Genome-wide association study for yield and quality of granulated cassava processed product.

The starchy storage roots of cassava are commonly processed into a variety of products, including cassava granulated processed products (gari). The commercial value of cassava roots depends on the yield and quality of processed products, directly influencing the acceptance of new varieties by farmers, processors, and consumers. This study aims to estimate genetic advance through phenotypic selection and identify genomic regions associated and candidate genes linked with gari yield and quality. Higher single nucleotide polymorphism (SNP)-based heritability estimates compared to broad-sense heritability estimates were observed for most traits highlighting the influence of genetic factors on observed variation. Using genome-wide association analysis of 188 clones, genotyped using 53,150 genome-wide SNPs, nine SNPs located on seven chromosomes were significantly associated with peel loss, gari yield, color parameters for gari and eba, bulk density, swelling index, and textural properties of eba. Future research will focus on validating and understanding the functions of identified genes and their influence on gari yield and quality traits.

Genetic and environmental effects on processing productivity and food product yield: drudgery of women's work.

BACKGROUND: Cassava processing is a crucial source of livelihood for rural farmers and processors in Nigeria and Cameroon. This study investigated the varietal effect on the processing productivity of women farmer processors within their working environment and compared this with the food product quality as evaluated by the processors and the field yield. Field trials were established in Nigeria (Benue and Osun state) and Cameroon (Littoral region). Eight cassava genotypes were evaluated. These eight varieties included newly bred genotypes, commercial checks and varieties provided and preferred by the processors. The roots of these genotypes were harvested and processed into gari and eba by processors. The time of each processing step was recorded. Processors assessed the quality of the roots and food products using pairwise ranking. RESULTS: In the field trials in Cameroon and Nigeria (Benue state), the newly bred genotypes showed superior performance in terms of dry matter content and fresh and dry yield. During processing, genotypes showed significant variation for most assessed parameters in both countries. Some newly bred varieties exhibited lower productivity that can make them more prone to drudgery than the local commercial checks and the varieties provided and preferred by the processors. Newly bred varieties were mostly ranked higher or equal to processors' preferred varieties concerning fresh root and food product quality. In the Cameroon location there were significant varietal differences in processing productivity and drudgery index which suggest that the particular processing methods there - such as pressing methods and fermentation time - cause these varietal differences to matter more. CONCLUSIONS: The varieties that were tested were observed to differ in yield, product quality, processing productivity, and potential drudgery levels. Some breeders' germplasms displayed a combination of increased yields and good product quality and good processor productivity. Those varieties that showed low processor productivity should be avoided during selection to avoid increased labour burden and associated drudgery of women processors. Further research is recommended to enhance food product color, latent culinary qualities, and processing productivity of newly bred varieties to improve acceptability and reduce processing drudgery for women. © 2023 The Authors. Journal of The Science of Food and Agriculture published by John Wiley & Sons Ltd on behalf of Society of Chemical Industry.

Exploring genetic variability, heritability, and trait correlations in gari and eba quality from diverse cassava varieties in Nigeria.

BACKGROUND: Gari (especially in Nigeria) is an important West African food product made from cassava. It is an affordable, precooked, dry, easy to prepare and store food product. Eba is a stiff dough produced by reconstituting gari in hot water. Gari and eba quality is an important driver of varietal acceptance by farmers, processors, and consumers. RESULTS: This study characterized the genetic variability, heritability, and correlations among quality-related traits of fresh roots, gari, and eba. Thirty-three diverse genotypes, including landraces and released and advanced breeding genotypes, were used in this study. In total, 40 traits categorized into fresh root quality, colour, functional, and texture properties trait groups were assessed. We observed broad phenotypic variability among the genotypes used in this study. Dry matter content had a positive (P < 0.05) correlation with gari%, bulk density and a negative correlation with eba hardness and gumminess. Broad-sense heritability across all environments varied considerably among the different trait groups: 62% to 79% for fresh root quality, 0% to 96% for colour, 0% to 79% for functional and 0% to 57% for texture properties. CONCLUSIONS: The stable broad-sense heritability found for gari%, gari and eba colour, bulk density, swelling index, and hardness measured using instrumental texture profile analysis coupled with sufficient variability in the population indicate good potential for genetic improvement of these traits through recurrent selection. Also, it is possible to genetically improve gari%, bulk density, and swelling power by simultaneously improving the dry matter content of fresh roots. © 2023 The Authors. Journal of The Science of Food and Agriculture published by John Wiley & Sons Ltd on behalf of Society of Chemical Industry.

