Towards a comprehensive characterization of durum wheat landraces in Moroccan traditional agrosystems: analysing genetic diversity in the light of geography, farmers’ taxonomy and tetraploid wheat domestication history

Background: Crop diversity managed by smallholder farmers in traditional agrosystems is the outcome of historical and current processes interacting at various spatial scales, and influenced by factors such as farming practices and environmental pressures. Only recently have studies started to consider the complexity of these processes instead of simply describing diversity for breeding purposes. A first step in that aim is to add multiple references to the collection of genetic data, including the farmers' varietal taxonomy and practices and the historical background of the crop. Results: On the basis of interview data collected in a previous study, we sampled 166 populations of durum wheat varieties in two traditional Moroccan agrosystems, in the Pre-Rif and Atlas Mountains regions. Using a common garden experiment, we detected a high phenotypic variability on traits indicative of taxonomical position and breeding status, namely spike shape and plant height. Populations often combined modern (short) with traditional-like (tall) statures, and classical durum squared spike shape (5 flowers/spikelet) with flat spike shape (3 flowers/spikelet) representative of primitive domesticated tetraploid wheat (ssp. dicoccum). By contrast, the genetic diversity assessed using 14 microsatellite markers was relatively limited. When compared to the genetic diversity found in a large collection of tetraploid wheat, it corresponded to free-threshing tetraploid wheat. Within Morocco, the two studied regions differed for both genetic diversity and variety names. Within regions, neither geography nor variety names nor even breeding status constituted strong barriers to gene exchange despite a few significant patterns. Conclusions: This first assessment of morphological and genetic diversity allowed pointing out some important factors that may have influenced the structure and evolutionary dynamics of durum wheat in Morocco: the significance of variety names, the occurrence of mixtures within populations, the relative strength of seed exchange between farmers and local adaptation, as well as the fate of modern varieties once they have been introduced. Further, multidisciplinary studies at different spatial scales are needed to better understand these complex agrosystems of invaluable importance for food security

Quantitative trait loci of frost tolerance and physiologically related trait in faba bean (Vicia faba L.)

Abstract In faba bean, field based winter-hardiness is a complex trait that is significantly correlated to frost tolerance. Frost tolerance could be used to indirectly select for faba bean winter-hardiness. The aim of this study was to identify putative QTL associated with frost tolerance and auxiliary traits and to quantify the efficiency of marker assisted selection. Thus, 101 recombinant inbred lines derived from the cross between two frost tolerant lines were tested for their hardened and unhardened frost tolerance and for their leaf fatty acid content in both treatments. Significant differences among the RIL were observed for all studied traits. For frost tolerance, five putative QTL were detected; three for unhardened frost tolerance that explained 40.7% (8.6% after crossvalidation, CV) of its genotypic variance and two for hardened frost tolerance that explained 21.8% (1.0% after CV). For fatty acid content, three QTL were detected for oleic acid content in unhardened leaves that explained 62.9% (40.6% after CV) of its genotypic variance. This fatty acid was significantly correlated with unhardened frost tolerance. The unbiased genotypic variance explained enabled to draw realistic prospects of MAS for frost tolerance. In this study, combined MAS was more efficient than classical phenotypic selection and was expected to be higher on larger populations at early generations. Moreover, favourable alleles inherited from the exotic line BPL 4628 could be introgressed to European winter-hardy beans for further improvement

Impact du relief et des circuits semenciers locaux sur la diversité agro-morphologique du blé dur (Triticum turgidum ssp. durum) dans la vallée d'Er Rich à Imilchil (Maroc)

