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Benali A, El Haddad N, Patil SB, Goyal A, Hejjaoui K, El Baouchi A, Gaboun F, Taghouti M, Ouhssine M, Kumar S. Impact of Terminal Heat and Combined Heat-Drought Stress on Plant Growth, Yield, Grain Size, and Nutritional Quality in Chickpea ( Cicer arietinum L.). Plants (Basel) 2023; 12:3726. [PMID: 37960082 PMCID: PMC10650860 DOI: 10.3390/plants12213726] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/02/2023] [Revised: 09/14/2023] [Accepted: 09/15/2023] [Indexed: 11/15/2023]
Abstract
Chickpea is the third most consumed pulse and provides a kit of essential nutrients for an exponential population. High temperatures and drought stress are two major abiotic stresses that cause serious effects on chickpea growth and development. The comprehension of abiotic stresses' impact on chickpea productivity and nutritional quality will permit the selection of promising genotypes. The current study aimed to assess the impact of heat and drought stresses on plant growth, grain yield and its components, grain size, and nutritional quality in chickpea. For this purpose, 43 international chickpea genotypes were evaluated under normal, heat, and combined heat-drought stress conditions. The findings revealed a significant decrease of over 50% in plant height, biological yield, and seed yield under both stress conditions. Grain size and hundred-seed weight were the most heritable traits under normal, heat, and combined heat-drought stress. Proteins were accumulated under both stresses, evolving from 20.26% for normal conditions to 22.19% for heat stress and to 21.94% for combined heat-drought stress. For minerals, significant variation between treatments was observed for Mn, Mg, and Na. Our results also showed a significant impact of genotype and genotype-environment interaction factors only on K content. Using selection indices, 22 genotypes were identified as highly tolerant to the combined heat-drought stress, while eleven genotypes were heat-tolerant. Mineral profile analysis according to the contrasting tolerance clusters revealed decreased potassium content in susceptible genotypes, indicating genetic potential in the studied chickpea collection, ensuring tolerance to both stresses while maintaining good grain quality.
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Affiliation(s)
- Aouatif Benali
- Laboratory of Agro-Physiology, Biotechnology, Environment and Quality, Department of Biology, Faculty of Sciences, IbnTofail University, Kenitra 14000, Morocco;
- National Institute of Agricultural Research (INRA), Rabat-Instituts, Rue Hafiane Cherkaoui, Rabat 10101, Morocco
- International Center for Agricultural Research in the Dry Areas (ICARDA), Rabat-Instituts, Rue Hafiane Cherkaoui, Rabat 10101, Morocco; (N.E.H.); (S.B.P.); (A.G.)
| | - Noureddine El Haddad
- International Center for Agricultural Research in the Dry Areas (ICARDA), Rabat-Instituts, Rue Hafiane Cherkaoui, Rabat 10101, Morocco; (N.E.H.); (S.B.P.); (A.G.)
| | - Somanagouda B. Patil
- International Center for Agricultural Research in the Dry Areas (ICARDA), Rabat-Instituts, Rue Hafiane Cherkaoui, Rabat 10101, Morocco; (N.E.H.); (S.B.P.); (A.G.)
| | - Aakash Goyal
- International Center for Agricultural Research in the Dry Areas (ICARDA), Rabat-Instituts, Rue Hafiane Cherkaoui, Rabat 10101, Morocco; (N.E.H.); (S.B.P.); (A.G.)
| | - Kamal Hejjaoui
- AgroBioSciences, Mohammed VI Polytechnic University, Ben Guerir 43150, Morocco; (K.H.)
| | - Adil El Baouchi
- AgroBioSciences, Mohammed VI Polytechnic University, Ben Guerir 43150, Morocco; (K.H.)
| | - Fatima Gaboun
- National Institute of Agricultural Research (INRA), Rabat-Instituts, Rue Hafiane Cherkaoui, Rabat 10101, Morocco
| | - Mouna Taghouti
- National Institute of Agricultural Research (INRA), Rabat-Instituts, Rue Hafiane Cherkaoui, Rabat 10101, Morocco
| | - Mohammed Ouhssine
- Laboratory of Agro-Physiology, Biotechnology, Environment and Quality, Department of Biology, Faculty of Sciences, IbnTofail University, Kenitra 14000, Morocco;
| | - Shiv Kumar
- International Center for Agricultural Research in the Dry Areas (ICARDA), New Delhi 110012, India
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Khayi S, Armitage AD, Gaboun F, Meftah-kadmiri I, Lahlali R, Fokar M, Mentag R. Chromosome-scale assembly uncovers genomic compartmentation of Fusarium oxysporum f. sp. albedinis, the causal agent of Bayoud disease in date palm. Front Microbiol 2023; 14:1268051. [PMID: 37886058 PMCID: PMC10599148 DOI: 10.3389/fmicb.2023.1268051] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2023] [Accepted: 09/25/2023] [Indexed: 10/28/2023] Open
Abstract
Date palm (Phoenixdactylifera) is the most significant crop across North Africa and the Middle East. However, the crop faces a severe threat from Bayoud disease caused by the fungal pathogen Fusarium oxysporum f. sp. albedinis (FOA). FOA is a soil-borne fungus that infects the roots and vascular system of date palms, leading to widespread destruction of date palm plantations in North Africa over the last century. This is considered the most devastating pathogen of oasis agriculture in North Africa and responsible for loss of 13 million trees in Algeria and Morocco alone. In this study, we present a chromosome-scale high-quality genome assembly of the virulent isolate Foa 44, which provides valuable insights into understanding the genetic basis of Bayoud disease. The genome assembly consists of 11 chromosomes and 40 unplaced contigs, totalling 65,971,825 base pairs in size. It exhibits a GC ratio of 47.77% and a TE (transposable element) content of 17.30%. Through prediction and annotation, we identified 20,416 protein-coding genes. By combining gene and repeat densities analysis with alignment to Fusarium oxysporum f. sp. lycopersici (FOL) 4287 isolate genome sequence, we determined the core and lineage-specific compartments in Foa 44, shedding light on the genome structure of this pathogen. Furthermore, a phylogenomic analysis based on the 3,292 BUSCOs core genome revealed a distinct clade of FOA isolates within the Fusarium oxysporum species complex (FOSC). Notably, the genealogies of the five identified Secreted In Xylem (SIX) genes (1, 6, 9, 11 and 14) in FOA displayed a polyphyletic pattern, suggesting a horizontal inheritance of these effectors. These findings provide a valuable genomics toolbox for further research aimed at combatting the serious biotic constraints posed by FOA to date palm. This will pave the way for a deeper understanding of Bayoud disease and facilitate the development of effective diagnostic tools and control measures.
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Affiliation(s)
- Slimane Khayi
- Biotechnology Research Unit, Regional Center of Agricultural Research of Rabat, National Institute of Agricultural Research, Rabat, Morocco
| | - Andrew D. Armitage
- Natural Resources Institute, University of Greenwich, Chatham Maritime, Greenwich, United Kingdom
| | - Fatima Gaboun
- Biotechnology Research Unit, Regional Center of Agricultural Research of Rabat, National Institute of Agricultural Research, Rabat, Morocco
| | - Issam Meftah-kadmiri
- Plant and Microbial Biotechnology Center, Moroccan Foundation of Advanced Science Innovation and Research MAScIR, Ben Guerir, Morocco
- Plant and Soil Microbiome Sub-Program, AgroBioSciences, Mohammed VI Polytechnic University (UM6P), Ben Guerir, Morocco
| | - Rachid Lahlali
- Phytopathology Unit, Department of Plant Protection, Ecole Nationale D’Agriculture de Meknes, Meknès, Morocco
- Plant Pathology Laboratory, AgroBioSciences, College of Sustainable Agriculture and Environmental Sciences, Mohammed VI Polytechnic University, Ben Guerir, Morocco
| | - Mohamed Fokar
- Center for Biotechnology and Genomics, Texas Tech University, Lubbock, TX, United States
| | - Rachid Mentag
- Biotechnology Research Unit, Regional Center of Agricultural Research of Rabat, National Institute of Agricultural Research, Rabat, Morocco
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Ibrahimi M, Brhadda N, Ziri R, Fokar M, Iraqi D, Gaboun F, Labhilili M, Habach A, Meziani R, Elfadile J, Abdelwahd R, Diria G. Analysis of genetic diversity and population structure of Moroccan date palm (Phoenix dactylifera L.) using SSR and DAMD molecular markers. J Genet Eng Biotechnol 2023; 21:66. [PMID: 37217693 DOI: 10.1186/s43141-023-00516-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2023] [Accepted: 05/06/2023] [Indexed: 05/24/2023]
Abstract
BACKGROUND Date palm, oasis pivot, plays a vital socio-economic part in the southern area of Morocco. However, with climate change and drought intensity and frequency increasing, the Moroccan palm grove is threatened with significant genetic degradation. Genetic characterization of this resource is key element for the development of effective conservation and management strategies in the current circumstances of climate change and various biotic and abiotic stresses. To evaluate the genetic diversity of date palm populations collected from different Moroccan oases, we used simple sequence repeats (SSR) and directed amplification of mini-satellite DNA (DAMD) markers. Our results showed that used markers could efficiently assess genetic diversity in Phoenix dactylifera L. RESULTS A total of 249 and 471 bands were respectively scored for SSR and DAMD, of which 100% and 92.9% were polymorphic. The polymorphic information content (PIC = 0.95), generated by the SSR primer was nearly identical to that generated by the DAMD primer (PIC = 0.98). The resolving power (Rp) was higher in DAMD than SSR (29.46 and 19.51, respectively). Analysis of the molecular variance (AMOVA) based on the combined data sets for both markers revealed a higher variance within populations (75%) than among populations (25%). Principal coordinate analysis (PCoA) and the ascendant hierarchical classification showed that the population of Zagora and Goulmima regions were the closest populations. The STRUCTURE analysis clustering of the 283 tested samples into seven clusters based on their genetic composition. CONCLUSION The results drawn from this study will orient genotypes selection strategies for a successful future breeding and conservation program, particularly under climate change context.
