Genomic diversity in pearl millet inbred lines derived from landraces and improved varieties.

BACKGROUND: Genetic improvement of pearl millet is lagging behind most of the major crops. Development of genomic resources is expected to expedite breeding for improved agronomic traits, stress tolerance, yield, and nutritional quality. Genotyping a breeding population with high throughput markers enables exploration of genetic diversity, population structure, and linkage disequilibrium (LD) which are important preludes for marker-trait association studies and application of genomic-assisted breeding. RESULTS: Genotyping-by-sequencing (GBS) libraries of 309 inbred lines derived from landraces and improved varieties from Africa and India generated 54,770 high quality single nucleotide polymorphism (SNP) markers. On average one SNP per 29 Kb was mapped in the reference genome, with the telomeric regions more densely mapped than the pericentromeric regions of the chromosomes. Population structure analysis using 30,208 SNPs evenly distributed in the genome divided 309 accessions into five subpopulations with different levels of admixture. Pairwise genetic distance (GD) between accessions varied from 0.09 to 0.33 with the average distance of 0.28. Rapid LD decay implied low tendency of markers inherited together. Genetic differentiation estimates were the highest between subgroups 4 and 5, and the lowest between subgroups 1 and 2. CONCLUSIONS: Population genomic analysis of pearl millet inbred lines derived from diverse geographic and agroecological features identified five subgroups mostly following pedigree differences with different levels of admixture. It also revealed the prevalence of high genetic diversity in pearl millet, which is very useful in defining heterotic groups for hybrid breeding, trait mapping, and holds promise for improving pearl millet for yield and nutritional quality. The short LD decay observed suggests an absence of persistent haplotype blocks in pearl millet. The diverse genetic background of these lines and their low LD make this set of germplasm useful for traits mapping.

GWAS unveils features between early- and late-flowering pearl millets.

BACKGROUND: Pearl millet, a nutritious food for around 100 million people in Africa and India, displays extensive genetic diversity and a high degree of admixture with wild relatives. Two major morphotypes can be distinguished in Senegal: early-flowering Souna and late-flowering Sanio. Phenotypic variabilities related to flowering time play an important role in the adaptation of pearl millet to climate variability. A better understanding of the genetic makeup of these variabilities would make it possible to breed pearl millet to suit regions with different climates. The aim of this study was to characterize the genetic basis of these phenotypic differences. RESULTS: We defined a core collection that captures most of the diversity of cultivated pearl millets in Senegal and includes 60 early-flowering Souna and 31 late-flowering Sanio morphotypes. Sixteen agro-morphological traits were evaluated in the panel in the 2016 and 2017 rainy seasons. Phenological and phenotypic traits related with yield, flowering time, and biomass helped differentiate early- and late-flowering morphotypes. Further, using genotyping-by-sequencing (GBS), 21,663 single nucleotide polymorphisms (SNPs) markers with more than 5% of minor allele frequencies were discovered. Sparse non-negative matrix factorization (sNMF) analysis confirmed the genetic structure in two gene pools associated with differences in flowering time. Two chromosomal regions on linkage groups (LG 3) (~ 89.7 Mb) and (LG 6) (~ 68.1 Mb) differentiated two clusters among the early-flowering Souna. A genome-wide association study (GWAS) was used to link phenotypic variation to the SNPs, and 18 genes were linked to flowering time, plant height, tillering, and biomass (P-value < 2.3E-06). CONCLUSIONS: The diversity of early- and late-flowering pearl millet morphotypes in Senegal was captured using a heuristic approach. Key phenological and phenotypic traits, SNPs, and candidate genes underlying flowering time, tillering, biomass yield and plant height of pearl millet were identified. Chromosome rearrangements in LG3 and LG6 were inferred as a source of variation in early-flowering morphotypes. Using candidate genes underlying these features between pearl millet morphotypes will be of paramount importance in breeding for resilience to climatic variability.

Current Status of Pearl Millet Downy Mildew Prevalence across Agroecological Zones of Senegal.

