Genome-wide scanning enabled SNP discovery, linkage disequilibrium patterns and population structure in a panel of fonio (Digitaria exilis [Kippist] Stapf) germplasm

White fonio (Digitaria exilis) is a staple food for millions of people in arid and semi-arid areas of West Africa. Knowledge about nutritional and health benefits, insights into morphological diversity, and the recent development of genomic resources call for a better understanding of the genetic structure of the extant germplasm gathered throughout the region in order to set up a robust breeding program. We assessed the genetic diversity and population structure of 259 fonio individuals collected from six countries from West Africa (Nigeria, Benin, Guinea, Mali, Burkina Faso and Niger) in this study using 688 putative out of 21,324 DArTseq-derived SNP markers. Due to the inbreeding and small population size, the results revealed a substantial level of genetic variability. Furthermore, two clusters were found irrespective of the geographic origins of accessions. Moreover, the high level of linkage disequilibrium (LD) between loci observed resulted from the mating system of the crop, which is often associated with a low recombination rate. These findings fill the gaps about the molecular diversity and genetic structure of the white fonio germplasm in West Africa. This was required for the application of genomic tools that can potentially speed up the genetic gain in fonio millet breeding for complex traits such as yield, and other nutrient contents

Identification of High-Yielding Iron-Biofortified Open-Pollinated Varieties of Pearl Millet in West Africa

Pearl millet is a predominant food and fodder crop in West Africa. This study was carried out to test the newly developed open-pollinated varieties (OPVs) for field performance and stability for grain yield, grain iron (Fe), and grain zinc (Zn) contents across 10 locations in West Africa (i.e., Niger, Nigeria, Mali, Burkina Faso, Senegal, and Ghana). The test material consisted of 30 OPVs, of which 8 are Fe/Zn biofortified. The experiment was conducted in a randomized complete block design in three replications. ANOVA revealed highly significant variability for grain yield and micronutrient traits. The presence of genotype x environment (G x E) indicated that the expressions of traits are significantly influenced by both genetic and G x E factors, for grain Fe and Zn contents. Days to 50% flowering and plant height showed less G x E, suggesting these traits are largely under genetic control. The genotypes CHAKTI (46 days), ICTP 8203 (46 days), ICMV 177002 (50 days), ICMV 177003 (48 days), and Moro (53 days) had exhibited early flowering across locations leading to early physiological maturity. CHAKTI (1.42 t/ha yield; 62.24 mg/kg of grain Fe, 47.29 mg/kg of grain Zn) and ICMP 177002 (1.19 t/ha yield, 62.62 mg/kg of grain Fe, 46.62 mg/kg of grain Zn) have performed well for grain yield and also for micronutrients, across locations, compared with the check. Additive Main Effect and Multiplicative Interaction (AMMI) ANOVA revealed the highly significant genotypic differences, the mean sum of squares of environment, and its interaction with the genotypes. Based on the AMMI stability value (ASV), the most stable genotype is SOSAT-C88 (ASV = 0.04) for grain yield and resistance to downy mildew; mean grain yield and stability rankings (YSI) revealed that the genotypes CHAKTI, SOSAT-C88, and ICMV IS 99001 were high yielding and expressed stability across regions. The strong correlation (r = 0.98**) of grain Fe and Zn contents that merits Fe-based selection is highly rewarding. CHAKTI outperformed over other genotypes for grain yield (71% higher), especially with early maturing varieties in West Africa, such as GB 8735, LCIC 9702, and Jirani, and for grain Fe (16.11% higher) and Zn (7% higher) contents across locations, and made a candidate of high-iron variety to be promoted for combating the micronutrient malnutrition in West and Central Africa (WCA)

Bovine Tuberculosis Prevalence Survey on Cattle in the Rural Livestock System of Torodi (Niger)