Phenotypic diversity of 101 durum wheat landrace populations collected from the oasis of the Oriental Atlas Mountains (Morocco) was studied. Nine characters (morphological and agronomic) were measured on the 3030 lines (30 lines per population). The frequencies of each phenotypic class were used for the estimate and the analysis of diversity, by considering the geographical zones of origin and the gradients of altitude. The Shannon-Weaver diversity index (H’) showed a wide variability for all considered traits. This index varies from one area to another and from one altitudinal class to another. The mean H’ recorded for all areas was 0.62, indicating the presence of a high degree of polymorphism among the studied durum wheat landrace populations. The results of the multiple component analysis and the hierarchical clustering showed that the geographical proximity and altitude play a main function in the discrimination and the structure of the studied durum wheat populations. The information gathered from this study could be used in conventional breeding programs and in situ conservation of the diversity. La diversité phénotypique de 101 populations locales de blé dur issues des oasis de montagnes de l’Atlas oriental (Maroc) a été étudiée. Neuf caractères (morphologiques et agronomiques) ont été mesurés sur les 3030 lignées (30 lignées par population). Les fréquences de chaque classe phénotypique ont été utilisées pour l’estimation et l’analyse de la diversité, en considérant les zones géographiques d’origine et les gradients d’altitude. L’indice de diversité de Shannon-Weaver (H’) a montré une forte variabilité pour l’ensemble des caractères considérés. Cet indice varie d’une zone à une autre et d’une classe d’altitude à une autre. Le H’ moyen obtenu pour l’ensemble des zones est de 0,62, indiquant la présence d’un degré élevé de polymorphisme au sein des populations locales de blé dur collectées. Les résultats de l’analyse en composantes multiples ainsi que de la classification hiérarchique ont montré que la proximité géographique et l’altitude jouent un rôle majeur dans la discrimination ainsi que sur la structuration des populations de blé dur étudiées. Les informations recueillies à partir de ces résultats peuvent être exploitées dans des programmes de sélection conventionnels et de conservation in situ de la diversité. Mots clés: Populations locales, diversité phénotypique, structuration, conservation in situ, blé dur (Triticum turgidum ssp. durum)

Detaillierte genetische Analyse der Winterhärte und damit verbundenerMerkmale bei der Ackerbohne (Vicia faba L.)

