The potential of cowpea (Vigna unguiculata [L] Walp) to contribute to food security and livelihood sustenance of sub-Sahara Africans is constantly threatened by many biotic and abiotic stresses that are aggravated by climate change. To address these threats, cowpea breeding programs in the subregion prioritize climate-resilience traits and resistance to biotic stresses. However, before successful trait discovery and implementation, it is essential to characterize diversity and population structure of cowpea germplasm. To test the hypothesis that assembled cowpea germplasm exhibits limited and narrow genetic diversity with a well-defined population structure, we assessed the level of genetic variability and characterized the population structure of 188 cowpea genotypes using 5147 Single Nucleotide Polymorphism (SNP) markers. The structure results revealed five major genetic groups with moderate levels of genetic diversity and an admixture level of 17 %. Discriminant analysis and phylogenetic analysis supported this finding, indicating the presence of distinct groups within the cowpea population. The analysis of molecular variance (AMOVA) showed 27 % among population variance, 64 % within-population variance, and 9 % within individual variance. While considering the origin, the AMOVA showed 16 % among population variance, 75 % among individual variance, and 9 % within individual variance. This study provides valuable insights for future cowpea improvement programs by facilitating the selection of suitable progenitors for population development, and contributing in the conservation of cowpea genetic resources. Addressing these challenges and enhancing cowpea's diversity and resilience are crucial steps towards ensuring food security and sustainable livelihoods in sub-Saharan Africa.

Bambara groundnut is a legume mainly cultivated for these seeds in Africa. In the Sahelian zone, it sometimes suffered of significant yield losses linked to drought. The objective of this study is to identify the adapted genotypes to water deficit stress. The experimental design is randomly made up of four complete randomized blocks. Three variants of stress were applied during the growth of the plants, namely a water deficit stress for 14 days, a stress of 10 days and another stress of 7 days and a constantly watered control. The study revealed a systematic decline in yield under water deficit stress conditions in all ten accessions. However, the yields of accessions Ti 049 and Th 113 were the least affected, with decreases of -7.71% and -8.76% respectively compared to the control. However, the Di-3 082 accession recorded the greatest drop in yield (-36.06%). According to the indices determined, it appears that the genotypes Th 113, Ti 047, Ti 049 and Ma-2-65 are the most tolerant to water deficit stress, with considerable yield potential. Accession Di-3 082 was identified as the most sensitive to water deficit stress.

The bambara groundnut [Vigna subterranea (L.) Verdc. (Fabaceae)] is a legume mainly cultivated by women, for the nutritional quality of these seeds. It is a so-called minor culture and the improvement of the plant and its popularization remains to be promoted. The objective of this present work is to evaluate the genetic variability of bambara groundnut accessions. The experiment was carried out according to a completely randomized block device with four replications. Twenty-two (22) characters including four (4) phenological, four (4) morphological and fourteen (14) related to yield were evaluated for accessions characterization. Descriptive analysis showed significant differences. The coefficients of variation ranged from 3.51% (maturity date) to 38.87% (shell weight). Significantly high values (CV˃20%) for 8 of the metric parameters were observed. Pod weight per plant and seed weight per plant (r=0.943), yield in kg/ha (r=0.943); seed weight per plant and yield in kg/ha (r=0.999) showed the strongest correlations. The phenotypic and genotypic coefficients of variation were high for dry biomass weight (PCV=42.23%; GCV=28.40%), shell weight (PCV=63.46%; GCV=22.46%) and 100-seed weight (PCV=25.57%; GCV=25.25%). Maturity date (95.77%) and 100-seed weight (99.84%) had high heritabilities. Broad-sense heritability and genetic gain are high for 100-seed weight (H2=99.84%; GA=52.58%). The Ascending hierarchical classification produced four groups of which group 4 is the most efficient in yield with short (20.58cm) early accessions (80.32 days). Groups 1 and 2 include, late accessions (~22cm) with respectively maturity dates (DM=85.67 days and DM=86.53 days.

In the current genomic era, the search and deployment of new semi-dwarf alleles have continued to develop better plant types in all cereals. We characterized an agronomically optimal semi-dwarf mutation in Zea mays L. and a parallel polymorphism in Sorghum bicolor L.We cloned the maize brachytic1 (br1-Mu) allele by a modified PCR-based Sequence Amplified Insertion Flanking Fragment (SAIFF) approach. Histology and RNA-Seq elucidated the mechanism of semi-dwarfism. GWAS linked a sorghum plant height QTL with the Br1 homolog by resequencing a West African sorghum landraces panel.The semi-dwarf br1-Mu allele encodes an MYB transcription factor78 that positively regulates stalk cell elongation by interacting with the polar auxin pathway. Semi-dwarfism is due to differential splicing and low functional Br1 wild-type transcript expression. The sorghum ortholog, SbBr1, co-segregates with the major plant height QTL qHT7.1 and is alternatively spliced. The high frequency of the Sbbr1 allele in African landraces suggests that African smallholder farmers used the semi-dwarf allele to improve plant height in sorghum long before efforts to introduce Green Revolution-style varieties in the 1960s.Surprisingly, variants for differential splicing of Brachytic1 were found in both commercial maize and smallholder sorghum, suggesting parallel tuning of plant architecture across these systems.

