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 diversity and inter-trait relationship of tropical extra-early maturing quality protein maize inbred lines under low soil nitrogen stress

Information on the genetic diversity, population structure, and trait associations of germplasm resources is crucial for predicting hybrid performance. The objective of this study was to dissect the genetic diversity and population structure of extra-early yellow and orange quality protein maize (QPM) inbred lines and identify secondary traits for indirect selection for enhanced grain yield under low-soil nitrogen (LN). One hundred and ten inbred lines were assessed under LN (30 kg ha ^-1) and assayed for tryptophan content. The lines were genotyped using 2500 single nucleotide polymorphism (SNP) markers. Majority (85.4%) of the inbred lines exhibited wide pairwise genetic distances between 0.4801 and 0.600. Genetic distances were wider between yellow and orange endosperm lines and predicted high heterosis in crosses between parents of different endosperm colors. The unweighted pair group method with arithmetic mean (UPGMA) and the admixture model-based population structure method both grouped the lines into five clusters. The clustering was based on endosperm color, pedigree, and selection history but not on LN tolerance or tryptophan content. Genotype by trait biplot analysis revealed association of grain yield with plant height and ear height. TZEEQI 394 and TZEEIORQ 73A had high expressivity for these traits. Indirect selection for high grain yield among the inbred lines could be achieved using plant and ear heights as selection criteria. The wide genetic variability observed in this study suggested that the inbred lines could be important sources of beneficial alleles for LN breeding programs in SSA.

Genetic Studies on the Inheritance of Storage-Induced Cooking Time in Cowpeas [Vigna unguiculata (L.) Walp]

Cowpeas provide food and income for many small-holder farmers in Africa. Cowpea grains contain substantial quantities of protein, carbohydrates, vitamins, and fiber. In areas where subsistence farming is practiced, cowpea's protein is cheaper than that obtained from other sources such as fish, meat, poultry or dairy products and combines well with cereal grains in diets. However, long-cooking times, typical of many grain legumes, is a major limitation to the utilization of cowpeas especially among the low-income and growing middle-income population of Africa. Long periods of cooking cowpeas lead to loss of nutrients, loss of useful time and increased greenhouse gas emission through increased burning of firewood. Fast-cooking cowpeas has the potential to deliver highly nutritious food to the hungry within shorter periods, encourage less use of firewood, improve gender equity, increase the consumption of cowpeas, trigger an increase in demand for cowpeas and thus incentivize cowpea production by smallholder farmers in Sub-Saharan Africa. In this study, the inheritance of storage-induced cooking time in cowpeas was investigated. Two sets of bi-parental crosses were conducted involving three cowpea genotypes: CRI-11(1)-1, C9P(B) and TVu7687. Generation means from six generations were used to determine the phenotypic and genotypic variances and coefficients of variation. Broad and narrow sense heritabilities and genetic advance percentage of mean were estimated. Generation mean analysis showed that additive, dominant, additive-additive, additive-dominant, and dominant-dominant gene actions were significant (p < 0.001). Fast-cooking trait was dominant over the long-cooking trait. Broad sense heritability for crosses C9P(B) × CRI-11(1)-1 and TVu7687 × CRI-11(1)-1 were 0.94 and 0.99 respectively while narrow sense heritabilities were 0.84 and 0.88 respectively. Genetic advances were 27.09 and 40.40 respectively. High narrow-sense heritabilities and moderate genetic advance for the fast-cooking trait indicated the presence of additive genes in the trait and the possibility of introgressing the trait into farmer-preferred varieties using conventional selection methods. However, due to significant epistatic gene effects observed, effective selection for fast-cooking trait would be appropriate at advanced generations.

Varietal Response to Groundnut Rosette Disease and the First Report of Groundnut ringspot virus in Ghana

Twelve cultivars of groundnut were screened in field trials for resistance to groundnut rosette disease (GRD), caused by coinfection with Groundnut rosette assistor virus (GRAV), Groundnut rosette virus (GRV), and its satellite RNA in the coastal savannah of Ghana. 'Oboshie' groundnut was rated as highly resistant; 'Bremaowuo', 'Nkatefufuo', and 'Behenase' as resistant; and 'Nkosuor', 'Kumawu', and 'Otuhia' as moderately resistant. GRAV infection rates of 11.8 to 61.8% (dry season) and 13.9 to 100% (wet season) were found, which included symptomless plants, suggesting that some lacked coinfection with GRV and its satellite. Chlorotic ringspot and line-pattern symptoms were observed, suggesting infection with Groundnut ringspot virus (GRSV). Virus identity was confirmed by enzyme-linked immunosorbent assay, reverse-transcription polymerase chain reaction, and amplicon sequencing. This is the first report of GRSV in Ghana. GRSV infection rates were 0.0 to 69.5% (dry season) and 26.1 to 69.5% (wet season). Mixed infections of GRAV and GRSV were common in all cultivars except Nkosuor and Bremaowuo in the dry season. Most cultivars graft inoculated with GRD showed significantly reduced height, leaf area, chlorophyll content, dry haulm weight, and seed yield compared with healthy plants. The sources of resistance to GRD and possibly GRAV and GRSV identified in this study could be exploited in groundnut breeding programs.