Efficient sugar utilization and transition from oxidative to substrate-level phosphorylation in high starch storage roots of African cassava genotypes.

Cassava's storage roots represent one of the most important sources of nutritional carbohydrates worldwide. Particularly, smallholder farmers in sub-Saharan Africa depend on this crop plant, where resilient and yield-improved varieties are of vital importance to support steadily increasing populations. Aided by a growing understanding of the plant's metabolism and physiology, targeted improvement concepts already led to visible gains in recent years. To expand our knowledge and to contribute to these successes, we investigated storage roots of eight cassava genotypes with differential dry matter content from three successive field trials for their proteomic and metabolic profiles. At large, the metabolic focus in storage roots transitioned from cellular growth processes toward carbohydrate and nitrogen storage with increasing dry matter content. This is reflected in higher abundance of proteins related to nucleotide synthesis, protein turnover, and vacuolar energization in low starch genotypes, while proteins involved in sugar conversion and glycolysis were more prevalent in high dry matter genotypes. This shift in metabolic orientation was underlined by a clear transition from oxidative- to substrate-level phosphorylation in high dry matter genotypes. Our analyses highlight metabolic patterns that are consistently and quantitatively associated with high dry matter accumulation in cassava storage roots, providing fundamental understanding of cassava's metabolism as well as a data resource for targeted genetic improvement.

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.

Climate change challenges, plant science solutions.

Climate change is a defining challenge of the 21st century, and this decade is a critical time for action to mitigate the worst effects on human populations and ecosystems. Plant science can play an important role in developing crops with enhanced resilience to harsh conditions (e.g. heat, drought, salt stress, flooding, disease outbreaks) and engineering efficient carbon-capturing and carbon-sequestering plants. Here, we present examples of research being conducted in these areas and discuss challenges and open questions as a call to action for the plant science community.

Validation of KASP markers associated with cassava mosaic disease resistance, storage root dry matter and provitamin A carotenoid contents in Ugandan cassava germplasm.

Introduction: The intrinsic high heterozygosity of cassava makes conventional breeding ineffective for rapid genetic improvement. However, recent advances in next generation sequencing technologies have enabled the use of high-density markers for genome-wide association studies, aimed at identifying single nucleotide polymorphisms (SNPs) linked to major traits such as cassava mosaic disease (CMD) resistance, dry matter content (DMC) and total carotenoids content (TCC). A number of these trait-linked SNPs have been converted to Kompetitive allele-specific polymerase chain reaction (KASP) markers for downstream application of marker assisted selection. Methods: We assayed 13 KASP markers to evaluate their effectiveness in selecting for CMD, DMC and TCC in 1,677 diverse cassava genotypes representing two independent breeding populations in Uganda. Results: Five KASP markers had significant co-segregation with phenotypes; CMD resistance (2), DMC (1) and TCC (2), with each marker accounting for at least 30% of the phenotypic variation. Markers located within the chromosomal regions for which strong marker-trait association loci have been characterised (chromosome 12 markers for CMD, chromosome 1 markers for DMC and TCC) had consistently superior ability to discriminate the respective phenotypes. Discussion: The results indicate varying discriminatory abilities of the KASP markers assayed and the need for their context-based use for MAS, with PSY2_572 particularly effective in selecting for high TCC. Availing the effective KASP markers on cost-effective genotyping platforms could facilitate practical implementation of marker-assisted cassava breeding for accelerated genetic gains for CMD, DMC and provitamin A carotenoids.

