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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., Using a socially inclusive ‘mother baby trial’ approach, farmer processors in two states in Nigeria grew and processed a diverse set of cassava varieties and evaluated the root and food product quality and provided quality criteria through pairwise ranking. This evaluation was linked to fresh roots agronomic data as well as the laboratory measurements on the food product gari to inform breeding.

Despite the significance of cassava as food, feed and industrial root crop, little is known regarding the gene action determining root dry matter content (RDMC), fresh root yield, and tolerance to cassava mosaic disease (CMD), cassava green mite (CGM), and cassava mealy bug (CMB). Thus, a study was conducted to determine the general and specific combining abilities for disease, pest, RDMC, root yield and related traits by crossing 10 parents in a 6 × 4 line by tester design. The F1 progenies and their parents were assessed in-field in a randomized complete block design (RCBD) with three replicates. Findings implied sufficient genetic variability for all traits studied. Family TMEB419×IBA030305 had the highest RDMC of 35.47%, whilst family TMEB7×IBA0000203 had the least RDMC (23.87%). Genotypes IBA020588, IBA916132 and TMEB419 were the best parents for improvement of harvest index (HI) and RDMC due to its high positive and significant GCA effects. Genotype IBA000203 contributed the highest to increased plant height, whereas TMEB1, TMEB47 and ZAR010116 had significant negative GCA effects. ZAR010116 was the best tester for HI. Families TMEB778×ZAR010116 (34.23) and IBA020588×ZAR010116 (32.78) were the best performing families for mean RDMC, with parent ZAR010116, exhibiting the highest GCA effect for RDMC. Families TMEB419×ZAR000156, IBA916132×ZAR000156 and IBA020588×IBA000156 had low mean CMD scores of 1.1, 1.2 and 1.2, respectively. The preponderance of non-additive gene actions indicated that selection of superior plants should be postponed to later generation. Key words: Cassava, genetic improvement, agronomic traits, combining ability, heritability, progeny performance.

This study compared the relationship of different phenotyping methods including iCheckTM CAROTENE (iCheck), Chromameter, colour chart and visible/near-infrared spectroscopy (Vis/NIRS) used in quantifying total carotenoids content (TCC) in fresh cassava roots. Using a total of 194 cassava clones harvested from the International Institute of Tropical Agriculture (IITA), Ibadan, we compared the repeatability precision, accuracy of measurement and correlations of these phenotyping methods. From the results, Vis/NIRS-analyzed TCC had high and positive correlations with Chromameter and Color chart (r = 0.91 and 0.71, respectively). On the other hand, the result revealed somewhat moderate correlation (r = 0.67) between Vis/NIRS and iCheck measurements. Vis/NIRS, iCheck and chromameter methods gave high and nearly equal heritability estimates (0.95, 0.98 and 0.98, respectively) illustrating high repeatability precision of these methods; an indication that they can be used for germplasm selection in the early stages of breeding. Conversely, with Bland-Altman plot at 95% confidence level, the accuracy of iCheck was not comparable with that of Vis/ NIRS. The information derived from this analysis directly contributes towards the genetic improvement of root quality traits in cassava and facilitates the sharing of data across cassava breeding consortium.

Understanding the genetic diversity among accessions and germplasm is an important requirement for crop development as it allows for the selection of diverse parental combinations for enhancing genetic gain in varietal selection, advancement and release. The study aimed to characterize 183 provitamin A cassava (Manihot esculentaCrantz) accessions and five Sierra Leonean varieties using morphological traits, total carotenoid content and SNP markers to develop a collection for conservation and further use in the cassava breeding program. Both morphological parameters and 5634 SNP markers were used to assess the diversity among the provitamin-A cassava accessions and varieties. Significant differences were observed among the accessions for most of the traits measured. The first five PCs together accounted for 70.44% of the total phenotypic variation based on yield and yield components among the 183 provitamin-A cassava accessions and five Sierra Leonean varieties. The present study showed that provitamin-A cassava accessions in Sierra Leone have moderate to high diversity based on morphological and molecular assessment studies. The similarity index among the 187 and 185 cassava accessions grouped them into 6 and 9 distinct clusters based on morphological and molecular analyses, respectively. A significant positive, but low correlation (r = 0.104;p

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 in developing countries. Dry matter content is a major component of dry yield and thus underlies overall variety performance and acceptability by growers, processors, and consumers. SNP markers linked to these traits have recently been discovered through several genome-wide association studies but have not been deployed for marker-assisted selection (MAS). Assessment of marker performance in diverse genetic backgrounds is an important step towards their deployment for routine MAS. In the present study, seven previously identified markers for these traits were converted to a robust set of uniplex allele-specific 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 marker effectiveness in multiple backgrounds, therefore, further strengthening its value in cassava biofortification to ensure nutritional security as well as dry matter content productivity. Our study provides a framework to guide future marker development, thus leading to more routine use of markers in MAS in cassava improvement programs.

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.

