Genetic progress in cowpea [Vigna unguiculata (L.) Walp.] stemming from breeding modernization efforts at the International Institute of Tropical Agriculture.

Genetic gain has been proposed as a quantifiable key performance indicator that can be used to monitor breeding programs' effectiveness. The cowpea breeding program at the International Institute of Tropical Agriculture (IITA) has developed and released improved varieties in 70 countries globally. To quantify the genetic changes to grain yield and related traits, we exploited IITA cowpea historical multi-environment trials (METs) advanced yield trial (AYT) data from 2010 to 2022. The genetic gain assessment targeted short duration (SD), medium duration (MD), and late duration (LD) breeding pipelines. A linear mixed model was used to calculate the best linear unbiased estimates (BLUE). Regressed BLUE of grain yield by year of genotype origin depicted realized genetic gain of 22.75 kg/ha/year (2.65%), 7.91 kg/ha/year (0.85%), and 22.82 kg/ha/year (2.51%) for SD, MD, and LD, respectively. No significant gain was realized in 100-seed weight (Hsdwt). We predicted, based on 2022 MET data, that recycling the best genotypes at AYT stage would result in grain yield gain of 37.28 kg/ha/year (SD), 28.00 kg/ha/year (MD), and 34.85 kg/ha/year (LD), and Hsdwt gain of 0.48 g/year (SD), 0.68 g/year (MD), and 0.55 g/year (LD). These results demonstrated a positive genetic gain trend for cowpea, indicating that a yield plateau has not yet been reached and that accelerated gain is expected with the recent integration of genomics in the breeding program. Advances in genomics include the development of the reference genome, genotyping platforms, quantitative trait loci mapping of key traits, and active implementation of molecular breeding.

A Mid-Density Single-Nucleotide Polymorphism Panel for Molecular Applications in Cowpea (Vigna unguiculata (L.) Walp).

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 panel's 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 panel's 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.

A Genome-Wide Scan Divulges Key Loci Involved in Resistance to Aphids (Aphis craccivora) in Cowpea (Vigna unguiculata).

Cowpea aphids (Aphis craccivora Koch) double as a direct damaging pest and a virus vector to cowpea, threatening the economic yield of the crop. Given the multiple ecotypes, different alleles have been implicated in aphid resistance, necessitating the identification of key genes involved. The present study implemented a genome-wide scan using 365 cowpea mini-core accessions to decipher loci involved in resistance to aphid ecotype from Kano, Nigeria. Accessions were artificially inoculated with A. craccivora in insect-proof cages and damage severity assessed at 21 days after infestation. Significant phenotypic differences based on aphid damage severity were registered among the accessions. Skewed phenotypic distributions were depicted in the population, suggesting the involvement of major genes in the control of resistance. A genome-wide scan identified three major regions on chromosomes Vu10, Vu08 and Vu02, and two minor ones on chromosomes Vu01 and Vu06, that were significantly associated with aphid resistance. These regions harbored several genes, out of which, five viz Vigun01g233100.1, Vigun02g088900.1, Vigun06g224900.1, Vigun08g030200.1 and Vigun10g031100.1 were the most proximal to the peak single nucleotide polymorphisms (SNPs) positions. These genes are expressed under stress signaling, mechanical wounding and insect feeding. The uncovered loci contribute towards establishing a marker-assisted breeding platform and building durable resistance against aphids in cowpea.

Molecular Fingerprinting and Hybridity Authentication in Cowpea Using Single Nucleotide Polymorphism Based Kompetitive Allele-Specific PCR Assay.

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.

Genetic worth of multiple sets of cowpea breeding lines destined for advanced yield testing.

The objective of this study was to determine genetic potentials in eight sets of cowpea lines for grain yield (GY), hundred seed weight (HSDWT) and days to 50% flowering (DT50FL). A total of 614 F6 genotypes constituting the sets, grouped by maturity, were evaluated across two locations in Northern Nigeria, in an alpha lattice design, two replications each. Data were recorded on GY, HSDWT and DT50FL.Variance components, genotypic coefficient of variation (GCV), and genetic advance (GA) were used to decode the magnitude of genetic variance within and among sets. Genetic usefulness (Up) which depends on mean and variance to score the genetic merits in historically bi-parental populations was applied to groups of breeding lines with mixed parentage. Principal component analysis (PCA) was used to depict contribution of traits to observed variations. GY and DT50FL explained the variance within and between sets respectively. Genotypes were significantly different, although genotype-by-location and set-by-location interaction effects were also prominent. Genetic variance (δ2 G) and GCV were high for GY in Prelim2 (δ2 G = 45,897; GCV = 19.58%), HSDWT in Prelim11 (δ2 G = 7.137; GCV = 17.07%) and DT50F in Prelim5 (δ2 G = 4.54; GCV = 4.4%). Heritability varied among sets for GY (H = 0.21 to 0.57), HSDWT (H = 0.76 to 0.93) and DT50FL (H = 0.20 to 0.81). GA and percentage GA (GAPM) were high for GY in Prelim2 (GAPM = 24.59%; GA = 269.05Kg/ha), HSDWT in Prelim11 (GAPM = 28.54%; GA = 4.47 g), and DT50F in Prelim10 (GAPM = 6.49%; GA = 3.01 days). These sets also registered high values of genetic usefulness, suggesting potential application in non-full sib populations. These approaches can be used during preliminary performance tests to reinforce decisions in extracting promising lines and choose among defined groups of lines. SUPPLEMENTARY INFORMATION: The online version contains supplementary material available at (10.1007/s10681-020-02763-y).