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Amelework, A.B.;  Bairu, M.W. Genetic Analysis and Breeding of Cassava. Encyclopedia. Available online: (accessed on 17 June 2024).
Amelework AB,  Bairu MW. Genetic Analysis and Breeding of Cassava. Encyclopedia. Available at: Accessed June 17, 2024.
Amelework, Assefa B., Michael W. Bairu. "Genetic Analysis and Breeding of Cassava" Encyclopedia, (accessed June 17, 2024).
Amelework, A.B., & Bairu, M.W. (2022, June 28). Genetic Analysis and Breeding of Cassava. In Encyclopedia.
Amelework, Assefa B. and Michael W. Bairu. "Genetic Analysis and Breeding of Cassava." Encyclopedia. Web. 28 June, 2022.
Genetic Analysis and Breeding of Cassava

Cassava (Manihot esculenta Crantz) is the sixth most important food crop and consumed by 800 million people worldwide. In Africa, cassava is the second most important food crop after maize and Africa is the worlds’ largest producer. Though cassava is not one of the main commodity crops in South Africa, it is becoming a popular crop among farming communities in frost-free areas, due to its climate-resilient nature. The potential of the available genetic and genomic resources for breeding and genetic improvement of cassava for enhanced resistance to biotic stresses are discussed.

biotic stresses genetic diversity genomic tools Manihot esculenta

1. Introduction

With increasing climate variability, cassava has attained significant importance in worldwide agriculture. It is an attractive food security and commercial crop for subsistence farmers with limited resources and it can grow in marginal soils [1]. Cassava roots are the main carbohydrate storage organs and store up to 85% starch on a dry weight basis [2]. Cassava roots contain a starch content of 40% higher than rice and 25% more than maize [3]. The importance of cassava for food security, climate risk mitigation, import substitution for industrial starch, livestock feed, and biofuel feed stock to South Africa’s economy has been reviewed by Amelework et al. [4].
It is estimated that in South Africa, maize accounts for approximately 95% of the country’s starch production, with 37% of the produce being used for food, 40% for feed, 18% for export, and 5% for starch. Due to drought and competition between industries utilizing maize products, the local starch industries failed to meet the starch demand of the country. Hence, South Africa is importing more than 66,000 tons of starch annually [5]. It was reported that cassava starch is preferred in South Africa in terms of imports and it fetches a higher price on the market than maize, potato, or wheat [4]. Hence, grasping the industrial potential of cassava in the starch industry would satisfy local starch demands, avoid computation among staple food commodities, and reduce import volume.
The Agricultural Research Council, together with the State partners, undertook basic research to determine the suitability of cassava as a food, feed, and industrial crop. The research was undertaken as participatory trials with farmers in KwaZulu-Natal, Limpopo, and Mpumalanga. The knowledge of the farmers about the resilience of the crop and its potential to alleviate their food security problem in these provinces and their surroundings triggered extremely high demand (Unpublished).

2. Origin and Domestication of Cassava

Cassava belongs to the family Euphorbiaceae, sub-family Crotonoideae, tribe Manihotae, and genus Manihot. The genus has two sections, the Arborae, containing tree species, and the Fructicosae, comprising slow-growing shrubs adapted to savannah grassland or desert conditions [6]. The genus Manihot is a large family of flowering plants with 300 genera and around 8000 species [7]. Of the many species that belong to the genus Manihot, Manihot esculenta Crantz is the most economically important species and widely cultivated for food and industrial applications [8].
Cassava is believed to have been domesticated before 4000 BC, and its center of origin is hypothesized to be South America [9]. The questions about the wild progenitor of cassava, the area where the wild progenitor evolved and was initially cultivated have been obscured. Originally, it was speculated that cassava could be ascended and evolved via periodic introgression of genes involving a number of wild species (compile-species) [10]. However, later it was reported that a wild species, Manihot flabellifolia (Pohl), was found to be the closest wild relative to cassava [11]. Many studies have supported the ancestral relationship of the modern cultivated cassava and the wild subspecies M. esculenta ssp. Flabellifolia [12][13][14][15].
The exact geographical origin of the crop has been disputed for many years following the appearance of new evidence. Geographic origin infers the distribution and habitats of the wild cassava species [14]. Although controversial results have been reported, the southern border of the Amazon basin currently stands as the recognized center of origin for M. esculenta [8][15][16]. A large number of wild Manihot species have been reported to be found in Brazil. Hence, this region is the likely primary center of diversity of cassava [17]. The domestication process involved selection for root size, growth habit, stem number, and ability of clonal propagation through stem cuttings [18]. During the 16th century, Portuguese traders introduced cassava to Africa and later to Asia [18]. It was initially cultivated in the Democratic Republic of Congo and adopted as a famine-reserve crop. Currently, cassava is cultivated in about 40 African countries, stretching over a wide belt from Madagascar in the Southeast to Cape Verde in the Northwest [19].