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Affiliation(s)
- Maha Ibrahimi
- Biotechnology Unit, Regional Center of Agricultural Research of Rabat, National Institute of Agricultural Research (INRA), Rabat, Morocco
- Laboratory of Plant, Animal and Agro-Industry Productions, Faculty of Sciences, University of Ibn Tofail, Kenitra, Morocco
| | - Najiba Brhadda
- Laboratory of Plant, Animal and Agro-Industry Productions, Faculty of Sciences, University of Ibn Tofail, Kenitra, Morocco
| | - Rabea Ziri
- Laboratory of Plant, Animal and Agro-Industry Productions, Faculty of Sciences, University of Ibn Tofail, Kenitra, Morocco
| | - Mohamed Fokar
- Center for Biotechnology and Genomics, Texas Tech University, Lubbock, TX, USA
| | - Driss Iraqi
- Biotechnology Unit, Regional Center of Agricultural Research of Rabat, National Institute of Agricultural Research (INRA), Rabat, Morocco
| | - Fatima Gaboun
- Biotechnology Unit, Regional Center of Agricultural Research of Rabat, National Institute of Agricultural Research (INRA), Rabat, Morocco
| | - Mustapha Labhilili
- Biotechnology Unit, Regional Center of Agricultural Research of Rabat, National Institute of Agricultural Research (INRA), Rabat, Morocco
| | - Aicha Habach
- Biotechnology Unit, Regional Center of Agricultural Research of Rabat, National Institute of Agricultural Research (INRA), Rabat, Morocco
| | - Reda Meziani
- UR Oasis Systems, National Laboratory of Date Palm Tissues Culture, Regional Center of Agricultural Research of Errachidia, National Institute of Agricultural Research (INRA), Rabat, Morocco
| | - Jamal Elfadile
- UR Oasis Systems, National Laboratory of Date Palm Tissues Culture, Regional Center of Agricultural Research of Errachidia, National Institute of Agricultural Research (INRA), Rabat, Morocco
| | - Rabha Abdelwahd
- Biotechnology Unit, Regional Center of Agricultural Research of Rabat, National Institute of Agricultural Research (INRA), Rabat, Morocco
| | - Ghizlane Diria
- Biotechnology Unit, Regional Center of Agricultural Research of Rabat, National Institute of Agricultural Research (INRA), Rabat, Morocco.
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Saghir K, Abdelwahd R, Iraqi D, Lebkiri N, Gaboun F, El Goumi Y, Ibrahimi M, Abbas Y, Diria G. Assessment of genetic diversity among wild rose in Morocco using ISSR and DAMD markers. J Genet Eng Biotechnol 2022; 20:150. [DOI: 10.1186/s43141-022-00425-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2022] [Accepted: 10/08/2022] [Indexed: 11/06/2022]
Abstract
Abstract
Background
Morocco is considered one of the main biodiversity hotspots in the Mediterranean region and contains various plant species including wild and domestic Rosa. This genus is the most important among cultivated ornamental plants in the world, with a high economic value in cosmetics, pharmaceutical industries, and floriculture. In the present study, genetic diversity among the collected accessions of wild Rosa species in Morocco was assessed using Inter-Simple Sequence Repeat (ISSR) and Directed Amplification of Minisatellites DNA (DAMD) markers.
Results
Results confirmed that both markers used have a good efficiency to assess genetic diversity in wild roses. Ten ISSR and eight DAMD primers amplified 276 and 203 loci, with an average of 27.4 and 25 polymorphic alleles per primer, respectively. The polymorphic information content (PIC) values were 0.34 with ISSR and 0.31 with DAMD. Analysis of molecular variance (AMOVA) showed that genetic variation in wild rose occurs mainly within populations (86%) rather than between populations (14%). The region of Azrou (Middle Atlas of Morocco) is the area that registered the highest genetic diversity in the present study with He = 0.21. The 39 rose accessions were divided into three main groups with among-group similarity of 30%. Principal component analysis and the hierarchical classification were consistent with genetic relationships derived by structure analysis.
Conclusion
The findings revealed that the patterns of grouping are weakly correlated with geographical origin. ISSR and DAMD markers showed that the accessions have a good genetic diversity.
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Bennani S, Birouk A, Jlibene M, Sanchez-Garcia M, Nsarellah N, Gaboun F, Tadesse W. Drought-Tolerance QTLs Associated with Grain Yield and Related Traits in Spring Bread Wheat. Plants (Basel) 2022; 11:plants11070986. [PMID: 35406966 PMCID: PMC9002858 DOI: 10.3390/plants11070986] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/17/2022] [Revised: 03/03/2022] [Accepted: 03/14/2022] [Indexed: 06/12/2023]
Abstract
The present research aims to identify the efficient combination of drought-tolerance selection criteria and associated quantitative trait loci. A panel of 197 bread wheat genotypes was evaluated for yield- and drought-tolerance-related traits in two environments (favorable and semiarid) for 2 years (2015-2016). Grain number, biomass, number of fertile spikes per plant and ground cover exhibited a significant correlation with grain yield and constitute potential secondary selection criteria for yield under drought conditions. About 73 significant marker-trait associations were detected along various chromosomal positions. The markers "wsnp_Ex_Rep_c67786_66472676" and "ExcalibuR_c24593_1217" exhibited important genetic gains associated with yield increase under drought (11 and 7%, respectively). The markers "KukRi_c94792_127" and "wsnp_Ex_c298_580660" showed a significant correlation with grain yield, biomass and grain number and were associated with a significant increase in yield performance at the semiarid site (+6 and +7%, respectively). The ground cover was found associated with grain yield and biomass through the markers "wsnp_Ex_Rep_c67786_66472676" (+11%) and "KukRi_c49927_151" (+10%). One marker "TduRuM_contig25432_1377" on chromosome 5B at 20 cM was consistently correlated with the number of fertile spikes across both environments. Further research should be considered to validate the efficiency of these markers to undertake selection for drought tolerance under various environments and genetic backgrounds.
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Affiliation(s)
- Sahar Bennani
- Plant Breeding and Conservation of Phytogenetic Genetic Resources Department, National Institute of Agricultural Research, Rabat 10101, Morocco;
| | - Ahmed Birouk
- Department of Production, Protection and Biotechnology of Plants, Agronomy and Veterinary Hassan II Institute, Rabat 10101, Morocco;
| | - Mohammed Jlibene
- National Federation of Milling, Casablanca 20000, Morocco; (M.J.); (N.N.)
| | - Miguel Sanchez-Garcia
- Biodiversity and Crop Improvement Program, International Center for Agricultural Research in the Dry Areas, Rabat 10101, Morocco; (M.S.-G.); (W.T.)
| | | | - Fatima Gaboun
- Plant Breeding and Conservation of Phytogenetic Genetic Resources Department, National Institute of Agricultural Research, Rabat 10101, Morocco;
| | - Wuletaw Tadesse
- Biodiversity and Crop Improvement Program, International Center for Agricultural Research in the Dry Areas, Rabat 10101, Morocco; (M.S.-G.); (W.T.)
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Zelmat L, Mansi JM, Aouzal S, Gaboun F, Khayi S, Ibriz M, El Guilli M, Mentag R. Genetic Diversity and Population Structure of Moroccan Isolates Belong to Alternaria spp. Causing Black Rot and Brown Spot in Citrus. Int J Genomics 2021; 2021:9976969. [PMID: 34859097 PMCID: PMC8632404 DOI: 10.1155/2021/9976969] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2021] [Revised: 09/21/2021] [Accepted: 10/12/2021] [Indexed: 11/23/2022] Open
Abstract
Alternaria alternata is one of the most important fungi causing various diseases on citrus worldwide. In Morocco, Alternaria black rot (ABR) and Alternaria brown spot (ABS) are two major diseases causing serious losses in commercial cultivars of citrus. The aim of the present work was to study the genetic diversity and the population structure of isolates belonging to sect. Alternaria obtained from infected citrus fruits, collected from seven provinces at different locations in Morocco (markets, packinghouses, and orchards). Forty-five isolates were analyzed by sequence-related amplified polymorphism (SRAP) markers, and cluster analysis of DNA fragments was performed using UPGMA method and Jaccard coefficient. Cluster analysis revealed that isolates were classified in four distinct groups. AMOVA revealed also a large extent of variation within sect. Alternaria isolates (99%). The results demonstrate that no correlation was found among SRAP pattern, host, and geographical origin of these isolates. Population structure analyses showed that the Alternaria isolates from the same collection origin had almost a similar level of admixture.