Abstract Drought is a key constraint on plant productivity and threat to food security. Sorghum ( Sorghum bicolor L. Moench), a global staple food and forage crop, is among the most drought‐adapted cereal crops, but its adaptation is not yet well understood. This study aims to better understand the genetic basis of preflowering drought in sorghum and identify loci underlying variation in water use and yield components under drought. A panel of 219 diverse sorghum from West Africa was phenotyped for yield components and water use in an outdoor large‐tube lysimeter system under well‐watered (WW) versus a preflowering drought water‐stressed (WS) treatment. The experimental system was validated based on characteristic drought response in international drought tolerant check genotypes and genome‐wide association studies (GWAS) that mapped the major height locus at QHT7.1 and Dw3. GWAS further identified marker trait associations (MTAs) for drought‐related traits (plant height, flowering time, forage biomass, grain weight, water use) that each explained 7–70% of phenotypic variance. Most MTAs for drought‐related traits correspond to loci not previously reported, but some MTA for forage biomass and grain weight under WS co‐localized with staygreen post‐flowering drought tolerance loci (Stg3a and Stg4). A globally common allele at S7_50055849 is associated with several yield components under drought, suggesting that it tags a major pleiotropic variant controlling assimilate partitioning to grain versus vegetative biomass. The GWAS revealed oligogenic variants for drought tolerance in sorghum landraces, which could be used as trait predictive markers for improved drought adaptation.

ABSTRACTDrought is a key constraint on plant productivity and threat to food security. Sorghum (Sorghum bicolorL. Moench), a global staple food and forage crop, is among the most drought-adapted cereal crops, but its adaptation is not yet well understood. This study aims to better understand the genetic basis of preflowering drought in sorghum and identify loci underlying variation in water use and yield components under drought. A panel of 219 diverse sorghum from West Africa was phenotyped for yield components and water use in an outdoor large-tube lysimeter system under well-watered (WW) versus a preflowering drought water-stressed (WS) treatment. The experimental system was validated based on characteristic drought response in international drought tolerance check genotypes and genome-wide association studies (GWAS) that mapped the major height locus atQHT7.1andDw3. GWAS further identified marker trait associations (MTAs) for drought-related traits (plant height, flowering time, forage biomass, grain weight, water use) that each explained 7–70% of phenotypic variance. Most MTAs for drought-related traits correspond to loci not previously reported, but some MTA for forage biomass and grain weight under WS co-localized with staygreen post-flowering drought tolerance loci (Stg3aandStg4). A globally common allele at S7_50055849 is associated with several yield components under drought, suggesting that it tags a major pleiotropic variant controlling assimilate partitioning to grain versus vegetative biomass. The GWAS findings revealed oligogenic variants for drought tolerance in sorghum landraces which could be used as trait predictive markers for improved drought adaptation.

Local landrace and breeding germplasm is a useful source of genetic diversity for regional and global crop improvement initiatives. Sorghum (Sorghum bicolor L. Moench) in western Africa (WA) has diversified across a mosaic of cultures and end uses and along steep precipitation and photoperiod gradients. To facilitate germplasm utilization, a West African sorghum association panel (WASAP) of 756 accessions from national breeding programs of Niger, Mali, Senegal, and Togo was assembled and characterized. Genotyping-by-sequencing (GBS) was used to generate 159,101 high-quality biallelic single nucleotide polymorphisms (SNPs), with 43% in intergenic regions and 13% in genic regions. High genetic diversity was observed within the WASAP (pi =.00045), only slightly less than in a global diversity panel (GDP) (pi = .00055). Linkage disequilibrium (LD) decayed to background level (r(2) < .1) by similar to 50 kb in the WASAP. Genome-wide diversity was structured both by botanical type and by populations within botanical type with eight ancestral populations identified. Most populations were distributed across multiple countries, suggesting several potential common gene pools across the national programs. Genome-wide association studies (GWAS) of days to flowering (DFLo) and plant height (PH) revealed eight and three significant quantitative trait loci (QTL), respectively, with major height QTL at canonical height loci Dw3 and SbHT7.1. Colocalization of two of eight major flowering time QTL with flowering genes previously described in U.S. germplasm (Ma6 and SbCN8) suggests that photoperiodic flowering in West African sorghum is conditioned by both known and novel genes. This genomic resource provides a foundation for genomics-enabled breeding of climate-resilient varieties in WA.

