Fatima Gaboun

H3ABioNet, a sustainable Pan-African Bioinformatics Network for Human Heredity and Health in Africa

The application of genomics technologies to medicine and biomedical research is increasing in popularity, made possible by new high-throughput genotyping and sequencing technologies and improved data analysis capabilities. Some of the greatest genetic diversity among humans, animals, plants, and microbiota occurs in Africa, yet genomic research outputs from the continent are limited. The Human Heredity and Health in Africa (H3Africa) initiative was established to drive the development of genomic research for human health in Africa, and through recognition of the critical role of bioinformatics in this process, spurred the establishment of H3ABioNet, a pan-African bioinformatics network for H3Africa. The limitations in bioinformatics capacity on the continent have been a major contributory factor to the lack of notable outputs in high-throughput biology research. Although pockets of high-quality bioinformatics teams have existed previously, the majority of research institutions lack experienced faculty who can train and supervise bioinformatics students. H3ABioNet aims to address this dire need, specifically in the area of human genetics and genomics, but knock-on effects are ensuring this extends to other areas of bioinformatics. Here, we describe the emergence of genomics research and the development of bioinformatics in Africa through H3ABioNet.

Development and Characterization of Microsatellite Loci for the Moroccan Endemic Endangered Species Argania spinosa (Sapotaceae)

Premise of the study: Microsatellite loci were developed for the Moroccan endemic endangered species Argania spinosa with a combination of a typical library enrichment procedure and a 454 GS FLX Titanium–based high-throughput sequencing approach. Methods and Results: A genomic DNA library was enriched and further screened using (GA)15, (GTA)8, and (TTC)8 biotin-labeled probes coupled with chemi-luminescence detection. To increase simple sequence repeat (SSR) loci number, an ultra-high-throughput sequencing-based approach was used. Evaluation of all primer pairs was performed with labeled dUTP on an ABI 3130xl sequencer. Eleven polymorphic SSR loci were selected out of 79 SSR regions and extensively characterized on 150 individuals from eight populations. Total alleles ranged from six to 19 alleles per locus while expected heterozygosity ranged from 0.618 to 0.869. Conclusions: The SSRs developed here will be used to further characterize the genetic diversity of A. spinosa across its distribution range, mainly in the southern part of Morocco and southwestern Algeria. They may also be transferable to other Sapotaceae species.

Validation of simple sequence repeats associated with quality traits in durum wheat

Over recent years, quality has become an important commercial issue for durum wheat breeders. Modern breeding methods are most efficient for producing and supplying the best quality raw materials to the pasta industry. Here we assessed the effectiveness of molecular marker-assisted selection of quality traits in durum wheat. To this end, DNA and quality trait markers were jointly used to analyze quality-related traits in a durum wheat collection. A total of 132 durum wheat (Triticum turgidum ssp. durum) Mediterranean landraces, international lines, and Moroccan cultivars were analyzed for seven important qualityrelated traits including thousand-kernel weight (TKW), test weight (TW), gluten strength, yellow pigment (YP), and grain protein content (GPC). Additionally, 18 simple sequence repeat (SSR) markers previously reported to be associated with different quality traits were analyzed. Of these, 14 (78%) were polymorphic and four were monomorphic. There were between two and seven alleles per locus, with an average of four alleles per locus. The average phenotypic variation value (R2) ranged from 2.81 to 20.43%. Association analysis identified nine markers significantly associated with TKW, TW, and YP, followed by eight markers associated with GPC, six markers associated with yellow index b, four markers associated with brightness L, and three markers associated with SDS-sedimentation volume. This study highlights the efficiency of SSR technology, which holds promise for a wide range of applications in marker-assisted wheat breeding programs.