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Affiliation(s)
- Lamyaa Zelmat
- Plant Pathology and Postharvest Quality laboratory, Plant Protection Research Unit, Regional Center of Agricultural Research of Kénitra, National Institue of Agricultural Research, El Menzeh Km 9, 14000, Kénitra, Morocco
- Biotechnology Research Unit, Regional Center of Agricultural Research of Rabat, National Institute of Agricultural Research, Avenue Ennasr, BP 415 Rabat Principale, 10090, Rabat, Morocco
- Department of Biology, Genetics and Biometrics Laboratory, Faculty of Sciences, Ibn Tofail University, Kénitra, Morocco
| | - Joseph Mbasani Mansi
- Biotechnology Research Unit, Regional Center of Agricultural Research of Rabat, National Institute of Agricultural Research, Avenue Ennasr, BP 415 Rabat Principale, 10090, Rabat, Morocco
- Department of Biology, Higher Institute of Medical Techniques (ISTM) Kinshasa, Democratic Republic of the Congo
| | - Sarra Aouzal
- Biotechnology Research Unit, Regional Center of Agricultural Research of Rabat, National Institute of Agricultural Research, Avenue Ennasr, BP 415 Rabat Principale, 10090, Rabat, Morocco
- Agro-Food and Health Laboratory, Faculty of Science and Techniques, Hassan First University of Settat, Settat, Morocco
| | - Fatima Gaboun
- Biotechnology Research Unit, Regional Center of Agricultural Research of Rabat, National Institute of Agricultural Research, Avenue Ennasr, BP 415 Rabat Principale, 10090, Rabat, Morocco
| | - Slimane Khayi
- Biotechnology Research Unit, Regional Center of Agricultural Research of Rabat, National Institute of Agricultural Research, Avenue Ennasr, BP 415 Rabat Principale, 10090, Rabat, Morocco
| | - Mohammed Ibriz
- Department of Biology, Genetics and Biometrics Laboratory, Faculty of Sciences, Ibn Tofail University, Kénitra, Morocco
| | - Mohammed El Guilli
- Plant Pathology and Postharvest Quality laboratory, Plant Protection Research Unit, Regional Center of Agricultural Research of Kénitra, National Institue of Agricultural Research, El Menzeh Km 9, 14000, Kénitra, Morocco
| | - Rachid Mentag
- Biotechnology Research Unit, Regional Center of Agricultural Research of Rabat, National Institute of Agricultural Research, Avenue Ennasr, BP 415 Rabat Principale, 10090, Rabat, Morocco
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Ait lhaj Z, Bchitou R, Gaboun F, Abdelwahd R, Benabdelouahab T, Kabbour MR, Pare P, Diria G, Bakhy K. Moroccan Strawberry Tree ( Arbutus unedo L.) Fruits: Nutritional Value and Mineral Composition. Foods 2021; 10:foods10102263. [PMID: 34681311 PMCID: PMC8534792 DOI: 10.3390/foods10102263] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2021] [Revised: 07/12/2021] [Accepted: 07/12/2021] [Indexed: 12/02/2022] Open
Abstract
The strawberry tree (Arbutus unedo L.), grown throughout the Mediterranean, produces edible fruit; as it is easily bruised, the sweet, reddish fruit is used mostly to prepare jams, marmalades and alcoholic beverages. As the genus is paraphyletic, phytochemical analysis can assist in defining the fruit composition with the species Arbutus unedo L. (A. unedo). Here we report on the carbohydrate, total sugar, protein, fat, fiber, ash, and mineral content of wild fruit, harvested from 45 specimens from five locations. The dominant nutrients were carbohydrates (78.2–84.8 g/100 g), total sugars (52.1–67.2 g/100 g) and dietary fiber (11.0–20.1 g/100 g). Other important nutrients supplied by A. unedo fruit include P, K, and Fe. The fruit was observed to contain health-promoting components providing 42 and 36%, of recommended daily allowance (RDA) for fiber and zinc, respectively, as well as iron and manganese, at levels exceeding minimum RDA. The free-sugar profile revealed high glucose followed by fructose content with minor amounts of sucrose (14, 11, and 6 g/100 g, respectively). Significant differences both between regions and within individuals were observed for several traits. The richness of fruit nutrients in A. unedo confers nutritional value and as such, a promising alternative fruit source.
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Affiliation(s)
- Zakaria Ait lhaj
- Research Unit on Plant Breeding and Conservation of Plant Genetic Resources and Biotechnology, National Institute of Agricultural Research (INRA), Rabat BP 6570, Morocco; (Z.A.l.); (F.G.); (R.A.); (T.B.); (M.R.K.); (G.D.)
- Center of Materials Science, Nanostructures Laboratory, Process Engineering and Environment, Faculty of Sciences, Université Mohammed V de Rabat Siège, Rabat 10000, Morocco;
| | - Rahma Bchitou
- Center of Materials Science, Nanostructures Laboratory, Process Engineering and Environment, Faculty of Sciences, Université Mohammed V de Rabat Siège, Rabat 10000, Morocco;
| | - Fatima Gaboun
- Research Unit on Plant Breeding and Conservation of Plant Genetic Resources and Biotechnology, National Institute of Agricultural Research (INRA), Rabat BP 6570, Morocco; (Z.A.l.); (F.G.); (R.A.); (T.B.); (M.R.K.); (G.D.)
| | - Rabha Abdelwahd
- Research Unit on Plant Breeding and Conservation of Plant Genetic Resources and Biotechnology, National Institute of Agricultural Research (INRA), Rabat BP 6570, Morocco; (Z.A.l.); (F.G.); (R.A.); (T.B.); (M.R.K.); (G.D.)
| | - Tarik Benabdelouahab
- Research Unit on Plant Breeding and Conservation of Plant Genetic Resources and Biotechnology, National Institute of Agricultural Research (INRA), Rabat BP 6570, Morocco; (Z.A.l.); (F.G.); (R.A.); (T.B.); (M.R.K.); (G.D.)
| | - Mohammed Rachid Kabbour
- Research Unit on Plant Breeding and Conservation of Plant Genetic Resources and Biotechnology, National Institute of Agricultural Research (INRA), Rabat BP 6570, Morocco; (Z.A.l.); (F.G.); (R.A.); (T.B.); (M.R.K.); (G.D.)
| | - Paul Pare
- Department of Chemistry & Biochemistry, Texas Tech University, Lubbock, TX 79409, USA;
| | - Ghizlane Diria
- Research Unit on Plant Breeding and Conservation of Plant Genetic Resources and Biotechnology, National Institute of Agricultural Research (INRA), Rabat BP 6570, Morocco; (Z.A.l.); (F.G.); (R.A.); (T.B.); (M.R.K.); (G.D.)
| | - Khadija Bakhy
- Research Unit on Plant Breeding and Conservation of Plant Genetic Resources and Biotechnology, National Institute of Agricultural Research (INRA), Rabat BP 6570, Morocco; (Z.A.l.); (F.G.); (R.A.); (T.B.); (M.R.K.); (G.D.)
- Correspondence: ; Tel.: +212-267-8981-039
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Amghar I, Ibriz M, Ibrahimi M, Boudra A, Gaboun F, Meziani R, Iraqi D, Mazri MA, Diria G, Abdelwahd R. In Vitro Root Induction from Argan ( Argania spinosa (L.) Skeels) Adventitious Shoots: Influence of Ammonium Nitrate, Auxins, Silver Nitrate and Putrescine, and Evaluation of Plantlet Acclimatization. Plants (Basel) 2021; 10:plants10061062. [PMID: 34073152 PMCID: PMC8227970 DOI: 10.3390/plants10061062] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 03/03/2021] [Revised: 03/24/2021] [Accepted: 03/29/2021] [Indexed: 06/12/2023]
Abstract
Argania spinosa (L.) Skeels is an endangered plant species endemic to Morocco. In recent years, attempts to develop in vitro regeneration systems for this species were made. However, rooting and acclimatization of in vitro plants have been a bottleneck for successful propagation. In the present study, the effects of different concentrations of auxins, putrescine, silver nitrate (AgNO3) and ammonium nitrate on the in vitro rooting of adventitious shoots of two argan genotypes "Mejji" and "R'zwa", were evaluated. The highest rooting percentages (86.6% in "Mejji" and 84.4% in "R'zwa") were observed on Murashige and Skoog (MS) medium modified by reducing the ammonium nitrate concentration and supplemented with 1.5 mg L-1 indole-3-butyric acid (IBA), 0.5 mg L-1 1-naphthalene acetic acid (NAA), 2 mg L-1 AgNO3 and 160 mg L-1 putrescine. This medium resulted in the development of a good root system after only 10 days of culture. Plantlet acclimatization was carried out using different substrate mixtures, and high survival rates (100%) were observed when the substrate contained either peat alone or a sand-peat mixture (1:1, w/w). The high percentages of rooting and acclimatization reported in the present study are of high importance for rapid and large-scale propagation of this endangered species.
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Affiliation(s)
- Ilham Amghar
- UR Biotechnologie, CRRA-Rabat, Institut National de la Recherche Agronomique, BP 6570, Rabat 10101, Morocco; (I.A.); (M.I.); (F.G.); (D.I.); (G.D.)
- Laboratoire de Génétique et Biométrie, Département de Biologie, Faculté des Sciences de Kénitra, Université Ibn Tofail, BP 133, Kenitra 14000, Morocco;
| | - Mohammed Ibriz
- Laboratoire de Génétique et Biométrie, Département de Biologie, Faculté des Sciences de Kénitra, Université Ibn Tofail, BP 133, Kenitra 14000, Morocco;
| | - Maha Ibrahimi
- UR Biotechnologie, CRRA-Rabat, Institut National de la Recherche Agronomique, BP 6570, Rabat 10101, Morocco; (I.A.); (M.I.); (F.G.); (D.I.); (G.D.)
| | | | - Fatima Gaboun
- UR Biotechnologie, CRRA-Rabat, Institut National de la Recherche Agronomique, BP 6570, Rabat 10101, Morocco; (I.A.); (M.I.); (F.G.); (D.I.); (G.D.)
| | - Reda Meziani
- Laboratoire National de Culture des Tissus du Palmier Dattier, UR Systèmes Oasiens, CRRA-Errachidia, Institut National de la Recherche Agronomique, Avenue Moulay Ali Cherif, BP 2, Errachidia 52000, Morocco;
| | - Driss Iraqi
- UR Biotechnologie, CRRA-Rabat, Institut National de la Recherche Agronomique, BP 6570, Rabat 10101, Morocco; (I.A.); (M.I.); (F.G.); (D.I.); (G.D.)
| | - Mouaad Amine Mazri
- Laboratoire de Biotechnologie Végétale, UR Agro-Biotechnologie, CRRA-Marrakech, Institut National de la Recherche Agronomique, BP 533, Marrakech 40000, Morocco;
| | - Ghizlane Diria
- UR Biotechnologie, CRRA-Rabat, Institut National de la Recherche Agronomique, BP 6570, Rabat 10101, Morocco; (I.A.); (M.I.); (F.G.); (D.I.); (G.D.)
| | - Rabha Abdelwahd
- UR Biotechnologie, CRRA-Rabat, Institut National de la Recherche Agronomique, BP 6570, Rabat 10101, Morocco; (I.A.); (M.I.); (F.G.); (D.I.); (G.D.)