Introgression of alleles from wild relatives has often been adaptive in plant breeding. However, the significance of historical hybridization events in modern breeding is often not clear. Cassava (Manihot esculenta) is among the most important staple foods in the world, sustaining hundreds of millions of people in the tropics, especially in sub-Saharan Africa. Widespread genotyping makes cassava a model for clonally propagated root and tuber crops in the developing world, and provides an opportunity to study the modern benefits and consequences of historical introgression. We detected large introgressed Manihot glaziovii genome-segments in a collection of 2742 modern cassava landraces and elite germplasm, the legacy of a 1930s era breeding to combat disease epidemics. African landraces and improved varieties were, on average, 3.8% (max 13.6%) introgressed. Introgressions accounted for a significant (mean 20%, max 56%) portion of the heritability of tested traits. M. glaziovii alleles on the distal 10 Mb of chr. 1 increased dry matter and root number. On chr. 4, introgressions in a 20 Mb region improved harvest index and brown streak disease tolerance. We observed the introgression frequency on chr. 1 double over three cycles of selection, and that later stage trials selectively excluded homozygotes from consideration as varieties. This indicates a heterozygous advantage of introgressions. However, we also found that maintaining large recombination-suppressed introgressions in the heterozygous state allowed the accumulation of deleterious mutations. We conclude that targeted recombination of introgressions would increase the efficiency of cassava breeding by allowing simultaneous fixation of beneficial alleles and purging of genetic load.

Cassava (Manihot esculenta Crantz) is a crucial staple crop, and provides carbohydrate energy to more than half a billion people in the tropics. Cassava mosaic disease (CMD) is the most important disease of cassava in Africa. Since Sri Lanka Cassava Mosaic Virus (SLCMV) was first reported in South East Asia in 2015, establishing sustainable solutions to CMD has become a top priority for the cassava program at the International Center for Tropical Agriculture (CIAT) and its partners. In the present study, we screened two populations for CMD resistance: VNM142, 142 clones collected from farms throughout Vietnam, and CIAT102, 102 clones resistant to CMD or mites, which were introduced from CIAT. High broad-sense heritability was observed in all the trials (&gt, 0.80). From the population VNM142, eight clones showed high CMD resistance with CMD severity scores less than 2.0. Two resistant clones had the same DNA fingerprinting with the accessions CR63 (PER262 or TAI9) and KM57 (VNM8) in the genebank, respectively. To our knowledge, this is the first report of CMD resistance in the genebank at CIAT. We also used the two populations to validate the CMD markers S12_7926132 and S14_4626854. Both markers explained 51% of the population variance in the segregating population CIAT102, but only 11% in the diverse population VNM142. Thus, we concluded that the two CMD markers could not be used to select for CMD resistance in diverse populations, but could predict the CMD resistance in segregating populations when the susceptible parents do not have resistant marker alleles and the resistance of the CMD2 donors is confirmed.

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. We were able to predict all genetic variances and most covariances with non-zero accuracy. We also tested a directional dominance model and found significant inbreeding depression for most traits and a boost in total merit accuracy for root yield. We predicted 47,083 possible crosses of 306 parents and contrasted them to those previously tested to show how mate selection can reveal new potential within the germplasm. We enable breeders to consider the potential of crosses to produce future parents (progeny with excellent breeding values) and varieties (progeny with top performance).Author SummaryBreeders typically use truncation selection and invest significant resources evaluating progeny to find exceptional genotypes. We extended genetic variance and trait covariance prediction to include dominance and predicting the multivariate selection index variance. We enable mate selection based on potential to produce future parents (progeny with excellent breeding values) and/or varieties (progeny with top performance). Using cross-validation, we demonstrate that genetic variances and covariances can be predicted with non-zero accuracy in cassava, a staple tropical root crop.

Over 800 million people across the tropics rely on cassava as a major source of calories. While the root dry matter content (RDMC) of this starchy root crop is important for both producers and consumers, characterization of RDMC by traditional methods is time-consuming and laborious for breeding programs. Alternate phenotyping methods have been proposed but lack the accuracy, cost, or speed ultimately needed for cassava breeding programs. For this reason, we investigated the use of a low-cost, handheld NIR spectrometer for field-based RDMC prediction in cassava. Oven-dried measurements of RDMC were paired with 21,044 scans of roots of 376 diverse clones from 10 field trials in Nigeria and grouped into training and test sets based on cross-validation schemes relevant to plant breeding programs. Mean partial least squares regression model performance ranged from R2p = 0.62 - 0.89 for within-trial predictions, which is within the range achieved with laboratory-grade spectrometers in previous studies. Relative to other factors, model performance was highly impacted by the inclusion of samples from the same environment in both the training and test sets. Random forest variable importance analysis of root spectra revealed increased importance in a region previously identified as predictive of water content in plants (~950 - 990 nm). With appropriate model calibration, the tested spectrometer will allow for field-based collection of spectral data with a smartphone for accurate RDMC prediction and potentially other quality traits, a step that could be easily integrated into existing harvesting workflows of cassava breeding programs.CORE IDEASA low-cost, handheld near-infrared spectrometer was tested for phenotyping of cassava rootsPlant breeding-relevant cross-validation schemes were used for predictionsHigh prediction accuracies were achieved for cassava root dry matter contentA spectral region predictive of plant water content was identified as important

The use of standard laboratory methods for trait evaluation is expensive and challenging, especially for low-resource breeding programs. For carotenoid assessment, rather than the standard HPLC method, these programs mostly rely on proxy approaches for quantitative total carotenoid content (TCC) assessment. To ensure data transferability and consistency, calibration models were developed using TCC iCheck and Chroma Meter proxy methods for the adoption of the alternative near-infrared phenotyping method in cassava. Calibration was developed for dry matter content (DMC) using a simple and inexpensive sampling procedure associated with the proxy TCC protocols. The partial least square (PLS) and random forest (RF) models were compared for the two traits, and the correlation (r) between the actual and predicted values in the training and validation (in bracket) sets of r = 0.85 (0.76) and r = 0.98 (0.82) with PLS and RF, respectively, for iCheck, and r = 0.99 (0.96) and r = 0.99 (0.96) with PLS and RF, respectively, for Chroma Meter, was obtained. The calibration result of r = 0.93 (0.83) and r = 0.99 (0.81) using PLS and RF, respectively, was obtained for DMC. This effort is valuable in carotenoids improvement and supports the ongoing effort in adopting portable spectrometers for rapid and cheap phenotyping in cassava.

