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.

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.

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.

Time to Load Up-Resistance Training Can Improve the Health of Women with Polycystic Ovary Syndrome (PCOS): A Scoping Review.

BACKGROUND: Guidelines for the management of polycystic ovary syndrome (PCOS) focus on lifestyle changes, incorporating exercise. Whilst evidence suggests that aerobic exercise may be beneficial, less is known about the effectiveness of resistance training (RT), which may be more feasible for those that have low fitness levels and/or are unable to tolerate/participate in aerobic exercise. OBJECTIVES: To identify the available evidence on RT in women with PCOS and to summarise findings in the context of a scoping review. ELIGIBILITY CRITERIA: Studies utilising pre-post designs to assess the effectiveness of RT in PCOS; all outcomes were included. SOURCES OF EVIDENCE: Four databases (PubMed, CENTRAL, CINAHL and SportDiscus) were searched and supplemented by hand searching of relevant papers/reference lists. CHARTING METHODS: Extracted data were presented in tables and qualitatively synthesised. RESULTS: Searches returned 42 papers; of those, 12 papers were included, relating to six studies/trials. Statistical changes were reported for multiple pertinent outcomes relating to metabolic (i.e., glycaemia and fat-free mass) and hormonal (i.e., testosterone and sex hormone-binding globulin) profiles. CONCLUSIONS: There is a striking lack of studies in this field and, despite the reported statistical significance for many outcomes, the documented magnitude of changes are small and the quality of the evidence questionable. This highlights an unmet need for rigorously designed/reported and sufficiently powered trials.

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.

Influence of traditional processing and genotypes on the antioxidant and antihyperglycaemic activities of yellow-fleshed cassava.

Yellow-fleshed cassava root (YFCR) is processed into traditional products that may influence its bioactivities. In this study, the antioxidant and anti-hyperglycaemic activities of three traditional products (lafun, fufu and gari) from five genotypes (IITA-TMS-IBA070337, 182961, 182962, 182986, 183044) of YFCR were evaluated. The YFCR genotypes were grown at the International Institute of Tropical Agriculture (IITA) research field, Ibadan. The bioactive constituents (total carotenoids, total phenolics, tannins and total flavonoids), antioxidant [2,2-azinobis (3-ethyl-benzothiazoline-6-sulfonic acid) radical cation (ABTS•+) and 1,1-diphenyl-2- picrylhydrazyl radical (DPPH•) scavenging capacities, and reducing power], and starch-digesting enzymes (α-amylase and α-glucosidase) inhibitory activities of the products were determined using standard laboratory methods. The glucose response of the products was assessed in human subjects. The concentrations of the bioactive constituents of the products from different genotypes varied significantly (p < 0.05). The ABTS•+ and DPPH• scavenging capacities and the reducing power of the products also differed significantly (p < 0.05), such that the lafun from IITA-TMS-IBA182962, IITA-TMS-IBA070337 and IITA-TMS-IBA070337 had the strongest ABTS•+ and DPPH• scavenging capacities, and reducing power, respectively. The α-amylase and α-glucosidase inhibitory activities of the three products differed significantly (p < 0.05), with the lafun from IITA-TMS-IBA070337 and IITA-TMS-IBA07033 having the strongest α-amylase and α-glucosidase inhibitory activity, respectively. Also, the lafun from IITA-TMS-182986 had the least glucose response, while the fufu from IITA-TMS-IBA070337 had the highest glucose response. Overall, the lafun from different genotypes of YFCR had the most potent antioxidant and starch-digesting enzymes inhibitory activities and the least glucose responses. Hence, lafun may be a promising dietary intervention targeting oxidative stress, hyperglycaemia, and their resultant type 2 diabetes.

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.

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.

Breeding Schemes: What Are They, How to Formalize Them, and How to Improve Them?

