Determination of genomic regions associated with early storage root formation and bulking in cassava.

Early cassava storage root formation and bulking is a medium of escape that farmers and processors tend to adopt in cases of abiotic and biotic stresses like drought, flood, and destruction by domestic animals. In this study, 220 cassava genotypes from the International Institute of Tropical Agriculture (IITA), National Root Crops Research Institute (NRCRI), International Center for Tropical Agriculture (CIAT), local farmers (from farmer's field), and NextGen project were evaluated in three locations (Umudike, Benue, and Ikenne). The trials were laid out using a split plot in a randomized incomplete block design (alpha lattice) with two replications in 2 years. The storage roots for each plant genotype were sampled or harvested at 3, 6, 9, and 12 month after planting (MAP). All data collected were analyzed using the R-statistical package. The result showed moderate to high heritability among the traits, and there were significant differences (p< 0.05) among the performances of the genotypes. The genome-wide association mapping using the BLINK model detected 45 single-nucleotide polymorphism (SNP) markers significantly associated with the four early storage root bulking and formation traits on Chromosomes 1, 2, 3, 4, 5, 6, 8, 9, 10, 13, 14, 17, and 18. A total of 199 putative candidate genes were found to be directly linked to early storage root bulking and formation. The functions of these candidate genes were further characterized to regulate i) phytohormone biosynthesis, ii) cellular growth and development, and iii) biosynthesis of secondary metabolites for accumulation of starch and defense. Genome-wide association study (GWAS) also revealed the presence of four pleiotropic SNPs, which control starch content, dry matter content, dry yield, and bulking and formation index. The information on the GWAS could be used to develop improved cassava cultivars by breeders. Five genotypes (W940006, NR090146, TMS982123, TMS13F1060P0014, and NR010161) were selected as the best early storage root bulking and formation genotypes across the plant age. These selected cultivars should be used as sources of early storage root bulking and formation in future breeding programs.

Novel SNP markers and other stress-related genomic regions associated with nitrogen use efficiency in cassava.

Cassava productivity is constrained by low soil nitrogen, which is predominant in most cassava-growing regions in the tropics and subtropical agroecology. Improving the low nitrogen tolerance of cassava has become an important breeding objective. The current study aimed to develop cassava varieties with improved nitrogen use efficiency by identifying genomic regions and candidate genes linked to nitrogen use efficiency in cassava. A genome-wide association study (GWAS) was performed using the Genome Association and Prediction Integrated Tool (GAPIT). A panel of 265 diverse cassava genotypes was phenotyped for 10 physiological and agronomic traits under optimum and low-nitrogen regimes. Whole-genome genotyping of these cassava cloneswas performed using the Diversity Arrays Technology (DArTseq) sequencing platform. A total of 68,814 single nucleotide polymorphisms (SNPs) were identified, which were spread across the entire 18 chromosomes of the cassava genome, of which 52 SNPs at various densities were found to be associated with nitrogen use efficiency in cassava and other yield-related traits. The putative genes identified through GWAS, especially those with significant associated SNP markers for NUE and related traits have the potential, if deployed appropriately, to develop cassava varieties with improved nitrogen use efficiency, which would translate to a reduction in the economic and environmental cost of cassava production.

Cassava retting ability and textural attributes of fufu for demand-driven cassava breeding.