Pearl millet is a dominant staple cereal crop for smallholder farmers in Senegal. However, the crop is constrained by various nonbiotic and biotic stresses such as downy mildew disease. To assess the prevalence of this disease in Senegal, a field survey was conducted during the rainy season of 2017 across eight main pearl millet production regions following latitudinal gradient with different climatic conditions. Results showed that downy mildew prevalence was higher in Kaolack (incidence = 68.19%), Kaffrine (incidence = 77.19%), Tambacounda (incidence = 97.03%), Sedhiou (incidence = 82.78%), and Kolda (incidence = 98.01%) than Thies (incidence = 28.21%), Diourbel (incidence = 24.46%), and Fatick (incidence = 37.75%) regions. The field survey revealed an incidence as high as 98% and 28% of infected area in surveyed fields. Significant correlations between geographic coordinates, disease incidence, and infected areas were also observed. This study provided information that could help to understand the prevalence of downy mildew in pearl millet in Senegal.

Intercropping millet with low-density cowpea improves millet productivity for low and medium N input in semi-arid central Senegal.

Cereal-legume intercropping has been traditionally practiced across West Africa by farmers and provides resilience of agriculture to climate variability. Intensification of these extensive intercropping systems in order to meet future food demand is critical. This study aims at evaluating the agronomic performance of the intensification of millet-cowpea intercropping with low cowpea density, and its variation with climate variability, using an on-station experiment in Bambey, Senegal. Two trials (irrigated vs rainfed) were set up to compare millet sole- and inter-cropping with a grain and a fodder variety of cowpea, in 2018 and 2019. Two levels of fertilization were tested: 0 kg(N) ha-1 and 69 kg(N) ha-1. The two cropping years were contrasting and water stress around flowering and/or during grain filling (indicated by the Fraction of Transpirable Soil Water) was higher in 2019 than in 2018 in the rainfed experiment. In both experiment and for all treatments, land equivalent ratio (LER) in the intercropping was 1.6 and 1.4 for grain and biomass respectively. Millet aboveground biomass was significantly higher in intercropping than in sole cropping in the irrigated experiment but not in the rainfed experiment. In the rainfed experiment, the interaction between cropping system and year was significant, so that millet aboveground biomass was greater in intercropping than in sole cropping in 2018 (year of lower water stress) but not in 2019 (year of higher water stress). The effect of fertilization on millet aboveground biomass did not significantly interact with cropping system (sole vs intercrop). For grain yield, fertilization interacted significantly with the cropping system in the irrigated trial: the benefits of intercropping on millet grain yield were greater with 69 kg(N) ha-1 than with 0 kg(N) ha-1. This significant interaction could not be observed in the rainfed trial, potentially due to water stress. These results show that the level of water stress (related here to the year and to the rainfed or irrigated experiment) and that of fertilization modulate the performance of millet-cowpea intercropping in the semi-arid context of Senegal. Overall, fertilization had a stronger effect on millet grain yield than intercropping. The two strategies (intercropping and mineral fertilization) can be complementary to achieve sustainable intensification of cropping system in semi-arid areas of West Africa.

Ethnobotanical study of cowpea (Vigna unguiculata (L.) Walp.) in Senegal.

Cowpea (Vigna unguiculata) plays a key role in family farming systems in Senegal. It makes an essential contribution to economic, nutritional and food security. Although it is crucial, little is known about how farmers classify the diversity of local varieties or about the social practices associated with them. The aim of this study is to characterize the farming practices associated with growing cowpea in Senegal. Surveys were conducted involving 335 rural farmers living in 37 villages, spread across seven regions that produce cowpea. An average of ten farmers were randomly selected in each village. The results reveal that cowpea is a key feature of cropping systems in the studied area. Our findings highlight the high diversity of local cowpea varieties with 59 local names inventoried. In 75% of cases, the name refers to the seed's morphology or color. Cowpea production is more diverse in Diourbel and Louga and less diverse in the south. More than half the farmers (57%) acquired their cowpea seeds (early, semi-early and late maturity varieties) outside their village, either from markets, seed suppliers or NGOs. This new understanding of farmers' expertize in the management of cowpea and its local variability will help to valorize local diversity in breeding programs.

Pearl Millet Genome: Lessons from a Tough Crop.

Pearl millet is an important cereal for food security in the arid regions of Africa and India. The recently published genome of this tough cereal crop has shed new light on its history and adaptation to dry, hot climates and paves the way for much-needed genomic-based breeding efforts.