3. Genetic Diversity in Cassava

Genetic improvement begins with the collection and evaluation of diverse genetic resources [1]. Various evolutionary forces such as mutations, migration, hybridization, and polyploidization are responsible for creating variation in plants [20]. In cassava, it is believed that the wide range of genetic diversity was generated through natural and artificial hybridization between the wild Manihot spp. and cultivated cassava or through apomixes [21]. Jennings [22] suggested that the high genetic diversity of cassava has resulted from migration followed by natural hybridization. Fregene et al. [23], on the other hand, indicated that genetic diversity was dictated by specific geographic adaptation, while Asante and Offei [24] argued that geographical region might have little effect on genetic diversity in cassava.
Currently, several national and international research institutes hold large collections of cassava germplasm. The International Centre for Tropical agriculture (CIAT) in Colombia comprises more than 6000 cassava accessions collected mainly (97%) from Latin America and of which 30% of the accessions are of Brazilian origin [25]. The International Institute for Tropical Agriculture (IITA) in Nigeria, on the other hand, consists of more than 2000 genotypes largely of West African origin [26]. Understanding the nature and magnitude of genetic variation present within and among individuals, populations, species, and gene pools is crucial for the efficient management of genetic resources [27]. Genetic diversity is assessed with morphological, biochemical, and/or molecular markers. However, the environment and genotype by environment interaction effects limit the effectiveness of genetic diversity studies using morphological and biochemical markers [28]. Molecular markers permit the detection of genetic differences among closely related and wild species. Various DNA marker systems have been developed and utilized to assess the genetic diversity of cassava germplasm (Table 1).
Table 1. Genetic diversity analyses studies reported in cassava.
Marker System No Acc. Evaluated Species References
RFLP 80 M. esculentaM. glazioviiM. Caerulescens [29]
AFLP 105 M. esculenta ssp. esculentaM. esculenta ssp. Flabellifolia
M. aesculifoliaM. carthaginensisM. tristisM. brachyloba
RAPD 31 Cultivated cassava [30]
RAPD/AFLP 53 M. esculentaM. flabellifoliaM. peruviana, M. glaziovii,
M. reptansM. chlorosticaM. aesculifoliaM. michaelis
AFLP 76 Cultivated cassava [32]
SSR 212 M. esculenta ssp. flabellifoliaM. pruinosa [15]
RAPD 24 M. esculenta ssp. esculenta [33]
Isozyme 46 Cultivated cassava [34]
SSR 117 Cultivated cassava [35]
SSR 185 Cultivated cassava [36]
SSR 37 Cultivated cassava [37]
SSR 55 Provitamin-A cassava [38]
SSR 54 Cultivated cassava [39]
SSR 1401 M. esculenta [40]
SSR 163 M. esculenta [41]
ISSR 17 Landraces [42]
SSR 596 M. esculenta ssp. esculentaM. esculenta ssp. flabellifolia [43]
SNP 1580 Cultivated and wild cassava [44]
SNP 3000 Cultivated cassava [45]
SSR 120 M. esculenta [46]
SSR 157 Cultivated cassava [47]
SNP 183 Provitamin-A cassava [48]
SNP 105 Cultivated cassava [49]
SSR 89 Cultivated cassava [50]
SNP 102 Cultivated cassava [51]
The success of genetic improvement of any trait depends on the nature of variability present within the trait [52]. In modern cassava breeding, a source population with high frequencies of alleles associated with desirable characters are developed through collection or hybridization of genotypes derived from selected elite clones [1]. New improved cultivars can be developed following selection of superior clones from segregating populations [53].