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9
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Farouk I, Alsaleh A, Motowaj J, Gaboun F, Belkadi B, Filali Maltouf A, Kehel Z, Elouafi I, Nsarellah N, M Nachit M. Detection of grain yield QTLs in the durum population Lahn/Cham1 tested in contrasting environments. ACTA ACUST UNITED AC 2021; 45:65-78. [PMID: 33597823 PMCID: PMC7877719 DOI: 10.3906/biy-2008-41] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2020] [Accepted: 11/19/2020] [Indexed: 11/03/2022]
Abstract
Durum wheat (Triticum turgidum L. var durum) is tetraploid wheat (AABB); it is the main source of semolina and other pasta products. Grain yield in wheat is quantitatively inherited and influenced by the environment. The genetic map construction constitutes the essential step in identifying quantitative trait loci (QTLs) linked to complex traits, such as grain yield. The study aimed to construct a genetic linkage map of two parents that are widely grown durum cultivars (Lahn and Cham1) in the Mediterranean basin, which is characterized by varying climate changes. The genetic linkage map of Lahn/Cham1 population consisted of 112 recombinant inbred lines (RILs) and was used to determine QTLs linked to the grain yield in 11 contrasting environments (favorable, cold, dry, and hot). Simple sequence repeat (SSR) molecular markers were used to construct an anchor map, which was later enriched with single nucleotide polymorphisms (SNPs). The map was constructed with 247 SSRs and enriched with 1425 SNPs. The map covered 6122.22 cM. One hundred and twenty-six QTLs were detected on different chromosomes. Chromosomes 2A and 4B harbored the most significant grain yield QTLs. Furthermore, by comparison with several wheat mapping populations, all the A and B chromosomes of Lahn/Cham1 QTLs contributed to grain yield. The results showed that the detected QTLs can be used as a potential candidate for marker-assisted selection in durum breeding programs.
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Affiliation(s)
- Issame Farouk
- Laboratory of Microbiology and Molecular Biology, Department of Biology, Med V University, Rabat Morocco
| | - Ahmad Alsaleh
- Department of Science and Technology Bozok University, Yozgat Turkey
| | - Jihan Motowaj
- ICARDA, The International Center for Agricultural Research in the Dry Areas, Rabat Morocco
| | - Fatima Gaboun
- INRA, National Institute of Agronomical Research, Unity of Biotechnology Research, Rabat Morocco
| | - Bouchra Belkadi
- Laboratory of Microbiology and Molecular Biology, Department of Biology, Med V University, Rabat Morocco
| | - Abdelkarim Filali Maltouf
- Laboratory of Microbiology and Molecular Biology, Department of Biology, Med V University, Rabat Morocco
| | - Zakaria Kehel
- ICARDA, The International Center for Agricultural Research in the Dry Areas, Rabat Morocco
| | - Ismahane Elouafi
- ICBA, International Center for Biosaline Agriculture, Dubai United Arab Emirates
| | - Nasserelhaq Nsarellah
- INRA, National Institute of Agronomical Research, Unity of Biotechnology Research, Rabat Morocco
| | - Miloudi M Nachit
- ICARDA, The International Center for Agricultural Research in the Dry Areas, Rabat Morocco
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10
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Khayi S, Gaboun F, Pirro S, Tatusova T, El Mousadik A, Ghazal H, Mentag R. Complete Chloroplast Genome of Argania spinosa: Structural Organization and Phylogenetic Relationships in Sapotaceae. Plants (Basel) 2020; 9:E1354. [PMID: 33066261 PMCID: PMC7602116 DOI: 10.3390/plants9101354] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/18/2020] [Revised: 06/24/2020] [Accepted: 06/25/2020] [Indexed: 01/02/2023]
Abstract
Argania spinosa (Sapotaceae), an important endemic Moroccan oil tree, is a primary source of argan oil, which has numerous dietary and medicinal proprieties. The plant species occupies the mid-western part of Morocco and provides great environmental and socioeconomic benefits. The complete chloroplast (cp) genome of A. spinosa was sequenced, assembled, and analyzed in comparison with those of two Sapotaceae members. The A. spinosa cp genome is 158,848 bp long, with an average GC content of 36.8%. The cp genome exhibits a typical quadripartite and circular structure consisting of a pair of inverted regions (IR) of 25,945 bp in length separating small single-copy (SSC) and large single-copy (LSC) regions of 18,591 and 88,367 bp, respectively. The annotation of A. spinosa cp genome predicted 130 genes, including 85 protein-coding genes (CDS), 8 ribosomal RNA (rRNA) genes, and 37 transfer RNA (tRNA) genes. A total of 44 long repeats and 88 simple sequence repeats (SSR) divided into mononucleotides (76), dinucleotides (7), trinucleotides (3), tetranucleotides (1), and hexanucleotides (1) were identified in the A. spinosa cp genome. Phylogenetic analyses using the maximum likelihood (ML) method were performed based on 69 protein-coding genes from 11 species of Ericales. The results confirmed the close position of A. spinosa to the Sideroxylon genus, supporting the revisiting of its taxonomic status. The complete chloroplast genome sequence will be valuable for further studies on the conservation and breeding of this medicinally and culinary important species and also contribute to clarifying the phylogenetic position of the species within Sapotaceae.
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Affiliation(s)
- Slimane Khayi
- CRRA-Rabat, National Institute for Agricultural Research (INRA), Rabat 10101, Morocco;
| | - Fatima Gaboun
- CRRA-Rabat, National Institute for Agricultural Research (INRA), Rabat 10101, Morocco;
| | - Stacy Pirro
- Iridian Genomes, Inc., Bethesda, MD 20817, USA;
| | - Tatiana Tatusova
- National Center for Biotechnology Information, National Institutes of Health, Bethesda, MD 20817, USA;
| | - Abdelhamid El Mousadik
- Laboratory of Biotechnology and Valorization of Natural Resources (LBVRN), Faculty of Sciences, University Ibn Zohr, Agadir 80000, Morocco;
| | - Hassan Ghazal
- National Center for Scientific and Technological Research (CNRST), Rabat 10102, Morocco;
| | - Rachid Mentag
- CRRA-Rabat, National Institute for Agricultural Research (INRA), Rabat 10101, Morocco;
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11
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Drissi Touzani C, Fellahi S, Fassi Fihri O, Gaboun F, Khayi S, Mentag R, Lico C, Baschieri S, El Houadfi M, Ducatez M. Complete genome analysis and time scale evolution of very virulent infectious bursal disease viruses isolated from recent outbreaks in Morocco. Infect Genet Evol 2019; 77:104097. [PMID: 31678239 DOI: 10.1016/j.meegid.2019.104097] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/27/2019] [Revised: 10/02/2019] [Accepted: 10/27/2019] [Indexed: 12/25/2022]
Abstract
Emerging of very virulent infectious bursal disease virus (vvIBDV) genotype in poultry flocks in Morocco were characterized. VP2 sequence analysis showed that the strains of Moroccan vvIBDV genotypes clustered separately from classic and vaccine strains reference of IBDV. The full-length genome of four Moroccan vvIBDV strains was determined, in order to get a more exhaustive molecular characterization allowing to conduct the evolution time scale and speculations on their origin. In a phylogenetic tree, nucleotide sequences of segment A and B formed a common branch with those vvIBDV references strains published in GenBank, but they clearly grouped into a distinct subcluster. An alignment of deduced amino acid sequences segment B, confirmed the presence of the conserved TDN tripeptide found in all of the vvIBDV genotype and revealed the presence of 2 substitutions I472L and E688D specific for the vvIBDV Moroccan isolates. The deduced amino acid sequences of segment A genes showed the presence of the "signature" typical of the vvIBDV genotype and revealed the presence of 7 aa substitutions specific for the vvIBDV Moroccan strains. The evolution rate for IBDV VP2 gene was estimated at 5.875 × 10-4 substitutions/site/year. The estimation of the time to most common recent ancestor of Moroccan vvIBDV based on the VP2 sequences available was 31 years, corresponding to 3 years earlier than the first vvIBDV case detection in layers in the country.
