Gilles Bezançon

Diversity of wild and cultivated pearl millet accessions (Pennisetum glaucum [L.] R. Br.) in Niger assessed by microsatellite markers

Genetic diversity of crop species in sub-Sahelian Africa is still poorly documented. Among such crops, pearl millet is one of the most important staple species. In Niger, pearl millet covers more than 65% of the total cultivated area. Analyzing pearl millet genetic diversity, its origin and its dynamics is important for in situ and ex situ germplasm conservation and to increase knowledge useful for breeding programs. We developed new genetic markers and a high-throughput technique for the genetic analysis of pearl millet. Using 25 microsatellite markers, we analyzed genetic diversity in 46 wild and 421 cultivated accessions of pearl millet in Niger. We showed a significantly lower number of alleles and lower gene diversity in cultivated pearl millet accessions than in wild accessions. This result contrasts with a previous study using iso-enzyme markers showing similar genetic diversity between cultivated and wild pearl millet populations. We found a strong differentiation between the cultivated and wild groups in Niger. Analyses of introgressions between cultivated and wild accessions showed modest but statistically supported evidence of introgressions. Wild accessions in the central region of Niger showed introgressions of cultivated alleles. Accessions of cultivated pearl millet showed introgressions of wild alleles in the western, central, and eastern parts of Niger.

Association Studies Identify Natural Variation at PHYC Linked to Flowering Time and Morphological Variation in Pearl Millet

The identification of genes selected during and after plant domestication is an important research topic to enhance knowledge on adaptative evolution. Adaptation to different climates was a key factor in the spread of domesticated crops. We conducted a study to identify genes responsible for these adaptations in pearl millet and developed an association framework to identify genetic variations associated with the phenotype in this species. A set of 90 inbred lines genotyped using microsatellite loci and AFLP markers was used. The population structure was assessed using two different Bayesian approaches that allow inbreeding or not. Association studies were performed using a linear mixed model considering both the population structure and familial relationships between inbred lines. We assessed the ability of the method to limit the number of false positive associations on the basis of the two different Bayesian methods, the number of populations considered and different morphological traits while also assessing the power of the methodology to detect given additive effects. Finally, we applied this methodology to a set of eight pearl millet genes homologous to cereal flowering pathway genes. We found significant associations between several polymorphisms of the pearl millet PHYC gene and flowering time, spike length, and stem diameter in the inbred line panel. To validate this association, we performed a second association analysis in a different set of pearl millet individuals from Niger. We confirmed a significant association between genetic variation in this gene and these characters.

Selection for Earlier Flowering Crop Associated with Climatic Variations in the Sahel

Climate changes will have an impact on food production and will require costly adaptive responses. Adapting to a changing environment will be particularly challenging in sub-Saharan Africa where climate change is expected to have a major impact. However, one important phenomenon that is often overlooked and is poorly documented is the ability of agro-systems to rapidly adapt to environmental variations. Such an adaptation could proceed by the adoption of new varieties or by the adaptation of varieties to a changing environment. In this study, we analyzed these two processes in one of the driest agro-ecosystems in Africa, the Sahel. We performed a detailed study in Niger where pearl millet is the main crop and covers 65% of the cultivated area. To assess how the agro-system is responding to recent recurrent drought, we analyzed samples of pearl millet landraces collected in the same villages in 1976 and 2003 throughout the entire cultivated area of Niger. We studied phenological and morphological differences in the 1976 and 2003 collections by comparing them over three cropping seasons in a common garden experiment. We found no major changes in the main cultivated varieties or in their genetic diversity. However, we observed a significant shift in adaptive traits. Compared to the 1976 samples, samples collected in 2003 displayed a shorter lifecycle, and a reduction in plant and spike size. We also found that an early flowering allele at the PHYC locus increased in frequency between 1976 and 2003. The increase exceeded the effect of drift and sampling, suggesting a direct effect of selection for earliness on this gene. We conclude that recurrent drought can lead to selection for earlier flowering in a major Sahelian crop. Surprisingly, these results suggest that diffusion of crop varieties is not the main driver of short term adaptation to climatic variation.