Genetic variability and genotype by environment interaction of two major cassava processed products in multi-environments.

Conversion of cassava (Manihot esculenta) roots to processed products such as gari and fufu before consumption is a common practice worldwide by cassava end-user for detoxification, prolonged shelf life or profitability. Fresh root and processed product yield are supposed to be equivalent for each genotype, however, that is not the case. Developing genotypes with high product conversion rate is an important breeding goal in cassava as it drives the adoption rates of new varieties. The objective of this study was to quantify the contribution of genetic and genotype-by-environment interaction (GEI) patterns on cassava root conversion rate to gari and fufu. Sixty-seven advanced breeding genotypes from the International Institute of Tropical Agriculture (IITA) were evaluated across eight environments in Nigeria. Root conversion rate means across trials ranges from 14.72 to 22.76% for gari% and 16.96-24.24% for fufu%. Heritability estimates range from 0.17 to 0.74 for trial bases and 0.71 overall environment for gari% and 0.03-0.65 for trial bases and 0.72 overall environment for fufu% which implies that genetic improvement can be made on these traits. Root conversion rate for both gari and fufu% showed a negative but insignificant correlation with fresh root yield and significant positive correlation to Dry Matter content. For all fitted models, environment and interaction had explained more of the phenotypic variation observed among genotypes for both product conversion rates showing the presence of a strong GEI. Wrickle ecovalence (Wi) stability analysis and Geometric Adaptability index (GAI) identified G40 (TMS14F1285P0006) as part of top 5 genotypes for gari% but no overlapping genotype was identified by both stability analysis for fufu%. This genotypic performance across environments suggests that it is possible to have genotype with dual-purpose for high gari and fufu conversion rate.

Predicting starch content in cassava fresh roots using near-infrared spectroscopy.

The cassava starch market is promising in sub-Saharan Africa and increasing rapidly due to the numerous uses of starch in food industries. More accurate, high-throughput, and cost-effective phenotyping approaches could hasten the development of cassava varieties with high starch content to meet the growing market demand. This study investigated the effectiveness of a pocket-sized SCiO™ molecular sensor (SCiO) (740-1070 nm) to predict starch content in freshly ground cassava roots. A set of 344 unique genotypes from 11 field trials were evaluated. The predictive ability of individual trials was compared using partial least squares regression (PLSR). The 11 trials were aggregated to capture more variability, and the performance of the combined data was evaluated using two additional algorithms, random forest (RF) and support vector machine (SVM). The effect of pretreatment on model performance was examined. The predictive ability of SCiO was compared to that of two commercially available near-infrared (NIR) spectrometers, the portable ASD QualitySpec® Trek (QST) (350-2500 nm) and the benchtop FOSS XDS Rapid Content™ Analyzer (BT) (400-2490 nm). The heritability of NIR spectra was investigated, and important spectral wavelengths were identified. Model performance varied across trials and was related to the amount of genetic diversity captured in the trial. Regardless of the chemometric approach, a satisfactory and consistent estimate of starch content was obtained across pretreatments with the SCiO (correlation between the predicted and the observed test set, (R2 P): 0.84-0.90; ratio of performance deviation (RPD): 2.49-3.11, ratio of performance to interquartile distance (RPIQ): 3.24-4.08, concordance correlation coefficient (CCC): 0.91-0.94). While PLSR and SVM showed comparable prediction abilities, the RF model yielded the lowest performance. The heritability of the 331 NIRS spectra varied across trials and spectral regions but was highest (H2 > 0.5) between 871-1070 nm in most trials. Important wavelengths corresponding to absorption bands associated with starch and water were identified from 815 to 980 nm. Despite its limited spectral range, SCiO provided satisfactory prediction, as did BT, whereas QST showed less optimal calibration models. The SCiO spectrometer may be a cost-effective solution for phenotyping the starch content of fresh roots in resource-limited cassava breeding programs.

Parsimonious genotype by environment interaction covariance models for cassava (Manihot esculenta).