Cassava is crucial for food security of millions of people in sub-Saharan Africa. The crop has great potential to contribute to African development and is increasing its income-earning potential for small-scale farmers and related value chains on the continent. Therefore, it is critical to increase cassava production, as well as its quality attributes. Technological innovations offer great potential to drive this envisioned change. This paper highlights genomic tools and resources available in cassava. The paper also provides a glimpse of how these resources have been used to screen and understand the pattern of cassava genetic diversity on the continent. Here, we reviewed the approaches currently used for phenotyping cassava traits, highlighting the methodologies used to link genotypic and phenotypic information, dissect the genetics architecture of key cassava traits, and identify quantitative trait loci/markers significantly associated with those traits. Additionally, we examined how knowledge acquired is utilized to contribute to crop improvement. We explored major approaches applied in the field of molecular breeding for cassava, their promises, and limitations. We also examined the role of national agricultural research systems as key partners for sustainable cassava production.

Significance Statement The high cyanogenic glucoside content in some cassava varieties prevents herbivory but can be toxic for human consumption. The identification of an intracellular transporter gene and its allelic variation allow us to identify cultivars with up to 30% reduced cyanogenic glucoside content in cassava root., Summary Manihot esculenta (cassava) is a root crop originating from South America that is a major staple in the tropics, including in marginal environments. This study focused on South American and African germplasm and investigated the genetic architecture of hydrogen cyanide (HCN), a major component of root quality. HCN, representing total cyanogenic glucosides, is a plant defense component against herbivory but is also toxic for human consumption. We genotyped 3354 landraces and modern breeding lines originating from 26 Brazilian states and 1389 individuals were phenotypically characterized across multi‐year trials for HCN. All plant material was subjected to high‐density genotyping using genotyping by sequencing. We performed genome‐wide association mapping to characterize the genetic architecture and gene mapping of HCN. Field experiments revealed strong broad‐ and narrow‐sense trait heritability (0.82 and 0.41, respectively). Two major loci were identified, encoding for an ATPase and a MATE protein, and contributing up to 7 and 30% of the HCN concentration in roots, respectively. We developed diagnostic markers for breeding applications, validated trait architecture consistency in African germplasm and investigated further evidence for the domestication of sweet and bitter cassava. Fine genomic characterization revealed: (i) the major role played by vacuolar transporters in regulating HCN content; (ii) the co‐domestication of sweet and bitter cassava major alleles are dependent upon geographical zone; and (iii) the major loci allele for high HCN in M. esculenta Crantz seems to originate from its ancestor, M. esculenta subsp. flabellifolia. Taken together, these findings expand our insights into cyanogenic glucosides in cassava roots and its glycosylated derivatives in plants.

Cassava is a root crop originating from South America and a major staple crop in the Tropics, including marginal environments. In this study, we focused on South American and African cassava germplasm and investigated the genetic architecture of Hydrogen Cyanide (HCN), a major component of tuber quality. HCN is a plant defense component against herbivory but also toxic for human consumption. We genotyped 3,354 landraces and modern breeding lines originating from 26 Brazilian states and 1,389 individuals were phenotypically characterized across multi-year trials for HCN. All plant material was subjected to high density genotyping using Genotyping-by-sequencing (GBS). We performed genome wide association mapping (GWAS) to characterize the genetic architecture and gene mapping of HCN. Field experiment revealed strong broad and narrow-sense trait heritability (0.82 and 0.41 respectively). Two major loci were identified, encoding for an ATPase and a MATE protein and contributing up to 7% and 30% of the cyanide concentration in roots, respectively. We developed diagnostic markers for breeding applications, validated trait architecture consistency in African germplasm and investigated further evidence for domestication of sweet and bitter cassava. Fine genomic loci characterization indicate; (i) a major role played by vacuolar transporter in regulating HCN content, (ii) co-domestication of sweet and bitter cassava major alleles to be geographical zone dependant, and (ii) major loci allele for high cyanide cassava in Manihot esculenta Crantz seems to originate from its ancestor, M. esculenta ssp. flabellifolia. Taken together these findings expand insights on cyanide in cassava and its glycosylated derivatives in plants.One-sentence summaryIdentification of an intracellular transporter gene and its allelic variation allow to point out cultivars with up to 30 percent decrease in cassava root cyanide content, toxic for human consumption.

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. Abstract 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.

The prevalence of vitamin A deficiency in sub-Saharan Africa necessitates effective approaches to improve provitamin A content of major staple crops. Cassava holds much promise for food security in sub-Saharan Africa, but a negative correlation between &beta, carotene, a provitamin A carotenoid, and dry matter content has been reported, which poses a challenge to cassava biofortification by conventional breeding. To identify suitable material for genetic transformation in tissue culture with the overall aim to increase &beta, carotene and maintain starch content as well as better understand carotenoid composition, root and leaf tissues from thirteen field-grown cassava landraces were analyzed for agronomic traits, carotenoid, chlorophyll, and starch content. The expression of five genes related to carotenoid biosynthesis were determined in selected landraces. Analysis revealed a weak negative correlation between starch and &beta, carotene content, whereas there was a strong positive correlation between root yield and many carotenoids including &beta, carotene. Carotenoid synthesis genes were expressed in both white and yellow cassava roots, but phytoene synthase 2 (PSY2), lycopene-&epsilon, cyclase (LCY&epsilon, ), and &beta, carotenoid hydroxylase (CHY&beta, ) expression were generally higher in yellow roots. This study identified lines with reasonably high content of starch and &beta, carotene that could be candidates for biofortification by further breeding or plant biotechnological means.

