MAGIC populations are powerful next generation mapping resources. We describe here the mating design and structure of the first MAGIC population in sorghum and test its utility for mapping. The population was developed by intercrossing 19 diverse founder lines, through a series of paired crosses with a genetic male sterile source, followed by 10 generations of random mating. At the final stage of random mating, one thousand random fertile plants in the population were identified and subjected to six generations of selfing to produce 1000 immortal MAGIC inbred lines. The development of this sorghum MAGIC population took over 15 years. Genotyping-by-sequencing of a subset of 200 MAGIC lines identified 79,728 SNPs, spanning high gene rich regions. Proportion of SNPs per chromosome ranged from 6% to 15%. Structure analyses produced no evidence of population stratification, portraying the desirability of this population for genome-wide association studies (GWAS). The 19 founders formed three clusters, each with considerable genetic diversity. Further analysis showed that 73% of founder alleles segregated in the MAGIC population. Linkage disequilibrium (LD) patterns depicted the MAGIC population to be highly recombined, with LD decaying to r² 0.2 at 40kb and down to r² 0.1 at 220kb. GWAS detected two known plant height genes: DWARF1 (Chr.9) and DWARF3 (Chr.7) and a potentially new plant height QTL (QTL-6) on Chromosome 6. The MAGIC population was found to be rich in allelic content with high fragmentation of its genome, making it fit for both gene mapping and effective marker-assisted breeding.

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 (F_IS) 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.

Optimization of a breeding program for increased genetic gain requires quality assurance (QA) and quality control (QC) at key phases of the breeding process. One vital phase in a breeding program that requires QC and QA is the choice of parents and successful hybridizations to combine parental attributes and create variations. The objective of this study was to determine parental diversity and confirm hybridity of cowpea F₁ progenies using KASP (Kompetitive Allele-Specific PCR)-based single nucleotide polymorphism (SNP) markers. A total of 1,436 F₁ plants were derived from crossing 220 cowpea breeding lines and landraces to 2 elite sister lines IT99K-573-1-1 and IT99K-573-2-1 as male parents, constituting 225 cross combinations. The progenies and the parents were genotyped with 17 QC SNP markers via high-throughput KASP genotyping assay. The QC markers differentiated the parents with mean efficiency of 37.90% and a range of 3.4–82.8%, revealing unique fingerprints of the parents. Neighbor-Joining cladogram divided the 222 parents into 3 clusters. Genetic distances between parents ranged from 0 to 3.74 with a mean of 2.41. Principal component analysis (PCA) depicted a considerable overlap between parents and F₁ progenies with more scatters among parents than the F₁s. The differentiation among parents and F₁s was best contributed to by 82% of the markers. As expected, parents and F₁s showed a significant contrast in proportion of heterozygous individuals, with mean values of 0.02 and 0.32, respectively. KASP markers detected true hybridity with 100% success rate in 72% of the populations. Overall, 79% of the putative F₁ plants were true hybrids, 14% were selfed plants, and 7% were undetermined due to missing data and lack of marker polymorphism between parents. The study demonstrated an effective application of KASP-based SNP assay in fingerprinting, confirmation of hybridity, and early detection of false F₁ plants. The results further uncovered the need to deploy markers as a QC step in a breeding program.

The yield of cowpea varieties is affected by environmental variability. Hence, candidate varieties must be tested for yield stability before release. This study assessed the impacts of genotypes, environments, and their interaction on the performance of elite cowpea lines for key adaptive, grain yield, and associated traits across different locations. A total of 42 elite genotypes were evaluated in five Nigerian environments, representing various savanna ecologies, during the 2021 growing season. The experimental design employed was an alpha lattice arrangement, with each genotype replicated three times. The results revealed significant differences among genotypes, environments, and genotype-by-environment interaction (G × E) for most traits, including days to maturity, 100-seed weight, and grain yield. The genotype and genotype-by-environment interaction (GGE) biplot showed G21 (IT14K-2111-2) and G25 (IT15K-2386-1) as the most stable genotypes across the five environments, G41 (IT11K-61-82) was best adapted to Ibadan and Shika, G5 (245-1) was best adapted to Bagauda and Gumel, and G30 (IT16K-2365-1) was best adapted to Bauchi. G21 (IT14K-2111-2) and G25 (IT15K-2386-1) could be recommended across the five test environments, whereas G41 (IT11K-61-82), G30 (IT16K-2365-1), and G5 (245-1) were specific to the adapted environments.

Cowpea is an important legume crop widely grown in sub‐Saharan Africa for food and feed. However, it is largely challenged by bruchid, a serious storage pest resulting in losses in quantity and quality of grains. Therefore, this research was designed to contribute to the breeding of cowpea resistance to bruchid through the identification of candidate genes associated with resistance to bruchid. A total of 217 mini‐core cowpea accessions were genotyped and phenotyped for their reactions to bruchid. To determine the genomic regions linked with bruchid resistance, 41,948 polymorphic SNP markers were used. Genome‐wide association study identified 11 SNPs linked to the average number of eggs, holes, insect emergence and development period and Dobie susceptibility index. Gene search via Phytozome identified six candidate genes (Vigun08g132300, Vigun08g158000, Vigun06g053700, Vigun02g131000, Vigun01g234900 and Vigun01g201900) associated with the resistance traits. These candidate genes could be incorporated into the farmers preferred but susceptible cowpea varieties to bruchid. The SNP markers associated with the resistance traits can be used in marker‐assisted breeding for accurate and rapid screening of cowpea resistant genotypes to bruchid.

Molecular markers are increasingly being deployed to accelerate genetic gain in crop plants. The objective of this study was to assess the potential of a mid-density genotyping panel for molecular applications in cowpea breeding. A core set of 2,602 targeted diversity array technology (DArTag) single-nucleotide polymorphisms (SNPs) was designed from an existing 51,128 Cowpea iSelect Consortium Array. The panels usefulness was assessed using 376 genotypes from different populations of known genetic backgrounds. The panel was informative, with over 78 of SNPs exceeding a minor allele frequency of 0.20. The panel decoded three stratifications in the constituted population, as was expected. Linkage disequilibrium (LD) decay was correctly depicted as slower in a biparental subset than in other populations. A known flower and seed coat color gene region was located on chromosome Vu07, suggesting that the mid-density panel may be used to hypothesize genomic regions underlying target traits in cowpea. Unexpected heterozygosity was detected in some lines and highly among F₁ progenies, divulging the panels potential application in germplasm purity and hybridity verification. The study unveils the potential of an excellent genomic resource that can be tapped to enhance the development of improved cowpea cultivars.