Als Körnerleguminose könnte die Fababohne (Vicia faba L.) die Abhängigkeit Europas von pflanzlichem Protein-Import reduzieren. Um diese Ackerfrucht zu fördern und genetisch zu verbessern wurde ein großes europäisches Projekt initiiert. Die gegenwärtige Studie betraf als Teil dieses Projektes die Toleranz der Fababohne gegen nordeuropäischen Winterbedingungen; der Winter ist ein Hauptfaktor für abiotischen Stress in diesen agro-ökologischen Regionen. Diese Studie hatte zum Ziel, die Winterhärte der Fababohne und auch Hilfsmerkmale für Winterhärte zu studieren, den Effekt von Härtung auf die Pflanzen zu bestimmen, QTL für Frosttoleranz zu entdecken und Heterosis für Frosttoleranz zu studieren. Umfangreiche Feldversuch mit einer repräsentativen Stichprobe von frosttoleranten und frostanfälligen Fababohnen-Genotypen erlaubten es, europäische Winter- Genotypen mit hoher Winterhärte und hohem Kornertrag zu identifizieren. Genotyp x Umwelt-Interaktionsanalysen mittels additive main effect and multiplicative interaction (AMMI) zeigten zusätzlich, dass diese Genotypen stabil für beide Merkmale waren; sie verfügten über eine allgemeine Adaptation an die meisten Umwelten. Künstliche und sogenannte provokative Frostprüfungen deuteten an, dass die Frosttoleranz eine signifikante aber keine erschöpfende Komponente der Winterhärte war (0,021 < |r| < 0,737**). Diese Prüfungen erlaubten es, hochgradig frosttolerante experimentelle Linien wie F7-95 zu identifizieren, aber auch europäische Genotypen, die als winterhart bekannt sind, und die entweder eine niedrige Frosttoleranz haben wie z.B. Bulldog/1 oder eine hohen Frosttoleranz wie z.B. Karl. Mit Blick auf Umwelten mit intermediärer Winterstrenge könnten diese künstlichen und provokativen Frostprüfungen benutzt werden, um indirekt die Winterhärte zu erfassen. Der Fettsäuregehalt in Blättern und deren Änderung aufgrund von Härtung, der Prolingehalt und der Membranstabilitätsindex waren signifikant mit der Frosttoleranz korreliert, was die physiologische Bedeutung dieser Merkmale für die Frosttoleranz bestätigt. Darüber hinaus zeigte die Analyse von Blättern und Stängeln, dass der Ölsäuregehalt ohne Härtung und die Veränderung im Ölsäuregehalt und im Linolsäure- plus Linolensäuregehalt in Blättern aufgrund von Härtung deren Frosttoleranz teilweise erklärte (0,347* < r < 0,543**). Obwohl in Stängeln signifikante Veränderung aufgrund von Härtung bei Ölsäure (-1,77%) undLinolensäure (+9,06%) beobachtet wurden, waren diese doch ohne Beziehung zur Frosttoleranz. Um eine Auslese auf Frosttoleranz und schlussendlich auch auf Winterhärte mit DNA-Markern zu unterstützen, wurden QTL-Analysen mit einer Population von 101 sog. rekombinierten Inzuchtlinien durchgeführt. Für alle untersuchten Merkmale wurde eine LOD-Schwelle von 3,25 zur Absicherung mutmaßlicher QTL benutzt. Für Frosttoleranz wurden vier solche mutmaßliche QTL entdeckt; zwei für Frosttoleranz ohne Härtung, die 28,3% (3,44% nach Kreuzvalidierung) der genotypischen Varianz erklärten und zwei für Frosttoleranz mit Härtung, die 12,5% (5,22% nach Kreuzvalidierung) erklärten. Mit Bezug auf physiologische Merkmale die mit Frosttoleranz korreliert waren, wurden drei QTL für Ölsäuregehalt in ungehärteten Blättern entdeckt, die 57,7% (37,2% nach Kreuzvalidierung) der genotypischen Varianz erklärten. Für den Gehalt an Prolin und löslichem Zucker wurde mit einer LOD-Schwelle von 3,25 kein QTL entdeckt. Der unverzerrte Anteil der genotypischen Varianz der nach Kreuzvalidierung erklärt wurde erlaubte es, die Aussichten einer markergestützten Selektion realistisch zu bewerten. Es zeigte sich, dass eine kombinierte markergestützte und phänotypische Selektion effizienter wäre als eine nur phänotypische Selektion und dass somit bedeutende Selektionsgewinne für Frosttoleranz in großen Populationen in den ersten Selektionsgenerationen erwartet werden können. Zusätzlich könnten günstige Allele die von BPL4628 vererbt werden benutzt werden, um die Frosttoleranz europäischer Winterbohnen weiter zu verbessern. Da die meisten zugelassenen Fababohnensorten synthetische oder sonstige Populationssorten sind, stellt Heterosis für Frosttoleranz einen wichtigen Aspekt dar. In einem diallelen Schema mit vier elterlichen Linien wurde signifikante Heterosis beobachtet. Eine Kreuzung zwischen zwei europäischen Linien zeigte allerdings keine Heterosis. Solange keine Hybridsorten produziert werden kann Heterosis für Frosttoleranz nicht vollständig ausgenutzt werden

Identification and Verification of QTL Associated with Frost Tolerance Using Linkage Mapping and GWAS in Winter Faba Bean

Frost stress is one of the abiotic stresses that causes a significant reduction in winter faba bean yield in Europe. The main objective of this work is to genetically improve frost tolerance in winter faba bean by identifying and validating QTL associated with frost tolerance to be used in marker-assisted selection (MAS). Two different genetic backgrounds were used: a biparental population (BPP) consisting of 101 inbred lines, and 189 genotypes from single seed descent (SSD) from the Gottingen Winter bean Population (GWBP). All experiments were conducted in a frost growth chamber under controlled conditions. Both populations were genotyped using the same set of 189 SNP markers. Visual scoring for frost stress symptoms was used to define frost tolerance in both populations. In addition, leaf fatty acid composition (FAC) and proline content were analyzed in BPP as physiological traits. QTL mapping (for BPP) and genome wide association studies (for GWBP) were performed to detect QTL associated with frost tolerance. High genetic variation between genotypes, and repeatability estimates, were found for all traits. QTL mapping and GWAS identified new putative QTL associated with promising frost tolerance and related traits. A set of 54 SNP markers common in both genetic backgrounds showed a high genetic diversity with polymorphic information content (PIC) ranging from 0.31 to 0.37 and gene diversity ranging from 0.39 to 0.50. This indicates that these markers may be polymorphic for many faba bean populations. Five SNP markers showed a significant marker-trait association with frost tolerance and related traits in both populations. Moreover, synteny analysis between Medicago truncatula (a model legume) and faba bean genomes was performed to identify candidate genes for these markers. Collinearity was evaluated between the faba bean genetic map constructed in this study and the faba bean consensus map, resulting in identifying possible genomic regions in faba bean which may control frost tolerance genes. The two genetic backgrounds were useful in detecting new variation for improving frost tolerance in winter faba bean. Of the five validated SNP markers, one (VF_Mt3g086600) was found to be associated with frost tolerance and FAC in both populations. This marker was also associated with winter hardiness and high yield in earlier studies. This marker is located in a gene of unknown function

