
Tolerance index	Measures the genotype’s drought tolerance based on tuber yield differences.	Yp − Ys	[143]
Yield stability index	Assesses stability by comparing tuber yields under stress to non-stress conditions	${\displaystyle \frac{\mathrm{Y}\mathrm{s}}{\mathrm{Y}\mathrm{p}}}$	[144]
Stress tolerance index	Quantify tuber yield performance and drought tolerance of cassava cultivars.	${\displaystyle \frac{\mathrm{Y}\mathrm{p}\times \mathrm{Y}\mathrm{s}}{{\overline{\mathrm{Y}}}_{\mathrm{p}}^2}}$	[145]
Yield index	Compares each genotype’s performance relative to the average of all the evaluated genotypes	${\displaystyle \frac{\mathrm{Y}\mathrm{s}}{{\overline{\mathrm{Y}}}_{\mathrm{s}}}}$	[146]
Mean productivity	Calculates the average tuber yield of a genotype.	${\displaystyle \frac{\mathrm{Y}\mathrm{p}+\mathrm{Y}\mathrm{s}}{2}}$	[147]
Geometric mean productivity	It accounts for variability in tuber yield performance across environments (drought stress and non-stress).	${(Yp\times Ys) }^{{\displaystyle \frac{1}{2}}}$	[147]
Harmonic mean	Measures cultivar performance based on mean yield response	${\displaystyle \frac{2(Ys\times Yp)}{Yp+Ys}}$	[148]

Y_s = tuber yield under drought stress; Y_p = tuber yield under non-stressed conditions.

5.6. Multiple Traits Selection

The simultaneous selection of multiple traits is crucial in cassava breeding programs aiming at developing and releasing desirable varieties with enhanced drought tolerance and WUE. Determining the association between physiological and agronomic traits, proteins and metabolites is crucial to inform effective selection strategies and improve drought tolerance and WUE. Cassava genotypes require a combination of traits, proteins and metabolites to thrive under different environmental conditions. Several authors have evaluated the association between yield-related traits and targeted traits such as the number of tubers and tuber weight [149,150,151,152]. Correlation analysis helps to identify key physiological traits, yield-related traits, proteins and metabolites that influence drought tolerance by evaluating their relationships. The high positive correlations between traits indicate shared genetic or physiological mechanisms and functional linkage, facilitating the identification of key traits, metabolites and proteins associated with drought tolerance. This understanding enables breeders to prioritize traits, account for potential trade-offs, and design more efficient selection strategies for sustained genetic improvement. Some authors have employed the principal component analysis to identify traits associated with enhanced tuber yield such as root number and diameter [149,150,152]. Therefore, correlation and principal component analysis provide complementary insights into the genetic and environmental determinants of cassava’s agronomic performance under drought stress.

Furthermore, path coefficient analysis has been conducted on crop cultivars assessed to evaluate traits that contribute directly and indirectly to improved tuber yield [153]. This technique helps to visualize trait interactions and trade-offs, assisting in making breeding strategies to develop drought-tolerant cassava genotypes. For instance, a study conducted by de Oliveira et al. [151], found that tuber diameter and number of tubers exhibited strong positive effects on tuber weight. Also, Setiawan et al. [153] suggested that plant height had a negative contribution to root yield, highlighting the potential significance of shorter cultivars in drought-prone environments. Therefore, path analysis remains an indispensable tool for dissecting complex traits and optimizing breeding strategies for drought-tolerant cassava.

6. Conclusions

Drought stress has a significant negative impact on cassava performance by reducing WUE, carbon assimilation and altering the expression of drought-responsive genes, proteins and metabolites. Despite the increasing threat of drought to global cassava production, progress in developing drought-tolerant and water-efficient varieties is still behind the pace of climate change, population growth and food security demands. The deployment of drought-tolerant and water use-efficient cassava genotypes represents a critical step toward achieving food security in drought-prone regions. Breeding programs should prioritize traits such as deep rooting systems, delayed leaf senescence and enhanced carbon assimilation capacity because they contribute to cassava’s drought tolerance. Integrating modern genomic, proteomic, metabolomic and rapid phenotyping tools can accelerate the identification of biomarkers for drought tolerance, improving the precision and efficiency of selection. Furthermore, combining these molecular approaches with agronomic management practices such as mulching, precision irrigation and the use of physiologically adaptive genotypes can optimize cassava performance in drought-prone regions. Future research should continue to leverage gene editing, multi-omics technologies, and precision phenotyping to develop climate-resilient cassava cultivars, supporting sustainable and productive farming systems.