Formalized breeding schemes are a key component of breeding program design and a gateway to conducting plant breeding as a quantitative process. Unfortunately, breeding schemes are rarely defined, expressed in a quantifiable format, or stored in a database. Furthermore, the continuous review and improvement of breeding schemes is not routinely conducted in many breeding programs. Given the rapid development of novel breeding methodologies, it is important to adopt a philosophy of continuous improvement regarding breeding scheme design. Here, we discuss terms and definitions that are relevant to formalizing breeding pipelines, market segments and breeding schemes, and we present a software tool, Breeding Pipeline Manager, that can be used to formalize and continuously improve breeding schemes. In addition, we detail the use of continuous improvement methods and tools such as genetic simulation through a case study in the International Institute of Tropical Agriculture (IITA) Cassava east-Africa pipeline. We successfully deploy these tools and methods to optimize the program size as well as allocation of resources to the number of parents used, number of crosses made, and number of progeny produced. We propose a structured approach to improve breeding schemes which will help to sustain the rates of response to selection and help to deliver better products to farmers and consumers.

Proximate Composition, Cyanide Content, and Carotenoid Retention after Boiling of Provitamin A-Rich Cassava Grown in Ghana.

Biofortified yellow-fleshed cassava is important in countries with high cassava consumption, to improve the vitamin A status of their populations. Yellow- and white-fleshed cassava were evaluated over three locations for proximate composition and cyanide content as well as retention of carotenoids after boiling. There was significant variation in the crude fiber, fat, protein and ash content of the genotypes. All but one of the yellow-fleshed cassava genotypes recorded higher protein values than the white-fleshed local genotypes across locations. The cyanide content of the genotypes varied between locations but was within the range of sweet cassava genotypes, but above the maximum acceptable recommended limit. Micronutrient retention is important in biofortified crops because a loss of micronutrients during processing and cooking reduces the nutritional value of biofortified foods. Total carotenoid content (TCC) ranged from 1.18-18.81 µg.g-1 and 1.01-13.36 µg.g-1 (fresh weight basis) for fresh and boiled cassava, respectively. All the yellow-fleshed cassava genotypes recorded higher TCC values in both the fresh and boiled state than the white-fleshed genotypes used as checks.

Popular Biofortified Cassava Cultivars Are Heavily Impacted by Plant Parasitic Nematodes, Especially Meloidogyne Spp.

The development of new biofortified cassava cultivars, with higher micronutrient contents, offers great potential to enhance food and nutrition security prospects. Among the various constraints affecting cassava production are plant parasitic nematodes (PPN), especially root-knot nematodes. In this study, six popular biofortified cultivars were field-evaluated for their response to PPN in Nigeria. A field naturally infested with a diversity of PPN but dominated by root-knot nematodes was used. Application of the nematicide carbofuran significantly reduced PPN densities, and at harvest, no root galling damage was observed, compared with untreated plots, which had heavy galling damage. Plant height, stem girth, plant weight, marketable storage root number and weight were significantly lower for most cultivars in untreated plots. Percentage yield losses in the range of 21.3-63.7% were recorded from two separate trials conducted for 12 months each. Lower total carotenoid and dry matter contents were associated with higher PPN densities in some biofortified cultivars, resulting in a loss of as much as 63% of total carotenoid and 52% of dry matter contents. The number and weight of rotted storage roots were significantly greater in untreated plots across cultivars, reducing in-field and post-harvest storability. This study demonstrates that natural field populations of PPN can substantially affect yield, quality and nutritional value of released biofortified cassava cultivars.

Genetic characterization of cassava (Manihot esculenta Crantz) genotypes using agro-morphological and single nucleotide polymorphism markers.