Cassava (Manihot esculenta Crantz) is one of the important staple foods in Sub-Saharan Africa. It produces starchy storage roots that provide food and income for several hundred million people, mainly in tropical agriculture zones. Increasing cassava storage root and starch yield is one of the major breeding targets with respect to securing the future food supply for the growing population of Sub-Saharan Africa. The Cassava Source–Sink (CASS) project aims to increase cassava storage root and starch yield by strategically integrating approaches from different disciplines. We present our perspective and progress on cassava as an applied research organism and provide insight into the CASS strategy, which can serve as a blueprint for the improvement of other root and tuber crops. Extensive profiling of different field-grown cassava genotypes generates information for leaf, phloem, and root metabolic and physiological processes that are relevant for biotechnological improvements. A multi-national pipeline for genetic engineering of cassava plants covers all steps from gene discovery, cloning, transformation, molecular and biochemical characterization, confined field trials, and phenotyping of the seasonal dynamics of shoot traits under field conditions. Together, the CASS project generates comprehensive data to facilitate conventional breeding strategies for high-yielding cassava genotypes. It also builds the foundation for genome-scale metabolic modelling aiming to predict targets and bottlenecks in metabolic pathways. This information is used to engineer cassava genotypes with improved source–sink relations and increased yield potential., The Plant Journal, 103 (5), ISSN:0960-7412, ISSN:1365-313X

We use DNA‐fingerprinting to estimate the poverty reduction effect of adoption of improved cassava varieties in Nigeria. We estimate the counterfactual household income distribution of cassava producers by combining farm‐level treatment effects with a market‐level model. Our results suggest that adoption of improved cassava varieties has led to a 4.6 percentage point reduction in poverty, though this is sensitive to the measurement of adoption status. Therefore, accurate measurement of adoption is crucial for a more credible estimate of the poverty reduction effect of adoption. Our analysis also suggests that farmers who are more likely to be adopters are also likely to face higher structural costs. Addressing structural barriers that make improved technologies less profitable for the poor would therefore be important to increase the poverty reduction effect of improved cassava varieties.

This article examines the impact that misreporting adoption status has on the identification and estimation of causal effects on productivity. In particular, by comparing measurement error-ridden self-reported adoption data with measurement-error-free DNA-fingerprinted adoption data, we investigate the extent to which such errors bias the causal effects of adoption on productivity. Taking DNA-fingerprinted adoption data as a benchmark, we find 25% “false negatives” and 10% “false positives” in farmers’ responses. Our results show that misreporting of adoption status is not exogenous to household characteristics, and produces a bias of about 22 percentage points in the productivity impact of adoption. Ignoring inherent behavioral adjustments of farmers based on perceived adoption status has a bias of 13 percentage points. The results of this article underscore the crucial role that correct measurement of adoption plays in designing policy interventions that address constraints to technology adoption in agriculture.

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.

Cassava (Manihot esculenta Crantz) is an important food security crop or resource for poor rural communities particularly in Africa. The crop’s ability to produce high yields even under poor conditions and storability of its roots underground for longer periods or until needed makes it a model ‘food security crop’. In Benin Republic, cassava has been recognized as one of the major crop contributing towards dynamic value chains generating incomes for small-holder farmers. The crop is grown all over the country, however, the increased production are mainly recorded from far south and central parts of the country. Genetic improvement of cassava in Benin Republic is limited because of poor knowledge of genetic diversity present within the country. The main objective of this study was to assess the genetic diversity and relationships among elite cassava varieties collected from different regions of Benin using fluorescently labelled simple sequence repeat (SSR) markers and to compare the results with farmer’s knowledge and morphological traits. A total of 96 cultivars collected from major cassava growing areas such as Southern and Central Benin were classified into 24 different groups using farmers’ knowledge, while classification based on 18 morphological traits resulted in five groups. In total, sixteen SSR markers were tested for molecular analysis of the ninety-six cassava varieties. Among the sixteen, twelve SSR markers gave good banding pattern and were used to genotype the varieties. An average of 3.58 and 0.47 for number of alleles and polymorphism information content respectively was observed. The observed heterozygosity (Ho) ranged from 0.23 to 1.0 with an average of 0.66 indicating moderate level of diversity among the cultivars. Based on the proportion of shared alleles and hierarchical clustering, the 96 elite cassava varieties were classified as 74 unique varieties. Principal component analysis and analysis of molecular variance revealed no significant variation between the regions thus, explaining regular exchange of planting materials among cassava farmers across various regions. The moderate level of genetic diversity in famer’s field, revealed in the present study, is a good indication of the need for broadening the genetic base of cassava in Benin Republic and establishing a formal breeding program in the country.

Summary Striga hermonthica is a parasitic weed that poses a serious threat to the production of economically important cereals in sub-Saharan Africa. The existence of genetic diversity within and between S. hermonthica populations presents a challenge to the successful development and deployment of effective control technologies against this parasitic weed. Understanding the extent of diversity between S. hermonthica populations will facilitate the design and deployment of effective control technologies against the parasite. In the present study, S. hermonthica plants collected from different locations and host crops in Kenya and Nigeria were genotyped using single nucleotide polymorphisms. Statistically significant genetic differentiation (FST = 0.15, P = 0.001) was uncovered between populations collected from the two countries. Also, the populations collected in Nigeria formed three distinct subgroups. Unique loci undergoing selection were observed between the Kenyan and Nigerian populations and among the three subgroups found in Nigeria. Striga hermonthica populations parasitising rice in Kenya appeared to be genetically distinct from those parasitising maize and sorghum. The presence of distinct populations in East and West Africa and in different regions in Nigeria highlights the importance of developing and testing Striga control technologies in multiple locations, including locations representing the geographic regions in Nigeria where genetically distinct subpopulations of the parasite were found. Efforts should also be made to develop relevant control technologies for areas infested with ‘rice-specific’ Striga spp. populations in Kenya.

