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Background: Gari and eba, forms of cassava semolina, are mainly consumed in Nigeria and other West African countries. This study aimed to define the critical quality traits of gari and eba, to measure their heritability, to define medium and high throughput instrumental methods for use by breeders, and to link the traits with consumer preferences. The definition of a food product's profiles, including its biophysical, sensory, and textural qualities, and the identification of the characteristics that determine its acceptability, are important if new genotypes are to be adopted successfully. Results: Eighty cassava genotypes and varieties (three different sets) from the International Institute of Tropical Agriculture (IITA) research farm were used for the study. Participatory processing and consumer testing data on different types of gari and eba products were integrated to prioritize the traits preferred by processors and consumers. The color, sensory, and instrumental textural properties of these products were determined using standard analytical methods, and standard operating protocols (SOPs) developed by the RTBfoods project (Breeding Roots, Tubers, and Banana Products for End-user Preferences, https://rtbfoods.cirad.fr). There were significant (P

Adapting to climate change in vulnerable coffee regions is crucial to maintain rural livelihoods. Among the solutions, coffee breeding strategies aim to produce coffee varieties with higher output performance than traditional varieties while reducing competition for land. This paper investigates the output performance of hybrid coffee (e.g., Starmaya and Centroamericano – H1), introgressed (e.g., Marsellesa and obatá) and traditional coffee (e.g., Caturra and Villa Sarchi) varieties. By using plot-level panel data among commercial farms in Costa Rica, we estimate the output performance of the three coffee varieties using pooled ordinary least squares and random effects models. We find that hybrid coffee varieties give 29-61% higher output than traditional coffee varieties. The results remain robust even after controlling for factor and climate inputs. Notwithstanding the larger productivity, hybrid coffee varieties demand more labor and inorganic fertilizers. While pesticide use may be reduced by hybrid's pest resistance, agroecological approaches for nutrient management are still needed to improve livelihoods and environmental outcomes. Headed towards longer-term studies, our paper presents the first evidence on the output performance of hybrid coffee varieties outside on-farm trials or experimental plots. These results suggest the potential of hybrid coffee varieties in promoting sustainable agriculture by improving the livelihood of coffee farmers, enhancing their adaptation against climate change and decreasing competition for land.

La culture de la banane Cavendish aux Antilles françaises opère une transition agroécologique depuis la fin des années 2000, incluant de nouvelles pratiques culturales pour limiter l'utilisation d'intrants chimiques et apporter de la diversité spécifique dans les systèmes. Parmi ces pratiques, l'effeuillage sévère est pratiqué pour maîtriser la cercosporiose noire du bananier plutôt que d'utiliser des fongicides foliaires ; des plantes de couverture sont utilisées en alternatives aux herbicides dans les parcelles et des engrais organiques riches en azote remplacent les engrais minéraux azotés. Mais ces pratiques peuvent réduire la production photosynthétique et la disponibilité des ressources azotées du sol, et de ce fait rendre les conditions de culture suboptimales. Un des leviers pour maintenir une performance agronomique satisfaisante malgré ces conditions suboptimales serait d'utiliser des cultivars adaptés à ces conditions de culture. Dans cette thèse, nous proposons d'utiliser une approche par traits fonctionnels pour caractériser une gamme de 12 cultivars de Cavendish issus du catalogue de Vitropic sur leur performance agronomique avec un effeuillage sévère et avec des ressources azotées limitées. Pour répondre à cet objectif nous supposons que des traits associés aux relations source-puits et à l'acquisition des ressources azotées permettraient de prédire la performance agronomique des cultivars avec un effeuillage sévère et avec des ressources azotées limitées. Nous avons, d'une part, mesuré les traits sur les cultivars dans un essai aux conditions de culture non limitantes, et d'autre part, mesuré la performance agronomique des bananiers dans quatre parcelles aux itinéraires techniques contrastés par la sévérité de l'effeuillage et par la disponibilité en azote. Nous avons ensuite comparé les valeurs des traits des cultivars avec leur performance dans les différentes parcelles pour valider ou rejeter les traits. Nous avons obtenu des valeurs de traits différentes entre les cultivars, suggérant des différences de rapport source-puits et des capacités d'acquisition des ressources azotées. Nous avons également mesuré des différences de variation des poids de régime entre les cultivars, en réponse à une diminution de la production photosynthétique, liées au nombre de fruit par régime. En effet, DC-01, un cultivar possédant beaucoup de fruits, a été le plus sensible à une diminution de la production photosynthétique. A l'inverse, Poyo, un cultivar possédant moins de fruits par régime, a maintenu son poids du régime malgré une diminution de la production photosynthétique. Enfin, nous avons observé des différences de stabilité des rendements entre les cultivars. Dans nos essais, Ruby et Mat-12 ont maintenu le même rendement malgré un effeuillage sévère et Gua- 02 a obtenu le meilleur comportement avec des ressources azotées limitées. Cependant, nos essais n'ont pas permis de valider les traits fonctionnels pour prédire les performances agronomiques avec un effeuillage sévère et avec des ressources azotées limitées. Néanmoins, la méthode d'évaluation variétale que nous avons utilisée est prometteuse pour la sélection de bananiers et pourrait être développer pour d'autres critères sélections. A partir de nos résultats, pour chaque cultivar, nous avons établi des conseils d'utilisation, en proposant des itinéraires techniques auxquels le cultivar serait le plus adapté.

All over the world, sugarcane breeding programs are developing new, high-yielding cultivars that are resistant to major diseases to improve the profitability and sustainability of the sugar-energy industries they serve. In Reunion Island, sugarcane genetic improvement efforts began in 1929. Many challenges had to be overcome. Continuous breeding efforts have been made to develop varietal resistances to control some major diseases and are still going on today. Given the extreme agroclimatic diversity that characterizes the different production areas of the industry, it was necessary to gradually develop a large network of seven decentralized breeding programs to support genetic progress throughout the whole industry. This article provides an overview of the sugarcane breeding program of Reunion. It describes historical achievements and gives detailed information about germplasm development, variety exchanges, breeding program and selection scheme and procedures. A review is also made on applied genetics research activities supporting variety improvement. Further progress depends on the optimized functioning of the current breeding program, which has never been so largely extended in terms of target environments. The article discusses prospects of genomics breeding applications in the complex genetic context of sugarcane, which will require large multidisciplinary collaborations.