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Affiliation(s)
- Charifa Drissi Touzani
- Unité de Pathologie Aviaire, Département de Pathologie et Santé Publique Vétérinaires, IAV Hassan II, BP 6202. Rabat- Instituts, 10000 Rabat, Morocco.
| | - Siham Fellahi
- Unité de Pathologie Aviaire, Département de Pathologie et Santé Publique Vétérinaires, IAV Hassan II, BP 6202. Rabat- Instituts, 10000 Rabat, Morocco.
| | - Ouafaa Fassi Fihri
- Unité de Pathologie Aviaire, Département de Pathologie et Santé Publique Vétérinaires, IAV Hassan II, BP 6202. Rabat- Instituts, 10000 Rabat, Morocco.
| | - Fatima Gaboun
- Unité de Biotechnologie, CRRA-Rabat, Institut National de la Recherche Agronomique INRA, Avenue Mohamed Belarbi Alaoui B.P 6356, Rabat- Instituts, 10101 Rabat, Morocco.
| | - Slimane Khayi
- Unité de Biotechnologie, CRRA-Rabat, Institut National de la Recherche Agronomique INRA, Avenue Mohamed Belarbi Alaoui B.P 6356, Rabat- Instituts, 10101 Rabat, Morocco.
| | - Rachid Mentag
- Unité de Biotechnologie, CRRA-Rabat, Institut National de la Recherche Agronomique INRA, Avenue Mohamed Belarbi Alaoui B.P 6356, Rabat- Instituts, 10101 Rabat, Morocco.
| | - Chiara Lico
- Laboratory of Biotechnology, Agenzia Nazionale per le Nuove tecnologie, l'Energia e lo Sviluppo economico sostenibile (ENEA), C.R. Casaccia, Via Anguillarese 301, 00123 Rome, Italy.
| | - Selene Baschieri
- Laboratory of Biotechnology, Agenzia Nazionale per le Nuove tecnologie, l'Energia e lo Sviluppo economico sostenibile (ENEA), C.R. Casaccia, Via Anguillarese 301, 00123 Rome, Italy.
| | - Mohammed El Houadfi
- Unité de Pathologie Aviaire, Département de Pathologie et Santé Publique Vétérinaires, IAV Hassan II, BP 6202. Rabat- Instituts, 10000 Rabat, Morocco.
| | - Mariette Ducatez
- Université de Toulouse, INRA, ENVT, IHAP, F- 31076 Toulouse, France.
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12
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Mbasani-Mansi J, Ennami M, Briache FZ, Gaboun F, Benbrahim N, Triqui ZEA, Mentag R. Characterization of genetic diversity and population structure of Moroccan lentil cultivars and landraces using molecular markers. Physiol Mol Biol Plants 2019; 25:965-974. [PMID: 31402820 PMCID: PMC6656841 DOI: 10.1007/s12298-019-00673-5] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/01/2019] [Revised: 04/23/2019] [Accepted: 05/01/2019] [Indexed: 06/10/2023]
Abstract
Knowledge of genetic diversity and population structure is a crucial step for an efficient use of available material in a plant breeding program and for germplasm conservation strategies. Current study undertakes an assessment of the genetic variations and population structure of Moroccan lentil including nine landraces and eight released varieties using sequence-related amplified polymorphism (SRAP) and random amplified polymorphism DNA (RAPD) markers. Results revealed that the two markers used have a good efficiency to assess genetic diversity in lentil. A total of 115 and 90 bands were respectively scored for SRAP and RAPD, of which 98.3% and 93.3% were polymorphic. The polymorphic information content values were 0.350 with SRAP and 0.326 with RAPD. Analysis of molecular variance based on the combined data sets of both markers revealed lower variations within (35%) than among (65%) landraces (PhiPT = 0.652), implying significant genetic differentiation between landraces. Principal coordinate analysis and the ascendant hierarchical classification clustered samples into groups that were consistent with the geographical origin of the cultivars. Population structure corroborated the main groups and confirmed the high differentiation among them. Moroccan lentil germplasm showed a wide genetic diversity that might be conserved and assessed for tolerance to biotic and abiotic stresses.
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Affiliation(s)
- Joseph Mbasani-Mansi
- Biotechnology Research Unit, National Institute of Agricultural Research, Rabat, Morocco
- Department of Biology, Faculty of Sciences, Plant and Microbial Biotechnology, Biodiversity and Environment Research Center, Mohammed V University, Rabat, Morocco
| | - Mounia Ennami
- Biotechnology Research Unit, National Institute of Agricultural Research, Rabat, Morocco
| | - Fatima Zahra Briache
- Biotechnology Research Unit, National Institute of Agricultural Research, Rabat, Morocco
- Department of Biology, Faculty of Sciences, Plant and Microbial Biotechnology, Biodiversity and Environment Research Center, Mohammed V University, Rabat, Morocco
| | - Fatima Gaboun
- Biotechnology Research Unit, National Institute of Agricultural Research, Rabat, Morocco
| | - Nadia Benbrahim
- Plant Breeding, Conservation and Valorization of Phyto-Genetic Resources Research Unit, National Institute of Agricultural Research, Rabat, Morocco
| | - Zine El Abidine Triqui
- Department of Biology, Faculty of Sciences, Plant and Microbial Biotechnology, Biodiversity and Environment Research Center, Mohammed V University, Rabat, Morocco
| | - Rachid Mentag
- Biotechnology Research Unit, National Institute of Agricultural Research, Rabat, Morocco
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13
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Zhouri L, Kallida R, Shaimi N, Barre P, Volaire F, Gaboun F, Fakiri M. Evaluation of cocksfoot ( Dactylis glomerata L.) population for drought survival and behavior. Saudi J Biol Sci 2019; 26:49-56. [PMID: 30622406 PMCID: PMC6319197 DOI: 10.1016/j.sjbs.2016.12.002] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2016] [Revised: 10/27/2016] [Accepted: 12/01/2016] [Indexed: 11/22/2022] Open
Abstract
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.
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Key Words
- ADM, autumn recovery dry matter
- ANOVA, one-way analysis of variance procedure
- Cocksfoot
- DS, drought survival
- Drought resistance
- HD, heading date
- Hybrids
- PCA, Principal Component Analyses
- PH, plant height
- Plants survival
- S/Sp, Norton index
- SD, summer dormancy
- SDI, summer dormancy index
- Senesc, senescence
- SpB, spring biomass
- Summer dormancy
- TDM, total dry matter
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Affiliation(s)
- Latifa Zhouri
- Laboratory of Agri-Food and Health, Faculty of Sciences and Techniques, Hassan 1st University, BP 577, 26000 Settat, Morocco
- Research Unit Animal Production and Forage, INRA, RCAR-Rabat, P.O. Box 6570, Rabat Institutes, 10101 Rabat, Morocco
| | - Rajae Kallida
- Research Unit Animal Production and Forage, INRA, RCAR-Rabat, P.O. Box 6570, Rabat Institutes, 10101 Rabat, Morocco
| | - Naima Shaimi
- Research Unit Plant Breeding, Conservation and Valorization of Plant Genetic Resources, INRA, RCAR-Rabat, P.O. Box 6570, Rabat Institutes, 10101 Rabat, Morocco
| | - Philippe Barre
- UR4 Multidisciplinary Research Unit Prairies and Forage Plants, National Institute for Agricultural Research, Lusignan, France
| | - Florence Volaire
- USC1338, Center of Functional and Evolutionary Ecology, UMR5175, National Institute for Agricultural Research, Montpellier, France
| | - Fatima Gaboun
- Research Unit Biotechnology, INRA, RCAR-Rabat, P.O. Box 6356, Rabat Institutes, 10101 Rabat, Morocco
| | - Malika Fakiri
- Laboratory of Agri-Food and Health, Faculty of Sciences and Techniques, Hassan 1st University, BP 577, 26000 Settat, Morocco
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14
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Drissi Touzani C, Fellahi S, Gaboun F, Fassi Fihri O, Baschieri S, Mentag R, El Houadfi M. Molecular characterization and phylogenetic analysis of very virulent infectious bursal disease virus circulating in Morocco during 2016-2017. Arch Virol 2018; 164:381-390. [PMID: 30367293 DOI: 10.1007/s00705-018-4076-3] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2018] [Accepted: 09/30/2018] [Indexed: 11/25/2022]
Abstract
Very virulent infectious bursal disease virus (vvIBDV), the cause of significant economic losses in many poultry-producing areas, has been present in Morocco since 1991. In spite of the introduction of vaccination, disease outbreaks are frequently observed. To ascertain if vaccines failure may be due to the emergence of new strains, the aim of this study was to perform for the first time the molecular characterization of vvIBDV strains circulating in Morocco by focusing on the hypervariable region (HVR) of the VP2 protein, which is frequently used for molecular epidemiology and phylogenetic studies. Field samples of haemorrhagic bursae of Fabricius were collected for molecular characterization in different parts of the country during 2016-2017 from 48 chicken flocks showing symptoms of disease. In a phylogenetic tree, nucleotide sequences containing the VP2 HVR of 13 samples that were positive for vvIBDV formed a common branch with those of vvIBDV references strains published in GenBank, but they clearly grouped into a distinct subcluster. An alignment of the deduced amino acid sequences, in addition to confirming the presence of the "signature" typical of the vvIBDV HVR, also revealed the presence of substitutions in hydrophilic loops that are known to be involved in the elicitation of neutralizing antibodies. One of these substitutions is unique to the Moroccan isolates. These results represent the first molecular characterization of vvIBDV isolates in Morocco and may indicate that one of the causes of vaccine ineffectiveness is antigenic drift.
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Affiliation(s)
- Charifa Drissi Touzani
- Unité de Pathologie Aviaire, Département de Pathologie et Santé Publique Vétérinaire, IAV Hassan II, BP 6202, Rabat-Instituts, 10000, Rabat, Morocco
- Unité de Biotechnologie, CRRA-Rabat, Institut National de la Recherche Agronomique INRA, Avenue Mohamed Belarbi Alaoui, Rabat-Instituts, B.P 6356, 10101, Rabat, Morocco
| | - Siham Fellahi
- Unité de Pathologie Aviaire, Département de Pathologie et Santé Publique Vétérinaire, IAV Hassan II, BP 6202, Rabat-Instituts, 10000, Rabat, Morocco
| | - Fatima Gaboun
- Unité de Biotechnologie, CRRA-Rabat, Institut National de la Recherche Agronomique INRA, Avenue Mohamed Belarbi Alaoui, Rabat-Instituts, B.P 6356, 10101, Rabat, Morocco
| | - Ouafaa Fassi Fihri
- Unité de Pathologie Aviaire, Département de Pathologie et Santé Publique Vétérinaire, IAV Hassan II, BP 6202, Rabat-Instituts, 10000, Rabat, Morocco
| | - Selene Baschieri
- Laboratory of Biotechnology, Agenzia Nazionale per le Nuove tecnologie, l'Energia e lo Sviluppo economico sostenibile (ENEA), C.R. Casaccia, Via Anguillarese 301, 00123, Rome, Italy
| | - Rachid Mentag
- Unité de Biotechnologie, CRRA-Rabat, Institut National de la Recherche Agronomique INRA, Avenue Mohamed Belarbi Alaoui, Rabat-Instituts, B.P 6356, 10101, Rabat, Morocco
| | - Mohammed El Houadfi
- Unité de Pathologie Aviaire, Département de Pathologie et Santé Publique Vétérinaire, IAV Hassan II, BP 6202, Rabat-Instituts, 10000, Rabat, Morocco.