Mapping the distribution of maize streak virus genotypes across the forest and transition zones of Ghana

Throughout sub-Saharan Africa, maize streak virus strain A (MSV-A), the causal agent of maize streak disease (MSD), is an important biological constraint on maize production. In November/December 2010, an MSD survey was carried out in the forest and transition zones of Ghana in order to obtain MSV-A virulence sources for the development of MSD-resistant maize genotypes with agronomic properties suitable for these regions. In 79 well-distributed maize fields, the mean MSD incidence was 18.544 % and the symptom severity score was 2.956 (1 = no symptoms and 5 = extremely severe). We detected no correlation between these two variables. Phylogenetic analysis of cloned MSV-A isolates that were fully sequenced from samples collected in 51 of these fields, together with those sampled from various other parts of Africa, indicated that all of the Ghanaian isolates occurred within a broader cluster of West African isolates, all belonging to the highly virulent MSV-A1 subtype. Besides being the first report of a systematic MSV survey in Ghana, this study is the first to characterize the full-genome sequences of Ghanaian MSV isolates. The 51 genome sequences determined here will additionally be a valuable resource for the rational selection of representative MSV-A variant panels for MSD resistance screening.

Diversity in 113 cowpea [Vigna unguiculata (L) Walp] accessions assessed with 458 SNP markers

Single Nucleotide Polymorphism (SNP) markers were used in characterization of 113 cowpea accessions comprising of 108 from Ghana and 5 from abroad. Leaf tissues from plants cultivated at the University of Ghana were genotyped at KBioscience in the United Kingdom. Data was generated for 477 SNPs, out of which 458 revealed polymorphism. The results were used to analyze genetic dissimilarity among the accessions using Darwin 5 software. The markers discriminated among all of the cowpea accessions and the dissimilarity values which ranged from 0.006 to 0.63 were used for factorial plot. Unexpected high levels of heterozygosity were observed on some of the accessions. Accessions known to be closely related clustered together in a dendrogram drawn with WPGMA method. A maximum length sub-tree which comprised of 48 core accessions was constructed. The software package structure was used to separate accessions into three groups, and the programme correctly identified varieties that were known hybrids. The hybrids were those accessions with numerous heterozygous loci. The structure plot showed closely related accessions with similar genome patterns. The SNP markers were more efficient in discriminating among the cowpea germplasm than morphological, seed protein polymorphism and simple sequence repeat studies reported earlier on the same collection.

Complete genome sequencing of two causative viruses of cassava mosaic disease in Ghana

Cassava mosaic disease (CMV), caused by one or a combination of cassava mosaic geminiviruses, is ranked among the most important constraints to profitable and efficient production of cassava. Effective control measures require in-depth knowledge of the viral causative agent. Using rolling-circle amplification and unique enzymes, the full genome of two species of cassava mosaic geminivirus isolated from infected cassava plants in Ghana were cloned into pCambia 1300 and pET-28b. The sequences of the genome were determined on an ABI sequencer and a pairwise comparison was performed with other cassava-infecting geminiviruses from different countries. It was revealed that cassava grown in Ghana is attacked by two species of geminivirus in either single or mixed infections. These are the African cassava mosaic virus (ACMV) and the East African cassava mosaic virus (EACMV)-like, with high sequence similarity of 94% and 80%, respectively, between the DNA-A and DNA-B components of each virus, and 66% and 41% similarity of the common region (CR) (for A and B accordingly). The DNA-A of ACMV and EACMV-like contained 2781 and 2800 nucleotides, respectively, while their DNA-B components had 2725 and 2734 nucleotides, respectively. ACMV DNA-A was over 97% similar to those of other ACMVs from the continent. In contrast, EACMV-like DNA-A was over 98% similar to the isolates from Cameroon and other West African countries, and less than 88% similar to other EACMV species. Thus ACMV and EACMV-like were named African cassava mosaic virus-Ghana and East African cassava mosaic Cameroon virus-Ghana. Computer analysis revealed that their genome arrangement follows the typical old world bipartite begomovirus genome. The association of these two species and their interaction might account for the severe symptoms observed on infected plants in the field and in the greenhouse.