The assessment of cassava clones across multiple environments is often carried out at the uniform yield trial, a late evaluation stage, before variety release. This is to assess the differential response of the varieties across the testing environments, a phenomenon referred to as genotype-by-environment interaction (GEI). This phenomenon is considered a critical challenge confronted by plant breeders in developing crop varieties. This study used the data from variety trials established as randomized complete block design (RCBD) in three replicates across 11 locations in different agro-ecological zones in Nigeria over four cropping seasons (2016-2017, 2017-2018, 2018-2019, and 2019-2020). We evaluated a total of 96 varieties, including five checks, across 48 trials. We exploited the intricate pattern of GEI by fitting variance-covariance structure models on fresh root yield. The goodness-of-fit statistics revealed that the factor analytic model of order 3 (FA3) is the most parsimonious model based on Akaike Information Criterion (AIC). The three-factor loadings from the FA3 model explained, on average across the 27 environments, 53.5% [FA (1)], 14.0% [FA (2)], and 11.5% [FA (3)] of the genetic effect, and altogether accounted for 79.0% of total genetic variability. The association of factor loadings with weather covariates using partial least squares regression (PLSR) revealed that minimum temperature, precipitation and relative humidity are weather conditions influencing the genotypic response across the testing environments in the southern region and maximum temperature, wind speed, and temperature range for those in the northern region of Nigeria. We conclude that the FA3 model identified the common latent factors to dissect and account for complex interaction in multi-environment field trials, and the PLSR is an effective approach for describing GEI variability in the context of multi-environment trials where external environmental covariables are included in modeling.

Validation of KASP-SNP markers in cassava germplasm for marker-assisted selection of increased carotenoid content and dry matter content.

Provitamin A biofortification and increased dry matter content are important breeding targets in cassava improvement programs worldwide. Biofortified varieties contribute to the alleviation of provitamin A deficiency, a leading cause of preventable blindness common among pre-school children and pregnant women in developing countries particularly Africa. Dry matter content is a major component of dry yield and thus underlies overall variety performance and acceptability by growers, processors, and consumers. Single nucleotide polymorphism (SNP) markers linked to these traits have recently been discovered through several genome-wide association studies but have not been deployed for routine marker-assisted selection (MAS). This is due to the lack of useful information on markers' performances in diverse genetic backgrounds. To overcome this bottleneck, technical and biological validation of the loci associated with increased carotenoid content and dry matter content were carried out using populations independent of the marker discovery population. In the present study, seven previously identified markers for these traits were converted to a robust set of uniplex allele-specific polymerase chain reaction (PCR) assays and validated in two independent pre-breeding and breeding populations. These assays were efficient in discriminating marker genotypic classes and had an average call rate greater than 98%. A high correlation was observed between the predicted and observed carotenoid content as inferred by root yellowness intensity in the breeding (r = 0.92) and pre-breeding (r = 0.95) populations. On the other hand, dry matter content-markers had moderately low predictive accuracy in both populations (r< 0.40) due to the more quantitative nature of the trait. This work confirmed the markers' effectiveness in multiple backgrounds, therefore, further strengthening their value in cassava biofortification to ensure nutritional security as well as dry matter content productivity. Our study provides a framework to guide future marker validation, thus leading to the more routine use of markers in MAS in cassava improvement programs.

Exploring genotype by environment interaction on cassava yield and yield related traits using classical statistical methods.