Dearth of information on extent of genetic variability in cassava limits the genetic improvement of cassava genotypes in Sierra Leone. The aim of this study was to assess the genetic diversity and relationships within 102 cassava genotypes using agro-morphological and single nucleotide polymorphism markers. Morphological classification based on qualitative traits categorized the germplasm into five different groups, whereas the quantitative trait set had four groups. The SNP markers classified the germplasm into three main cluster groups. A total of seven principal components (PCs) in the qualitative and four PCs in the quantitative trait sets accounted for 79.03% and 72.30% of the total genetic variation, respectively. Significant and positive correlations were observed between average yield per plant and harvest index (r = 0.76***), number of storage roots per plant and harvest index (r = 0.33*), height at first branching and harvest index (0.26*), number of storage roots per plant and average yield per plant (r = 0.58*), height at first branching and average yield per plant (r = 0.24*), length of leaf lobe and petiole length (r = 0.38*), number of leaf lobe and petiole length (r = 0.31*), width of leaf lobe and length of leaf lobe (r = 0.36*), number of leaf lobe and length of leaf lobe (r = 0.43*), starch content and dry matter content (r = 0.99***), number of leaf lobe and root dry matter (r = 0.30*), number of leaf lobe and starch content (r = 0.28*), and height at first branching and plant height (r = 0.45**). Findings are useful for conservation, management, short term recommendation for release and genetic improvement of the crop.

Genetic variability, stability and heritability for quality and yield characteristics in provitamin A cassava varieties.

Cassava is widely consumed in many areas of Africa, including Ghana, and is a major part of most household diets. These areas are characterized by rampant malnutrition, because the tuberous roots are low in nutritional value. Provitamin A biofortified cassava varieties have been developed by the International Institute for Tropical Agriculture, but adoption of these varieties in Ghana will largely depend on their agronomic performance, including fresh root yield, dry matter content, resistance to major pests and diseases, mealiness, starch content and the stability of these traits. Eight provitamin A varieties with two white checks were planted in three environments for two seasons to determine stability and variability among the varieties for important traits. There were significant variations in performance between varieties and between environments for cassava mosaic disease, root number, fresh root yield and starch content. High broad-sense heritability and genetic advance were observed in all traits, except for storage root number, and could be exploited through improvement programs. This study identified the best performing enhanced provitamin A varieties for traits that are key drivers of variety adoption in Ghana. In view of this, some varieties can be recommended for varietal release after on-farm testing. The study also showed the possibility of tapping heterosis after careful selection of parents.

Gender-based constraints affecting biofortified cassava production, processing and marketing among men and women adopters in Oyo and Benue States, Nigeria.

This study identified gender-based constraints affecting the production, processing and marketing of biofortified cassava in two states in Nigeria, using a mixed methods approach. The study identified major differences between the two study sites (Benue and Oyo). The scale of production of biofortified cassava is higher in Oyo state among adult men because of their active involvement and collaboration with research institutes within the state and the ease of transporting products to Lagos State for designated diverse markets. However, in Benue state more adult and young women are engaged in cultivation, processing and marketing business to meet up with the increased demand due to higher consumer acceptance in this region. Gender analysis revealed that lack of access to hired-labour restricted the scale of production among women in especially Oyo state. Low product price and high price of processing equipment, poor market infrastructure and middle men exploitation were constraints significantly more mentioned by women in general. Majorly, the men identified limited processing facilities/equipment as the most important constraint affecting the demand of biofortified cassava roots, while generally women were more constrained by the shortage of basic amenities and trainings that hindered their processing efficiency. The study proposes integration of gender-responsive strategies to further enhance the delivery of biofortified cassava products in Nigeria.

Cassava Trait Preferences of Men and Women Farmers in Nigeria: Implications for Breeding.

Nigeria is the world's largest cassava producer, hosting a diverse array of cassava farmers and processors. Cassava breeding programs prioritize "common denominator" traits in setting breeding agendas, to impact the largest possible number of people through improved varieties. This approach has been successful, but cassava adoption rates are less than expected, with room for improvement by integrating traits in demand by farmers and processors. This paper aims to inform breeding priority setting, by examining trait and varietal preferences of men and women cassava farmer/processors. Men and women in eight communities in Southwest and Southeast Nigeria were consulted using mixed methods. Women and men had significantly different patterns of cassava use in the Southwest. Fifty-five variety names were recorded from the communities demonstrating high genetic diversity maintained by growers, especially in the Southeast. High yield, early maturity, and root size were most important traits across both regions, while traits women and men preferred followed gender roles: women prioritized product quality/cooking traits, while men placed higher priority on agronomic traits. Trait preference patterns differed significantly between the Southeast and Southwest, and showed differentiation based on gender. Patterns of access to stem sources were determined more by region and religion than gender.