Genetic structure of seventy cocoyam (Xanthosoma sagittifolium, Linn, Schott) accessions in Ghana based on RAPD

Seventy cocoyam accessions collected from the eastern and Volta regions of Ghana were studied using RAPD technique. Ten primers were used to study the genetic diversity and structure of the experimental material and a total of 120 different bands were detected. Levels of polymorphic fragments detected by the ten primers ranged from 69.2% to 100%. In the accessions from the eastern region, the mean observed and effective number of alleles per individual per population and mean Nei's gene diversity were 1.99+/-0.01, 1.53+/-0.12 and 0.312+/-0.05, respectively. Mean observed and effective number of alleles per individual per population and Nei's gene diversity were 1.76+/-0.17, 1.44+/-0.16 and 0.264+/-0.08, respectively for the accessions from the Volta region. Considering the entire collections, the mean observed and effective number of alleles per individual per population and Nei's gene diversity for primers were 1.99+/-0.02, 1.54+/-0.12 and 0.319+/-0.05, respectively. In terms of Nei's F-statistics in the subdivided populations for all primers, the overall gene diversity (Ht) ranged from 0.230 to 0.396 with a mean of 0.313+0.06, within sample gene diversity (Hs) ranged from 0.214 to 0.372 with a mean of 0.286+0.06, gene differentiation (Gst) ranged between 0.005 and 0.178 with a mean of 0.086. Geneflow estimate ranged between 2.309 and 99.500 with a mean of 5.314. The accessions grouped into three main clusters. Accession BD96/183 was the most diverse and may be incorporated into cocoyam breeding programs. The 70 accessions did not cluster into their distinct geographical regions suggesting that there may have been movement of germplasm across the two regions.

Molecular variation of Potato yellow vein virus isolates

To evaluate the variation of Potato yellow vein virus from potato fields, 12 isolates were collected from Colombia and one was collected from Peru. Double-stranded RNA was extracted from the plants and used as a template for RT-PCR amplification of the coat protein ( CP) gene and, in separate reactions the C-terminal region of the heat shock protein 70 homologue ( Hsp70h) gene and the N-terminal region of the p60 open reading frame. The CP amplicons were subjected to single-strand conformation polymorphism (SSCP) analysis and, together with the other amplicon, nucleotide sequence analysis. These analyses suggested that there is low genetic diversity in the PYVV isolates examined and that the Peruvian isolate of PYVV may have originated in Colombia.

First Report of East African Cassava Mosaic Begomovirus in Ghana

Virus species causing cassava mosaic disease have been categorized into three classes based on their reaction with monoclonal antibodies (MAbs) and their distribution (2). These viruses have different, scarcely overlapping distribution: African cassava mosaic begomovirus (ACMV) occurs in Africa west of the Rift Valley and in South Africa; East African cassava mosaic (EACMV) occurs in Africa east of the Rift Valley and in Madagascar; and Indian cassava mosaic virus (ICMV) occurs in India and Sri Lanka (2). During 1998, surveys were conducted in farmers' fields in Ghana to assess the incidence and reaction of local cassava cultivars to cassava mosaic disease. Leaf samples from symptomatic plants were indexed by triple antibody sandwich-enzyme-linked immunosorbent assay with crude extracts and monoclonal antibodies obtained from the International Institute of Tropical Agriculture (IITA). Each sample was assayed with monoclonal antibody SCR 23, which detects ACMV and EACMV, SCR 33, which detects ACMV, and SCR 58, which detects ICMV. None of the samples reacted with SCR 58. Two of the samples collected from the western region of Ghana produced strong reactions with MAb SCR23 but did not react with ACMV-specific MAb SCR 33. This result was consistent in three separate experiments conducted on the samples, confirming that the virus was EACMV and not ACMV. The results extend the work by Ogbe et al. (1) and provide further evidence of the occurrence of EACMV in west Africa. References: (1) F. O. Ogbe et al. Plant Dis 83:398, 1999. (2) M. M. Swanson and B. D. Harrison. Trop. Sci. 34:15, 1994.

The tobacco necrosis virus p7a protein is a nucleic acid-binding protein

The two centrally located open reading frames (ORFs) of necroviruses may, by analogy with the similarly located and related ORFs of carmoviruses, be expected to have a function in virus movement in plants. In the case of tobacco necrosis virus (TNV) strain D these proteins both have a molecular mass of approximately 7 kDa and are thus known as p7a and p7b. We overexpressed p7a in Escherichia coli, separated it from bacterial proteins and renatured it on gels, and showed that p7a was able to bind single-stranded RNA and single-stranded DNA, but was unable to bind double-stranded DNA. These protein-nucleic acid complexes were stable at moderately high salt concentrations. Protein p7b could not be expressed in a number of bacterial systems. We speculate that in TNV, unlike some other viruses which encode a single movement protein with separate functional domains for RNA binding and plasmodesmatal targeting, p7a and p7b may respectively provide these functions on separate proteins.