BACKGROUND: Cassava retting ability and the textural qualities of cooked fufu are important quality traits. Cassava retting is a complex process in which soaking causes tissue breakdown, starch release, and softening. The rate at which various traits linked to it evolve varies greatly during fufu processing. According to the literature, there is no standard approach for determining retting ability. The retting indices and textural properties of fufu were measured using both manual and instrumental approaches. RESULTS: Different protocols were developed to classify 64 and 11 cassava genotypes into various groups based on retting ability and textural qualities, respectively. The retting protocols revealed considerable genetic dissimilarities in genotype classification: foaming ability and water clarity should be measured at 24 h, while penetrometer, hardness, turbidity, pH, and total titratable acidity data are best collected after 36 h. The stepwise regression model revealed that pH, foaming ability, and dry matter content are the best multivariates (with the highest R2) for predicting cassava retting. These predictors were used to develop an index for assessing the retting ability of cassava genotypes. The retting index developed showed a significant relationship with dry matter content and fufu yield. The study also showed significant correlations between instrumental cohesiveness and sensory smoothness (r = -0.75), moldability (r = -0.62), and stretchability (r = 0.78). Instrumental cohesiveness can correctly estimate fufu smoothness (R2 = 0.56, P = 0.008) and stretchability (R2 = 0.60, P = 0.005). CONCLUSION: pH, foaming ability, and dry matter content are the best traits for predicting cassava retting ability, while instrumental cohesiveness can effectively estimate fufu smoothness and stretchability. © 2024 The Authors. Journal of The Science of Food and Agriculture published by John Wiley & Sons Ltd on behalf of Society of Chemical Industry.

Establishing the linkage between eba's instrumental and sensory descriptive profiles and their correlation with consumer preferences: implications for cassava breeding.

BACKGROUND: Gari and eba, forms of cassava semolina, are mainly consumed in Nigeria and other West African countries. This study aimed to define the critical quality traits of gari and eba, to measure their heritability, to define medium and high throughput instrumental methods for use by breeders, and to link the traits with consumer preferences. The definition of a food product's profiles, including its biophysical, sensory, and textural qualities, and the identification of the characteristics that determine its acceptability, are important if new genotypes are to be adopted successfully. RESULTS: Eighty cassava genotypes and varieties (three different sets) from the International Institute of Tropical Agriculture (IITA) research farm were used for the study. Participatory processing and consumer testing data on different types of gari and eba products were integrated to prioritize the traits preferred by processors and consumers. The color, sensory, and instrumental textural properties of these products were determined using standard analytical methods, and standard operating protocols (SOPs) developed by the RTBfoods project (Breeding Roots, Tubers, and Banana Products for End-user Preferences, https://rtbfoods.cirad.fr). There were significant (P < 0.05) correlations between instrumental hardness and sensory hardness and between adhesiveness and sensory moldability. Principal component analysis showed broad discrimination amongst the cassava genotypes and the association of the genotypes concerning the color and textural properties. CONCLUSIONS: The color properties of gari and eba, together with instrumental measures of hardness and cohesiveness, are important quantitative discriminants of cassava genotypes. © 2023 The Authors. Journal of The Science of Food and Agriculture published by John Wiley & Sons Ltd on behalf of Society of Chemical Industry.

Genotype-by-environment interaction and stability of root mealiness and other organoleptic properties of boiled cassava roots.

Genetic enhancement of cassava aimed at improving cooking and eating quality traits is a major goal for cassava breeders to address the demand for varieties that are desirable for the fresh consumption market segment. Adoption of such cassava genotypes by consumers will largely rely not only on their agronomic performance, but also on end-user culinary qualities such as root mealiness. The study aimed to examine genotype × environment interaction (GEI) effects for root mealiness and other culinary qualities in 150 cassava genotypes and detect genotypes combining stable performance with desirable mealiness values across environments using GGE biplot analysis. Experiments were conducted using an alpha-lattice design with three replications for two years in three locations in Nigeria. The analysis of variance revealed a significant influence of genotype, environment, and GEI on the performance of genotypes. Mealiness scores showed no significant relationship with firmness values of boiled roots assessed by a penetration test, implying that large-scale rapid and accurate phenotyping of mealiness of boiled cassava roots remains a major limitation for the effective development of varieties with adequate mealiness, a good quality trait for direct consumption (boil-and-eat) as well as for pounding into 'fufu'. The moderate broad-sense heritability estimate and relatively high genetic advance observed for root mealiness suggest that significant genetic gains can be achieved in a future hybridization program. The genotype main effects plus genotype × environment interaction (GGE) biplot analysis showed that the different test environments discriminated among the genotypes. Genotypes G80 (NR100265) and G120 (NR110512) emerged as the best performers for root mealiness in Umudike, whereas G13 (B1-50) and the check, G128 (TMEB693) performed best in Igbariam and Otobi. Based on the results of this study, five genotypes, G13 (B1-50), G34 (COB6-4), G46 (NR010161), the check, G128 (TMEB693), and G112 (NR110376), which were found to combine stability with desirable mealiness values, were the most suitable candidates to recommend for use as parents to improve existing cassava germplasm for root mealiness.

