Digitaria exilis, white fonio, is a minor but vital crop of West Africa that is valued for its resilience in hot, dry, and low-fertility environments and for the exceptional quality of its grain for human nutrition. Its success is hindered, however, by a low degree of plant breeding and improvement. We sequenced the fonio genome with long-read SMRT-cell technology, yielding a ∼761 Mb assembly in 3,329 contigs (N50, 1.73 Mb; L50, 126). The assembly approaches a high level of completion, with a BUSCO score of >99%. The fonio genome was found to be a tetraploid, with most of the genome retained as homoeologous duplications that differ overall by ∼4.3%, neglecting indels. The 2 genomes within fonio were found to have begun their independent divergence ∼3.1 million years ago. The repeat content (>49%) is fairly standard for a grass genome of this size, but the ratio of Gypsy to Copia long terminal repeat retrotransposons (∼6.7) was found to be exceptionally high. Several genes related to future improvement of the crop were identified including shattering, plant height, and grain size. Analysis of fonio population genetics, primarily in Mali, indicated that the crop has extensive genetic diversity that is largely partitioned across a north-south gradient coinciding with the Sahel and Sudan grassland domains. We provide a high-quality assembly, annotation, and diversity analysis for a vital African crop. The availability of this information should empower future research into further domestication and improvement of fonio.

As efforts are made to increase food security, millets are gaining increasing importance due to their excellent nutritional credentials. Among the millets, pearl millet is the predominant species possessing several health benefiting nutritional traits in its grain that are helpful in mitigating chronic illnesses such as type−2 diabetes and obesity. In this paper, we conducted metabolomic fingerprinting of 197 pearl millet inbred lines drawn randomly from within the world collection of pearl millet germplasm and report the extent of genetic variation for health benefitting metabolites in these genotypes. Metabolites were extracted from seeds and assessed using flow infusion high-resolution mass spectrometry (FIE-HRMS). Metabolite features (m/z), whose levels significantly differed among the germplasm inbred lines, were identified by ANOVA corrected for FDR and subjected to functional pathway analysis. A number of health-benefiting metabolites linked to dietary starch, antioxidants, vitamins, and lipid metabolism-related compounds were identified. Metabolic genome-wide association analysis (mGWAS) performed using the 396 m/z as phenotypic traits and the 76 K SNP as genotypic variants identified a total of 897 SNPs associated with health benefiting nutritional metabolite at the -log p-value ≤ 4.0. From these associations, 738 probable candidate genes were predicted to have an important role in starch, antioxidants, vitamins, and lipid metabolism. The mGWAS analysis focused on genes involved in starch branching (α-amylase, β-amylase), vitamin-K reductase, UDP-glucuronosyl, and UDP-glucosyl transferase (UGTs), L-ascorbate oxidase, and isoflavone 2′-monooxygenase genes, which are known to be linked to increases in human health benefiting metabolites. We demonstrate how metabolomic, genomic, and statistical approaches can be utilized to pinpoint genetic variations and their functions linked to key nutritional properties in pearl millet, which in turn can be bred into millets and other cereals crops using plant breeding methods.

Pigeonpea [Cajanus cajan (L.) Millspaugh] is a widely grown pulse with high seed protein content that contributes to food and nutritional security in the Indian subcontinent. The majority of pigeonpea varieties cultivated in India are of medium duration (<180 days to maturity), which makes it essential for breeders to focus on the development of stable high-yielding varieties. The diverse agroecological regime in the Indian subcontinent necessitates an efficient multi-environment study by taking into consideration genotype (G) × environment (E) interaction (GEI) that has a significant impact on traits like grain yield (GY) in developing high-yielding and widely adaptable varieties. In the present study, 37 pigeonpea genotypes were evaluated during the 2021 rainy season at ARS Badnapur, ARS Tandur, BAU Ranchi, GKVK Bengaluru, and ICRISAT Patancheru. The GEI was significant on the grain yield (p < 0.01), and hence, genotype + genotype × environment (GGE) and additive main effects and multiplicative interaction (AMMI) biplots along with AMMI stability value (ASV) and yield relative to environmental maximum (YREM) statistics were used to identify stable high-yielding genotypes. The interaction principal component analysis 1 and 2 (IPC1 and IPC2) explained 40.6% and 23.3% variations, respectively. Based on the rankings of genotypes, G37 (ICPL 20205), G35 (ICPL 20203), G8 (ICPL 19404), G17 (ICPL 19415), and G9 (ICPL 19405) were identified as ideal genotypes. Discriminativeness vs. representativeness identified GKVK Bengaluru as an ideal environment for comprehensive evaluation of test genotypes. However, ICPL 19405 was identified as the potentially stable high-yielding genotype for further testing and release across the test environments based on its mean grain yield (1,469.30 kg/ha), least ASV (3.82), and low yield stability index (YSI) of 13.