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15
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Khayi S, Azza NE, Gaboun F, Pirro S, Badad O, Claros MG, Lightfoot DA, Unver T, Chaouni B, Merrouch R, Rahim B, Essayeh S, Ganoudi M, Abdelwahd R, Diria G, Mdarhi MA, Labhilili M, Iraqi D, Mouhaddab J, Sedrati H, Memari M, Hamamouch N, Alché JDD, Boukhatem N, Mrabet R, Dahan R, Legssyer A, Khalfaoui M, Badraoui M, Van de Peer Y, Tatusova T, El Mousadik A, Mentag R, Ghazal H. First draft genome assembly of the Argane tree ( Argania spinosa). F1000Res 2018; 7:1310. [PMID: 32509273 PMCID: PMC7238458 DOI: 10.12688/f1000research.15719.2] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 04/22/2020] [Indexed: 11/20/2022] Open
Abstract
Background: The Argane tree ( Argania spinosa L. Skeels) is an endemic tree of mid-western Morocco that plays an important socioeconomic and ecologic role for a dense human population in an arid zone. Several studies confirmed the importance of this species as a food and feed source and as a resource for both pharmaceutical and cosmetic compounds. Unfortunately, the argane tree ecosystem is facing significant threats from environmental changes (global warming, over-population) and over-exploitation. Limited research has been conducted, however, on argane tree genetics and genomics, which hinders its conservation and genetic improvement. Methods: Here, we present a draft genome assembly of A. spinosa. A reliable reference genome of A. spinosa was created using a hybrid de novo assembly approach combining short and long sequencing reads. Results: In total, 144 Gb Illumina HiSeq reads and 7.6 Gb PacBio reads were produced and assembled. The final draft genome comprises 75 327 scaffolds totaling 671 Mb with an N50 of 49 916 kb. The draft assembly is close to the genome size estimated by k-mers distribution and covers 89% of complete and 4.3 % of partial Arabidopsis orthologous groups in BUSCO. Conclusion: The A. spinosa genome will be useful for assessing biodiversity leading to efficient conservation of this endangered endemic tree. Furthermore, the genome may enable genome-assisted cultivar breeding, and provide a better understanding of important metabolic pathways and their underlying genes for both cosmetic and pharmacological.
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Affiliation(s)
- Slimane Khayi
- Biotechnology Unit, National Institute of Agricultural Research (INRA), Rabat, Morocco, Morocco
| | - Nour Elhouda Azza
- Laboratory of Biotechnology and Valorization of Natural Resources (LBVRN), Faculty of Sciences, University Ibn Zohr, Agadir, Morocco.,Laboratory of Physiology, Genetics & Ethnopharmacology (LPGE), Faculty of Sciences, University Mohamed Premier, Oujda, Morocco
| | - Fatima Gaboun
- Biotechnology Unit, National Institute of Agricultural Research (INRA), Rabat, Morocco, Morocco
| | - Stacy Pirro
- Iridian Genomes, Inc., Bethesda, MD, 20817, USA
| | - Oussama Badad
- Laboratory of Physiology, Genetics & Ethnopharmacology (LPGE), Faculty of Sciences, University Mohamed Premier, Oujda, Morocco.,Department of Plant, Soil and Agricultural Systems, Southern Illinois University, Carbondale, IL, 62901, USA.,Laboratory of Plant Physiology, Faculty of Sciences, University Mohamed V in Rabat, Rabat, 10000, Morocco
| | - M Gonzalo Claros
- Department of Molecular Biology and Biochemistry, and Plataforma Andaluza de Bioinformática, University of Malaga, Malaga, Spain
| | - David A Lightfoot
- Department of Plant, Soil and Agricultural Systems, Southern Illinois University, Carbondale, IL, 62901, USA
| | - Turgay Unver
- International Biomedicine and Genome Institute (iBG-izmir), Dokuz Eylül University, Current address: Egitim Mah. Ekrem Guer Sok. 26/3 Balcova, Izmir, Turkey
| | - Bouchra Chaouni
- Laboratory of Physiology, Genetics & Ethnopharmacology (LPGE), Faculty of Sciences, University Mohamed Premier, Oujda, Morocco.,Laboratory of Plant Physiology, Faculty of Sciences, University Mohamed V in Rabat, Rabat, 10000, Morocco
| | - Redouane Merrouch
- National Center for Scientific and Technological Research (CNRST), Rabat, Morocco
| | - Bouchra Rahim
- National Center for Scientific and Technological Research (CNRST), Rabat, Morocco
| | - Soumaya Essayeh
- Polydisciplinary Faculty of Nador, University Mohamed Premier, Nador, Morocco
| | - Matika Ganoudi
- Biotechnology Unit, National Institute of Agricultural Research (INRA), Rabat, Morocco, Morocco
| | - Rabha Abdelwahd
- Biotechnology Unit, National Institute of Agricultural Research (INRA), Rabat, Morocco, Morocco
| | - Ghizlane Diria
- Biotechnology Unit, National Institute of Agricultural Research (INRA), Rabat, Morocco, Morocco
| | - Meriem Alaoui Mdarhi
- Biotechnology Unit, National Institute of Agricultural Research (INRA), Rabat, Morocco, Morocco
| | - Mustapha Labhilili
- Biotechnology Unit, National Institute of Agricultural Research (INRA), Rabat, Morocco, Morocco
| | - Driss Iraqi
- Biotechnology Unit, National Institute of Agricultural Research (INRA), Rabat, Morocco, Morocco
| | - Jamila Mouhaddab
- Laboratory of Biotechnology and Valorization of Natural Resources (LBVRN), Faculty of Sciences, University Ibn Zohr, Agadir, Morocco
| | - Hayat Sedrati
- National School of Computer Sciences & Systems Analysis, University Mohammed V in Rabat, Rabat, Morocco
| | - Majid Memari
- Research Computing and Cyber infrastructure, Computer Science Department, Southern Illinois University, Carbondale, IL, 62901, USA
| | - Noureddine Hamamouch
- Polydisciplinary Faculty, Sultan Moulay Slimane University, Beni-Mellal, Morocco
| | - Juan de Dios Alché
- Estación Experimental del Zaidín, Consejo Superior de Investigaciones Científicas (CSIC), Granada, Spain
| | - Noureddine Boukhatem
- Laboratory of Physiology, Genetics & Ethnopharmacology (LPGE), Faculty of Sciences, University Mohamed Premier, Oujda, Morocco
| | - Rachid Mrabet
- Biotechnology Unit, National Institute of Agricultural Research (INRA), Rabat, Morocco, Morocco
| | - Rachid Dahan
- Biotechnology Unit, National Institute of Agricultural Research (INRA), Rabat, Morocco, Morocco
| | - Adelkhaleq Legssyer
- Laboratory of Physiology, Genetics & Ethnopharmacology (LPGE), Faculty of Sciences, University Mohamed Premier, Oujda, Morocco
| | - Mohamed Khalfaoui
- National Center for Scientific and Technological Research (CNRST), Rabat, Morocco
| | - Mohamed Badraoui
- Biotechnology Unit, National Institute of Agricultural Research (INRA), Rabat, Morocco, Morocco
| | - Yves Van de Peer
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Ghent, B-9052 Ghent, Belgium, Belgium.,VIB Center for Plant Systems Biology, Technologiepark 927, Ghent, B-9052, Belgium.,Department of Genetics, Genomics Research Institute, University of Pretoria, Pretoria, 0028, South Africa
| | - Tatiana Tatusova
- National Center for Biotechnology Information, National Institutes of Health, Bethesda, MD, 20817, USA
| | - Abdelhamid El Mousadik
- Laboratory of Biotechnology and Valorization of Natural Resources (LBVRN), Faculty of Sciences, University Ibn Zohr, Agadir, Morocco
| | - Rachid Mentag
- Biotechnology Unit, National Institute of Agricultural Research (INRA), Rabat, Morocco, Morocco
| | - Hassan Ghazal
- Laboratory of Biotechnology and Valorization of Natural Resources (LBVRN), Faculty of Sciences, University Ibn Zohr, Agadir, Morocco.,Laboratory of Physiology, Genetics & Ethnopharmacology (LPGE), Faculty of Sciences, University Mohamed Premier, Oujda, Morocco.,Iridian Genomes, Inc., Bethesda, MD, 20817, USA.,National Center for Scientific and Technological Research (CNRST), Rabat, Morocco
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Khayi S, Azza NE, Gaboun F, Pirro S, Badad O, Claros MG, Lightfoot DA, Unver T, Chaouni B, Merrouch R, Rahim B, Essayeh S, Ganoudi M, Abdelwahd R, Diria G, Mdarhi MA, Labhilili M, Iraqi D, Mouhaddab J, Sedrati H, Memari M, Hamamouch N, Alché JDD, Boukhatem N, Mrabet R, Dahan R, Legssyer A, Khalfaoui M, Badraoui M, Van de Peer Y, Tatusova T, El Mousadik A, Mentag R, Ghazal H. First draft genome assembly of the Argane tree ( Argania spinosa). F1000Res 2018; 7:1310. [PMID: 32509273 DOI: 10.12688/f1000research.15719.1] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 08/02/2018] [Indexed: 11/20/2022] Open
Abstract
Background: The Argane tree ( Argania spinosa L. Skeels) is an endemic tree of mid-western Morocco that plays an important socioeconomic and ecologic role for a dense human population in an arid zone. Several studies confirmed the importance of this species as a food and feed source and as a resource for both pharmaceutical and cosmetic compounds. Unfortunately, the argane tree ecosystem is facing significant threats from environmental changes (global warming, over-population) and over-exploitation. Limited research has been conducted, however, on argane tree genetics and genomics, which hinders its conservation and genetic improvement. Methods: Here, we present a draft genome assembly of A. spinosa. A reliable reference genome of A. spinosa was created using a hybrid de novo assembly approach combining short and long sequencing reads. Results: In total, 144 Gb Illumina HiSeq reads and 7.6 Gb PacBio reads were produced and assembled. The final draft genome comprises 75 327 scaffolds totaling 671 Mb with an N50 of 49 916 kb. The draft assembly is close to the genome size estimated by k-mers distribution and covers 89% of complete and 4.3 % of partial Arabidopsis orthologous groups in BUSCO. Conclusion: The A. spinosa genome will be useful for assessing biodiversity leading to efficient conservation of this endangered endemic tree. Furthermore, the genome may enable genome-assisted cultivar breeding, and provide a better understanding of important metabolic pathways and their underlying genes for both cosmetic and pharmacological.