Cacao (Theobroma cacao L.) is an important Neotropical crop originating in South America and dispersed by European explorers, arriving in Madagascar in the late 19th century. Although Madagascar is an important producer of cocoa for the premium chocolate market, the varietal composition and genetic diversity in cacao germplasm from Madagascar, especially in traditional cacao farms, remains unknown. A total of 190 cacao accessions, including 40 farmer accessions collected from traditional cacao farms in Madagascar, and 150 accessions representing seven reference cacao populations, were analyzed using Single Nucleotide Polymorphism (SNP) markers. Multivariate analysis and Bayesian stratification resulted in the clustering of the 40 farmer accessions into three groups: Criollo, Amelonado and Trinitario. These three traditional varieties were commonly cultivated in tropical America in the 18th century, but most of them have been replaced by improved varieties. The present study demonstrated that Madagascar is distinctive in that all three traditional cacao varieties, Criollo, Amelonado and Trinitario, are still maintained on-farm for cocoa production, as in Mesoamerica and the Caribbean several hundred years ago. Results from the present study are significant in terms of understanding the early dispersal of cacao from tropical America and Asia to Africa, in addition to the well-documented route from Brazil to São Tomé & Príncipe. The results also provide new information for planning future conservation and utilization of cacao germplasm in Madagascar.

This review of the literature on varietal change in sub-Saharan Africa looks in detail at adoption of new varieties of bananas in Uganda, cassava in Nigeria, potato in Kenya, sweetpotato in Uganda and yams in C^ote d'Ivoire. The review explored three hypotheses about drivers of varietal change. There was a strong confirmation for the hypothesis that insufficient priority given to consumer-preferred traits by breeding programmes contributes to the limited uptake of modern varieties (MVs) and low varietal turnover. Lack of evidence meant the second hypothesis of insufficient attention to understanding and responding to gender differences in consumer preferences for quality and post-harvest traits was unresolved. The evidence on the third hypothesis about the informal seed system contributing to slow uptake of MVs was mixed. In some cases, the informal system has contributed to rapid uptake of MVs, but often it appears to be a barrier with inconsistent varietal naming a major challenge.

So far, the main Arabica coffee breeding programmes in Latin America have focused on the selection of varieties adapted to intensive full-sun farming systems. Meanwhile, little attention has been paid to breeding varieties specifically adapted to shade, which is the main characteristic of agroforestry systems (AFS). Yet the specialty coffee sector is currently expanding and seeking specific sensory qualities related to exotic varieties and no breeding programme exists to create new varieties for this type of market. Two trials were set up: one in full sun and the other under shade. F1 hybrids and their parents (pure lines and Ethiopian accessions) were studied in a factorial-crossing design to measure tree volume, yield (3 years), bean size, the bean NIRS signature and the final cupping score. Bean size and the final cupping score seemed to be relatively unaffected by shading. Strong maternal heritability was observed for bean size. In the trials, F1 hybrids produced “75–80%” more than the maternal lines and “40–50%” more than the male parents in the shade trial and in the full-sun trial, respectively. By choosing the F1 hybrid, it is possible to increase productivity under both shade and full sun while simultaneously achieving good sensory qualities. Selecting a F1 hybrid for “specialty coffee” seems exceptional. This raises a fundamental issue concerning the maternal heritability of seed biochemical composition. We conclude that selection under shade is essential for the selection of varieties adapted to AFS.

International audience; Self-incompatibility is an important evolutionary feature in angiosperms and has major implications for breeding strategies in horticultural crops. In citrus, when coupled with parthenocarpy, it enables the production of seedless fruits in a mono-varietal orchard. A gametophytic incompatibility system with one S locus was proposed for citrus, but its molecular mechanisms remain the subject of debate. The objective of this work was to locate the S locus by the analyzing segregation distortion in reciprocal crosses of two self-incompatible citrus sharing one self-incompatible allele and to compare this location with previously published models. High density genetic maps of ‘Fortune’ mandarin and ‘Ellendale tangor’ with, respectively, 2164 SNP and 1467 SNP markers, were constructed using genotyping by sequencing data. They are highly syntenic and collinear with the clementine genome. Complete rejection of one allele was only observed in male segregation in the two parents and in only one genomic area, at the beginning of chromosome 7 of the clementine reference genome. Haplotype data in the area surrounding the theoretical S locus were in agreement with previously proposed S genotypes. Overall, our results are in full agreement with the recently proposed gametophytic S-RNase system with the S locus at the beginning of chromosome 7 of the clementine reference genome.

Kava, the traditional beverage of the South Pacific Islands is prepared by cold water extraction of the fresh or dried roots and stumps of Piper methysticum Forst. (Piperaceae). Nutraceutical and pharmaceutical kava-based products manufactured in Europe from extracts obtained by solvents (acetone or ethanol) have been implicated in hepatotoxicity cases. Kava has been banned in Germany and, although the German Health Authorities have lost their case in the administrative court, the ban has produced a worldwide negative impact on kava's reputation as a safe product. Quality standards and control are now needed to enable the registration under the FAO/WHO Codex Alimentarius. The present paper reviews the most recent advances in analytical techniques (HPLC, NIRS, DNA analysis using SSRs and DArTs and HP-TLC) to detect unsuitable cultivars and raw material. These techniques are accurate and reliable but they are comparatively expensive and cumbersome for local traders and exporters in the South Pacific. A simple colorimetric test has been developed and represents a fairly convenient and cost efficient way of assessing the quality of traded kava. Possible strategies for improving the industry are discussed.

International audience; Enhancing rice yield in upland rice systems through genetic improvement remains a major challenge in the tropics. This review aims to provide the trends on upland rice cultivation over the last 30 years and recent distribution of upland rice in the tropics, and to report progress in studies on genetic improvement for enhancing productivity in Africa, Asia, and Latin America. While upland rice cultivation area has reduced in Asia and Latin America over the last 30 years, the area in Africa has increased. The current share of upland rice area in total rice area is related to rainfall and gross national income per capita, especially in Africa, and higher share is associated with lower rice self-sufficiency at national level. Breeding programs in Asia and Latin America have developed high-yielding varieties using indica materials as parents. In Africa, New Rice for Africa (NERICA) varieties were developed from crosses between improved tropical japonica and Oryza glaberrima. However, recent studies report that there is scope for improving existing NERICA using upland indica materials from Asia. In highlands of Africa, there are ongoing breeding programs using japonica varieties, such as the Nepalese Chhomrong Dhan. Key important plant traits used in the breeding programs are not largely different across regions, especially intermediate plant height and tillering capacity (which may be related to weed-suppressive ability), and high harvest index. In conclusion, we propose an international network for breeding upland rice with accelerating seed exchange across regions that could enhance upland rice productivity through genetic improvement.

