Approaches and progress in breeding drought-tolerant maize hybrids for tropical lowlands in west and central Africa.

Drought represents a significant production challenge to maize farmers in West and Central Africa, causing substantial economic losses. Breeders at the International Institute of Tropical Agriculture have therefore been developing drought-tolerant maize varieties to attain high grain yields in rainfed maize production zones. The present review provides a historical overview of the approaches used and progress made in developing drought-tolerant hybrids over the years. Breeders made a shift from a wide area testing approach, to the use of managed screening sites, to precisely control the intensity, and timing of drought stress for developing drought-tolerant maize varieties. These sites coupled with the use of molecular markers allowed choosing suitable donors with drought-adaptive alleles for integration into existing elite maize lines to generate new drought-tolerant inbred lines. These elite maize inbred lines have then been used to develop hybrids with enhanced tolerance to drought. Genetic gains estimates were made using performance data of drought-tolerant maize hybrids evaluated in regional trials for 11 years under managed drought stress, well-watered conditions, and across diverse rainfed environments. The results found significant linear annual yield gains of 32.72 kg ha-1 under managed drought stress, 38.29 kg ha-1 under well-watered conditions, and 66.57 kg ha-1 across multiple rainfed field environments. Promising hybrids that deliver high grain yields were also identified for areas affected by drought and variable rainfed growing conditions. The significant genetic correlations found among the three growing conditions highlight the potential to exploit the available genetic resources and modern tools to further enhance tolerance to drought in hybrids.

Hydroxamic acids: New players in the multifactorial mechanisms of maize resistance to Striga hermonthica.

Striga hermonthica is the most widespread and destructive plant parasite infesting maize and other major crops in sub-Saharan Africa where it causes severe yield losses and threatens food security. Several tolerant maize lines supporting reduced S. hermonthica emergence have been deployed. However, the molecular bases of such resistance are yet poorly understood. Based on a time course comparative gene expression analysis between susceptible and resistant maize lines we have confirmed resistance mechanisms known to be activated upon plant parasite infestation and identified potential novel players worth further investigation e.g. iron homeostasis and mitochondrial respiration-related genes. Most intriguingly, we show a previously unknown strategy of maize post-attachment resistance based on DIMBOA accumulation in S. hermonthica-infested maize roots. S. hermonthica infestation triggers positive regulation of gene expression in the hydroxamic acid (HA) pathway culminating with an accumulation of benzoxazinoids (BX), known for their antifeedant, insecticidal, antimicrobial, and allelopathic activities. We demonstrate that HA root content is positively correlated with S. hermonthica resistance in the resistant parent and its progenies and in unrelated maize lines. Downregulation of HA genes causes increased susceptibility to S. hermonthica infestation in loss-of-function maize mutants. While the mechanism of BX action in parasitic plant resistance is yet to be uncovered, the potential of this discovery for developing effective control and breeding strategies is enormous.

Heterotic grouping of provitamin A-enriched maize inbred lines for increased provitamin A content in hybrids.

BACKGROUND: The establishment of heterotic groups of inbred lines is crucial for hybrid maize breeding programs. Currently, there is no information on the heterotic patterns of the Provitamin A (PVA) inbred lines developed in the maize improvement program of the International Institute of Tropical Agriculture (IITA) to form productive PVA enriched hybrids for areas affected by vitamin A deficiency. This study assessed the feasibility of classifying PVA-enriched inbred lines into heterotic groups based on PVA content without compromising grain yield in hybrids. Sixty PVA inbred lines were crossed to two testers representing two existing heterotic groups. The resulting 120 testcrosses hybrids were evaluated for two years at four locations in Nigeria. RESULTS: The two testers effectively classified the inbred lines into two heterotic groups. The PVA-based general combining ability and specific combining ability (HSGCA) method assigned 31 and 27 PVA enriched maize inbred lines into HGB and HGA, respectively, leaving two inbred lines not assigned to any group. The yield-based HSGCA method classified 32 inbred lines into HGB and 28 inbred lines into HGA. Both PVA and yield-based heterotic grouping methods assigned more than 40% of the inbred lines into the same heterotic groups. Even though both PVA and yield-based heterotic grouping of the inbred lines differed from the clusters defined by the DArTag SNP markers, more than 40% of the inbred lines assigned to HGA were present in Cluster-1 and 60% of the inbred lines assigned to HGB were present in Cluster-3. Interestingly, the inbred lines assigned to the same heterotic groups based on PVA content and grain yield were distributed across the three Ward's clusters. The PVA-based HSGCA was identified as the most effective heterotic grouping method for breeding programs working on PVA biofortification. CONCLUSIONS: Selecting PVA enriched maize inbred lines with diverse genetic backgrounds from the three marker-based clusters may facilitate the development of productive hybrids with high PVA content and for generating source populations to develop more vigorous maize inbred lines with much higher concentrations of PVA.

Genetic structure analysis and identifying key founder inbred lines in diverse elite sub-tropical maize inbred lines.

Understanding the genetic relationships between the key founder inbred lines and derived inbred lines could provide insight into the breeding history and the structure of genetic diversity of the available elite inbred lines with desirable target traits. The maize improvement program at the International Institute of Tropical Agriculture (IITA) analyzed the pedigree information of 623 sub-tropical maize inbred lines generated at the IITA maize breeding program to identify the key founder inbred lines. We also used 5032 SNP markers to assess the genetic similarities of the founder inbred lines with their progenies subsequently developed for specific target traits. The results of pedigree analysis and SNP markers-based similarity scores identified 20 key founder inbred lines with significant contributions to the development of drought tolerant, early maturing, productive, Striga resistant, provitamin A enriched, and quality protein maize inbred lines. In our breeding program, line TZMi501 belonging to a flint heterotic group (HGA), and TZMi407-S and TZMi214, representing the dent heterotic group (HGB), were identified as the most useful founder inbred lines. The 623 inbred lines were consistently separated into four clusters based on Ward's hierarchical clustering, structure, and principal component analyses, with the 20 founder inbred lines spread into all clusters. The founder inbred lines were more genetically related to the productive inbred lines but showed genetic divergence from the provitamin A enriched inbred lines. These results provide a better understanding of the breeding history of the sub-tropical maize inbred lines to facilitate parental selection aligned to existing heterotic groups for use in breeding programs targeting the improvement of essential traits in maize.

