Genomic prediction and quantitative trait locus discovery in a cassava training population constructed from multiple breeding stages

Open Access Article; Published online: 11 Dec 2019Assembly of a training population (TP) is an important component of effective genomic selection‐based breeding programs. In this study, we examined the power of diverse germplasm assembled from two cassava (Manihot esculenta Crantz) breeding programs in Tanzania at different breeding stages to predict traits and discover quantitative trait loci (QTL). This is the first genomic selection and genome‐wide association study (GWAS) on Tanzanian cassava data. We detected QTL associated with cassava mosaic disease (CMD) resistance on chromosomes 12 and 16; QTL conferring resistance to cassava brown streak disease (CBSD) on chromosomes 9 and 11; and QTL on chromosomes 2, 3, 8, and 10 associated with resistance to CBSD for root necrosis. We detected a QTL on chromosome 4 and two QTL on chromosome 12 conferring dual resistance to CMD and CBSD. The use of clones in the same stage to construct TPs provided higher trait prediction accuracy than TPs with a mixture of clones from multiple breeding stages. Moreover, clones in the early breeding stage provided more reliable trait prediction accuracy and are better candidates for constructing a TP. Although larger TP sizes have been associated with improved accuracy, in this study, adding clones from Kibaha to those from Ukiriguru and vice versa did not improve the prediction accuracy of either population. Including the Ugandan TP in either population did not improve trait prediction accuracy. This study applied genomic prediction to understand the implications of constructing TP from clones at different breeding stages pooled from different locations on trait accuracy

GENETICS OF RESISTANCE TO GROUNDNUT ROSETTE VIRUS DISEASE

Groundnut Rosette Virus disease (GRD) has long been regarded a major limiting biotic constraint to groundnut production in Sub-Saharan Africa (SSA). The disease is caused by a complex of three viral components that interact in a synergistic fashion resulting into severe crop losses. A study was conducted to better understand the genetics of inheritance of GRD resistance. Nineteen groundnut genotypes among which twelve F2 families populations arising from a 3x4 North Carolina II mating design, were evaluated for their percentage disease severity (PDS) and incidence (PDI). There was significant genetic variability for resistance to GRD among the materials studied with more significant additive gene action as compared to non additive. However, since specific combining ability effects were not so consistent among the F2 family populations, evaluation and testing of progenies alongside with their parents would be more meaningful and selection in the early generations would be the most effective strategy. Further, narrow sense heritability of 53% suggests that prerformance of groundnut progenies could be partly predicted by both parental and individual cross means.La rosette, une maladie virale de l\u2019arachide (GRD) a pendant longtemps \ue9t\ue9 consid\ue9r\ue9e comme une contrainte biotique majeur \ue0 la production de l\u2019arachide en Afrique Sub Saharienne (SSA). La maladie est caus\ue9e par un complexe de trois composants viraux qui interagissent de fa\ue7on synerg\ue9tique causant ainsi de pertes lourdes de la culture. Une \ue9tude \ue9tait men\ue9e afin de mieux comprendre l\u2019acquisition g\ue9n\ue9tique de la r\ue9sistance de GRD. Dix neuf g\ue9notypes d\u2019arachides parmi douze populations de famille F2 provenant de la disposition du mating 3x4 de Nord Caroline II \ue9taient \ue9valu\ue9s sur base de leur pourcentage de s\ue9verit\ue9 (PDS) et incidence maladie (PDI). Une variabilit\ue9 significative de la r\ue9sistance au GRD parmi le mat\ue9riel \ue9tudi\ue9 avec plus d\u2019 action additive significative du g\ue8ne en comparaison \ue0 la non additive. Par ailleurs, du fait que les effets de combinaison des aptitudes n\u2019\ue9taient pas consistants parmi les populations de familles F2, l\u2019\ue9valuation et le test des prog\ue9nies avec leurs parents pourraient \ueatre plus significatif et la s\ue9lection parmi les g\ue9n\ue9rations pr\ue9coces pourrait \ueatre une strat\ue9gie la plus efficace. Aussi, l\u2019heritabilit\ue9 de 53% sugg\ue8re que la performance des prog\ue9nies d\u2019arachide pourrait partiellement \ueatre pr\ue9dit par le moyen de croisements parentaux et individuals

Cassava Brown Streak Disease response and association with agronomic traits in elite Nigerian cassava cultivars

