Diallel Analysis and Heritability of Grain Yield, Yield Components, and Maturity Traits in Cowpea (Vigna unguiculata (L.) Walp.).

Information on combining ability and reciprocal effects (REC) facilitates efficient utilization of genetic materials in a breeding program. This study was conducted (at the CSIR-Savanna Agricultural Research Institute, Ghana) to determine general combining ability (GCA) and specific combining ability (SCA), heritability, genetic advance, GCA, and SCA effects as well as the relationship between parents per se performance and progenies for yield components and maturity traits in cowpea. The test populations were derived using a 5 × 5 complete diallel cross of parents with different yield attributes and maturity durations. The results indicated that GCA was predominant for number of days to 90% pod maturity, plant height at maturity, and hundred-seed weight. This showed that genes with additive effects conditioned these traits. Padi-Tuya, Songotra, and IT86D-610 were identified as good general combiners for grain yield, while Sanzi-Nya was identified as a general combiner for developing extra-early duration cowpea varieties. Crosses Songotra × Sanzi-Nya, SARC-1-57-2 × IT86D-610, Songotra × SARC-1-57-2, and Padi-Tuya × Songotra were identified as good specific combiners for days to 50% flowering, pod length, pods per plant, pod yield, grain yield, and seeds per pod. The findings from this study provide useful information on the inheritance of early maturity and yield traits in cowpea. This can be exploited to develop high yielding and early maturing cowpea varieties as climate smart strategy to mitigate climate change via breeding methods such as pedigree selection and marker assisted backcrossing (MABC). Pedigree selection method is being used to develop varieties from the hybrid with high and significant SCA for grain yield, whereas the development of extra-early duration varieties via MABC with Sanzi-Nya (general combiner for earliness traits) as a donor parent is ongoing.

A multi-parent advanced generation inter-cross (MAGIC) population for genetic analysis and improvement of cowpea (Vigna unguiculata L. Walp.).

Multi-parent advanced generation inter-cross (MAGIC) populations are an emerging type of resource for dissecting the genetic structure of traits and improving breeding populations. We developed a MAGIC population for cowpea (Vigna unguiculata L. Walp.) from eight founder parents. These founders were genetically diverse and carried many abiotic and biotic stress resistance, seed quality and agronomic traits relevant to cowpea improvement in the United States and sub-Saharan Africa, where cowpea is vitally important in the human diet and local economies. The eight parents were inter-crossed using structured matings to ensure that the population would have balanced representation from each parent, followed by single-seed descent, resulting in 305 F8 recombinant inbred lines each carrying a mosaic of genome blocks contributed by all founders. This was confirmed by single nucleotide polymorphism genotyping with the Illumina Cowpea Consortium Array. These lines were on average 99.74% homozygous but also diverse in agronomic traits across environments. Quantitative trait loci (QTLs) were identified for several parental traits. Loci with major effects on photoperiod sensitivity and seed size were also verified by biparental genetic mapping. The recombination events were concentrated in telomeric regions. Due to its broad genetic base, this cowpea MAGIC population promises breakthroughs in genetic gain, QTL and gene discovery, enhancement of breeding populations and, for some lines, direct releases as new varieties.

Genome resources for climate-resilient cowpea, an essential crop for food security.

Cowpea (Vigna unguiculata L. Walp.) is a legume crop that is resilient to hot and drought-prone climates, and a primary source of protein in sub-Saharan Africa and other parts of the developing world. However, genome resources for cowpea have lagged behind most other major crops. Here we describe foundational genome resources and their application to the analysis of germplasm currently in use in West African breeding programs. Resources developed from the African cultivar IT97K-499-35 include a whole-genome shotgun (WGS) assembly, a bacterial artificial chromosome (BAC) physical map, and assembled sequences from 4355 BACs. These resources and WGS sequences of an additional 36 diverse cowpea accessions supported the development of a genotyping assay for 51 128 SNPs, which was then applied to five bi-parental RIL populations to produce a consensus genetic map containing 37 372 SNPs. This genetic map enabled the anchoring of 100 Mb of WGS and 420 Mb of BAC sequences, an exploration of genetic diversity along each linkage group, and clarification of macrosynteny between cowpea and common bean. The SNP assay enabled a diversity analysis of materials from West African breeding programs. Two major subpopulations exist within those materials, one of which has significant parentage from South and East Africa and more diversity. There are genomic regions of high differentiation between subpopulations, one of which coincides with a cluster of nodulin genes. The new resources and knowledge help to define goals and accelerate the breeding of improved varieties to address food security issues related to limited-input small-holder farming and climate stress.