Variety advancement decisions for root quality and yield-related traits in cassava are complex due to the variable patterns of genotype-by-environment interactions (GEI). Therefore, studies focused on the dissection of the existing patterns of GEI using linear-bilinear models such as Finlay-Wilkinson (FW), additive main effect and multiplicative interaction (AMMI), and genotype and genotype-by-environment (GGE) interaction models are critical in defining the target population of environments (TPEs) for future testing, selection, and advancement. This study assessed 36 elite cassava clones in 11 locations over three cropping seasons in the cassava breeding program of IITA based in Nigeria to quantify the GEI effects for root quality and yield-related traits. Genetic correlation coefficients and heritability estimates among environments found mostly intermediate to high values indicating high correlations with the major TPE. There was a differential clonal ranking among the environments indicating the existence of GEI as also revealed by the likelihood ratio test (LRT), which further confirmed the statistical model with the heterogeneity of error variances across the environments fit better. For all fitted models, we found the main effects of environment, genotype, and interaction significant for all observed traits except for dry matter content whose GEI sensitivity was marginally significant as found using the FW model. We identified TMS14F1297P0019 and TMEB419 as two topmost stable clones with a sensitivity values of 0.63 and 0.66 respectively using the FW model. However, GGE and AMMI stability value in conjunction with genotype selection index revealed that IITA-TMS-IBA000070 and TMS14F1036P0007 were the top-ranking clones combining both stability and yield performance measures. The AMMI-2 model clustered the testing environments into 6 mega-environments based on winning genotypes for fresh root yield. Alternatively, we identified 3 clusters of testing environments based on genotypic BLUPs derived from the random GEI component.

Breedbase: a digital ecosystem for modern plant breeding.

Modern breeding methods integrate next-generation sequencing and phenomics to identify plants with the best characteristics and greatest genetic merit for use as parents in subsequent breeding cycles to ultimately create improved cultivars able to sustain high adoption rates by farmers. This data-driven approach hinges on strong foundations in data management, quality control, and analytics. Of crucial importance is a central database able to (1) track breeding materials, (2) store experimental evaluations, (3) record phenotypic measurements using consistent ontologies, (4) store genotypic information, and (5) implement algorithms for analysis, prediction, and selection decisions. Because of the complexity of the breeding process, breeding databases also tend to be complex, difficult, and expensive to implement and maintain. Here, we present a breeding database system, Breedbase (https://breedbase.org/, last accessed 4/18/2022). Originally initiated as Cassavabase (https://cassavabase.org/, last accessed 4/18/2022) with the NextGen Cassava project (https://www.nextgencassava.org/, last accessed 4/18/2022), and later developed into a crop-agnostic system, it is presently used by dozens of different crops and projects. The system is web based and is available as open source software. It is available on GitHub (https://github.com/solgenomics/, last accessed 4/18/2022) and packaged in a Docker image for deployment (https://hub.docker.com/u/breedbase, last accessed 4/18/2022). The Breedbase system enables breeding programs to better manage and leverage their data for decision making within a fully integrated digital ecosystem.

Genome-wide association analysis reveals new insights into the genetic architecture of defensive, agro-morphological and quality-related traits in cassava.

KEY MESSAGE: More than 40 QTLs associated with 14 stress-related, quality and agro-morphological traits were identified. A catalogue of favourable SNP markers for MAS and a list of candidate genes are provided. Cassava (Manihot esculenta) is one of the most important starchy root crops in the tropics due to its adaptation to marginal environments. Genetic progress in this clonally propagated crop can be accelerated through the discovery of markers and candidate genes that could be used in cassava breeding programs. We carried out a genome-wide association study (GWAS) using a panel of 5130 clones developed at the International Institute of Tropical Agriculture-Nigeria. The population was genotyped at more than 100,000 SNP markers via genotyping-by-sequencing (GBS). Genomic regions underlying genetic variation for 14 traits classified broadly into four categories: biotic stress (cassava mosaic disease and cassava green mite severity); quality (dry matter content and carotenoid content) and plant agronomy (harvest index and plant type) were investigated. We also included several agro-morphological traits related to leaves, stems and roots with high heritability. In total, 41 significant associations were uncovered. While some of the identified loci matched with those previously reported, we present additional association signals for the traits. We provide a catalogue of favourable alleles at the most significant SNP for each trait-locus combination and candidate genes occurring within the GWAS hits. These resources provide a foundation for the development of markers that could be used in cassava breeding programs and candidate genes for functional validation.

Genomic mating in outbred species: predicting cross usefulness with additive and total genetic covariance matrices.