Phenotypic biodiversity of an endemic wild pear, Pyrus mamorensis Trab., in North-Western Morocco using morphological descriptors

In this paper, we report on morphological diversity, ecology and flowering phenological records of an endangered and an endemic species of Morocco Pyrus mamorensis Trab. For this study, a survey was undertaken in North-Western Morocco (Mamora forest and Zaër region) whereby 67 accessions of P. mamorensis were sampled. A set of 33 genotypes of Pyrus spp. from the international collection INRA-Angers (France) of the genus Pyrus were also analyzed. The variability of the total of 100 accessions was assessed by twenty-six characters including fourteen qualitative and twelve quantitative traits. The results demonstrated high levels of morphological variation in the sampled accessions of P. mamorensis and established the relationships among the local germplasm using the UPGMA cluster analysis and the factorial discriminant analysis. Furthermore, we were able to distinguish three types of flowering in the Mamora forest: early, intermediate and late flowering type. Otherwise, the UPGMA classification comparing local accessions of P. mamorensis to the international collection led to the formation of four major groups showing the closest correspondence to their geographical origins: (1) The North African species represented by P. mamorensis, (2) The East Asian pea species, (3) The West Asian species and (4) The European species. These findings suggest the importance of implementing a conservation strategy preserving the genetic resources of wild pear in North-Western Morocco.

Evaluation of cocksfoot (Dactylis glomerata L.) population for drought survival and behavior

Climate change models predict frequent and intense droughts in the world. Development of drought-tolerant species and cultivars is necessary to cope with such changes. Forage grass species are affected, especially in the Mediterranean region. The aim of the present study was to investigate the diversity for drought survival, summer dormancy, and productivity within a cocksfoot population. The study was conducted in Morocco, under field conditions from 2011 to 2013. 283 genotypes of cocksfoot and parents were tested, characterized for dry matter yield, heading date, plant height, senescence, summer dormancy, and drought survival. Results exhibited a large variability between traits. 79% of the population had survived after severe drought summer while 57% yielded more than both parents. Also, 63% of the progeny had an intermediate score of summer dormancy estimated by senescence score. Large variability was also noticed for heading date and plant height. Several accessions combined a high yield and persistence under severe summer drought. Which explain the significant correlation (r = 0.18, P < 0.005) founded between total dry matter accumulated in 2013 and plant survival. Accordingly, our results showed that we can rise persistent and resilient genotypes among population with a good level of biomass.

Variability and genetic structure of a natural population of Citrus psorosis virus

In this study, we examined the population structure and genetic diversity of Citrus psorosis virus (CPsV) in Morocco. Analysis of the coat protein partial sequences of 34 isolates collected in the three main citrus-growing areas of Morocco showed that CPsV grouped in three major groups, with low within-group nucleotide diversity. Analyses indicated that CPsV genetic diversity is not structured by the geographic origin of the CPsV isolates. The genetic variation resulting from mutations depends on evolutionary forces that have contributed to the shaping of the genetic structure and diversity of the CPsV populations analyzed here: negative selective pressure for amino acid variation, recombination between variants or mixed infection, genetic drift induced by the founder effect associated with the transmission process, and migration explained by the exchange of infected propagative plant material.

Host differentiation and variability of Orobanche crenata populations from legume species in Morocco as revealed by cross infestation and molecular analysis

BACKGROUND Orobanche crenata represents a major biotic constraint to production of faba bean and lentil in Morocco. While this parasitic plant attacks both of these crops, the extent to which Orobanche biotypes specialise in parasitising specific crops is unknown. To address this question, we studied O. crenata that grew on different hosts and quantified their host specificity to faba bean and lentil. The virulence of O. crenata populations on each host was investigated through field trials, pot and Petri dishes assays. Genetic diversity of the parasite populations was also assessed through molecular analyses. RESULTS The two legume species showed distinct patterns of specificity. Faba bean was more susceptible to both O. crenata populations, while the specificity for lentil by lentil-grown O. crenata was evident at the final stage of the parasite life cycle as shown by correspondence factorial analyses. Considerable internal variation (81%) within O. crenata populations parasitising both legume species was observed by molecular analyses, but significant divergence (19%; Ø = 0.189; P = 0.010) among the populations was detected. CONCLUSION These results indicate that O. crenata can adapt to specific host species, which is important knowledge when developing integrated pest management practices for parasitic weed control.