Open Access Journal; Published online: 22 Nov 2021Cassava mosaic geminiviruses (CMGs) and cassava brown streak viruses (CBSVs) cause the highest yield losses in cassava production in Africa. In particular, cassava brown streak disease (CBSD) is and continues to be a significant constraint to optimal cassava production in Eastern and Southern Africa. While CBSD has not been reported in West Africa, its recent rapid spread and damage to cassava productivity in Eastern, and Southern Africa is alarming. The aim of this study was to evaluate Nigerian cassava genotypes in order to determine their responses to CBSD, in the event that it invades Nigeria, the world’s largest cassava producer. The study gathered information on whether useful CBSD resistance alleles are present in the elite Nigerian cassava accessions. A total of 1,980 full-sib cassava seedlings from 106 families were assessed in the field at the seedling stage for a year. A subset of 569 clones were selected and assessed for another year at the clonal stage in Namulonge, central Uganda, a known hotspot for CBSD screening. Results indicated that foliar and root incidences and severities varied significantly (p ≤ 0.01, p ≤ 0.001) except for CBSD foliar incidence at 6 months (CBSD6i). Highest and lowest plot-based heritability estimates for CBSD were registered for CBSD root severity (CBSDrs) (0.71) and CBSD6i (0.5). Positive and highly significant correlations were noted between CBSD root incidence (CBSDri) and CBSDrs (r = 0.90∗∗∗). Significant positive correlations were also noted between CBSD foliar severity at 3 months (CBSD3s) and CBSD foliar incidence at 6 months (CBSD6i ) (r = 0.77∗∗∗), CBSD3s and CBSDrs (r = 0.35∗∗∗). Fresh root weight (FreshRW) negatively correlated with CBSDri and CBSDrs, respectively (r = −0.21∗∗∗ and r = −0.22∗∗∗). Similarly, CBSD3s correlated negatively with cassava mosaic disease severity at 3 (CMD3s) and 6 months (CMD6s), respectively (r = −0.25∗∗∗ and r = −0.21∗∗∗). Fifteen clones were selected using a non-weighted summation selection index for further screening. In conclusion, results revealed that the elite Nigerian accessions exhibited significant susceptibility to CBSD within 2 years of evaluation period. It is expected that this information will aid future breeding decisions for the improvement of CBSD resistance among the Nigerian cassava varieties

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

Open Access Journal; Published online: 23 Nov 2022Introduction The intrinsic high heterozygosity of cassava makes conventional breeding ineffective for rapid genetic improvement. However, recent advances in next-generation sequencing technologies have enabled the use of high-density markers for genome-wide association studies, aimed at identifying single nucleotide polymorphisms (SNPs) linked to major traits such as cassava mosaic disease (CMD) resistance, dry matter content (DMC) and total carotenoids content (TCC). A number of these trait-linked SNPs have been converted to Kompetitive allele-specific polymerase chain reaction (KASP) markers for downstream application of marker assisted selection. Methods We assayed 13 KASP markers to evaluate their effectiveness in selecting for CMD, DMC and TCC in 1,677 diverse cassava genotypes representing two independent breeding populations in Uganda. Results Five KASP markers had significant co-segregation with phenotypes; CMD resistance (2), DMC (1) and TCC (2), with each marker accounting for at least 30% of the phenotypic variation. Markers located within the chromosomal regions for which strong marker-trait association loci have been characterised (chromosome 12 markers for CMD, chromosome 1 markers for DMC and TCC) had consistently superior ability to discriminate the respective phenotypes. Discussion The results indicate varying discriminatory abilities of the KASP markers assayed and the need for their context-based use for MAS, with PSY2_572 particularly effective in selecting for high TCC. Availing the effective KASP markers on cost-effective genotyping platforms could facilitate practical implementation of marker-assisted cassava breeding for accelerated genetic gains for CMD, DMC and provitamin A carotenoids

Training population optimization for prediction of cassava brown streak disease resistance in west African clones