Pyramiding aphid resistance genes into the elite cowpea variety, Zaayura, using marker-assisted backcrossing.

The cowpea aphid (Aphis cracivora) is a cosmopolitan insect pest that causes economic damage on cowpea. Although the pest persists at all the growth stages of the crop, in West Africa, aphids are the only major insect pests that farmers regularly control at the vegetative stage. Thus, deploying aphid-resistant crop varieties can reduce farmers' expenditure on insecticide. The availability of different biotypes of the pest and reports of resistance breakdown necessitates pyramiding of sources of aphid resistance to develop a more robust genotype for durable resistance. Two aphid-resistance genes, sourced from SARC-1-57-2 and IT97K-556-6, were introgressed through gene pyramiding technique into a farmers' preferred cowpea variety, Zaayura, using marker-assisted backcrossing. A simple sequence repeat (SSR) marker, CP 171F/172R, and an allele-specific single nucleotide polymorphism (SNP) marker, 1_0912, were used for foreground selection of the SARC-1-57-2 and IT97K-556-6 aphid resistance genes, respectively. A stepwise backcross approach was used to introgress the major aphid resistance QTL (QAc-vu7.1) from IT97K-556-6 into Zaayura using the marker 1_0912 coupled with intermittent screening under artificial aphid infestation. After the fourth backcross generation, three heterozygous BC4F1 of Zaayura/TT97K-556-6 were intercrossed to Zaayura Pali to develop intercross F1 (ICF1). Three true ICF1 hybrids allowed to self to produce ICF2. Five (5) out of 48 ICF2 plants which were genotyped with the two foreground markers had the two aphid resistance genes fixed in the double homozygous dominant state. For background selection, out of 192 allele-specific markers screened, only 47 polymorphic markers were identified and used for the background analysis of the pyramided lines. The recurrent parent genome recovery ranged from 72 to 93.8 %. ICF2_Zaa/556/SARC-P6 had the highest recurrent parent genome and the least heterozygosity among the five improved lines. The five pyramided lines showed superior resistance under artificial aphid infestation as compared to the two donor parents with damage scores ranging from 2.0 to 2.3. On the field, however, there were no significant differences between the pyramided lines and their recurrent parent for all the agronomic traits measured except for grain yield. The pyramided lines do not only stand the chance of being released as new varieties but are also valuable genetic resources for other breeding programs that seek to improve cowpea for aphid resistance.

Quantitative trait loci and genomic prediction for grain sugar and mineral concentrations of cowpea [Vigna unguiculata (L.) Walp.].

Development of high yielding cowpea varieties coupled with good taste and rich in essential minerals can promote consumption and thus nutrition and profitability. The sweet taste of cowpea grain is determined by its sugar content, which comprises mainly sucrose and galacto-oligosaccharides (GOS) including raffinose and stachyose. However, GOS are indigestible and their fermentation in the colon can produce excess intestinal gas, causing undesirable bloating and flatulence. In this study, we aimed to examine variation in grain sugar and mineral concentrations, then map quantitative trait loci (QTLs) and estimate genomic-prediction (GP) accuracies for possible application in breeding. Grain samples were collected from a multi-parent advanced generation intercross (MAGIC) population grown in California during 2016-2017. Grain sugars were assayed using high-performance liquid chromatography. Grain minerals were determined by inductively coupled plasma-optical emission spectrometry and combustion. Considerable variation was observed for sucrose (0.6-6.9%) and stachyose (2.3-8.4%). Major QTLs for sucrose (QSuc.vu-1.1), stachyose (QSta.vu-7.1), copper (QCu.vu-1.1) and manganese (QMn.vu-5.1) were identified. Allelic effects of major sugar QTLs were validated using the MAGIC grain samples grown in West Africa in 2017. GP accuracies for minerals were moderate (0.4-0.58). These findings help guide future breeding efforts to develop mineral-rich cowpea varieties with desirable sugar content.