Impact du relief et des circuits semenciers locaux sur la diversité agro-morphologique du blé dur (Triticum turgidum ssp. durum) dans la vallée d’Er Rich – Imilchil (Maroc)

Phenotypic diversity of 101 durum wheat landrace populations collected from the oasis of the Oriental Atlas Mountains (Morocco) was studied. Nine characters (morphological and agronomic) were measured on the 3030 lines (30 lines per population). The frequencies of each phenotypic class were used for the estimate and the analysis of diversity, by considering the geographical zones of origin and the gradients of altitude. The Shannon-Weaver diversity index (H’) showed a wide variability for all considered traits. This index varies from one area to another and from one altitudinal class to another. The mean H’ recorded for all areas was 0.62, indicating the presence of a high degree of polymorphism among the studied durum wheat landrace populations. The results of the multiple component analysis and the hierarchical clustering showed that the geographical proximity and altitude play a main function in the discrimination and the structure of the studied durum wheat populations. The information gathered from this study could be used in conventional breeding programs and in situ conservation of the diversity

Diversité agro-morphologique et gestion variétale par les agriculteurs du blé dur (Triticum turgidum ssp. durum) dans le Pré-Rif marocain

Le blé dur est une culture stratégique au Maroc. La caractérisation et l’évaluation des variétés cultivées dans différents agro-écosystèmestraditionnels permettent la sauvegarde et la réhabilitation de ce patrimoine génétique ainsi que son utilisation dans desprogrammes de sélection. Dans ce contexte, une collection de 59 populations traditionnelles de blé dur issues de la région du Pré-Rif a été étudiée en utilisant neuf traits agro-morphologiques. La diversité phénotypique a été déterminée par l’indice de diversitéShannon-Weaver (H’) à différents niveaux (Totalité de l’échantillon, par typologie du blé et par nom variétal). Les H’ estimés ontmontré une large variabilité phénotypique pour les différents traits avec un H’ moyen de 0,78. Les résultats de l’analyse des correspondancesmultiples et de la classification hiérarchique ont montré une nette distinction entre les variétés modernes et traditionnelles.Les caractères agro-morphologiques ne permettent pas de différencier les variétés traditionnelles entre elles. Les résultats de ce travailont permis de révéler la grande diversité phénotypique des variétés de blé dur qui ne correspond que partiellement aux noms desvariétés du fait de l’existence d’homonymes et de synonymes dans les noms donnés par les agriculteurs.Durum wheat is a strategic crop in Morocco. Characterization and evaluation of cultivated varieties in different traditional agroecosystemsallows safeguard and rehabilitation of this genetic heritage and its use in breeding programs. In this context, a collectionof 59 traditional populations of durum wheat from the Pre-Rif region was studied using nine agro-morphological traits. Phenotypicdiversity was determined by the Shannon-Weaver diversity index (H’) at different levels (totality of sample, by type of wheat andvarietal names). Estimated H’ showed a wide genetic variability for different traits with a mean of H’=0.78. The results of the multiplecorrespondence analysis and hierarchical clustering showed a clear distinction between modern and traditional varieties. In traditionalvarieties, agro-morphological traits do not differentiate between varieties. The results of this work revealed the great phenotypic andnominative diversity of durum wheat varieties as well as the existence of homonyms and synonyms in the names given by farmers