Genetic diversity and population structure of an African yam bean (Sphenostylis stenocarpa) collection from IITA GenBank.

African yam bean, AYB (Sphenostylis stenocarpa), 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.

Genetic Diversity and Population Structure of Cowpea [Vigna unguiculata (L.) Walp.] Germplasm Collected from Togo Based on DArT Markers.

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.

Genetic Diversity and Population Structure of Maize Inbred Lines with Varying Levels of Resistance to Striga Hermonthica Using Agronomic Trait-Based and SNP Markers.

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.

Genetic diversity and population structure of a mini-core subset from the world cowpea (Vigna unguiculata (L.) Walp.) germplasm collection.

The International Institute of Tropical Agriculture maintains the world's largest collection of cowpea germplasm of over 15,000 accessions. A sub-set of 298 lines from the loosely composed mini core collection of 370 landraces were genotyped based on genotyping by sequencing (GBS). Ward's minimum variance hierarchical cluster analysis, model-based ancestry analysis and discriminant analysis of principal component (DAPC) were carried out on this sub-set. Three clusters were identified by the different clustering methods. Principal component analysis further supported the three clusters especially when accessions are scattered along the axes of the first two principal components. The first two principal components explained a total of 22.30% of the variation. Cluster one comprises 115 accessions from the largest number of countries and has the highest gene diversity, heterozygosity and polymorphic information content (PIC) values. Cluster two is made up of 102 accessions, 90 percent of which are from West and Central Africa. Analysis of molecular variance shows that the most variation is among accessions and lowest among clusters. No cluster is made exclusively of accessions from a single country. Based on SNP markers, the sub set of cowpea mini core germplasm collection used in this study encompasses the diversity in the crop.

Isolation, identification and in silico analysis of alpha-amylase gene of Aspergillus niger strain CSA35 obtained from cassava undergoing spoilage.

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.

Genetic Gains in Grain Yield of a Maize Population Improved through Marker Assisted Recurrent Selection under Stress and Non-stress Conditions in West Africa.

Marker-assisted recurrent selection (MARS) is a breeding method used to accumulate favorable alleles that for example confer tolerance to drought in inbred lines from several genomic regions within a single population. A bi-parental cross formed from two parents that combine resistance to Striga hermonthica with drought tolerance, which was improved through MARS, was used to assess changes in the frequency of favorable alleles and its impact on inbred line improvement. A total of 200 testcrosses of randomly selected S1 lines derived from the original (C0) and advanced selection cycles of this bi-parental population, were evaluated under drought stress (DS) and well-watered (WW) conditions at Ikenne and under artificial Striga infestation at Abuja and Mokwa in Nigeria in 2014 and 2015. Also, 60 randomly selected S1 lines each derived from the four cycles (C0, C1, C2, C3) were genotyped with 233 SNP markers using KASP assay. The results showed that the frequency of favorable alleles increased with MARS in the bi-parental population with none of the markers showing fixation. The gain in grain yield was not significant under DS condition due to the combined effect of DS and armyworm infestation in 2015. Because the parents used for developing the bi-parental cross combined tolerance to drought with resistance to Striga, improvement in grain yield under DS did not result in undesirable changes in resistance to the parasite in the bi-parental maize population improved through MARS. MARS increased the mean number of combinations of favorable alleles in S1 lines from 114 in C0 to 124 in C3. The level of heterozygosity decreased by 15%, while homozygosity increased by 13% due to the loss of some genotypes in the population. This study demonstrated the effectiveness of MARS in increasing the frequency of favorable alleles for tolerance to drought without disrupting the level of resistance to Striga in a bi-parental population targeted as a source of improved maize inbred lines.

Genetic Gains in Yield and Yield Related Traits under Drought Stress and Favorable Environments in a Maize Population Improved Using Marker Assisted Recurrent Selection.

The objective of marker assisted recurrent selection (MARS) is to increase the frequency of favorable marker alleles in a population before inbred line extraction. This approach was used to improve drought tolerance and grain yield (GY) in a biparental cross of two elite drought tolerant lines. The testcrosses of randomly selected 50 S1 lines from each of the three selection cycles (C0, C1, C2) of the MARS population, parental testcrosses and the cross between the two parents (F1) were evaluated under drought stress (DS) and well watered (WW) well as under rainfed conditions to determine genetic gains in GY and other agronomic traits. Also, the S1 lines derived from each selection types were genotyped with single nucleotide polymorphism (SNP) markers. Testcrosses derived from C2 produced significantly higher grain field under DS than those derived from C0 with a relative genetic gain of 7% per cycle. Also, the testcrosses of S1 lines from C2 showed an average genetic gain of 1% per cycle under WW condition and 3% per cycle under rainfed condition. Molecular analysis revealed that the frequency of favorable marker alleles increased from 0.510 at C0 to 0.515 at C2, while the effective number of alleles (Ne) per locus decreased from C0 (1.93) to C2 (1.87). Our results underscore the effectiveness of MARS for improvement of GY under DS condition.