Diverse crops are both outbred and clonally propagated. Breeders typically use truncation selection of parents and invest significant time, land, and money evaluating the progeny of crosses to find exceptional genotypes. We developed and tested genomic mate selection criteria suitable for organisms of arbitrary homozygosity level where the full-sibling progeny are of direct interest as future parents and/or cultivars. We extended cross variance and covariance variance prediction to include dominance effects and predicted the multivariate selection index genetic variance of crosses based on haplotypes of proposed parents, marker effects, and recombination frequencies. We combined the predicted mean and variance into usefulness criteria for parent and variety development. We present an empirical study of cassava (Manihot esculenta), a staple tropical root crop. We assessed the potential to predict the multivariate genetic distribution (means, variances, and trait covariances) of 462 cassava families in terms of additive and total value using cross-validation. Most variance (89%) and covariance (70%) prediction accuracy estimates were greater than zero. The usefulness of crosses was accurately predicted with good correspondence between the predicted and the actual mean performance of family members breeders selected for advancement as new parents and candidate varieties. We also used a directional dominance model to quantify significant inbreeding depression for most traits. We predicted 47,083 possible crosses of 306 parents and contrasted them to those previously tested to show how mate selection can reveal the new potential within the germplasm. We enable breeders to consider the potential of crosses to produce future parents (progeny with top breeding values) and varieties (progeny with top own performance).

Genetic Diversity and Population Structure of Cowpea [Vigna unguiculata (L.) Walp.] Germplasm Collected from Togo Based on DArT Markers.

Crop genetic diversity is a sine qua non for continuous progress in the development of improved varieties, hence the need for germplasm collection, conservation and characterization. Over the years, cowpea has contributed immensely to the nutrition and economic life of the people in Togo. However, the bulk of varieties grown by farmers are landraces due to the absence of any serious genetic improvement activity on cowpea in the country. In this study, the genetic diversity and population structure of 255 cowpea accessions collected from five administrative regions and the agricultural research institute of Togo were assessed using 4600 informative diversity array technology (DArT) markers. Among the regions, the polymorphic information content (PIC) ranged from 0.19 to 0.27 with a mean value of 0.25. The expected heterozygosity (He) varied from 0.22 to 0.34 with a mean value of 0.31, while the observed heterozygosity (Ho) varied from 0.03 to 0.07 with an average of 0.05. The average inbreeding coefficient (FIS) varied from 0.78 to 0.89 with a mean value of 0.83, suggesting that most of the accessions are inbred. Cluster analysis and population structure identified four groups with each comprising accessions from the six different sources. Weak to moderate differentiation was observed among the populations with a genetic differentiation index varying from 0.014 to 0.117. Variation was highest (78%) among accessions within populations and lowest between populations (7%). These results revealed a moderate level of diversity among the Togo cowpea germplasm. The findings of this study constitute a foundation for genetic improvement of cowpea in Togo.

Understanding cassava varietal preferences through pairwise ranking of gari-eba and fufu prepared by local farmer-processors.

Within communities in Osun and Imo States of Nigeria, farmer-processors grew and processed a diverse set of improved and landrace cassava varieties into the locally popular foods, gari, eba and fufu. Local and 15 main varieties were grown in a 'mother and baby trials' design in each state. Mother trials with three replications were processed by farmer-processors renown in their community for their processing skills. Baby trials were managed and processed by other farmer-processors. The objective was to identify food quality criteria to inform demand-led breeding to benefit users, especially women, given their key roles in processing. Farmer-processors evaluated the overall quality of fresh roots and derived food products through pairwise comparisons. Improved varieties had higher fresh and dry root yield. Overall, landraces ranked first for quality of gari and eba, but several improved varieties were also appreciated for good quality. Landraces in Osun had higher gari yield and a higher swelling power compared to improved varieties. Colour (browning), bulk density, swelling power, solubility and water absorption capacity were the criteria most related to food product ranking by farmer-processors. Evaluation of varieties under farmer-processors' conditions is crucial for providing guidance to breeders on critical selection criteria.