BACKGROUND: Bovine tuberculosis (BTB) is a widespread zoonosis in developing countries but has received little attention in sub-Saharan Africa, especially in Niger. Recent investigations confirmed the high incidence of the disease in cattle slaughtered in an abattoir in Niamey. The fact that most of the animals in which M. bovis has been identified were from the rural area of Torodi implied the existence of a probable source of BTB in this region. This study aimed to determine the prevalence of BTB infection in cattle and to identify risk factors for infection in human and cattle populations in Torodi. METHODS AND PRINCIPAL FINDINGS: A survey was carried out at the level of households keeping livestock (n = 51). The questionnaire was related to the potential risk factors and the presence of clinical signs of TB both in animals and humans. Comparative Intradermal Tuberculin Test was conducted to determine the TB status in cattle (n = 393). The overall apparent individual animal prevalence of tuberculin reactors was 3.6% (CI: 95%, 1.9-5.9), whereas the individual true prevalence was estimated at 0.8% (CI: 95%, 0.0-5.0). Using a multivariate logistic regression analysis and a classification tree analysis, the only household level risk factor that significantly influenced the presence of BTB in cattle was the presence of animals coughing in the herd (OR = 4.7, 95% CI: 1.12-19.71, p-value = 0.034). The lack of the practice of quarantine was borderline significant (OR = 4.2, 95% CI: 0.96-18.40, p-value = 0.056). CONCLUSION/SIGNIFICANCE: The study confirmed that BTB is endemic in cattle in Torodi and the risk of the transmission of the disease to humans is potentially high. For the control of the disease in livestock, slaughtering of infected animals and the compensation of the owners is needed. Collaboration between the veterinary and the medical sectors, in the diagnosis, monitoring, prevention and control of BTB is strongly encouraged

Combining ability studies of grain Fe and Zn contents of pearl millet (Pennisetum glaucum L.) in West Africa

Micronutrient malnutrition is a major challenge in Africa, where half a million children die each year because of lack of micronutrients in their food. Pearl millet is an important food and fodder crop for the people living in the Semi-Arid regions of West Africa. The present study was conducted to determine the stability, combining ability, and gene action conditions of the high level of Fe and Zn content in grain and selected agronomic traits. Hence, eight genotypes were selected based on the availability of grain Fe and Zn contents and crossed in a full diallel mating design. Progenies from an 8 × 8 diallel mating along with the parents were evaluated in an alpha lattice design with three replications in three locations for two years. The parental lines Jirani, LCIC 9702 and MORO, had positive significant general combining ability (GCA) effects for grain Fe concentration, while Jirani and MORO had positive significant GCA effects for grain Zn concentration. For the specific combining ability (SCA), among the 56 hybrids evaluated, only the hybrids LCIC 9702 × Jirani and MORO × ZANGO had positive significant SCA effects for grain Fe concentration across locations, and for grain Zn concentration, the hybrids Gamoji × MORO, LCIC 9702 × Jirani, and ICMV 167006 × Jirani had positive significant SCA effects. The reciprocal effects were significant for grain Zn concentration, grain yield, flowering time, plant height, test weight, and downy mildew incidence, suggesting that the choice of a female or male parent is critical in hybrid production. Grain Fe and Zn concentration, flowering time, plant height, panicle length, panicle girth, panicle compactness, and downy mildew incidence were found to be predominantly under additive gene action, while grain yield and test weight were predominantly under non-additive gene action. A highly positive correlation was found between grain Fe and Zn concentrations, which implies that improving grain Fe trait automatically improves the grain Zn content. The stability analysis revealed that the hybrid ICMV 167006 × Jirani was the most stable and high-yielding with a high level of grain Fe and Zn micronutrients.</jats:p

Identification of High-Yielding Iron-Biofortified Open-Pollinated Varieties of Pearl Millet in West Africa