Genetic basis of pearl millet adaptation along an environmental gradient investigated by a combination of genome scan and association mapping

Identifying the molecular bases of adaptation is a key issue in evolutionary biology. Genome scan is an efficient approach for identifying important molecular variation involved in adaptation. Association mapping also offers an opportunity to gain insight into genotype–phenotype relationships. Using these two approaches coupled with environmental data should help to come up with a refined picture of the evolutionary process underlying adaptation. In this study, we first conducted a selection scan analysis on a transcription factor gene family. We focused on the MADS‐box gene family, a gene family which plays a crucial role in vegetative and flower development. Twenty‐one pearl millet populations were sampled along an environmental gradient in West Africa. We identified one gene, i.e. PgMADS11, using Bayesian analysis to detect selection signatures. Polymorphism at this gene was also associated with flowering time variation in an association mapping framework. Finally, we found that PgMADS11 allele frequencies were closely associated with annual rainfall. Overall, we determined an efficient way to detect functional polymorphisms associated with climate variation in non‐model plants by combining genome scan and association mapping. These results should help monitor the impact of recent climatic changes on plant adaptation.

Role of seed flow on the pattern and dynamics of pearl millet (Pennisetum glaucum [L.] R. Br.) genetic diversity assessed by AFLP markers: a study in south-western Niger

We studied the regional genetic diversity and seed exchange dynamics of pearl millet landraces in south-western Niger. The genetic study was based on AFLP markers. We found significant genetic differentiation between landraces in different geographical areas of south-western Niger. However, the degree of differentiation was low insofar as only 1.9% of the total molecular diversity was due to regional differentiation, suggesting a relatively high gene flow. Anthropologic studies on farming practices have suggested that seed exchanges between farmers on a large geographical scale probably make a considerable contribution to this result. In order to test this hypothesis, the effects of seed exchange on the genetic diversity of landraces was analyzed on seed samples from two distant villages in contrasting areas of south-western Niger. Seeds imported by farmers into the southern village of Sina Koara did not differ significantly from locally grown landraces. By contrast, in the northern village of Alzou, several samples were genetically different from locally grown landraces and closer to southern accessions. These data suggest that the seed flow is preferentially from south to north, i.e. from an area with more favorable rainfall conditions. The potential consequences for the genetic diversity and adaptation of northern pearl millet landraces are discussed.

Highlighting the occurrence of tetraploidy in Acacia senegal (L.) Willd. and genetic variation patterns in its natural range revealed by DNA microsatellite markers

Acacia senegal (L.) Willd. is the main species producing the internationally traded gum arabic. Genetic studies of this species are rare and until now the chromosome number was thought to be diploid (2n = 2x = 26). Here, using chromosome number counting, we demonstrate for the first time that tetraploids (2n = 4x = 52) also occur in A. senegal. Nuclear and chloroplast microsatellite markers were used to estimate and compare genetic variation within this newly described polyploidy complex in the Sudano-Sahelian region in Africa. Genetic diversity was higher in diploids, suggesting that the formation of tetraploids is recent and that mutation–drift equilibrium has not yet been reached. The two cytotypes do not have the same genetic structure and are genetically differentiated. Among tetraploids, populations are greatly differentiated and do not share the same chlorotypes. Based on these results, we discuss recurrent formation of tetraploids from different diploid progenitors across the distribution range of A. senegal in the Sudano-Sahelian zone.

Impact of natural and human selection on the frequency of the F1 hybrid between cultivated and wild pearl millet (Pennisetum glaucum (L.) R. Br.)

AbstractIn the Sahel, pearl millet yields are affected by the proportion of hybrid phenotype plants resulting from genetic mixing between domesticated and wild forms. Man counteracts this mixing by applying a production method, the efficiency of which is quantified in this study. Under experimental conditions, cultivated and wild pearl millet were hybridised in order to obtain cultivated pearl millet seeds including a known proportion of F1 hybrids tagged by two different allozymes. These seeds were sown in the field and the cultivation was conducted following practices common in the Sahel. The evolution of the survival rate of plants and the frequency of hybrids were followed over several stages during the season: sowing, germinating, emergence, thinning, flowering and maturing of the seeds. Owing to plant mortality in the experiment, the average tendency was a hybrid frequency that decreased steadily in the first part of the growing season from 42% during germination, to 37% at emergence. It then fell to 17% after the thinning of the plantlets by the farmer. At the end of the cycle, after thinning, only 11% of mature plants were hybrids. Thus, under the combined pressures of natural and human selection, the frequency of hybrids in the field declined drastically. In interaction with natural pressure, the farmers practices of selection of seeds, sowing in pockets and thinning have the combined effect of heavily selecting the cultivated genotype and limiting without completely preventing the introgression of wild pearl millet genes into the cultivated genome.