In low-input rice-maize rotation systems in the hills of central Madagascar, farmers deal with erratic rainfall, poor soils, high soil erosion risks and infestation by the parasitic weed Striga asiatica (L.) Kuntze. Practices combining zero-tillage with permanent soil cover by intercropped legumes and crop residue mulches — known as Conservation Agriculture (CA)— are proposed as remedy against soil and climatic constraints. Implications of these practices for S. asiatica are unknown. A 4-season factorial experiment compared the current farmer practice of rice − maize rotation, involving seasonal tillage and crop residue removal (CONV), with three rice − maize rotation systems following CA with different cover crops, i.e. Vigna unguiculata (cowpea) and Mucuna pruriens (CACM), Vigna umbellata (ricebean) (CARB), and Stylosanthes guianensis (CAST). Performance of two rice varieties, NERICA-4 and −9, with partial S. asiatica resistance, were compared with the locally popular B22. Parasite emergence time, numbers, and seed bank sizes were recorded. In all CA practices S. asiatica infection was significantly reduced. Best results were obtained with Stylosanthes guianensis (CAST). This species also suppressed ordinary weeds much better than other cover crops. With CAST, average parasite emergence was delayed by 7.5 days (in rice) and 6.3 days (in maize) and infection levels were reduced by 79% (in rice) and 92% (in maize) compared to the conventional farmer practice (CONV). NERICA varieties delayed S. asiatica emergence by 5.7 days (NERICA-9) and 9.7 days (NERICA-4) and reduced infection levels by 57% (NERICA-9) and 91% (NERICA-4) compared to B22. In maize the residual effect of resistance of NERICA-4 resulted in a delay of 7.5 days in S. asiatica emergence and a reduction of 60% in parasite numbers. The best combinations delay S. asiatica emergence by 17.8 days (CAST + NERICA-9) and 19.1 days (CARB + NERICA-4) and reduce the parasite infection levels by 96% (CAST + NERICA-9 or −4) to 98% (CARB + NERICA-4) in rice, compared to CONV + B22. After two full rice-maize rotation cycles S. asiatica seed numbers in the soil (0–10 cm) were 76% (CACM), 78% (CAST) and 86% (CARB) lower than under CONV. Even the combination of zero-tillage, crop residue mulching, cover crops and resistant rice varieties does not entirely prevent S. asiatica parasitism and seed bank increase. Additional measures, targeted to escaping weeds, would be required for fully effective and long-term control.

Sugarcane yellow mite, Oligonychus sacchari (Prostigmata: Tetranychidae), is one of the main detrimental pests in sugarcane growing areas in Iran. The early populations of mites colonize on the lower surfaces of sugarcane leaves. Because of high reproductive potential, multi-generation are produced per year under warm and humid temperature during sugarcane growing season. This pest imposes economic damage to sugar industries. Field trials were conducted on evaluation of varietal resistance of five sugarcane varieties against yellow mite during two successive seasons 2014–2015 and 2015–2016 in sugarcane fields at Salman Farsi Agro-industry unit in Ahwaz, Iran. After initiation of O. sacchari activity in fields, in each plot, fifteen leaves were selected at random and number of living mites was recorded. The results showed that there were significant differences among tested varieties. The variety IRC99-02 was the most susceptible in tested years by CP57-614 in the total number of living mites and dry-leaf even though CP69-1062 was the most resistant variety.

Stable and sufficient food supplies are increasingly threatened by climatic variability, in particular extreme heat events. Intraspecific crop diversity may be an important biological resource to both understand and maintain crop resilience to extreme conditions. Here using data from a mass field experiment screening for heat tolerance in sweet potato (Ipomoea batatas), we identify 132 heat-tolerant cultivars and breeding lines (6.7%) out of 1,973 investigated. Sweet potato is the world's fifth most important food crop, and mean conditions experienced by sweet potato by 2070 are predicted to be 1 to 6 degrees C warmer, negatively impacting most genotypes. We identify canopy temperature depression, chlorophyll content and storage root-flesh colour as predictors of heat tolerance and, therefore, as potential traits for breeding consideration. These results highlight the role of intraspecific biodiversity for the productivity and resilience of food and agricultural systems in the face of climate change. Mass field testing of heat tolerance in 1,973 cultivars of sweet potato (Ipomoea batatas) from 50 countries identifies tolerant cultivars and reveals tolerance-predictive traits for breeding consideration. The work highlights the role of intraspecific diversity for future crop resilience.

The adoption of new cultivars depends largely on the extent to which the breeding objectives set to identify the new cultivars align with the farmers' preferences. There is documented potential of improved cultivars to enhance productivity and income in the developing world, but their adoption among smallholders remains low. Here, we attempt to understand if in the case of Morocco the low level of adoption of new durum wheat (Triticum durum Desf.) cultivars can be partially explained by a misalignment of breeders objectives. Factorial analysis was applied to data obtained through a set of interviews with 90 wheat breeders from 49 countries and a case study of 861 durum wheat growers in Morocco, to reveal the existence of five breeders and four farmers classes based on relative importance assigned to five mega-traits: grain yield potential, yield stability, abiotic stress tolerance, biotic stress resistance, industrial quality, and household use. Weighted indexes were derived based on the average rate of preference shown by each interviewee belonging to that specific class, and hierarchically clustered to reveal poor matching between North African breeders and Moroccan farmers. Further, these indexes were applied to the actual performances of 23 durum wheat elite lines to reveal 71% to 87% matching. However, breeders' and farmers' classes had preferences for different genotypes. Together, these results indicate that a certain degree of misalignment exist between farmers and breeders' objectives, and that the use of participatory farmers-weighted indexes could help raise the level of adoption.

International audience; This study aimed to understand the response of photosynthesis and growth to e-CO2 conditions (800 vs. 400 mu mol mol(-1)) of rice genotypes differing in source-sink relationships. A proxy trait called local C source-sink ratio was defined as the ratio of flag leaf area to the number of spikelets on the corresponding panicle, and five genotypes differing in this ratio were grown in a controlled greenhouse. Differential CO2 resources were applied either during the 2 weeks following heading (EXP1) or during the whole growth cycle (EXP2). Under e-CO2, low source-sink ratio cultivars (LSS) had greater gains in photosynthesis, and they accumulated less nonstructural carbohydrate in the flag leaf than high source-sink ratio cultivars (HSS). In EXP2, grain yield and biomass gain was also greater in LSS probably caused by their strong sink. Photosynthetic capacity response to e-CO2 was negatively correlated across genotypes with local C source-sink ratio, a trait highly conserved across environments. HSS were sink-limited under e-CO2, probably associated with low triose phosphate utilization (TPU) capacity. We suggest that the local C source-sink ratio is a potential target for selecting more CO2-responsive cultivars, pending validation for a broader genotypic spectrum and for field conditions.