Cassava (Manihot esculenta Crantz) is an important staple food crop in Africa and South America; however, ubiquitous deleterious mutations may severely decrease its fitness. To evaluate these deleterious mutations, we constructed a cassava haplotype map through deep sequencing 241 diverse accessions and identified >28 million segregating variants. We found that (i) although domestication has modified starch and ketone metabolism pathways to allow for human consumption, the concomitant bottleneck and clonal propagation have resulted in a large proportion of fixed deleterious amino acid changes, increased the number of deleterious alleles by 26%, and shifted the mutational burden toward common variants; (ii) deleterious mutations have been ineffectively purged, owing to limited recombination in the cassava genome; (iii) recent breeding efforts have maintained yield by masking the most damaging recessive mutations in the heterozygous state but have been unable to purge the mutation burden; such purging should be a key target in future cassava breeding.

Cassava is widely cultivated due to its high drought tolerance and high carbohydrate-containing storage roots. The lack of uniformity and irregular shape of storage roots within and between genotypes poses significant constraints on harvesting and post-harvest processing. Routine assessment of storage root size and shape in breeding plots relies on visual scores.Here, we phenotyped the Genetic gain and offspring (C1) populations from the International Institute of Tropical Agriculture (IITA) breeding program for root shape and size-related traits using image analysis of storage root photographs taken in the field.In our study, using univariate genome-wide association analysis, we detected for most shape and size related traits, significant QTL regions located on chromosomes 1 and 12. The QTL region on chromosome 12 has been previously associated, using IITA breeding populations, to cassava mosaic disease (CMD) resistance.Because the uniformity in size and shape of cassava roots is an important breeding goal, we calculated the standard deviation of individual root measurements per clone. The use of standard deviation measurements allowed the identification of new significant QTL for Perimeter, Feret and Aspect Ratio on chromosomes 6, 9 and 16. Using genomic prediction cross validation, the accuracies of root size and shape-related traits were lower than those previously reported for dry matter content (DM) and cassava mosaic virus resistance (CMD). Predictive accuracies of the mean values of root size and shape image-extracted traits were mostly higher than yield trait prediction accuracies in the C1 population. This study aimed to evaluate the feasibility of the image phenotyping protocol and to assess the use of genome-wide analyses for size and shape image-extracted traits. The methodology described here and the results obtained in this study are promising and open up the opportunity to apply high-throughput methods in cassava.

Cassava mosaic disease (CMD) is a major viral disease adversely affecting cassava production in Africa and Asia. Genomic regions conferring resistance to the disease have been mapped in African cassava germplasm through biparental quantitative trait loci (QTL) mapping and genome-wide association studies. To facilitate the utilization of these markers in breeding pipelines to support selections, proof-of-concept technical and biological validation research was carried out using independent pre-breeding and breeding populations. Kompetitive Allele-Specific Polymerase Chain Reaction (KASP) assays were designed from three single nucleotide polymorphism (SNP) markers linked to a major resistance locus on chromosome 12 (S12_7926132, S12_7926163) and a minor locus on chromosome 14 (S14_4626854). The designed assays were robust and easy to score with &gt, 99% genotype call rate. The overall predictive accuracy (proportion of true positives and true negatives) of the markers (S12_7926132 and S14_4626854) was 0.80 and 0.78 in the pre-breeding and breeding population, respectively. On average, genotypes that carried at least one copy of the resistant allele at the major CMD2 locus had a significantly higher yield advantage. Nevertheless, variation was observed in prediction accuracies for the major locus (S12_7926132) among sub-families from the two populations, suggesting the need for context-specific utilization, for example, by screening for co-segregation of favorable SNP alleles with resistance in the parents being used for crosses. Availability of these validated SNP markers on the uniplex KASP genotyping platform represents an important step in translational genetics toward marker-assisted selection to accelerate introgression of favorable resistant alleles in breeding populations.

Cassava (Manihot esculenta Crantz) is a clonally propagated staple food crop in the tropics. Genomic selection (GS) has been implemented at three breeding institutions in Africa to reduce cycle times. Initial studies provided promising estimates of predictive abilities. Here, we expand on previous analyses by assessing the accuracy of seven prediction models for seven traits in three prediction scenarios: cross-validation within populations, cross-population prediction and cross-generation prediction. We also evaluated the impact of increasing the training population (TP) size by phenotyping progenies selected either at random or with a genetic algorithm. Cross-validation results were mostly consistent across programs, with nonadditive models predicting of 10% better on average. Cross-population accuracy was generally low (mean = 0.18) but prediction of cassava mosaic disease increased up to 57% in one Nigerian population when data from another related population were combined. Accuracy across generations was poorer than within-generation accuracy, as expected, but accuracy for dry matter content and mosaic disease severity should be sufficient for rapid-cycling GS. Selection of a prediction model made some difference across generations, but increasing TP size was more important. With a genetic algorithm, selection of one-third of progeny could achieve an accuracy equivalent to phenotyping all progeny. We are in the early stages of GS for this crop but the results are promising for some traits. General guidelines that are emerging are that TPs need to continue to grow but phenotyping can be done on a cleverly selected subset of individuals, reducing the overall phenotyping burden.