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Affiliation(s)
- Slimane Khayi
- Biotechnology Unit, National Institute of Agricultural Research (INRA), Rabat, Morocco, Morocco
| | - Nour Elhouda Azza
- Laboratory of Biotechnology and Valorization of Natural Resources (LBVRN), Faculty of Sciences, University Ibn Zohr, Agadir, Morocco.,Laboratory of Physiology, Genetics & Ethnopharmacology (LPGE), Faculty of Sciences, University Mohamed Premier, Oujda, Morocco
| | - Fatima Gaboun
- Biotechnology Unit, National Institute of Agricultural Research (INRA), Rabat, Morocco, Morocco
| | - Stacy Pirro
- Iridian Genomes, Inc., Bethesda, MD, 20817, USA
| | - Oussama Badad
- Laboratory of Physiology, Genetics & Ethnopharmacology (LPGE), Faculty of Sciences, University Mohamed Premier, Oujda, Morocco.,Department of Plant, Soil and Agricultural Systems, Southern Illinois University, Carbondale, IL, 62901, USA.,Laboratory of Plant Physiology, Faculty of Sciences, University Mohamed V in Rabat, Rabat, 10000, Morocco
| | - M Gonzalo Claros
- Department of Molecular Biology and Biochemistry, and Plataforma Andaluza de Bioinformática, University of Malaga, Malaga, Spain
| | - David A Lightfoot
- Department of Plant, Soil and Agricultural Systems, Southern Illinois University, Carbondale, IL, 62901, USA
| | - Turgay Unver
- International Biomedicine and Genome Institute (iBG-izmir), Dokuz Eylül University, Current address: Egitim Mah. Ekrem Guer Sok. 26/3 Balcova, Izmir, Turkey
| | - Bouchra Chaouni
- Laboratory of Physiology, Genetics & Ethnopharmacology (LPGE), Faculty of Sciences, University Mohamed Premier, Oujda, Morocco.,Laboratory of Plant Physiology, Faculty of Sciences, University Mohamed V in Rabat, Rabat, 10000, Morocco
| | - Redouane Merrouch
- National Center for Scientific and Technological Research (CNRST), Rabat, Morocco
| | - Bouchra Rahim
- National Center for Scientific and Technological Research (CNRST), Rabat, Morocco
| | - Soumaya Essayeh
- Polydisciplinary Faculty of Nador, University Mohamed Premier, Nador, Morocco
| | - Matika Ganoudi
- Biotechnology Unit, National Institute of Agricultural Research (INRA), Rabat, Morocco, Morocco
| | - Rabha Abdelwahd
- Biotechnology Unit, National Institute of Agricultural Research (INRA), Rabat, Morocco, Morocco
| | - Ghizlane Diria
- Biotechnology Unit, National Institute of Agricultural Research (INRA), Rabat, Morocco, Morocco
| | - Meriem Alaoui Mdarhi
- Biotechnology Unit, National Institute of Agricultural Research (INRA), Rabat, Morocco, Morocco
| | - Mustapha Labhilili
- Biotechnology Unit, National Institute of Agricultural Research (INRA), Rabat, Morocco, Morocco
| | - Driss Iraqi
- Biotechnology Unit, National Institute of Agricultural Research (INRA), Rabat, Morocco, Morocco
| | - Jamila Mouhaddab
- Laboratory of Biotechnology and Valorization of Natural Resources (LBVRN), Faculty of Sciences, University Ibn Zohr, Agadir, Morocco
| | - Hayat Sedrati
- National School of Computer Sciences & Systems Analysis, University Mohammed V in Rabat, Rabat, Morocco
| | - Majid Memari
- Research Computing and Cyber infrastructure, Computer Science Department, Southern Illinois University, Carbondale, IL, 62901, USA
| | - Noureddine Hamamouch
- Polydisciplinary Faculty, Sultan Moulay Slimane University, Beni-Mellal, Morocco
| | - Juan de Dios Alché
- Estación Experimental del Zaidín, Consejo Superior de Investigaciones Científicas (CSIC), Granada, Spain
| | - Noureddine Boukhatem
- Laboratory of Physiology, Genetics & Ethnopharmacology (LPGE), Faculty of Sciences, University Mohamed Premier, Oujda, Morocco
| | - Rachid Mrabet
- Biotechnology Unit, National Institute of Agricultural Research (INRA), Rabat, Morocco, Morocco
| | - Rachid Dahan
- Biotechnology Unit, National Institute of Agricultural Research (INRA), Rabat, Morocco, Morocco
| | - Adelkhaleq Legssyer
- Laboratory of Physiology, Genetics & Ethnopharmacology (LPGE), Faculty of Sciences, University Mohamed Premier, Oujda, Morocco
| | - Mohamed Khalfaoui
- National Center for Scientific and Technological Research (CNRST), Rabat, Morocco
| | - Mohamed Badraoui
- Biotechnology Unit, National Institute of Agricultural Research (INRA), Rabat, Morocco, Morocco
| | - Yves Van de Peer
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Ghent, B-9052 Ghent, Belgium, Belgium.,VIB Center for Plant Systems Biology, Technologiepark 927, Ghent, B-9052, Belgium.,Department of Genetics, Genomics Research Institute, University of Pretoria, Pretoria, 0028, South Africa
| | - Tatiana Tatusova
- National Center for Biotechnology Information, National Institutes of Health, Bethesda, MD, 20817, USA
| | - Abdelhamid El Mousadik
- Laboratory of Biotechnology and Valorization of Natural Resources (LBVRN), Faculty of Sciences, University Ibn Zohr, Agadir, Morocco
| | - Rachid Mentag
- Biotechnology Unit, National Institute of Agricultural Research (INRA), Rabat, Morocco, Morocco
| | - Hassan Ghazal
- Laboratory of Biotechnology and Valorization of Natural Resources (LBVRN), Faculty of Sciences, University Ibn Zohr, Agadir, Morocco.,Laboratory of Physiology, Genetics & Ethnopharmacology (LPGE), Faculty of Sciences, University Mohamed Premier, Oujda, Morocco.,Iridian Genomes, Inc., Bethesda, MD, 20817, USA.,National Center for Scientific and Technological Research (CNRST), Rabat, Morocco
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Rabeh K, Gaboun F, Belkadi B, Filali-Maltouf A. In Silico development of new SSRs primer for aquaporin linked to drought tolerance in plants. Plant Signal Behav 2018; 13:e1536630. [PMID: 30380988 PMCID: PMC6279315 DOI: 10.1080/15592324.2018.1536630] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/05/2023]
Abstract
Plants are exposed to various stress factors including biotic and abiotic stresses. Drought is a limiting factor that minimizes the development and growth of several plants in arid and semi-arid regions. Stress response is usually occur at different levels, Morphological, physiological and biochemical while at the molecular level a large number of genes are involved. This study aims at developing a new SSR primer for aquaporin related to drought stress in plants. A total of 177 complete coding sequences (CDS) available in the NCBI database are downloaded. After analyzing with BLAST, 163 sequences are selected. 1294 SSR derived from these sequences are characterized with MISA and indicating that all sequences contained SSRs. The most abundant SSR has been tetra-nucleotide repeat motif (36%) and among all the tetra-nucleotide repeats, the motif AAAG/CTTT was the most common type, whereas in tri-nucleotide, the motif CCG/CGG has been the predominate type. By using Primer3, 1120 primer pairs are generated and after analyzing, only 735 non redundant primer pairs that present the good characteristics are selected. Among them, some of the pairs of primers are randomly selected and validated on DNA of various species using PCR and agarose gel.
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Affiliation(s)
- Karim Rabeh
- Laboratory of Microbiology and Molecular Biology, Faculty of Sciences, Mohammed V University, Rabat, Morocco
| | - Fatima Gaboun
- Biotechnology Unit, National Institute for Agronomic Research (INRA), Rabat, Morocco
| | - Bouchra Belkadi
- Laboratory of Microbiology and Molecular Biology, Faculty of Sciences, Mohammed V University, Rabat, Morocco
| | - Abdelkarim Filali-Maltouf
- Laboratory of Microbiology and Molecular Biology, Faculty of Sciences, Mohammed V University, Rabat, Morocco
- CONTACT Abdelkarim Filali-Maltouf ; a.