Pearl millet is a predominant food and fodder crop in West Africa. This study was carried out to test the newly developed open-pollinated varieties (OPVs) for field performance and stability for grain yield, grain iron (Fe), and grain zinc (Zn) contents across 10 locations in West Africa (i.e., Niger, Nigeria, Mali, Burkina Faso, Senegal, and Ghana). The test material consisted of 30 OPVs, of which 8 are Fe/Zn biofortified. The experiment was conducted in a randomized complete block design in three replications. ANOVA revealed highly significant variability for grain yield and micronutrient traits. The presence of genotype × environment (G × E) indicated that the expressions of traits are significantly influenced by both genetic and G × E factors, for grain Fe and Zn contents. Days to 50% flowering and plant height showed less G × E, suggesting these traits are largely under genetic control. The genotypes CHAKTI (46 days), ICTP 8203 (46 days), ICMV 177002 (50 days), ICMV 177003 (48 days), and Moro (53 days) had exhibited early flowering across locations leading to early physiological maturity. CHAKTI (1.42 t/ha yield; 62.24 mg/kg of grain Fe, 47.29 mg/kg of grain Zn) and ICMP 177002 (1.19 t/ha yield, 62.62 mg/kg of grain Fe, 46.62 mg/kg of grain Zn) have performed well for grain yield and also for micronutrients, across locations, compared with the check. Additive Main Effect and Multiplicative Interaction (AMMI) ANOVA revealed the highly significant genotypic differences, the mean sum of squares of environment, and its interaction with the genotypes. Based on the AMMI stability value (ASV), the most stable genotype is SOSAT-C88 (ASV = 0.04) for grain yield and resistance to downy mildew; mean grain yield and stability rankings (YSI) revealed that the genotypes CHAKTI, SOSAT-C88, and ICMV IS 99001 were high yielding and expressed stability across regions. The strong correlation (r = 0.98∗∗) of grain Fe and Zn contents that merits Fe-based selection is highly rewarding. CHAKTI outperformed over other genotypes for grain yield (71% higher), especially with early maturing varieties in West Africa, such as GB 8735, LCIC 9702, and Jirani, and for grain Fe (16.11% higher) and Zn (7% higher) contents across locations, and made a candidate of high-iron variety to be promoted for combating the micronutrient malnutrition in West and Central Africa (WCA).</jats:p

Location of the study zone (Torodi) in Niger.

<p>Location of the study zone (Torodi) in Niger.</p

Classification tree produced using CART with target variable “CITT” (1 having at least one animal tested positive by CITT within the household; 0: not having animals tested positive by CITT within the household).

<p>Classification tree representing the important factors influencing CITT positivity. Target variable is “CITT” (1 having at least one animal tested positive by CITT within the household; 0: not having animals tested positive by CITT within the household). The following variables were selected by the tree as important factors: herd size with a cut off of 19 cattle in the herd; Handling (quarantine: keeping newly arrived animals out of the herd – mixed: new animals mixed with the other animals); Animals chronic cough (0 = absence of animals with chronic cough in the herd and 1 = presence of animals with chronic cough).</p

Genome-Wide Scanning Enabled SNP Discovery, Linkage Disequilibrium Patterns and Population Structure in a Panel of Fonio (Digitaria exilis [Kippist] Stapf) Germplasm

White fonio (Digitaria exilis) is a staple food for millions of people in arid and semi-arid areas of West Africa. Knowledge about nutritional and health benefits, insights into morphological diversity, and the recent development of genomic resources call for a better understanding of the genetic structure of the extant germplasm gathered throughout the region in order to set up a robust breeding program. We assessed the genetic diversity and population structure of 259 fonio individuals collected from six countries from West Africa (Nigeria, Benin, Guinea, Mali, Burkina Faso and Niger) in this study using 688 putative out of 21,324 DArTseq-derived SNP markers. Due to the inbreeding and small population size, the results revealed a substantial level of genetic variability. Furthermore, two clusters were found irrespective of the geographic origins of accessions. Moreover, the high level of linkage disequilibrium (LD) between loci observed resulted from the mating system of the crop, which is often associated with a low recombination rate. These findings fill the gaps about the molecular diversity and genetic structure of the white fonio germplasm in West Africa. This was required for the application of genomic tools that can potentially speed up the genetic gain in fonio millet breeding for complex traits such as yield, and other nutrient contents.</jats:p

Within herd apparent prevalence in local cattle (n = 393) in the rural zone of Torodi, Niger.

<p>Apparent prevalence (AP) and estimation of the true prevalence (TP) of bovine tuberculosis among local cattle (n = 393) in the rural zone of Torodi, Niger. TP was calculated using the value of Sensitivity and Specificity for the cut-off of >4 mm according to Ameni et al. (2008).</p><p>*Number of households in which animals were tested by comparative intra-dermal tuberculin testing (CITT).</p

Univariate analysis of raw data indicating potential risk factors associated with bovine tuberculosis (BTB) in cattle and humans in the rural area of Torodi, Niger.

<p>*These values had <i>P</i>-value<0.25 and were identified as potential risk factors for inclusion in the multivariable analysis; Ref: indicate that the level is taken as the reference to which others are compared; ND: not determined;</p><p>**Target variable for multivariate analysis and CART analysis.</p