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Soybean (Glycine max (L.) Merr.) is an important legume crop with high commercial value widely cultivated globally. Thus, the genetic characterization of the existing soybean germplasm will provide useful information for enhanced conservation, improvement and future utilization. This study aimed to assess the extent of genetic diversity of soybean elite breeding lines and varieties developed by the soybean breeding programme of the International Institute of Tropical Agriculture (IITA), Ibadan, Nigeria. The genetic diversity of 65 soybean genotypes was studied using single-nucleotide polymorphism (SNP) markers. The result revealed that 2446 alleles were detected, and the indicators for allelic richness and diversity had good differentiating power in assessing the diversity of the genotypes. The three complementary approaches used in the study grouped the germplasm into three major clusters based on genetic relatedness. The analysis of molecular variance revealed that 71% (P < 0.001) variation was due to among individual genotypes, while 11% (P < 0.001) was ascribed to differences among the three clusters, and the fixation index (FST) was 0.11 for the SNP loci, signifying moderate genetic differentiation among the genotypes. The identified private alleles indicate that the soybean germplasm contains diverse variability that is yet to be exploited. The SNP markers revealed high diversity in the studied germplasm and found to be efficient for assessing genetic diversity in the crop. These results provide valuable information that might be utilized for assessing the genetic variability of soybean and other legume crops germplasm by breeding programmes.

Understanding the genetic diversity of cowpea (Vigna unguiculata L. Walp.) landraces is useful for effective characterization and ex-situ conservation of germplasm. The analysis of genetic diversity of eighteen cowpea landraces collected from five agro-ecological zones in Nigeria was reported in this study. Five individuals per landrace were genotyped with six polymorphic microsatellite markers. Three to 5 alleles with a mean of 3.833 were detected. Mean Polymorphic information content (PIC) and observed heterozygosity of the markers were 0.5721 and 0.2433, respectively. Analysis of Molecular Variance (AMOVA) showed that variation due to agroecological zone constituted 24%, while variations among and within landraces as well as within individuals constituted 25%, 17% and 33%, respectively. Landraces collected from the humid rainforest zone showed high within landrace diversity and were not significantly different (P ≥ 0.001) from other landraces collected from the same zone. Landraces from the savannah zones showed low within landrace diversity and homozygous across all loci. Consequently, among landrace diversity was higher in the savannah zone with landraces collected from guinea savannah been the most diverse, followed by landraces from the derived savannah and Sudan savannah. Mantel test showed positive and significant correlation (r= 0.377, p= 0.01) between genetic and geographical distance of landrace collections. The findings are important for up-to-date characterizations of cowpea germplasm in Nigeria for improved breeding programs. Keywords: Genetic diversity, cowpea, Alleles, Polymorphic information content, AMOVA

African yam bean, AYB (Sphenostylisstenocarpa), is an underutilized legume of tropical Africa. AYB can boost food and nutritional security in sub-Saharan Africa through its nutrient-rich seeds and tubers. However, inadequate information on germplasm with desirable agro-morphological traits, including insufficient data at the genomic level, has prevented the full exploitation of its food and breeding potentials. Notably, assessing the genetic diversity and population structure in a species is a prerequisite for improvement and eventual successful exploitation. The present study evaluated the population structure and genetic diversity of 169 accessions from the International Institute of Tropical Agriculture (IITA) collection using 26 phenotypic characters and 1789 single nucleotide polymorphism (SNP) markers. The phenotypic traits and SNP markers revealed their usefulness in uniquely distinguishing each AYB accession. The hierarchical cluster of phenotypes grouped accessions into three sub-populations; SNPs analysis also clustered the accessions into three sub-populations. The genetic differentiation (FST) among the three sub-populations was sufficiently high (0.14–0.39) and significant at P = 0.001. The combined analysis revealed three sub-populations; accessions in sub-population 1 were high yielding, members in sub-population 2 showed high polymorphic loci and heterozygosity. This study provides essential information for the breeding and genetic improvement of AYB.

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.

Host-specific interactions can maintain genetic and phenotypic diversity in parasites that attack multiple host species. Host diversity, in turn, may promote parasite diversity by selection for genetic divergence or plastic responses to host type. The parasitic weed purple witchweed [Striga hermonthica (Delile) Benth.] causes devastating crop losses in sub-Saharan Africa and is capable of infesting a wide range of grass hosts. Despite some evidence for host adaptation and host-by-Striga genotype interactions, little is known about intraspecific Striga genomic diversity. Here we present a study of transcriptomic diversity in populations of S. hermonthica growing on different hosts (maize [Zea mays L.] vs. grain sorghum [Sorghum bicolor (L.) Moench]). We examined gene expression variation and differences in allelic frequency in expressed genes of aboveground tissues from populations in western Nigeria parasitizing each host. Despite low levels of host-based genome-wide differentiation, we identified a set of parasite transcripts specifically associated with each host. Parasite genes in several different functional categories implicated as important in host–parasite interactions differed in expression level and allele on different hosts, including genes involved in nutrient transport, defense and pathogenesis, and plant hormone response. Overall, we provide a set of candidate transcripts that demonstrate host-specific interactions in vegetative tissues of the emerged parasite S. hermonthica. Our study shows how signals of host-specific processes can be detected aboveground, expanding the focus of host–parasite interactions beyond the haustorial connection.