Background Root and tuber crops are a major food source in tropical Africa. Among these crops are several species in the monocotyledonous genus Dioscorea collectively known as yam, a staple tuber crop that contributes enormously to the subsistence and socio-cultural lives of millions of people, principally in West and Central Africa. Yam cultivation is constrained by several factors, and yam can be considered a neglected “orphan” crop that would benefit from crop improvement efforts. However, the lack of genetic and genomic tools has impeded the improvement of this staple crop. Results To accelerate marker-assisted breeding of yam, we performed genome analysis of white Guinea yam (Dioscorea rotundata) and assembled a 594-Mb genome, 76.4% of which was distributed among 21 linkage groups. In total, we predicted 26,198 genes. Phylogenetic analyses with 2381 conserved genes revealed that Dioscorea is a unique lineage of monocotyledons distinct from the Poales (rice), Arecales (palm), and Zingiberales (banana). The entire Dioscorea genus is characterized by the occurrence of separate male and female plants (dioecy), a feature that has limited efficient yam breeding. To infer the genetics of sex determination, we performed whole-genome resequencing of bulked segregants (quantitative trait locus sequencing [QTL-seq]) in F1 progeny segregating for male and female plants and identified a genomic region associated with female heterogametic (male = ZZ, female = ZW) sex determination. We further delineated the W locus and used it to develop a molecular marker for sex identification of Guinea yam plants at the seedling stage. Conclusions Guinea yam belongs to a unique and highly differentiated clade of monocotyledons. The genome analyses and sex-linked marker development performed in this study should greatly accelerate marker-assisted breeding of Guinea yam. In addition, our QTL-seq approach can be utilized in genetic studies of other outcrossing crops and organisms with highly heterozygous genomes. Genomic analysis of orphan crops such as yam promotes efforts to improve food security and the sustainability of tropical agriculture. Electronic supplementary material The online version of this article (doi:10.1186/s12915-017-0419-x) contains supplementary material, which is available to authorized users.

Cassava is a widely grown staple in Sub-Saharan Africa and consumed as a cheap source of calories, but the crop is deficient in micronutrients including pro-vitamin A carotenoids. This challenge is currently being addressed through biofortification breeding that relies on phenotypic selection. Gene-based markers linked to pro-vitamin A content variation are expected to increase the rate of genetic gain for this critical trait. We sequenced four candidate carotenoid genes from 167 cassava accessions representing the diversity of elite breeder lines from IITA. Total carotenoid content was determined using spectrophotometer and total β-carotene was quantified by high-performance liquid chromatography. Storage root yellowness due to carotenoid pigmentation was assessed. We carried out candidate gene association analysis that accounts for population structure and kinship using genome-wide single nucleotide polymorphisms (SNPs) generated through genotyping-by-sequencing. Significant SNPs were used to design competitive allele-specific PCR assays and validated on the larger population for potential use in marker-assisted selection breeding. Candidate gene sequencing of the genes β-carotene hydroxylase (crtRB), phytoene synthase (PSY2), lycopene epsilon cyclase (lcyE), and lycopene beta cyclase (lcyB) yielded a total of 37 SNPs. Total carotenoid content, total β-carotene, and color parameters were significantly associated with markers in the PSY2 gene. The SNPs from lcyE were significantly associated with color while those of lcyB and crtRB were not significantly associated with carotenoids or color parameters. These validated and breeder-friendly markers have potential to enhance the efficiency of selection for high β-carotene cassava, thus accelerating genetic gain.

Cassava (Manihot esculenta Crantz) is a clonally propagated staple food crop in the tropics. Genomic selection (GS) reduces selection cycle times by the prediction of breeding value for selection of unevaluated lines based on genome-wide marker data. GS has been implemented at three breeding programs in sub-Saharan Africa. Initial studies provided promising estimates of predictive abilities in single populations using standard prediction models and scenarios. In the present study we expand on previous analyses by assessing the accuracy of seven prediction models for seven traits in three prediction scenarios: (1) cross-validation within each population, (2) cross-population prediction and (3) cross-generation prediction. We also evaluated the impact of increasing training population size by phenotyping progenies selected either at random or using a genetic algorithm. Cross-validation results were mostly consistent across breeding programs, with non-additive models like RKHS predicting an average of 10% more accurately. Accuracy was generally associated with heritability. Cross-population prediction accuracy was generally low (mean 0.18 across traits and models) but prediction of cassava mosaic disease severity increased up to 57% in one Nigerian population, when combining data from another related population. Accuracy across-generation was poorer than within (cross-validation) as expected, but indicated that accuracy should be sufficient for rapid-cycling GS on several traits. Selection of prediction model made some difference across generations, but increasing training population (TP) size was more important. In some cases, using a genetic algorithm, selecting one third of progeny could achieve accuracy equivalent to phenotyping all progeny. Based on the datasets analyzed in this study, it was apparent that the size of a training population (TP) has a significant impact on prediction accuracy for most traits. We are still in the early stages of GS in this crop, but results are promising, at least for some traits. The TPs need to continue to grow and quality phenotyping is more critical than ever. General guidelines for successful GS are emerging. Phenotyping can be done on fewer individuals, cleverly selected, making for trials that are more focused on the quality of the data collected.Abbreviations(GS)Genomic selection(GBS)genotype-by-sequencing(IITA)International Institute of Tropical Agriculture(NRCRI)National Root Crops Research Institute(NaCRRI)National Crops Resources Research Institute(GEBVs)genomic estimated breeding values(TP)training population(RTWT)fresh root weight(RTNO)root number(SHTWT)fresh shoot weight(HI)harvest index(DM)dry matter(CMD)content cassava mosaic disease(MCMDS)mean CMD severity(VIGOR)early vigor