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Ennami M, Briache FZ, Gaboun F, Abdelwahd R, Ghaouti L, Belqadi L, Westwood J, Mentag R. Host differentiation and variability of Orobanche crenata populations from legume species in Morocco as revealed by cross-infestation and molecular analysis. Pest Manag Sci 2017; 73:1753-1763. [PMID: 28139072 DOI: 10.1002/ps.4536] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/28/2016] [Revised: 11/22/2016] [Accepted: 01/24/2017] [Indexed: 06/06/2023]
Abstract
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. © 2017 Society of Chemical Industry.
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Affiliation(s)
- Mounia Ennami
- National Institute of Agricultural Research (INRA), Biotechnology Unit, CRRA-Rabat, Morocco
- Agronomic and Veterinary Institute Hassan II (IAV), Plant Biotechnology Department, Rabat, Morocco
| | - Fatima Zahra Briache
- National Institute of Agricultural Research (INRA), Biotechnology Unit, CRRA-Rabat, Morocco
| | - Fatima Gaboun
- National Institute of Agricultural Research (INRA), Biotechnology Unit, CRRA-Rabat, Morocco
| | - Rabha Abdelwahd
- National Institute of Agricultural Research (INRA), Biotechnology Unit, CRRA-Rabat, Morocco
| | - Lamiae Ghaouti
- Agronomic and Veterinary Institute Hassan II (IAV), Plant Biotechnology Department, Rabat, Morocco
| | - Loubna Belqadi
- Agronomic and Veterinary Institute Hassan II (IAV), Plant Biotechnology Department, Rabat, Morocco
| | - James Westwood
- Virginia Tech, Department of Plant Pathology, Physiology and Weed Science, Blacksburg, VA, USA
| | - Rachid Mentag
- National Institute of Agricultural Research (INRA), Biotechnology Unit, CRRA-Rabat, Morocco
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Amallah L, Taghouti M, Rhrib K, Gaboun F, Arahou M, Hassikou R, Diria G. Validation of simple sequence repeats associated with quality traits in durum wheat. ACTA ACUST UNITED AC 2016. [DOI: 10.1007/s12892-016-0096-2] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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Mulder NJ, Adebiyi E, Alami R, Benkahla A, Brandful J, Doumbia S, Everett D, Fadlelmola FM, Gaboun F, Gaseitsiwe S, Ghazal H, Hazelhurst S, Hide W, Ibrahimi A, Jaufeerally Fakim Y, Jongeneel CV, Joubert F, Kassim S, Kayondo J, Kumuthini J, Lyantagaye S, Makani J, Mansour Alzohairy A, Masiga D, Moussa A, Nash O, Ouwe Missi Oukem-Boyer O, Owusu-Dabo E, Panji S, Patterton H, Radouani F, Sadki K, Seghrouchni F, Tastan Bishop Ö, Tiffin N, Ulenga N. H3ABioNet, a sustainable pan-African bioinformatics network for human heredity and health in Africa. Genome Res 2015; 26:271-7. [PMID: 26627985 PMCID: PMC4728379 DOI: 10.1101/gr.196295.115] [Citation(s) in RCA: 78] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2015] [Accepted: 11/25/2015] [Indexed: 11/24/2022]
Abstract
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.
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Affiliation(s)
- Nicola J Mulder
- Computational Biology Group, Department of Integrative Biomedical Sciences, Institute of Infectious Disease and Molecular Medicine, Faculty of Health Sciences, University of Cape Town, Cape Town, South Africa 7925
| | - Ezekiel Adebiyi
- Covenant University Bioinformatics Research (CUBRe) and Department of Computer and Information Sciences, Covenant University, Ota, Ogun State, Nigeria, P.M.B. 1023
| | - Raouf Alami
- Centre National de Transfusion Sanguine, Rabat, Morocco 10100
| | | | - James Brandful
- Noguchi Memorial Institute for Medical Research, University of Ghana, Ghana, LG
| | - Seydou Doumbia
- University of Sciences, Techniques and Technology of Bamako, Bamako, Mali BPE 3206
| | - Dean Everett
- Malawi-Liverpool-Wellcome Trust Clinical Research Programme, Blantyre, Malawi, 3/Institute of Infection and Global Health, University of Liverpool, Liverpool L69 3BX, United Kingdom
| | - Faisal M Fadlelmola
- Centre for Bioinformatics and Systems Biology, Faculty of Science, University of Khartoum/Future University of Sudan, Khartoum, Sudan 11115
| | - Fatima Gaboun
- Institut National de Recherche Agronomique, Rabat, Morocco 10000
| | | | | | - Scott Hazelhurst
- Sydney Brenner Institute for Molecular Bioscience, University of the Witwatersrand, Johannesburg, South Africa 2193
| | - Winston Hide
- Harvard T.H. Chan School of Public Health, Boston, Massachusetts 02115, USA/Sheffield Institute for Translational Neuroscience, Department of Neuroscience, University of Sheffield, Sheffield S10 2HQ, United Kingdom
| | - Azeddine Ibrahimi
- Faculté de Médecine et de Pharmacie de Rabat, Université Mohammed V Souissi, Rabat, Morocco 10100
| | | | - C Victor Jongeneel
- National Center for Supercomputing Applications and Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, USA
| | - Fourie Joubert
- Department of Biochemistry, University of Pretoria, Pretoria, South Africa 0083
| | - Samar Kassim
- Medical Biochemistry and Molecular Biology Department, Faculty of Medicine, Ain Shams University, Cairo, Egypt 11566
| | | | - Judit Kumuthini
- Centre for Proteomic and Genomic Research, Cape Town, South Africa 7925
| | | | - Julie Makani
- Muhimbili University of Health and Allied Sciences, Dar es Salaam, Tanzania 00255
| | | | - Daniel Masiga
- International Centre of Insect Physiology and Ecology, Nairobi, Kenya 00100
| | - Ahmed Moussa
- Abdelmalek Essaadi University, ENSA, Tangier, Morocco 90000
| | - Oyekanmi Nash
- National Biotechnology Development Agency, Abuja, Nigeria 10099
| | | | - Ellis Owusu-Dabo
- Kumasi Centre for Collaborative Research in Tropical Medicine/Kwame Nkrumah University of Science and Technology, Kumasi, Ghana, PMB
| | - Sumir Panji
- Computational Biology Group, Department of Integrative Biomedical Sciences, Institute of Infectious Disease and Molecular Medicine, Faculty of Health Sciences, University of Cape Town, Cape Town, South Africa 7925
| | - Hugh Patterton
- University of the Free State, Bloemfontein, South Africa 9300
| | | | - Khalid Sadki
- Faculty of Sciences of Rabat, University Mohammed V of Rabat, Rabat, Morocco 10000
| | | | - Özlem Tastan Bishop
- Research Unit in Bioinformatics, Department of Biochemistry and Microbiology, Rhodes University, Grahamstown, South Africa 6140
| | - Nicki Tiffin
- South African National Bioinformatics Institute/Medical Research Council of South Africa Bioinformatics Unit, University of the Western Cape, Cape Town, South Africa 7530
| | - Nzovu Ulenga
- Management and Development for Health, Dar es Salaam, Tanzania, 61
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El Bahloul Y, Dauchot N, Machtoun I, Gaboun F, Van Cutsem P. Development and characterization of microsatellite loci for the Moroccan endemic endangered species Argania spinosa (Sapotaceae). Appl Plant Sci 2014; 2:apps.1300071. [PMID: 25202614 PMCID: PMC4103133 DOI: 10.3732/apps.1300071] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/30/2013] [Accepted: 12/09/2013] [Indexed: 05/25/2023]
Abstract
UNLABELLED 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.
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Affiliation(s)
- Yasmina El Bahloul
- Plant Breeding Unit Rabat Regional Research Center, National Institute of Agronomy Research, Institut National de la Recherche Agronomique (INRA) Maroc, B.P. 6570 Rabat-Instituts, 10101 Rabat, Morocco
| | - Nicolas Dauchot
- Unit of Research in Plant Biology, University of Namur, rue de Bruxelles 61, B-5000 Namur, Belgium
| | - Ikrame Machtoun
- Plant Breeding Unit Rabat Regional Research Center, National Institute of Agronomy Research, Institut National de la Recherche Agronomique (INRA) Maroc, B.P. 6570 Rabat-Instituts, 10101 Rabat, Morocco
| | - Fatima Gaboun
- Plant Breeding Unit Rabat Regional Research Center, National Institute of Agronomy Research, Institut National de la Recherche Agronomique (INRA) Maroc, B.P. 6570 Rabat-Instituts, 10101 Rabat, Morocco
| | - Pierre Van Cutsem
- Unit of Research in Plant Biology, University of Namur, rue de Bruxelles 61, B-5000 Namur, Belgium
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Said AA, Simard MH, Denance C, Oukabli A, Gaboun F, Modafar CE. Molecular characterization of an endangered wild pear, Pyrus mamorensis Trab., from North-Western Morocco. N Biotechnol 2012. [DOI: 10.1016/j.nbt.2012.08.366] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
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Bennani K, Thami Alami I, Bendaou N, Saidi N, Gaboun F, Al Faiz C. Conservation and multivariate analysis utility in characterization of ecogegraphical relationships of Trifolium and Lotus species. Afr J Ecol 2011. [DOI: 10.1111/j.1365-2028.2010.01220.x] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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Lage M, Gaboun F, Bakhy K, Dakak H, Zouahri A, Cantrell C. SUSTAINABLE PRODUCTION OF HIGH QUALITY SAFFRON (CROCUS SATIVUS L.) IN SOME MOROCCAN AREAS. ACTA ACUST UNITED AC 2010. [DOI: 10.17660/actahortic.2010.850.39] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
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