Anchoring durum wheat diversity in the reality of traditional agricultural systems: varieties, seed management, and farmers’ perception in two Moroccan regions

Background: Traditional agrosystems are the places were crop species have evolved and continue to evolve under a combination of human and environmental pressures. A better knowledge of the mechanisms underlying the dynamics of crop diversity in these agrosystems is crucial to sustain food security and farmers’ self-reliance. It requires as a first step, anchoring a description of the available diversity in its geographical, environmental, cultural and socio-economic context. [br/] Methods: We conducted interviews with farmers cultivating durum wheat in two contrasted traditional agrosystems of Morocco in the Pre-Rif (163 farmers) and in the oases of the Atlas Mountains (110 farmers). We documented the varietal diversity of durum wheat, the main characteristics of the farms, the farming and seed management practices applied to durum wheat, and the farmers’ perception of their varieties. [br/] Results: As expected in traditional agrosystems, farmers largely practiced diversified subsistence agriculture on small plots and relied on on-farm seed production or informal seed exchange networks. Heterogeneity nevertheless prevailed on many variables, especially on the modernization of practices in the Pre-Rif region. Fourteen (resp. 11) traditional and 5 (resp. 3) modern varieties were identified in the Pre-Rif region (resp. in the Atlas Mountains). The majority of farmers grew a single variety, and most traditional varieties were distributed in restricted geographical areas. At the farm level, more than half of the varieties were renewed in the last decade in the Pre-Rif, a more rapid renewal than in the Atlas Mountain. Modern varieties were more prevalent in the Pre-Rif region and were integrated in the traditional practices of seed production, selection and exchange. They were clearly distinguished by the farmers from the landraces, the last ones being appreciated for their quality traits. [br/] Conclusions: The surveyed traditional agrosystems constitute open, dynamic and heterogeneous entities. We suggest that competing factors could favour or limit the cultivation of improved varieties and the erosion of original durum wheat diversity. This first description opens the way to focused further investigations, including complementing variety names with cultural, genetic and phenotypic information and unravelling the multidimensional factors and consequences of modern variety adoption

Seedling and adult stage resistance to net form of net blotch (NFNB) in spring barley and stability of adult stage resistance to NFNB in Morocco

International audienceThis study was conducted to identify stable resistance to net form of net blotch (NFNB) in spring barley in Moroccan environments. Seedling resistance to NFNB was evaluated by inoculating 336 barley genotypes with two NFNB isolates LDNH04Ptt-19 and TD-10 in the greenhouse. These genotypes were evaluated for adult plant resistance to NFNB under seven environments in Morocco in 2015 and 2016. The disease severity was estimated at GS 77-87 on barley leaves using a double-digit scale. To investigate stability of resistance, 149 barley genotypes were subjected to AMMI analysis. At the seedling stage, differential responses of barley genotypes to different NFNB isolates were identified, whereas genotypes had variable stability to NFNB resistance at the adult stages. Five genotypes, AM-68, AM-95, AM-250, AM-267 and AM-322, were resistant to both NFNB isolates at the seedling stage. There were significant (p < .001) effects of genotype (G) and G x E interaction on NFNB severity for barley genotypes at the adult stage. The principal components, IPCA1 and IPCA2, accounted for 48.4% and 18.7% variation for NFNB severity, respectively. The AMMI stability values (ASVs) ranged from 0.01 to 15.5, and fifty-nine barley genotypes had stable responses (ASV <= 0.05) across all seven environments. Specifically, two stable genotypes, AM-187 and AM-244, had lower mean NFNB severities across all environments, suggesting a quantitative resistance in these genotypes. Divergent environmental responses of NFNB severity were measured in Sidi El Ayedi 2015 and Sidi Allal Tazi 2016, suggesting that these environments may be suitable to capture resistance to diverse pathotypes. These stable genotypes are valuable resources for introgression of both qualitative resistance and quantitative resistance to NFNB in future