Genome-Wide Association Mapping of Correlated Traits in Cassava: Dry Matter and Total Carotenoid Content.

Cassava is a starchy root crop cultivated in the tropics for fresh consumption and commercial processing. Primary selection objectives in cassava breeding include dry matter content and micronutrient density, particularly provitamin A carotenoids. These traits are negatively correlated in the African germplasm. This study aimed at identifying genetic markers associated with these traits and uncovering whether linkage and/or pleiotropy were responsible for observed negative correlation. A genome-wide association mapping using 672 clones genotyped at 72,279 single nucleotide polymorphism (SNP) loci was performed. Root yellowness was used indirectly to assess variation in carotenoid content. Two major loci for root yellowness were identified on chromosome 1 at positions 24.1 and 30.5 Mbp. A single locus for dry matter content that colocated with the 24.1 Mbp peak for carotenoids was identified. Haplotypes at these loci explained 70 and 37% of the phenotypic variability for root yellowness and dry matter content, respectively. Evidence of megabase-scale linkage disequilibrium (LD) around the major loci of the two traits and detection of the major dry matter locus in independent analysis for the white- and yellow-root subpopulations suggests that physical linkage rather that pleiotropy is more likely to be the cause of the negative correlation between the target traits. Moreover, candidate genes for carotenoid () and starch biosynthesis ( and ) occurred in the vicinity of the identified locus at 24.1 Mbp. These findings elucidate the genetic architecture of carotenoids and dry matter in cassava and provide an opportunity to accelerate breeding of these traits.

Tracking crop varieties using genotyping-by-sequencing markers: a case study using cassava (Manihot esculenta Crantz).

BACKGROUND: Accurate identification of crop cultivars is crucial in assessing the impact of crop improvement research outputs. Two commonly used identification approaches, elicitation of variety names from farmer interviews and morphological plant descriptors, have inherent uncertainty levels. Genotyping-by-sequencing (GBS) was used in a case study as an alternative method to track released varieties in farmers' fields, using cassava, a clonally propagated root crop widely grown in the tropics, and often disseminated through extension services and informal seed systems. A total of 917 accessions collected from 495 farming households across Ghana were genotyped at 56,489 SNP loci along with a "reference library" of 64 accessions of released varieties and popular landraces. RESULTS: Accurate cultivar identification and ancestry estimation was accomplished through two complementary clustering methods: (i) distance-based hierarchical clustering; and (ii) model-based maximum likelihood admixture analysis. Subsequently, 30% of the identified accessions from farmers' fields were matched to specific released varieties represented in the reference library. ADMIXTURE analysis revealed that the optimum number of major varieties was 11 and matched the hierarchical clustering results. The majority of the accessions (69%) belonged purely to one of the 11 groups, while the remaining accessions showed two or more ancestries. Further analysis using subsets of SNP markers reproduced results obtained from the full-set of markers, suggesting that GBS can be done at higher DNA multiplexing, thereby reducing the costs of variety fingerprinting. A large proportion of discrepancy between genetically unique cultivars as identified by markers and variety names as elicited from farmers were observed. Clustering results from ADMIXTURE analysis was validated using the assumption-free Discriminant Analysis of Principal Components (DAPC) method. CONCLUSION: We show that genome-wide SNP markers from increasingly affordable GBS methods coupled with complementary cluster analysis is a powerful tool for fine-scale population structure analysis and variety identification. Moreover, the ancestry estimation provides a framework for quantifying the contribution of exotic germplasm or older improved varieties to the genetic background of contemporary improved cultivars.