Cassava (Manihot esculenta (L.) Crantz) is a starchy root crop cultivated in the tropics for fresh consumption and commercial processing. Dry matter content and micronutrient density, particularly of provitamin A – traits that are negatively correlated – are among the primary selection objectives in cassava breeding. This study aimed at identifying genetic markers associated with these traits and uncovering the potential underlying cause of their negative correlation – whether linkage and/or pleiotropy. A genome-wide association mapping using 672 clones genotyped at 72,279 SNP loci was carried out. Root yellowness was used indirectly to assess variation in carotenoid content. Two major loci for root yellowness was identified on chromosome 1 at positions 24.1 and 30.5 Mbp. A single locus for dry matter content that co-located with the 24.1 Mbp peak for carotenoid content was identified. Haplotypes at these loci explained a large proportion of the phenotypic variability. Evidence of mega-base-scale linkage disequilibrium 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 (phytoene synthase) and starch biosynthesis (UDP-glucose pyrophosphorylase and sucrose synthase) occurred in the vicinity of the identified locus at 24.1 Mbp. These findings elucidate on the genetic architecture of carotenoids and dry matter in cassava and provides an opportunity to accelerate genetic improvement of these traits.CORE IDEASCassava, a starchy root crop, is a major source of dietary calories in the tropics.Most varieties consumed are poor in micronutrients, including pro-vitamin A.These two traits are governed by few major loci on chromosome one.Genetic linkage, rather than pleiotropy, is the most likely cause of their negative correlation.

Compared with other reduced-representation sequencing methods, library construction for genotyping-by-sequencing (GBS) is simpler and less expensive. However, elimination of sizeselection steps results in libraries of more variable fragment size than with other reduced-representation methods, affecting several aspects of the data. To test the effect of restriction enzyme choice on library quality, we made GBS libraries with PstI (6-cutter), PstI/TaqI (4-cutter), or ApeKI (4.5-cutter) from the same set of DNAs from a cassava (Manihot esculenta Crantz) biparental population. Tag and single nucleotide polymorphism (SNp) counts were limited by the number of cut sites rather than by read number. Depth per locus was very skewed for the PstI library, such that most SNps had low read depth but a subset had very high read depth. In contrast, the ApeKI and PstI/TaqI libraries had less variable distributions of read depth and yielded far more scorable SNps. our results suggest that 6-cutter enzymes may be most appropriate for genotyping a modest number of markers at a high multiplexing level, or for very large genomes, and perform better when used in a double digest with a 4-cutter enzyme. M.T. Hamblin, Dep. of Plant Breeding and Genetics, Cornell Univ., Ithaca, NY; and I.Y. Rabbi, International Institute for Tropical Agriculture (IITA), Ibadan, Nigeria. This work was supported by the projects “Genomic Selection, the Next Frontier for Rapid Gains in Maize and Wheat Improvement” through funds from The Bill and Melinda Gates Foundation, and “Next Generation Cassava Breeding” through funds from The Bill and Melinda Gates Foundation and the Department for International Development of the United Kingdom. Received 27 Feb. 2014. *Corresponding author (mth3@cornell.edu). Abbreviations: GBS, genotyping-by-sequencing; PCR, polymerase chain reaction; RRL, reduced representation library, SNP, single nucleotide polymorphism. Published in Crop Sci. 54:2603–2608 (2014). doi: 10.2135/cropsci2014.02.0160 Freely available online through the author-supported open-access option. © Crop Science Society of America | 5585 Guilford Rd., Madison, WI 53711 USA All rights reserved. No part of this periodical may be reproduced or transmitted in any form or by any means, electronic or mechanical, including photocopying, recording, or any information storage and retrieval system, without permission in writing from the publisher. Permission for printing and for reprinting the material contained herein has been obtained by the publisher. Published May 15, 2015

Cassava (Manihot esculenta L.) is one of the most important food crops in the tropics, but yields are far below their potential. The gene pool of cas- sava contains natural genetic diversity relevant to many important breeding goals, but breeding progress has been slow, partly because of insuf- ficient genomic resources. As a first step toward implementing genomewide genetic studies that will facilitate rapid genetic gain through breed- ing, we genotyped-by-sequencing a set of 182 full-sibs population of cassava that segregated in several traits: resistance to the cassava mosaic disease (CMD) and yield under CMD pressure; increased carotenoid content in storage roots; color of stem exterior and anthocyanin pigmen- tation in the petioles, inner root skin, and api- cal leaves. Employing a rare-cutting restriction enzyme, PstI, in a genotyping-by-sequencing (GBS) library preparation, we obtained 2478 segregating single nucleotide polymorphisms (SNPs), of which 1257 passed standard filter - ing for missing genotypes and deviation from expected genotypic frequencies. We mapped 772 SNPs across 19 linkage groups and anchored 313 unique scaffolds from the version 4.1 of the cassava genome assembly. Most of the stud- ied morphological traits as well as resistance to CMD and root carotenoid content showed quali- tative inheritance. As expected, quantitative trait loci analysis for these traits revealed single loci surrounded by small confidence intervals. Yield under CMD was associated with the CMD resis- tance locus. We show that GBS is a powerful genotyping tool that provides a sufficient number of markers for unraveling the genetic architecture of Mendelian traits in cassava in addition to the development of a robust genetic map that can help anchor unassembled genomic scaffolds.