Cassava Brown Streak Disease Response and Association With Agronomic Traits in Elite Nigerian Cassava Cultivars.

Cassava mosaic geminiviruses (CMGs) and cassava brown streak viruses (CBSVs) cause the highest yield losses in cassava production in Africa. In particular, cassava brown streak disease (CBSD) is and continues to be a significant constraint to optimal cassava production in Eastern and Southern Africa. While CBSD has not been reported in West Africa, its recent rapid spread and damage to cassava productivity in Eastern, and Southern Africa is alarming. The aim of this study was to evaluate Nigerian cassava genotypes in order to determine their responses to CBSD, in the event that it invades Nigeria, the world's largest cassava producer. The study gathered information on whether useful CBSD resistance alleles are present in the elite Nigerian cassava accessions. A total of 1,980 full-sib cassava seedlings from 106 families were assessed in the field at the seedling stage for a year. A subset of 569 clones were selected and assessed for another year at the clonal stage in Namulonge, central Uganda, a known hotspot for CBSD screening. Results indicated that foliar and root incidences and severities varied significantly (p ≤ 0.01, p ≤ 0.001) except for CBSD foliar incidence at 6 months (CBSD6i ). Highest and lowest plot-based heritability estimates for CBSD were registered for CBSD root severity (CBSD rs ) (0.71) and CBSD6i (0.5). Positive and highly significant correlations were noted between CBSD root incidence (CBSD ri ) and CBSD rs (r = 0.90***). Significant positive correlations were also noted between CBSD foliar severity at 3 months (CBSD3s ) and CBSD foliar incidence at 6 months (CBSD6i ) (r = 0.77***), CBSD3s and CBSD rs (r = 0.35***). Fresh root weight (Fresh RW ) negatively correlated with CBSD ri and CBSD rs , respectively (r = -0.21*** and r = -0.22***). Similarly, CBSD3s correlated negatively with cassava mosaic disease severity at 3 (CMD3s ) and 6 months (CMD6s ), respectively (r = -0.25*** and r = -0.21***). Fifteen clones were selected using a non-weighted summation selection index for further screening. In conclusion, results revealed that the elite Nigerian accessions exhibited significant susceptibility to CBSD within 2 years of evaluation period. It is expected that this information will aid future breeding decisions for the improvement of CBSD resistance among the Nigerian cassava varieties.

Quality attributes of fufu in South-East Nigeria: guide for cassava breeders.

Fufu is a popular traditional fermented wet paste food product from cassava. We examined consumer preferences and quality attributes of fufu in Abia and Imo States of South-East Nigeria, with special attention to gender differences, for the purpose of providing guidance to breeders. Data were analysed by the use of descriptive and inferential statistics. Participants for the interview were randomly selected from a list of farmers in the study area. Individual (II) interviews were conducted among eighty participants comprising twenty-six men (32.5%) and fifty-four women (67.5%). Preferences along the food chain from raw roots to final product were also obtained. Major traits influencing gender-specific consumer preferences are related to appearance, texture and smell. Smoothness, not sticky, easy to swallow and drawability of fufu appear to be major traits that drive acceptance by both men and women. Big roots and smooth skin are prioritised for raw material. Some quality characteristics are conditioned largely by variety traits, while others can be modified by adjusting the processing methods. The complexity of producing high-quality fufu makes it imperative to introduce a multidisciplinary approach into breeding programmes.

Genome-Wide Association Study of Root Mealiness and Other Texture-Associated Traits in Cassava.