Haplotype variation of cpDNA in the agamic grass complex Pennisetum section Brevivalvula (Poaceae)

The Brevivalvula section of the grass polyploid complex Pennisetum shows various reproductive systems, apomixis being the most widespread. Haplotype variation of chloroplast DNA was studied in the six morphological taxa (species) of this section by using RFLP analysis in 54 plants corresponding to 14 elementary taxa, each characterized on the basis of morphology and ploidy level. Two additional species, Pennisetum glaucum and P. purpureum, which belong to another section of the same genus, were analysed for comparison. In Brevivalvula, chloroplast DNA size was estimated to range between 130 and 133 kb. Thirteen of 15 distinct haplotypes identified in the study were specific to the Brevivalvula section. They were unequally distributed among the morphotypes, the ploidy levels and sampling sites. Within the Brevivalvula section, plants of P. setosum, which are perennial and reproduce vegetatively or by agamospermy, possessed a single specific haplotype. This species differed clearly from the five other morphological species, which are known to be annual, to show either sexual or agamospermic reproduction and which shared most of the 12 other haplotypes observed in the section, suggesting the occurrence of multiple hybridization events between the taxa. Chloroplast DNA variation was highly geographically structured, suggesting low seed dispersal between sites, whereas the substantial haplotype diversity observed in the sites may indicate that agamic reproduction is responsible for the maintenance of distinct genetically isolated clones. Haplotype classification using Wagner’s parsimony suggested the occurrence of bidirectional gene flow between the diploids and the polyploids, as reported already in other related apomictic complexes.

Differentiation between two sub-species of Acacia senegal complex: Acacia senegal (L.) Willd. and Acacia dudgeoni Craib ex Holland using morphological traits and molecular markers

The Acacia senegal complex is formed by closely related species of Acacia senegal (L.) Willd. These species share several botanical characters, so from a morphological point of view, there is no clear discontinuity between some of them. A. dudgeoni Craib ex Holland is one species of the A. senegal complex that was formerly described as A. senegal ssp. senegalensis var. samoryana (A. Chev.) Rob. In order to differentiate Acacia senegal from A. dudgeoni, we analyzed a range of morphological traits such as tree height and diameter in natural stands, and, at the nursery stage, seedling height, number of branches, main root depth, biomass dry weight and leaf characteristics. Within addition, molecular polymorphism analyses were conducted using 11 microsatellite markers. Leaf characteristics and molecular markers appear to be the most effective tools to distinguish A. senegal from A. dudgeoni. These tools can improve our understanding of the relationship between two species belonging to the same species complex.

Wild crop relative populations hot-spots of diversity are hot-spots of introgression in the case of pearl millet

Wild crop relatives are unique genetic resources for crop adaptation. Increasing pressure from agriculture threatens these populations both by reducing their habitats and by creating opportunities for wild-cultivated hybridization. In this study, we assessed the diversity of 38 wild pearl millet populations covering the whole known distribution of the species in Africa, which extends from Senegal to Sudan. Using genetic analyses of 10 cultivated varieties as control, we demonstrate the high diversity harbored by these wild populations. Diversity patterns suggest a diversity hot-spot in the southern part of the wild population’s range. However, this high wild genetic diversity could partly be explained by introgression from cultivated varieties. Such introgression is widespread in the Sahel. We validate the impact of cultivated introgression on the diversity of the wild population using a genetic introgression model. The introgression distorts the real assessment of the diversity of the wild population, and the burden of this gene flow compromises the long term survival of the wild populations’ original genome. Our study also questions the long term survival of the crop’s wild relatives.