Sour oranges (Citrus aurantium L.) are well known in the processing and cosmetics industries for the aromatic properties of their essential oils. Intercultivar genetic and aromatic diversity is not well documented. The objective of this study was to evaluate the impact of morphological selection and genetic mechanisms of varietal diversification (mutation or hybridization) on the aromatic and odor variability of sour orange essential oils. Forty-five sour orange accessions from INRAE-CIRAD citrus Biological Resources Center (France) were assessed for ten simple sequence repeat (SSR) and 54 single nucleotide polymorphism (SNP) markers, nine morphochemical fruit traits and with the aromatic components of leaf and peel essential oils. Thirty-nine sour oranges displayed no intercultivar molecular polymorphism and six genotypes originated from interspecific hybridizations involving sour orange, citron, pummelo or mandarin. The peel essential oil (PEO) diversity was low, in accordance with the genetic diversity. The predominance of limonene (&gt, 90%) prevents any possible correlation to be made between the composition and the variation in sensory profiles detected by panelists. Few compounds in the leaf essential oil (LEO), such as linalool, linalyl acetate, α-terpineol and geraniol were significantly different across sour oranges varieties. The morphological fruit attributes mainly used in varietal selection differed highly across the main genetically identical group of sour orange accessions. These results confirm that mutation can generate variability in aromatic compounds and aromas and that their exploitation requires an improvement in characterization processes.

High-yielding rice varieties (HYV) show strong compensation among sequentially developed yield components (YC). This phenotypic plasticity has adaptive value but for crop improvement, more information is needed on its effects on yield. SAMARA, a deterministic crop model predicting trait-trait and trait-environment interactions by simulating morphogenetic processes and competition among sinks for assimilates, was developed to study crop phenotypic plasticity. Dynamics of YC and morphology were observed on the HYV IR72 planted at standard and 4-fold greater density in 4 environments in the Philippines in 2012/13. Data for other years/seasons were obtained for model validation. Sequential path analysis was used to determine the phenotypic plasticity of traits consecutively contributing to yield. Tiller number at flowering (R2 = 0.94) and maturity (R2 = 0.84) and grain yield (R2 = 0.77) were predicted accurately for independent datasets. The model also predicted accurately density effects on aboveground dry weight (agdw), plant height, leaf size, spikelet number per panicle and filling percentage. Tiller and leaf mortality were over-estimated under high density. Overall, the model predicted satisfactorily the sequential compensation processes among YCs. They led to stable grain yield despite large morphological differences among density treatments and environments. Sensitivity analysis of simulation outcomes vs. variation in crop parameters indicated that modified genotypic tillering ability, phyllochron or leaf size had little effect on final grain yield because of compensations by other traits, although IR72 appeared to have an optimal combination of parameter values. Larger effects on grain yield were predicted for variation of parameters affecting the sensitivity of leaf and tiller mortality to assimilate resources and the ability to mobilize stem non-structural carbohydrates during grain filling. The model will be used next to perform physiological trait dissection and plasticity analyses for diverse genotypes.

BGPI : équipe 2 / 5; International audience; Efficient strategies for limiting the impact of pathogens on crops require a good understanding of the factors underlying the evolution of compatibility range for the pathogens and host plants, i.e., the set of host genotypes that a particular pathogen genotype can infect and the set of pathogen genotypes that can infect a particular host genotype. Until now, little is known about the evolutionary and ecological factors driving compatibility ranges in systems implicating crop plants. We studied the evolution of host and pathogen compatibility ranges for rice blast disease, which is caused by the ascomycete Magnaporthe oryzae. We challenged 61 rice varieties from three rice subspecies with 31 strains of M. oryzae collected worldwide from all major known genetic groups. We determined the compatibility range of each plant variety and pathogen genotype and the severity of each plant pathogen interaction. Compatibility ranges differed between rice subspecies, with the most resistant subspecies selecting for pathogens with broader compatibility ranges and the least resistant subspecies selecting for pathogens with narrower compatibility ranges. These results are consistent with a nested distribution of R genes between rice subspecies.

To be able to account for sensory quality earlier in the assessment of a new banana hybrid in a selection scheme, the ability of instrumental parameters to predict the sensory perception of banana odour and aroma was investigated. Thirteen cultivated bananas and four new triploid hybrids were characterized by both sensory profiling and chemical analyses. PLS regression models were built using cultivated bananas, and the quality of predictions was validated using hybrids. Forty-one volatile compounds were detected in banana cultivars by SPME–GC–MS. Major differences were observed in the distribution of volatile compounds among cultivars. 3-methylbutyl esters were the most abundant in the 17 banana cultivars. PLS models were able to predict four odours (‘banana’, ‘fermented’, ‘grassy’, and ‘chemical’) and five aromas (‘banana’, ‘fermented’, ‘chemical’, ‘medicinal’, and ‘pineapple’) with a goodness of fit (R2) between 0.52 and 0.71. Two butanoate esters, 2-methylpropyl butanoate and 3-methylbutyl butanoate, mainly contributed to ‘banana’ odour and aroma. Two other esters, 3-methylbutyl acetate and ethyl 3-methylbutanoate contributed to the ‘fermented’, ‘chemical’, and ‘medicinal’ notes, suggesting that interactions between volatile compounds could lead to differences in the perception of odours and aromas. The ‘grassy’ odour was the only attribute which was negatively associated with volatile compounds. Total organic acids enhanced the ‘pineapple’ aroma, whereas it reduced the perception of the ‘banana’ aroma, suggesting interactions between volatile and non-volatile compounds or cognitive associations between aromas and sourness. In conclusion, PLS models can now be used for high throughput phenotyping to predict odours and aromas in dessert banana.

BGPI : équipe 7; International audience; Yellow leaf (YL) is a disease of sugarcane that is currently widespread throughout most American and Asian sugarcane-producing countries. However, its actual distribution in Africa remains largely unknown. A reverse-transcription loop-mediated isothermal amplification (RT-LAMP) assay was developed to facilitate and improve the detection of Sugarcane yellow leaf virus (SCYLV), the causal agent of YL. The RT-LAMP assay was found to be comparable with or superior to conventional RT-polymerase chain reaction (PCR) for the detection of SCYLV genotypes CUB and BRA in infected sugarcane 'C132-81' and 'SP71-6163', respectively. Additionally, 68 sugarcane samples that tested negative by RT-PCR were found positive by RT-LAMP, whereas the RT-LAMP assay failed to detect SCYLV in only 5 samples that tested positive by RT-PCR. Combining RT-PCR and RT-LAMP data enabled the detection of SCYLV in 86 of 183 Kenyan sugarcane plants, indicating high SCYLV prevalence throughout the country (ranging from 36 to 64% in individual counties). Seminested PCR assays were developed that enabled the amplification of a fragment encompassing the capsid protein coding region gene and its flanking 5' and 3' genomic regions. Sequences of this fragment for four Kenyan SCYLV isolates indicated that they shared 99.2 to 99.6% pairwise identity with one another and clearly clustered phylogenetically with SCYLV-BRA genotype isolates. To our knowledge, this is the first report of SCYLV in Kenya.