4. Breeding for Yield and Quality Related Traits

4.1. Starch Content

Starch has been the subject of intensive research over many decades. Cassava is the second most important source of starch worldwide, after maize, and the most traded one [54]. The average starch content of cassava is 84.5% on a dry weight basis and the average amylose content is 20.7%, ranging between 15.2 and 26.5% [55]. Cassava starch is the cheapest and the most preferred known form of starch with many positive characteristics such as high paste clarity, relatively good stability to retrogradation and swelling capacity, low protein complex, and good texture [56]. Novel starch properties such as amylose-free and high-amylose starch are of interest to the cassava community [57].
South Africa is a highly industrialized country and starch is widely used by the food, alcohol, textile, pharmaceutical, cosmetic, adhesive, paper, and plywood industries. The Republic is Africa’s largest producer of starch and exports starch to neighboring countries. The starch industries in South Africa have been producing starch mainly (95%) from maize. There is a huge competition among industries utilizing maize products and other uses. Hence, the starch industry is not able to satisfy the local demands. Hence, South Africa has been importing thousands of tons of starch from Southeast Asia annually [5]. Exploitation of cassava as a source of starch will provide an alternative to the maize industry. Producing starch from cassava locally will satisfy local starch demands, avoid competition among staple food commodities, relieve the country’s economy from foreign currency strains, and reduce import volumes [4].

4.2. Dry Matter Content

Dry matter content is an important characteristic for the acceptance of cassava by producers, consumers, and processors. It is considered as the economic or true biological yield, which is controlled by polygenes [58]. The proportion of dry matter in cassava storage roots ranges from 17 to 47%, with the majority of the accessions lying between 20% and 40% [59] and values above 30% are considered to be high. Dry matter content is highly influenced by a number of genetic and environmental factors such as age of the crop, efficiency of the canopy to trap sunlight, season, and location effects [56]. The longer the plants stay on the field, the more dry matter and starch is accumulated. It was reported that yields of fresh and dry roots, as well as starch, increased progressively from 8 to 18 months after planting (MAP).
It was reported that, on average, nearly 90% of cassava root dry weight is carbohydrate, 4% crude fiber, 3% ash, 2% crude protein, and 1% fat [60]. Dry matter partitioning into different plant parts varies with the growth cycle of the plant. During the early growth stages of the plant, more dry matter is accumulated in the leaves than in the stems and storage roots [61]. However, at 4 MAP about 50–60% of the total dry matter is accumulated in the storage roots [61].
The total dry weight of a cassava plant is positively associated with dry weight of the storage roots, suggesting that both traits could be improved simultaneously [62]. However, dry matter content is not associated with fresh root yield. Okogbenin et al. [63] reported that dry matter content is positively and highly correlated with starch content and harvest index, suggesting the importance of the two traits for indirect selection. Adjebeng-Danquah et al. [64] also reported a significant positive correlation between early storage root yield and final root yield, indicating the possibility of selecting genotypes with high yield potential at 6 MAP. Under tropical conditions, maximum rate of dry matter accumulation was detected at 3–5 MAP [65], while at high attitudes maximum rate was observed at 7 MAP [66]. Similarly, Kawano et al. [67] reported that root dry matter content tended to be higher at 8 MAP compared to 12 MAP. Although the rate of dry matter accumulation varies with the genotypes and growing conditions, it was suggested that selection for dry matter content should not be performed before 4 MAP [61].

4.3. Early Bulking

Early bulking is an important trait in cassava, referring to the thickening of storage roots as they fill with assimilates after the plant satisfies its need for vegetative growth [63]. Early bulkers are those cultivars that are harvestable within 7–8 MAP. Breeders have been used early bulking as a drought tolerance mechanism [64]. Various researchers have different opinions on the onset and rate of bulking. Doku [68] suggested that cassava plants begin root bulking at 2 MAP but reasonable storage root mass was not reached until 6 MAP. However, according to El-Sharkawy [69], cassava root bulking starts at 3 MAP but roots become a major sink between 6 and 10 MAP. Similarly, Izumi et al. [70] reported that cassava root bulking starts at 3 MAP but rapid starch deposition does not occur before 6 MAP. Wholey and Cock [71] argued that although root bulking starts at 2 MAP, the rate of root bulking increased with time and varied with cultivars. It was suggested that earliness in cassava is associated with either early-onset or rapid rate of bulking or a combination of the two [71]. Various researchers who studied the rate of accumulation of storage root mass at different harvesting times indicated the existence of early bulking genotypes [63]. It was also reported that cultivars showing a high bulking rate over a long period of time produced more storage root yield than those with intermediate or low bulking rates for a short duration [64]. Suja et al. [72] also indicated that short-duration cultivars exhibit the maximum bulking rate during their early growing stage.
Cassava, being a tropical crop, prefers humid-warm climates with temperature ranges of 25–29 °C and an altitude below 1500 m. Cassava is highly sensitive to low temperatures below 18 °C [73]. Low temperature causes delayed sprouting of stem cuttings, reduced leaf expansion, low biomass accumulation, and decreased storage root yield [74]. In South Africa, the growing season is characterized by a hot rainy summer followed by a cold and dry winter. Frost is a major obstacle for cassava production and propagation in some parts of South Africa.
The most suitable areas for cassava production are northern KwaZulu-Natal, the eastern parts of the Limpopo, and Mpumalanga. Due to frost, the vast majority of the Eastern Cape, Western Cape, Northern Cape, and the Free State are not suitable for cassava cultivation. The frost days ranged from 30 days in the Eastern Cape to 120 days in the Free State and the Northern Cape. Successful cultivation of cassava throughout the republic requires cold tolerance and short growth cycle cultivars. All the cultivars currently in the system take more than 18 months to mature and are highly sensitive to cold. Therefore, early bulking cultivars, that fit into the growing season (i.e., matures within 7–9 MAP), or cold-tolerant cultivars that can grow in a prolonged growth period are in demand. Early maturing cassava genotypes that can escape the cold winter should be the focus of cassava breeding in South Africa.