Gender trait preferences among smallholder cowpea farmers in northern Ghana: lessons from a case study.

Introduction: This case study reports on how a gender responsive breeding program contributes to meeting the trait preference of men and women for improved cowpea varieties in northern Ghana. Methods: Fifty-eight early-maturing, medium-maturing and dual-purpose cowpea lines were planted at the CSIR-SARI research fields and women and men farmers invited for participatory plant breeding (PPB) in 2016. Selected lines from the PPB were further evaluated in 2017 using participatory varietal selection (PVS) in 5 districts in northern Ghana. In addition, 20 focus group discussions (FGDs) were held in 2018 in 10 randomly selected communities with 260 participants (130 women and 130 men) across the districts where the PVS had been held previously. Results and discussion: The study finds drought tolerance, short cooking time and pest resistance to be the most preferred cowpea traits among both men and women. The study also finds that gender differences exist in trait preference, especially for traits such as seed coat color, earliness, pod above canopy and indeterminate growth habit. As breeding programs focus on improving genetic gains for tolerance of biotic and abiotic stresses, equal attention must be given to breeding for traits desired by women.

Genetic control of earliness in cowpea (Vigna unguiculata (L) Walp).

Global climate change is expected to further intensify the already harsh conditions in the dry savannah ecological zones of sub-Saharan Africa, posing serious threats to food and income security of millions of smallholder farmers. Breeding cowpea for improved earliness could help minimize this risk, by ensuring that the crops complete their lifecycle before the cessation of rainfall. In this study, we crossed two sets of cowpea lines showing contrasting phenotypes for earliness in terms of days to 50% flowering (DFF). One set of the lines comprised three extra-early parents (viz.: Sanzi-Nya, Tobonaa and CB27, 30-35 DFF), and the other set consisted of three early-to-medium maturity lines (viz.: Kirkhouse-Benga, Wang-Kae and Padi-Tuya, 42-45 DFF). The derived crosses and their parents were evaluated for key earliness-related traits at Nyankpala and Manga sites of CSIR-Savanna Agricultural Research Institute (SARI), Ghana. To unravel the genetic control of measured traits, we compared the appropriateness of Chi-square goodness of fit tests using classical Mendelian ratios, and frequency distribution (histogram)-related statistics such as skewness and kurtosis. The Chi-square test suggested a single dominant gene mode of inheritance for earliness, whereas the quantitative methods implicated duplicate epistasis and complementary epistatic gene actions. Our results show that coercing segregating lines to fit into classical Mendelian ratios to determine the genetic control of earliness could be misleading, due to its subjectivity. Thus, the genetic control of earliness in cowpea is governed by complementary and duplicate epistasis. The most applicable breeding approach for traits influenced by duplicate epitasis is selection of desirable recombinants from segregating populations developed from bi-parental crosses. Complementary epitasis, as found in the Wang-Kae × CB27 cross, could be exploited in developing improved extra-early lines through backcrossing. Heritability and genetic advance estimates were high for days to first flower appearance (DFFA) and days to 95 % pod maturity (DNPM) in the Padi-Tuya × CB27 and Kirkhouse-Benga x CB27 crosses, indicating that breeding for extra-earliness is feasible. CB27 could be a good donor for introgression of earliness into medium to late maturing improved cowpea varieties, because crosses developed from it had high heritability and genetic advance estimates.

Identification of sources of resistance in cowpea lines to Macrophomina root rot disease in Northern Ghana.