In Kenya coffee quality is determined by the grade proportions and beverage quality which are influenced by various factors including variety, shade and altitude. The objective was to characterize the quality of coffee produced by farmers producing traditional varieties and Ruiru 11 under shade or under full sun in Muranga County. One hundred and five farmers from 13 farmers' Cooperative societies were sampled from an altitude of 1300 to 1900MASL. The type of shade was characterized and it was found that in some cases trees along the hedge were observed to cast shade on coffee. In other farms, big trees in the coffee fields provided shade to the coffee below. Cherry was harvested and wet processed. Green coffee was roasted to medium roast, weighed out as whole beans (five cups of each sample). A panel of five judges evaluated the sensory attributes of the samples. Ten sensory attributes assessed for each coffee on a ten point scale: Fragrance/Aroma, flavour, aftertaste, acidity, body, balance, uniformity, clean cup, sweetness and overall perception. Generally, traditional varieties had significantly better fragrance, flavour, acidity and overall perception as rated by the panel. Altitude and shade did not seem to have any significant effect on the sensory characteristics. In terms of defects, coffee berry borer attack was significantly observed irrespective of the variety or whether coffee was under some shade or in full sun. The results are discussed in relation to possible impact of variety, altitude, and shade on coffee quality observing that shade/agro-forestry is one of the upcoming changes of coffee production systems to mitigate against climate change.

The cowpea aphid, Aphis craccivora, is a major insect pest of cowpea in Africa. Volatile organic compounds (VOCs) mediate plant–arthropod interactions that could be used in the management of insect pests. In this study, we established the VOC profile involved in the interaction between A. craccivora and four cowpea cultivars, namely Ex‐Luanda, Katumani 80, Machakos 66 and Ken Kunde 1. Behavioural assays were conducted to study host preference and gas chromatography‐mass spectrometry (GC/MS) for chemical analysis of volatiles. In preference assays, alate A. craccivora had no significant preference for any of the four cowpea cultivars tested. However, in the olfactometer assays, the aphids showed a significant preference for odours from cultivar Ex‐Luanda compared to Katumani 80. Machakos 66 and Ken Kunde 1 elicited neutral responses. In pairwise comparisons, alate A. craccivora did not distinguish between odours of respective cowpea cultivars. GC/MS analysis identified 23 compounds in the volatiles of the four cowpea cultivars. Not all compounds were detected in all cowpea cultivars, and the detected compounds amounts varied in each cultivar. Of these, only four compounds (hexanal, (E)‐2‐hexenal, 1‐octen‐3‐ol and p‐xylene) were emitted in significantly different quantities in the four cultivars. A blend of hexanal and (E)‐2‐hexenal added to cowpea cultivar Ex‐Luanda decreased its attractiveness to A. craccivora compared to the control. Our findings showed differential attractiveness of VOCs of cowpea cultivars to A. craccivora, suggesting that VOCs could be used in the management of A. craccivora.

Summary Hybridizations between closely related species commonly occur in the domestication process of many crops. Banana cultivars are derived from such hybridizations between species and subspecies of the Musa genus that have diverged in various tropical Southeast Asian regions and archipelagos. Among the diploid and triploid hybrids generated, those with seedless parthenocarpic fruits were selected by humans and thereafter dispersed through vegetative propagation. Musa acuminata subspecies contribute to most of these cultivars. We analyzed sequence data from 14 M. acuminata wild accessions and 10 M. acuminata‐based cultivars, including diploids and one triploid, to characterize the ancestral origins along their chromosomes. We used multivariate analysis and single nucleotide polymorphism clustering and identified five ancestral groups as contributors to these cultivars. Four of these corresponded to known M. acuminata subspecies. A fifth group, found only in cultivars, was defined based on the ‘Pisang Madu’ cultivar and represented two uncharacterized genetic pools. Diverse ancestral contributions along cultivar chromosomes were found, resulting in mosaics with at least three and up to five ancestries. The commercially important triploid Cavendish banana cultivar had contributions from at least one of the uncharacterized genetic pools and three known M. acuminata subspecies. Our results highlighted that cultivated banana origins are more complex than expected – involving multiple hybridization steps – and also that major wild banana ancestors have yet to be identified. This study revealed the extent to which admixture has framed the evolution and domestication of a crop plant., Significance Statement Hybridizations between subspecies of Musa acuminata are at the origin of a diversity of banana cultivars whose genomes remain to be fully characterized for their ancestry. We developed a bioinformatics approach to decipher the genome ancestry mosaic in a set of banana cultivars including the commercially important Cavendish banana. We revealed that the cultivars resulted from multiple hybridization events involving known M. acuminata subspecies but also unknown contributors still to be discovered. These results bring essential information for breeding strategies in this crop that is particularly threatened by disease.

Modern rice cultivars are adapted to a range of environmental conditions and human preferences. At the root of this diversity is a marked genetic structure, owing to multiple foundation events. Admixture and recurrent introgression from wild sources have played upon this base to produce the myriad adaptations existing today. Genome-wide studies bring support to this idea, but understanding the history and nature of particular genetic adaptations requires the identification of specific patterns of genetic exchange. In this study, we explore the patterns of haplotype similarity along the genomes of a subset of rice cultivars available in the 3,000 Rice Genomes data set. We begin by establishing a custom method of classification based on a combination of dimensionality reduction and kernel density estimation. Through simulations, the behavior of this classifier is studied under scenarios of varying genetic divergence, admixture, and alien introgression. Finally, the method is applied to local haplotypes along the genome of a Core set of Asian Landraces. Taking the Japonica, Indica, and cAus groups as references, we find evidence of reciprocal introgressions covering 2.6% of reference genomes on average. Structured signals of introgression among reference accessions are discussed. We extend the analysis to elucidate the genetic structure of the group circum-Basmati: we delimit regions of Japonica, cAus, and Indica origin, as well as regions outlier to these groups (13% on average). Finally, the approach used highlights regions of partial to complete loss of structure that can be attributed to selective pressures during domestication.