Pearl millet (Pennisetum glaucum) is a staple food crop in Burkina Faso that is widely grown in the Sahelian and Sudano-Sahelian zones, characterised by poor soil conditions and erratic rainfall, and high temperatures. The objective of this study was to document farmers’ perceptions of the prevailing constraints affecting pearl millet production and related approaches to manage the parasitic weeds S. hermonthica. The study was conducted in the Sahel, Sudano-Sahelian zones in the North, North Central, West Central, Central Plateau, and South Central of Burkina Faso. Data were collected through a structured questionnaire and focus group discussions involving 492 participant farmers. Recurrent drought, S. hermonthica infestation, shortage of labour, lack of fertilisers, lack of cash, and the use of low-yielding varieties were the main challenges hindering pearl millet production in the study areas. The majority of the respondents (40%) ranked S. hermonthica infestation as the primary constraint affecting pearl millet production. Respondent farmers reported yield losses of up to 80% due to S. hermonthica infestation. 61.4% of the respondents in the study areas had achieved a mean pearl millet yields of <1 t/ha. Poor access and the high cost of introduced seed, and a lack of farmers preferred traits in the existing introduced pearl millet varieties were the main reasons for their low adoption, as reported by 32% of respondents. S. hermonthica management options in pearl millet production fields included moisture conservation using terraces, manual hoeing, hand weeding, use of microplots locally referred to as ‘zaï’, crop rotation and mulching. These management techniques were ineffective because they do not suppress the below ground S. hermonthica seed, and they are difficult to implement. Integrated management practices employing breeding for S. hermonthica resistant varieties with the aforementioned control measures could offer a sustainable solution for S. hermonthica management and improved pearl millet productivity in Burkina Faso.

Striga hermonthica, a member of the Orobanchaceae family, is an obligate root parasite of staple cereal crops, which poses a tremendous threat to food security, contributing to malnutrition and poverty in many African countries. Depleting Striga seed reservoirs from infested soils is one of the crucial approaches to minimize subterranean damage to crops. The dependency of Striga germination on the host-released strigolactones (SLs) has prompted the development of the “Suicidal Germination” strategy to reduce the accumulated seed bank of Striga. The success of aforementioned strategy depends not only on the activity of the applied SL analogs, but also requires suitable application protocol with simple, efficient, and handy formulation for rain-fed African agriculture. Here, we developed a new formulation “Emulsifiable Concentration (EC)” for the two previously field-assessed SL analogs Methyl phenlactonoate 3 (MP3) and Nijmegen-1. The new EC formulation was evaluated for biological activities under lab, greenhouse, mini-field, and field conditions in comparison to the previously used Atlas G-1086 formulation. The EC formulation of SL analogs showed better activities on Striga germination with lower EC₅₀ and high stability under Lab conditions. Moreover, EC formulated SL analogs at 1.0 µM concentrations reduced 89–99% Striga emergence in greenhouse. The two EC formulated SL analogs showed also a considerable reduction in Striga emergence in mini-field and field experiments. In conclusion, we have successfully developed a desired formulation for applying SL analogs as suicidal agents for large-scale field application. The encouraging results presented in this study pave the way for integrating the suicidal germination approach in sustainable Striga management strategies for African agriculture.

Background: The challenge of pigeonpea breeding lies in its photosensitivity and seasonal specificity. This poses a problem to the breeder, as it restricts to single generation advancement in a year. Currently, the cross to cultivar gap is twelve to thirteen years resulting in a limited number of varietal releases over the past six decades. Shortening the breeding cycle was need of the hour, unlikely achieved by conventional breeding. To overcome these hindrances speed breeding was a necessary leap. An experiment was planned to optimize the speed breeding coupled with single seed descent and seed or pod chip-based genotyping to shorten the breeding cycle in pigeonpea at ICRISAT, Hyderabad. Monitored photoperiod, light wavelength, temperature and crop management regime were the indicators attributing to the success of speed breeding. Result: A photoperiod of 13 h: 8 h: 13 h at vegetative: flowering and pod filling stages is ideal for shortening the breeding cycle. Broad spectrum light (5700 K LED) hastened early vegetative growth and pod formation. Whereas far-red (735 nm) light favoured early flowering. A significant difference between the photoperiods, genotypes as well as photoperiod x genotype interaction for both days to flowering and plant height was noted. Conclusion: The optimized protocol serves as a road map for rapid generation advancement in pigeonpea. Deploying this protocol, it is possible to advance 2–4 generations per year. The breeding cycle can be reduced to 2–4 years which otherwise takes 7 years under conventional breeding. Single Seed Descent and seed or pod chip-based genotyping for early generation marker assisted selection, strengthened the precision of this technique aiding in high throughput line development.