Striga hermonthica is a serious biotic stress limiting maize production in sub-Saharan Africa. The limited information on the patterns of genetic diversity among maize inbred lines derived from source germplasm with mixed genetic backgrounds limits the development of inbred lines, hybrids, and synthetics with durable resistance to S. hermonthica. This study was conducted to assess the level of genetic diversity in a panel of 150 diverse maize inbred lines using agronomic and molecular data and also to infer the population structure among the inbred lines. Ten Striga-resistance-related traits were used for the phenotypic characterization, and 16,735 high-quality single-nucleotide polymorphisms (SNPs), identified by genotyping-by-sequencing (GBS), were used for molecular diversity. The phenotypic and molecular hierarchical cluster analyses grouped the inbred lines into five clusters, respectively. However, the grouping patterns between the phenotypic and molecular hierarchical cluster analyses were inconsistent due to non-overlapping information between the phenotypic and molecular data. The correlation between the phenotypic and molecular diversity matrices was very low (0.001), which is in agreement with the inconsistencies observed between the clusters formed by the phenotypic and molecular diversity analyses. The joint phenotypic and genotypic diversity matrices grouped the inbred lines into three groups based on their reaction patterns to S. hermonthica, and this was able to exploit a broad estimate of the actual diversity among the inbred lines. The joint analysis shows an invaluable insight for measuring genetic diversity in the evaluated materials. The result indicates that wide genetic variability exists among the inbred lines and that the joint diversity analysis can be utilized to reliably assign the inbred lines into heterotic groups and also to enhance the level of resistance to Striga in new maize varieties.

In this investigation, a gene (CDF_Amyl) encoding extracellular α-amylase in Aspergillus niger strain CSA35 associated with cassava spoilage was amplified using specific primers and characterized in silico. The gene had a partial nucleotide sequence of 968 bp and encoded a protein of 222 aa residues with a molecular weight and isoelectric point of 25.13 kDa and 4.17, respectively. Its catalytic site was located in the active site domain. BLASTp analysis showed that the protein primary sequence of the α-amylase gene had 98% and 99% homologies with the α-amylase of A. niger and A. oryzae RIB40, respectively. The gene is more closely related to α-amylase genes from fungi than to bacterial, plant, or animal α-amylase genes. Restriction mapping of the gene showed it can be digested with restriction enzymes like NcoI, PstI, SmaI, and BcLI among others but not with EcoRI and EcoRV. Its protein product had a hydrophobicity score of − 0.43 but no transmembrane helix. The CDF_Amyl protein was subcellularly localized in the secretory pathway, an indication of its release into extracellular space after secretion. Also, the 3D structure of the CDF-Amyl protein was barrel-shaped with domains characteristic of α-amylases. The encoded α-amylase Vmax is 6.90 U/mg protein and Km is 6.70 mg/ml. It was concluded that the unique characteristics of the CDF_Amyl gene and its deduced protein could find applications in biotechnological, food and pharmaceutical industries where cloning and further modification of this gene would be required for product development and improvement.

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.

Strigahermonthica (Del.) Benth is a parasitic weed that devastates cereals in Sub-Saharan Africa. Several control measures have been proposed for the parasite, of these, host plant resistance is considered the most cost-effective for poor farmers. Some tolerant/resistant lines have been developed and these lines display tolerance/resistance mechanisms to the parasite. A series of studies was done to investigate some of the mechanisms through which a resistant (TZISTR1108) and a susceptible (5057) maize line responds to S. hermonthica infestation, as well as the effects of parasitism on these lines. In this study, TZISTR1108 stimulated the germination and attachment of fewer S. hermonthica plants than 5057, both in the laboratory and on the field. In TZISTR1108, the growth of the S. hermonthica plants, that successfully attached, was slowed. When compared to the un-infested plants, the infested resistant plants showed fewer effects of parasitism than the infested susceptible plants. The infested TZISTR1108 plants were more vigorous, taller and resembled their un-infected counterparts. There were substantial reductions in the stomatal conductance and nitrogen content of the 5057 upon infestation. The resistant inbred line showed multiple mechanisms of resistance to S. hermonthica infestation. It thrives better than the susceptible line by reducing the attachment of S. hermonthica and it delays the parasite&rsquo, s development.

Accurate estimation of genetic variability present in tropical maize inbreds with varying reactions to Strigahermonthica infestation is essential for efficient and sustainable utilization to ensure increased genetic gain in a breeding program. Thirty-six early maturing maize inbred lines and 156 single cross hybrids were evaluated under Striga-infested and non-infested conditions in Nigeria during the 2014 and 2015 cropping seasons. Under Striga infestation, grain yield ranged from 1134 kg ha−1 for TZEI 26 × TZEI 5 to 5362 kg ha−1 for TZdEI 173 × TZdEI 280. The average yield reduction of the hybrids under Striga infestation was 44% relative to the performance under non-infested environments. Using 4440 high-quality DArT markers, clustering and population structure analyses separated the inbred lines into three distinct groups based on the genetic distance indicating high level of genetic variability among the lines. The base index of the International Institute of Tropical Agriculture (IITA) identified 50% of the inbred lines as Striga resistant. The genetic diversity study provided an opportunity for selecting divergent parents for tagging candidate genes and quantitative trait loci for marker-assisted introgression of Striga resistance genes into early maturing tropical maize breeding populations. The most reliable secondary trait for indirect selection for grain yield under Striga infestation was the ear aspect.