International audience; Background and Aims Banana cultivars are derived from hybridizations involving Musa acuminata subspecies. The latter diverged following geographical isolation in distinct South-east Asian continental regions and islands. Observation of chromosome pairing irregularities in meiosis of hybrids between these subspecies suggested the presence of large chromosomal structural variations. The aim of this study was to characterize such rearrangements. Methods Marker (single nucleotide polymorphism) segregation in a self-progeny of the 'Calcutta 4' accession and mate-pair sequencing were used to search for chromosomal rearrangements in comparison with the M. acuminata ssp. malaccensis genome reference sequence. Signature segment junctions of the revealed chromosome structures were identified and searched in whole-genome sequencing data from 123 wild and cultivated Musa accessions. Key Results Two large reciprocal translocations were characterized in the seedy banana M. acuminata ssp. burmannicoides 'Calcutta 4' accession. One consisted of an exchange of a 240 kb distal region of chromosome 2 with a 7.2 Mb distal region of chromosome 8. The other involved an exchange of a 20.8 Mb distal region of chromosome 1 with a 11.6 Mb distal region of chromosome 9. Both translocations were found only in wild accessions belonging to the burmannicoides/burmannica/siamea subspecies. Only two of the 87 cultivars analysed displayed the 2/8 translocation, while none displayed the 1/9 translocation. Conclusion Two large reciprocal translocations were identified that probably originated in the burmannica genetic group. Accurate characterization of these translocations should enhance the use of this disease resistance-rich burmannica group in breeding programmes.

International audience; Introduction - The narrow knowledge of the genetic variability in cultivated pineapple in the Republic of Benin and in other West African countries limits its efficient use and its expansion in the international market; it also hinders the efficient development of pineapple while the crop is listed among the top three priority fruit species to be promoted in Africa. Materials and methods - In this study, we assessed pineapple morphological diversity of 55 accessions collected in Benin. Ten qualitative and twenty quantitative traits were used to describe them. Stepwise discriminant analysis and hierarchical cluster analysis were performed to identify quantitative morphological traits which best differentiate accessions and group them into cultivars/morphotypes. Results and discussion - Five pineapple cultivars were identified and characterized for Benin, including 'Smooth Cayenne', 'Baronne de Rothschild', 'Perola', 'Singapore Spanish', and 'Green Spanish'. We observed significant morphological variation among the cultivars. The collected materials were grouped in three clusters based on flowering date, fruit diameter, fruit shelf life, water content, leaf width, fruit weight and the crown height and weight. Correlation analyses between descriptors revealed positive relationships between fruits weight, peduncle diameter, and conicity index in 'Cayenne' and 'Spanish'. Conclusion - This study showed the existence of clear morphological variation among pineapple cultivars which could be used for fruit improvement through clonal selection and farmer training on propagule production and crop homogeneity. 'Singapore Spanish' and 'Green Spanish' could be promoted for their attractive shell color and long shelf life.

Panicum maximum est une graminee fourragere caracterisee par la coexistence sur une meme inflorescence de deux modes de reproduction : l'apomixie et la sexualite. Selectionneurs, multiplicateurs de semences et utilisateurs ont pour une meme raison, le rendement, tendance a n'employer qu'un nombre limite de varietes. Ceci aboutit rapidement a l'echelle d'un pays a une homogeneisation genetique. Chez une plante apomictique, l'homogeneite devient preponderante. Les possibilites d'adaptation a un changement des conditions exterieures sont alors limitees. L'etude des strategies adoptees par cette espece pour se maintenir et se diversifier dans des conditions aussi variables que celles qui regissent les ecosystemes tropicaux permet de cerner l'attitude que le selectionneur et l'utilisateur doivent prendre afin de minimiser les risques lors de son exploitation agronomique

The diversity of cultivated species results from a series of domestication events, gene flow between wild and cultivated compartments, effects of natural adaptive selection and also on human selection and diffusion dynamics at large scales, often over long periods. The impact of these processes on diversity depends not only on the biology of the species but is also strongly related to social context and human practices. This thesis contributes to the understanding of the influence of human on the dynamics of almond diversity in situ. The approach followed uses population genetics and anthropology to study the structuring of the genetic diversity of this allogamous perennial fruit species, grown in Lebanon. This study consists of three parts:In the first part, we sought to understand the processes of continuous diversification of cultivated almond trees based on evidence from archeology, history and evolutionary biology of almond trees in the Mediterranean Basin. We used a population genetics approach with many individuals representing each cultivar collected in Lebanon. Intensive sampling of Lebanese cultivars was compared to a large number of in situ grown trees from different Mediterranean regions. The results allowed us to distinguish the impact of different diffusion periods on the structure of genetic diversity.The second part assessed the cultural importance of the almond tree grown in Lebanon and identified its intraspecific diversity as perceived by the informants. Our results show heterogeneity of informants' knowledge that led to a flexible local taxonomy. The flexibility of local taxonomy is revealed by the presence of inclusive categories and the complexity of the nomenclature system.In the third part, we assessed the effect of the change in propagation practices on the structuration and dynamics of genetic diversity between two varieties and within each of the varieties studied.Our results show that the traditional cultivar, sexually propagated, is geographically structured. The introduction of clonal propagation mode by grafting was gradually adopted. At first, farmers maintained some genetic diversity through occasional sexual multiplication of the introduced cultivar. In contrast, introduction after grafting has reduced intra-varietal genetic diversity in recent orchards.This thesis shows how human knowledge and decisions at different spatial and temporal scales influence the structure and dynamics of the diversity of this species.; La diversité des espèces cultivées résulte d’une série d’évènements de domestication, de flux de gènes entre compartiments sauvages et cultivés, d’effets de la sélection adaptative naturelle et aussi de la sélection humaine et des dynamiques de diffusion à de larges échelles, souvent sur de longues périodes. L’impact de ces processus sur la diversité dépend non seulement de la biologie de l’espèce, mais elle est aussi fortement liée au contexte social et aux pratiques humaines. Cette thèse contribue à la compréhension de l’influence de l’Homme sur la dynamique de la diversité de l’amandier in situ. La démarche suivie fait appel à la génétique des populations et à l’anthropologie pour étudier la structuration de la diversité génétique de cette espèce fruitière pérenne allogame, cultivée au Liban. Cette étude comprend trois parties:Dans la première partie, nous avons cherché à comprendre les processus de diversification continue de l’amandier cultivée en se basant sur des évidences tirées de l'archéologie, de l'histoire et de la biologie évolutive de l’amandier dans le Bassin Méditerranéen. Nous avons utilisé une approche de génétique des populations avec de nombreux individus représentant chaque cultivar collecté auLiban. L'échantillonnage intensif de cultivars libanais a été comparé à un grand nombre d’arbres cultivés in situ provenant de différentes régions méditerranéennes. Les résultats nous ont permis de distinguer l’impact des différents périodes de diffusion sur la structure de la diversité génétique.La deuxième partie, a permis d’évaluer l’importance culturelle de l’amandier cultivé au Liban, et d’identifier sa diversité intra-spécifique telle qu’elle est perçue par les informateurs. Nos résultats montrent une hétérogénéité des connaissances des informateurs qui a mené à une taxonomie locale flexible. La flexibilité de la taxonomie locale est révélée par la présence de catégories englobantes et par la complexité du système de nomenclature.Dans la troisième partie, nous avons évalué l’effet du changement de pratiques de propagation sur la structuration et dynamique de la diversité génétique entre les variétés et à l’intérieur de chacune des deux variétés étudiées. Nos résultats montrent que le cultivar traditionnel, multiplié par semis, est structuré géographiquement. L’introduction du mode de propagation clonal par greffage a été adoptée graduellement. Au début, les agriculteurs ont maintenu une certaine diversité génétique par la multiplication sexuée occasionnelle du cultivar introduit. Par contre, l’introduction après l’adoption du greffage a réduit la diversité génétique intra-variétale dans les vergers récents.Cette thèse montre comment les connaissances et les décisions de l’Homme à différents échelles spatiales et temporelles influencent la structure et la dynamique de la diversité de cette espèce.