4.4. Cyanogenic Content

Cyanogenic glycosides (CN) are a group of chemical compounds that produced hydrogen cyanide following enzymatic breakdown [75]. There are at least 25 cyanogenic glycosides known to be found in the edible parts of plants [76]. Many species produce and sequester cyanogenic glycosides including cassava, sorghum, almonds, lima beans, flax, and white clover [77]. In plants, glycoside hydrolysis occurs when the plant tissues have been disrupted by herbivores, fungal attacks, or mechanical damage. Although many explanations have been given on the importance of CN in plants, the most probable physiological role of CN is a defense against herbivores, pathogens, competitors, and theft [78]. In support of this view, bitter cassava genotypes exhibited greater tolerance to CMD [79] and drought than sweet cassava.
The predominant cyanogenic compounds in cassava roots and leaves are linamarin (95%) and lotaustralin (5%) [80]. Depending on the genetic, physiological, climatic, and edaphic factors, the normal range of cyanogenic glycoside content in cassava ranged from 1 to 1300 mg per kg of dry weight [81]. However, some reports indicated that the total cyanogenic content of the roots was not correlated with the content in the leaves and stems of the same plant [82]. The levels of cyanogenic glycosides in cassava roots are generally lower than that in the leaves and stems [83]. It has been reported that cassava roots contain a cyanide content of 10–500 mg per kg of dry matter [84], while the leaves contain 53–1300 mg per kg of dry matter [85].
Cassava cultivars have been classified biochemically using cyanogenic glucoside content as bitter and sweet [10] depending on the presence or absence of toxic levels of cyanogenic glucosides, respectively. The bitter cultivars are characterized by their high cyanogenic content (100–400 mg per kilogram of fresh weight of roots) distributed throughout the storage roots, whereas those cultivars with very low cyanogenic content (15–50 mg per kilogram of fresh weight of roots) mainly confined in the peel are termed as sweet varieties [76]. The utilization of cassava as food and feed is limited by the toxic level of cyanogen. Consumption of raw or inadequately processed cassava can lead to chronic and acute health problems resulting from cyanide poisoning [78]. The World Health Organization (WHO) recommended 10 ppm or 10 mg hydrogen cyanide per kg of cassava flour as a safe level [86]. Sweet cassava roots can be eaten by peeling and cooking, whereas bitter varieties require more extensive processing such as peeling, washing, grating, fermenting, drying, or frying. Efforts have been made on breeding and selection of low-cyanogen varieties [80], the development of low-cyanogen mutants through mutagenesis [87], and genetic engineering [88].

4.5. Post-Harvest Physiological Deterioration (PPD)

PPD is a major constraint for the production, development, expansion, and exploitation of cassava as an industrial crop in many parts of the world [89]. It is the outcome of intricate interactions of simultaneously occurring cellular functions in the harvested cassava roots and results in considerable quantitative and qualitative post-harvest losses of the fresh cassava roots. Saravanan et al. [90] reported that the estimated yield losses of fresh cassava roots due to PPD are nearly a third of the total harvest worldwide. The expression of PPD is controlled by genotypic and environmental factors following microbial infections [91]. In Thailand where cassava is the most important industrial crop, PPD results in an economic loss of up to USD 35 million annually [92]. Rudi et al. [93] predicted that extending the shelf life of cassava to several weeks would reduce financial losses by USD 2.9 billion in Nigeria over a 20-year period. Studies indicated the presence of genetic variation for PPD among genotypes [94]. However, environmental factors such as the age of the plant, root conditions during harvest and thereafter, and storage conditions significantly influence the development and effects of PPD [95].


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