Cassava mosaic disease (CMD), caused by different species of cassava mosaic geminiviruses (CMGs), is the most important disease of cassava in Africa and the Indian sub-continent. The cultivated cassava species is protected from CMD by polygenic resistance introgressed from the wild species Manihot glaziovii and a dominant monogenic type of resistance, named CMD2, discovered in African landraces. The ability of the monogenic resistance to confer high levels of resistance in different genetic backgrounds has led recently to its extensive usage in breeding across Africa as well as pre-emptive breeding in Latin America. However, most of the landraces carrying the monogenic resistance are morphologically very similar and come from a geographically restricted area of West Africa, raising the possibility that the diversity of the single-gene resistance could be very limited, or even located at a single locus. Several mapping studies, employing bulk segregant analysis, in different genetic backgrounds have reported additional molecular markers linked to supposedly new resistance genes. However, it is not possible to tell if these are indeed new genes in the absence adequate genetic map framework or allelism tests. To address this important question, a high-density single nucleotide polymorphism (SNP) map of cassava was developed through genotyping-by-sequencing a bi-parental mapping population (N=180) that segregates for the dominant monogenic resistance to CMD. Virus screening using PCR showed that CMD symptoms and presence of virus were strongly correlated (r=0.98). Genome-wide scan and high-resolution composite interval mapping using 6756 SNPs uncovered a single locus with large effect (R2=0.74). Projection of the previously published resistance-linked microsatellite markers showed that they co-occurred in the same chromosomal location surrounding the presently mapped resistance locus. Moreover, their relative distance to the mapped resistance locus correlated with the reported degree of linkage with the resistance phenotype. Cluster analysis of the landraces first shown to have this type of resistance revealed that they are very closely related, if not identical. These findings suggest that there is a single source of monogenic resistance in the crop's genepool tracing back to a common ancestral clone. In the absence of further resistance diversification, the long-term effectiveness of the single gene resistance is known to be precarious, given the potential to be overcome by CMGs due to their fast-paced evolutionary rate. However, combining the quantitative with the qualitative type of resistance may ensure that this resistance gene continues to offer protection to cassava, a crop that is depended upon by millions of people in Africa against the devastating onslaught of CMGs.

This study was conducted to: (1) determine the amount and structure of the genetic diversity of cassava in southern, eastern and central (SEC) Africa using simple sequence repeat (SSR) markers, (2) determine the frequency and distribution of alleles putatively associated with resistance to cassava brown streak disease (CBSD) derived from the variety ‘Namikonga’, and (3) examine the genetic relationships among some CBSD resistant genotypes. The major findings from this study were: (1) little genetic differentiation was confirmed among countries (7%) with the majority of variation distributed among individuals (93%), (2) the frequency of alleles putatively associated with resistance to CBSD was found to be generally low (0.2 to 0.5) but widely dispersed in the cassava germplasm of the SEC Africa region implying that if validated the markers will be useful for marker-assisted breeding on a broad scale, (3) several distinct putative sources of resistance to CBSD seem to be present in the cassava germplasm of SEC Africa offering the potential to pyramid genes for more effective and durable resistance and (4) it may be more informative to assess cassava diversity in the SEC Africa region based on pedigree (if known) or genetic relatedness, rather than geographical origin. Key words: Cassava brown streak disease (CBSD), simple sequence repeat (SSR), genetic diversity, pedigree information.

Before implementation of genomic selection, evaluation of the potential accuracy of prediction can be obtained by cross-validation. In this procedure, a population with both phenotypes and genotypes is split into training and validation sets. The prediction model is fi tted using the training set, and its accuracy is calculated on the validation set. The degree of genetic relatedness between the training and validation sets may infl uence the expected accuracy as may the genotype × environment (G×E) interaction in those sets. We developed a method to assess these effects and tested it in cassava (Manihot esculenta Crantz). We used historical phenotypic data available from the International Institute of Tropical Agriculture Genetic Gain trial and performed genotyping by sequencing for these clones. We tested cross-validation sampling schemes preventing the training and validation sets from sharing (i) genetically close clones or (ii) similar evaluation locations. For 19 traits, plot-basis heritabilities ranged from 0.04 to 0.66. The correlation between predicted and observed phenotypes ranged from 0.15 to 0.47. Across traits, predicting for less related clones decreased accuracy from 0 to 0.07, a small but consistent effect. For 17 traits, predicting for different locations decreased accuracy between 0.01 and 0.18. Genomic selection has potential to accelerate gains in cassava and the existing training population should give a reasonable estimate of future prediction accuracies.

Cassava (Manihot esculenta Crantz) is a crucial, under-researched crop feeding millions worldwide, especially in Africa. Cassava mosaic disease (CMD) has plagued production in Africa for over a century. Biparental mapping studies suggest primarily a single major gene mediates resistance. To investigate this genetic architecture, we conducted the first genome-wide association mapping study in cassava with up to 6128 genotyping-by-sequenced African breeding lines and 42,113 reference genome-mapped single-nucleotide polymorphism (SNP) markers. We found a single region on chromosome 8 that accounts for 30 to 66% of genetic resistance in the African cassava germplasm. Thirteen additional regions with small effects were also identified. Further dissection of the major quantitative trait locus (QTL) on chromosome 8 revealed the presence of two possibly epistatic loci and/or multiple resistance alleles, which may account for the difference between moderate and strong disease resistances in the germplasm. Search of potential candidate genes in the major QTL region identified two peroxidases and one thioredoxin. Finally, we found genomic prediction accuracy of 0.53 to 0.58 suggesting that genomic selection (GS) will be effective both for improving resistance in breeding populations and identifying highly resistant clones as varieties.