UMR BFP - Equipe GFDF; International audience; Improved plant varieties are important in our attempts to face the challenges of a growing human population and limited planet resources. Plant breeding relies on meiotic crossovers to combine favourable alleles into elite varieties1. However, meiotic crossovers are relatively rare, typically one to three per chromosome2, limiting the efficiency of the breeding process and related activities such as genetic mapping. Several genes that limit meiotic recombination were identified in the model species Arabidopsis thaliana2. Mutation of these genes in Arabidopsis induces a large increase in crossover frequency. However, it remained to be demonstrated whether crossovers could also be increased in crop species hybrids. We explored the effects of mutating the orthologues of FANCM3, RECQ44 or FIGL15 on recombination in three distant crop species, rice (Oryza sativa), pea (Pisum sativum) and tomato (Solanum lycopersicum). We found that the single recq4 mutation increases crossovers about three-fold in these crops, suggesting that manipulating RECQ4 may be a universal tool for increasing recombination in plants. Enhanced recombination could be used with other state-of-the-art technologies such as genomic selection, genome editing or speed breeding6 to enhance the pace and efficiency of plant improvement.

Improving the genetic yield potential (YP) of tropical, irrigated rice varieties is a priority objective of rice breeding programs worldwide in the interest of achieving food security and maintaining political stability. But YP has stagnated at about 10 Mg ha−1 since the Green Revolution. We present a survey of researchers' current top yields across different environments and countries, experimentally investigate YP-related traits and radiation use efficiency (RUE) of 12 elite materials, and use a simple model to explore traits that would raise the yield ceiling. The survey indicated that maximal grain yield is between 5 and 12 Mg ha−1 depending on radiation during flowering and grain filling. The experiments conducted in several environments in the Philippines indicated that (1) different morphologies in terms of panicle number and size and leaf size lead to similar YP due to trait–trait compensation, and (2) differences in RUE are partly attributable to variation in terminal senescence which is strongly environment dependent. Simulations thus focused on post-floral physiological processes, namely dynamics of light interception, carbon assimilation and maintenance burden. Scenarios of different degree of stay-green indicated that terminal senescence is essential to limit N requirements and maintenance burden, but partial stay-green would strongly benefit RUE and YP, particularly if accompanied with increased leaf photosynthetic capacity. The need to increase pre-floral C and N reserves for grain filling is discussed, resulting in a concept to refine current ideotypes such as IRRI's New Plant Type and China's Super Hybrid Rice. In conclusion, current best tropical breeding products do not have higher YP than some varieties dating 30–40 years, and new concepts are needed in rice breeding. Breeding for such plants should be done under high N inputs.

Taro (Colocasia esculenta) and the greater yam (Dioscorea alata) are staples in Vanuatu. The aim of the present study was to assess the role of somaclonal variations in the varietal diversification of these two clonally propagated crops. The study was conducted in six villages located each on distinct islands of Vanuatu, Melanesia. Overall, 203 varieties of taro and 80 varieties of yam were collected and DArTs were used for analysis. The overall quality of the DArT markers was high for both species. The percentage of polymorphic clones detected on the DArT array was low for taro (3 %) and high (13 %) for yam, with respectively 202 and 499 polymorphic clones. Each variety was characterized by its multilocus genotype based on its DArT presence/absence profile. For taro, the 203 varieties were represented by 126 unique genotypes and 34 distinct multilocus lineages (MLLs). The high number of unique genotypes and the presence of few varieties sharing a clonal origin, generated a high varietal richness index (R = 0.83). For yam, the 80 varieties were represented by seven unique genotypes and 16 MLLs. The low number of unique genotypes and the presence of numerous varieties sharing a clonal origin generated a low varietal richness index (R = 0.26). Possible factors contributing to these contrasting results are discussed. DArT markers provide evidence that somaclonal variants of taro and yam are selected as new varieties. Strategies aiming at strengthening communities' capacity to adapt to forthcoming changes should consider the introduction of allelic diversity into farmers' varietal portfolios.

Depuis des millénaires, les migrations de populations et les échanges de matériel végétal ont placé le bananier dans des contextes écologiques très différents sur tous les continents. Les agriculteurs ont su valoriser les mutations naturelles résultant de la multiplication végétative. C'est cette combinaison de la reproduction naturelle et des sélections faites par l'homme depuis la nuit des temps qui est à l'origine de la diversité génétique actuelle.

'CARBAP K74' is a triploid plantain-like hybrid developed and selected in partnership between CARBAP and CIRAD. It results from a cross between an improved plantain-like tetraploid (AAAB) parental line and an improved cooking-type diploid (AA). Molecular studies showed that this hybrid is free of any endogenous banana streak virus (eBSV) sequence. An agronomic evaluation was performed over two crop cycles to quantify its productivity and evaluate its host reaction to pests and diseases. A first plot received non-limiting cropping conditions to allow it to reach its highest agronomic potential. A second plot reproduced traditional management in West and Central Africa with low inputs and traditional practices. Agronomic traits at flowering described a robust plant with great anchorage and large green leaf area. Bunch weights ranged from 10 to 50 kg across the two cropping conditions, with an average of 16.4 kg (14 t ha-1 year-1) under traditional management, and 34.3 kg (46 t ha-1 year-1) for non-limiting cropping conditions. In both plots, damage assessments highlighted a lower susceptibility to major pests and diseases of plantains. The agronomic potential of 'CARBAP K74' allows the production of acceptable yields with few inputs over several cycles without replanting, which confirms its interest for smallholders as well as for agroindustry. Furthermore, fruit post-harvest traits and consumer testing showed that 'CARBAP K74' is a promising candidate for consumption and processing. Thus, 'CARBAP K74' is an innovative promising hybrid, which could help farmers to achieve agronomic performance, limit environmental impacts of banana production and confront food security issues.