Published online: 29 Oct 2018; Open Access JournalCassava production in the central, southern and eastern parts of Africa is under threat by cassava brown streak virus (CBSV). Yield losses of up to 100% occur in cases of severe infections of edible roots. Easy illegal movement of planting materials across African countries, and long-range movement of the virus vector (Bemisia tabaci) may facilitate spread of CBSV to West Africa. Thus, effort to pre-emptively breed for CBSD resistance in W. Africa is critical. Genomic selection (GS) has become the main approach for cassava breeding, as costs of genotyping per sample have declined. Using phenotypic and genotypic data (genotyping-by-sequencing), followed by imputation to whole genome sequence (WGS) for 922 clones from National Crops Resources Research Institute, Namulonge, Uganda as a training population (TP), we predicted CBSD symptoms for 35 genotyped W. African clones, evaluated in Uganda. The highest prediction accuracy (r = 0.44) was observed for cassava brown streak disease severity scored at three months (CBSD3s) in the W. African clones using WGS-imputed markers. Optimized TPs gave higher prediction accuracies for CBSD3s and CBSD6s than random TPs of the same size. Inclusion of CBSD QTL chromosome markers as kernels, increased prediction accuracies for CBSD3s and CBSD6s. Similarly, WGS imputation of markers increased prediction accuracies for CBSD3s and for cassava brown streak disease root severity (CBSDRs), but not for CBSD6s. Based on these results we recommend TP optimization, inclusion of CBSD QTL markers in genomic prediction models, and the use of high-density (WGS-imputed) markers for CBSD predictions across population

New sources and stability of resistance to aphids in cowpea germplasm across locations in Uganda

Open Access ArticleThe cowpea aphid (Aphis craccivora Koch) is an economically important pest, whose feeding effects cause stunting, delayed flower initiation and yield reduction in cowpea (Vigna unguiculata L. Walp). Host plant resistance offers an alternative for controlling aphids; while simultaneously reducing reliance on chemical pesticides. The objective of this study was to evaluate a multi-parent advanced generation inter-cross (MAGIC) population of cowpea against aphids, across cowpea growing regions in Uganda. The study was arranged in alpha lattice design, with two replicates in three locations over two seasons (2018B and 2019A). Results revealed significant effects (P<0.001) for the main treatment effects, genotype x location and location x season interaction for both infestation and damage. The genotype x season interaction was significant (P<0.01) for both aphid infestation and damage; while the three-way interaction was only significant (P<0.001) for aphid infestation, but not for damage. The study identified five new resistant and stable genotypes from the MAGIC panel, including MAGIC131, MAGIC-132, MAGIC149, MAGIC170 and MAGIC280; and one resistant parent, SUVITA-2. The study further revealed MAGIC-125, MAGIC-171, MAGIC153, MAGIC-333, MAGIC177, MAGIC-292, MAGIC282, MAGIC249, MAGIC162, SEC 4W * SEC 5T, NAROCOWPEA 4, MAGIC-204, MAGIC-039, MAGIC060, MAGIC-097, NAROCOWPEA 3, MAGIC-233, MAGIC090 and MU 9 to be moderately resistant and high yielding genotypes. The above genotypes are recommended for use in the cowpea breeding programme, to develop improved resistant lines against aphids in Uganda

Prospects for Genomic Selection in Cassava Breeding

Article purchased; Published online: 28 Sept 2017Cassava (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

International agricultural research to reduce food risks: case studies on aflatoxins

Despite massive expansion of human and livestock populations, fuelled by agricultural innovations, nearly one billion people are hungry and 2 billion are sickened each year from the food they eat. Agricultural and food systems are intimately connected to health outcomes, but health policy and programs often stop at the clinic door. A consensus is growing that the disconnection between agriculture, health and nutrition is at least partly responsible for the disease burden associated with food and farming. Mycotoxins produced by fungi are one of the most serious food safety problems affecting staple crops (especially maize and groundnuts). Aflatoxins, the best studied of these mycotoxins, cause around 90,000 cases of liver cancer each year and are strongly associated with stunting and immune suppression in children. Mycotoxins also cause major economic disruptions through their impacts on trade and livestock production. In this paper we use the case of fungal toxins to explore how agricultural research can produce innovations, understand incentives and enable institutions to improve, simultaneously, food safety, food accessibility for poor consumers and access to markets for smallholder farmers, thus making the case for research investors to support research into agricultural approaches for enhancing food safety in value chains. We first discuss the evolution of food safety research within the CGIAR. Then we show how taking an epidemiological and economic perspective on aflatoxin research connects health and nutrition outcomes. Finally, we present three case studies illustrating the traditional strengths of CGIAR research: breeding better varieties and developing new technologies