Cassava breeders have made significant progress in developing new genotypes with improved agronomic characteristics such as improved root yield and resistance against biotic and abiotic stresses. However, these new and improved cassava (Manihot esculenta Crantz) varieties in cultivation in Nigeria have undergone little or no improvement in their culinary qualities; hence, there is a paucity of genetic information regarding the texture of boiled cassava, particularly with respect to its mealiness, the principal sensory quality attribute of boiled cassava roots. The current study aimed at identifying genomic regions and polymorphisms associated with natural variation for root mealiness and other texture-related attributes of boiled cassava roots, which includes fibre, adhesiveness (ADH), taste, aroma, colour, and firmness. We performed a genome-wide association (GWAS) analysis using phenotypic data from a panel of 142 accessions obtained from the National Root Crops Research Institute (NRCRI), Umudike, Nigeria, and a set of 59,792 high-quality single nucleotide polymorphisms (SNPs) distributed across the cassava genome. Through genome-wide association mapping, we identified 80 SNPs that were significantly associated with root mealiness, fibre, adhesiveness, taste, aroma, colour and firmness on chromosomes 1, 4, 5, 6, 10, 13, 17 and 18. We also identified relevant candidate genes that are co-located with peak SNPs linked to these traits in M. esculenta. A survey of the cassava reference genome v6.1 positioned the SNPs on chromosome 13 in the vicinity of Manes.13G026900, a gene recognized as being responsible for cell adhesion and for the mealiness or crispness of vegetables and fruits, and also known to play an important role in cooked potato texture. This study provides the first insights into understanding the underlying genetic basis of boiled cassava root texture. After validation, the markers and candidate genes identified in this novel work could provide important genomic resources for use in marker-assisted selection (MAS) and genomic selection (GS) to accelerate genetic improvement of root mealiness and other culinary qualities in cassava breeding programmes in West Africa, especially in Nigeria, where the consumption of boiled and pounded cassava is low.

Genotypic evaluation of twenty-eight high- and low-cyanide cassava in low-land tropics, southeast Nigeria.

A two-year field experiment was carried out in a randomized complete block design with two replications in 2015/16 and 2016/17 cropping seasons at the National Root Crops Research Institute, Umudike (05° 29'N; 07° 33'E; 122 m above sea level) in Nigeria. The objectives of the study were to assess growth, disease status and yield responses of twenty-eight (28) newly developed high- and low-cyanide cassava genotypes in low-land humid tropics of Umudike, Nigeria. Plant height, stem girth, canopy diameter, number of leaves/plant, cassava mosaic disease (CMD) and cassava bacterial blight (CBB) incidence and severity as well as bulking rate and fresh root yield varied significantly (P < 0.05) amongst the high- and low-cyanide cassava genotypes in both cropping seasons. Also, the results showed that bitter cassava genotypes exhibited greater tolerance to CMD than sweet cassava. However, there was no significant (P > 0.05) difference in bulking rate and fresh root yield between the two groups. The Pearson's and Spearman's ranked associations between fresh root yield of the cassava genotypes and other variables analysed across the two cropping seasons were highly significant (P ≤ 0.01) and positive contrary to the other variables. However, they exhibited different degrees of associations amongst themselves, especially CMD incidence that indicated highly significant and positive association with severity. The principal component analysis across the two cropping seasons indicated eigen-values of the four axes > unity with cumulative variance of 68.98 %. Most of the characters that contributed to the 22.35 % observed variability in principal component (PC1) were CMD incidence and severity, and number of leaves/plant while PC2 also exhibited high vector load from plant attributes such as number of leaves/plant, bulking rate ha-1 and canopy diameter. The bi-plot clustering indicated that genotypes (BI-56, NR110439 and B1-29) exhibited strong similarity amongst themselves across the tested variables. The combined fresh root yield sequence of the first ten high yielder genotypes was in the order: NR110439 > TMS010354 > NR110315 > NR 110238 > NR 110228 > NR 060169 > BI-117 > BI-50 > NR110084 > NR 110181. These cassava genotypes were considered to be better endowed genetically, hence their improvement can be encouraged to ensure high and sustainable root yield. A poly-linear and positive regression was recorded between CMD and root yield as well as between CBB and root yield indicating that they affected fresh root yield of high- and low-cyanide cassava genotypes and demands attention also in cassava improvement studies.