Macrophomina root rot disease (MRRD) caused by Macrophomina phaseolina is an emerging threat to the profitable cowpea production in northern Ghana. Recommended control methods including the use of fungicides are ineffective and expensive for resource poor farmers whilst biocontrol options are not commercially available. An integrated method based on host plant resistance is considered the cheapest and most effective method of managing the disease. This study sought to confirm and characterize previously identified MRRD isolates from Northern Ghana using molecular technology, and to identify cowpea with potential sources of resistance to the MRRD. A PCR assay of ten isolates of the cowpea root rot pathogen revealed all isolates belonged to the species M. phaseolina, whilst a nucleotide BLAST of eight isolates showed 98% similarity with the sequences of Macrophomina isolates from other host available in GenBank. A sick pot method evaluation of 49 cowpea lines found 10 lines resistant to MRRD on a 1-9 disease severity scale (disease score, less than 5). A selection of eight resistant lines (Suvita 2, Abagbaala, IT97K573-1-1, IT93K-503-1-1, Hewale, AV2 3224, Nhyira and T2T4), and a susceptible check (Songotra) were evaluated against 10 isolates of M. phaseolina using a sick pot method. All the genotypes except for the susceptible check were resistant to MRRD. Thus, these genotypes could be used in cowpea MRRD resistance breeding programs.

Genetic variability, heritability and correlation analysis among maturity and yield traits in Cowpea (Vigna unguiculata (L) Walp) in Northern Ghana.

Experimental studies were conducted to evaluate 16 advanced breeding lines of cowpea (Vigna unguiculata (L) Walp) for genetic variability, heritability and correlation between maturity and yield related traits. The genotypes exhibited significant (P < 0.05) differences for the eight traits evaluated viz., number of days to 50 % flowering, number of days to 90 % pod maturity, plant height at maturity, number of pods per plant, number of seeds per pod, pod yield, grain yield and hundred seed weight. SARI-3-11-100, SARI-6-2-6, SARVX-09-004 and IT07K-299-6 had grain yields of 1.99 ± 0.30, 1.88 ± 0.20, 1.95 ± 0.30 and 1.91 ± 0.20 t/ha, respectively, which were significantly higher than the check (Songotra) (1.68 ± 0.01 t/ha). In addition, SARI-5-5-5 matured significantly earlier than the check but no significant difference was observed for grain yield. The higher value of phenotypic component compared to the corresponding genotypic component for all the traits suggest that there was an environmental influence on the performance of the genotypes. Hence, the need for multi-location evaluation of the promising lines for onward release if found stable. The information provided in this study, can be exploited in cowpea breeding program.

Characterization of Groundnut (Arachis hypogaea L.) Test Locations Using Representative Testing Environments With Farmer-Preferred Traits.

In this study, the differential rankings of 36 groundnut genotypes under varying environmental conditions were studied at various levels of phenotype. Locations that are generally accepted by the crop- and soil-based research community to represent the entire Guinea and Sudan Savanna agro-ecological zones in Ghana were characterized, this time using a crop. The characterization was done based on four farmer-preferred traits (early and late leaf spot disease ratings, and haulm and pod yields) using three models (i.e., AMMI, GGE, and Finlay-Wilkinson regression). These models were used to capture specific levels of phenotype, namely, genotype-by-environment interaction (GE), genotype main effect plus GE (G+GE), and environment and genotype main effects plus GE (E+G+GE), respectively. The effect of three major environmental covariables was also determined using factorial regression. Location main effect was found to be highly significant (p < 0.001), confirming its importance in cultivar placement. However, unlike genotypes where the best is usually adjudged through statistical ranking, locations are judged against a benchmark, particularly when phenotyping for disease severity. It was also found that the locations represent one complex mega-environment, justifying the need to test new technologies, including genotypes in all of them before they can be approved for adoption nationally. Again, depending on the phenotypic level considered, genotypic rankings may change, causing environmental groupings to change. For instance, all locations clustered to form one group in 2017 for early and late leaf spot diseases and pod yield when GE was considered, but the groupings changed when G+GE was considered for the same traits in the same year. As a result, assessing genotypic performance at the various levels to arrive at a consensus decision is suggested. Genotypes ICGV-IS 141120 and ICGV-IS 13937 were found to be the best performing.