Uncovering the genomic basis of climate adaptation in traditional crop varieties can provide insight into plant evolution and facilitate breeding for climate resilience. In the African cereal sorghum (Sorghum bicolor L. [Moench]), the genomic basis of adaptation to the semiarid Sahelian zone versus the subhumid Soudanian zone is largely unknown. To address this issue, we characterized a large panel of 421 georeferenced sorghum landrace accessions from Senegal and adjacent locations at 213,916 single-nucleotide polymorphisms (SNPs) using genotyping-by-sequencing. Seven subpopulations distributed along the north-south precipitation gradient were identified. Redundancy analysis found that climate variables explained up to 8% of SNP variation, with climate collinear with space explaining most of this variation (6%). Genome scans of nucleotide diversity suggest positive selection on chromosome 2, 4, 5, 7, and 10 in durra sorghums, with successive adaptation during diffusion along the Sahel. Putative selective sweeps were identified, several of which colocalize with stay-green drought tolerance (Stg) loci, and a priori candidate genes for photoperiodic flowering and inflorescence morphology. Genome-wide association studies of photoperiod sensitivity and panicle compactness identified 35 and 13 associations that colocalize with a priori candidate genes, respectively. Climate-associated SNPs colocalize with Stg3a, Stg1, Stg2, and Ma6 and have allelic distribution consistent with adaptation across Sahelian and Soudanian zones. Taken together, the findings suggest an oligogenic basis of adaptation to Sahelian versus Soudanian climates, underpinned by variation in conserved floral regulatory pathways and other systems that are less understood in cereals.

Evolution of plants under climatic gradients may lead to clinal adaptation. Understanding the genomic basis of clinal adaptation in crops species could facilitate breeding for climate resilience. We investigated signatures of clinal adaptation in the cereal crop sorghum (Sorghum bicolor L. [Moench]) to the precipitation gradient in West Africa using a panel (n = 607) of sorghum accessions from diverse agroclimatic zones of Nigeria. Significant correlations were observed between common-garden phenotypes of three putative climate-adaptive traits (flowering time, plant height, and panicle length) and climatic variables. The panel was characterized at >400,000 single nucleotide polymorphisms (SNPs) using genotyping-by-sequencing (GBS). Redundancy analysis indicated that a small proportion of SNP variation can be explained by climate (1%), space (1%), and climate collinear with space (3%). Discriminant analysis of principal components identified three genetic groups that are distributed differently along the precipitation gradient. Genome-wide association studies were conducted with phenotypes and three climatic variables (annual mean precipitation, precipitation in the driest quarter, and annual mean temperature). There was no overall enrichment of associations near a priori candidate genes implicated in flowering time, height, and inflorescence architecture in cereals, but several significant associations were found near a priori candidates including photoperiodic flowering regulators SbCN12 and Ma6. Together, the findings suggest that a small (3%) but significant proportion of nucleotide variation in Nigerian sorghum landraces reflects clinal adaptation along the West African precipitation gradient.

Improving adaptation of staple crops in developing countries is important to ensure food security. In the West African country of Niger, the staple crop sorghum (Sorghum bicolor) is cultivated across diverse agroclimatic zones, but the genetic basis of local adaptation has not been described. The objectives of this study were to characterize the genomic diversity of sorghum from Niger and to identify genomic regions conferring local adaptation to agroclimatic zones and farmer preferences. We analyzed 516 Nigerien accessions for which local variety name, botanical race, and geographic origin were known. We discovered 144 299 single nucleotide polymorphisms (SNPs) using genotyping-by-sequencing (GBS). We performed discriminant analysis of principal components (DAPC), which identified six genetic groups, and performed a genome scan for loci with high discriminant loadings. The highest discriminant coefficients were on chromosome 9, near the putative ortholog of maize flowering time adaptation gene Vgt1. Next, we characterized differentiation among local varieties and used a genome scan of pairwise FST values to identify SNPs associated with specific local varieties. Comparison of varieties named for light- versus dark-grain identified differentiation near Tannin1, the major gene responsible for grain tannins. These findings could facilitate genomics-assisted breeding of locally adapted and farmer-preferred sorghum varieties for Niger.

Heterotic grouping based on combining ability for traits of interest, in addition to plant performance and genetic relationship among germplasm, would be useful in planning crosses in breeding programmes. This study aimed at determining the combining abilities of selected landraces for morphological and physiological traits under contrasted environments and identifying the suitable heterotic grouping method for superior hybrid production. For this purpose, nineteen accessions representing different origins and population structure among West African Sorghum Accessions Panel (WASAP) and two female lines, were used in « Line x tester » mating design to produce thirtyeight (38) hybrids. Analysis of variance showed significant general combining ability and specific combining ability effects for grain weight, plant height, days to flowering, panicle length and chlorophyll content implying existence of heterotic responses for these traits. Both additive and non-additive gene effects were important in controlling the inheritance of the traits. Parents K31.3, K37 and Ni331 were the best combiners for grain weight, providing the opportunity for breeders to improve grain yield under diverse environments. AVG-1 x K31.3 and AVG-1 x Tg148 were the superior hybrids. Combining ability based heterotic grouping methods classified sorghum accessions into four groups. The heterotic group's specific and general combining ability (HSGCA) method was the suitable in predicting hybrid superiority. This combining abilities based heterotic grouping study is an additional tool that breeders could use to identify the best parents for superior hybrids development in West Africa.Key Words: Combining ability, heterotic groups, sorghum, West Africa