The 'Plantain-Optim' dataset (came from the 'Plantain-Optim' experiment conducted from 2009 to 2011 at CARBAP experimental station in Cameroon. The main objective was to describe agronomic potential of nine plantain varieties, including five natural plantains commonly cropped in Cameroon, and four plantain-like hybrids. A completely randomized bloc permitted to compare growth, development and yield of 45 plants per variety split between five replicates. Cropping practices guarantied non-limiting and homogenous conditions. Each plant was measured every 15 days. Data described aerial organ sizes, foliar structure and bunch characteristics of the mother plant. The 'Plantain-Optim' dataset includes the complete individual growth of each studied plantain of the 'Plantain-Optim' experiment with a 15-day accuracy. It is a useful standard of plantain varietal diversity for comparison with others datasets. Varietal growth and development homogeneity, biomass production or foliar and bunch structures could be further investigated. Moreover, these accurate data on plantain growth could be valuable for plantain 3D modelling.

Aims: Genotypic mixtures have been receiving a growing interest as genetic diversity could increase crop productivity. Resource-use complementarity is an expected key underlying mechanism, provided that varieties in the mixture differ in resource-related traits, notably root traits. We aimed at examining how trait differences and resource-use complementarity drive biomass production of genotypic mixtures. Methods: Four rice (Oryza sativa) genotypes including two Near-Isogenic Lines only differing in root depth were grown in monoculture and in two-way mixtures in pots under two levels of phosphorus supply. We analyzed the relative difference between mixture biomass and the best monoculture biomass in relation to between-genotype phenotypic distance on ten resource-related traits. Results: Mixtures never outperformed the best monoculture. However, relative mixture productivity increased with increasing between-genotype distance in biovolume, specific leaf area and top soil root biomass. This was mainly driven by a “selection effect”: trait differences led to competitive ability differences and the dominant genotypes tended to gain more in mixture than the subdominant genotypes lost compared to monoculture. Conclusions: Rather than trying to minimize competition through resource-use complementarity, we argue that promoting interactions between genotypes that have different competitive abilities may be a more promising approach to design productive crop mixtures.

The Global Strategy for the Conservation and Use of Musa Genetic Resources (hereafter referred to as the ‘Global Strategy’) has been expanded in 2016 by Musa genetic resources and breeding experts within the framework of the Global Musa Genetic Resources Network, MusaNet. MusaNet’s mandate is to oversee the further development and monitoring of the implementation of the Global Strategy. The updated Global Strategy aims to provide a clear framework and roadmap to be used by the Musa community for the efficient and effective conservation of the globally important collections of Musa and to strengthen the utilization of the genetic resources toward an increased use of available diversity. It includes recommendations and priorities indicated in several consultation processes following the 2006 Global Musa Strategy and particularly the expertise and key groups represented, including the Regional Research Networks (BAPNET, BARNESA, Innovate Plantain and MusaLAC) and global networks such as ProMusa. The Global Strategy covers numerous topics dealing with Musa genetic resources, with the 12 chapters divided into four main parts: Diversity, Identity, Management and Use. Each chapter contains the sections titled Where we are now, Where do we want to go and How will we get there. For Musa researchers, including taxonomists and breeders, but also end users such as farmers, decisions on the management of banana diversity are often made with limited information. With this in mind, the Global Strategy is a core reference on the taxonomy, characterization, evaluation and genetic improvement of cultivars, leading to actions such as the selection of new and improved cultivars. The use of a more diverse genepool can lead to higher production while at the same time promote ecosystem services such as resilience to pest and disease and the effects of climate change.

Taro [Colocasia esculenta (L.) Schott] is a root crop which is an important staple food in many regions of the world, producing 10.5 million tonnes on 1.4 million hectares a year. The crop is cultivated in wet (rain fed) or irrigated conditions, requiring on average 2,500 mm water per year, and in many countries it is cultivated in flooded plots. it is estimated that taro production could decrease by 40 % as a result of the increase in drought and other severe events. In this work, Thirty three accessions, including local cultivars, selected and hybrid lines were submitted to long duration drought stress and screened for tolerance. Twelve physiological, morphological and agronomic traits were measured at harvest, and subject to multivariate analysis. Stress indices, Water Use Efficiency and Factorial Analysis were useful for discriminating accessions regarding drought tolerance and yield stability, and drought tolerant and susceptible cultivars were identified. Our results confirm that different taro cultivars have different drought avoidance and tolerance strategies to cope with water scarcity. Better yield performers minimised biomass and canopy loss, while tolerance was observed in cultivars that presented low potential yield, but efficiently transferred resources to enhance corm formation. Among the 33 accessions, two local cultivars showed high yield stability and could be considered as suitable parents for breeding programs, while two others are well adapted to drought, but with overall low yield potential.

The tropical root and tuber crops (aroids, cassava, sweet potato and yams) represent major contributions to food security in the Pacific Islands Countries (PICs) but are also cash crops for local and export markets. Conventional breeding is complex as the flowering ability of cultivars is erratic; they are predominantly allogamous, highly heterozygous with variable ploidy levels. Breeding is based on phenotypic recurrent selection with comprehensive characterisation and elimination of numerous hybrids evaluated across successive clonal generations for major agronomic traits. Over the last three decades, the PICs breeding programmes have been project-driven but have successfully delivered improved clones. The results obtained for Colocasia esculenta, Xanthosoma sagittifolium, Ipomoea batatas, Dioscorea spp., and Manihot esculenta, are reviewed. For each species, the technical bottlenecks and research priorities are identified and perspectives for further genetic improvement are discussed.

Sugarcane (Saccharum spp.) is a major crop for sugar and bioenergy production. Its highly polyploid, aneuploid, heterozygous, and interspecific genome poses major challenges for producing a reference sequence. We exploited colinearity with sorghum to produce a BAC-based monoploid genome sequence of sugarcane. A minimum tiling path of 4660 sugarcane BAC that best covers the gene-rich part of the sorghum genome was selected based on whole-genome profiling, sequenced, and assembled in a 382-Mb single tiling path of a high-quality sequence. A total of 25,316 protein-coding gene models are predicted, 17% of which display no colinearity with their sorghum orthologs. We show that the two species, S. officinarum and S. spontaneum, involved in modern cultivars differ by their transposable elements and by a few large chromosomal rearrangements, explaining their distinct genome size and distinct basic chromosome numbers while also suggesting that polyploidization arose in both lineages after their divergence., Sugarcane (Saccharum spp.) is a crop of major economic significance but has complex genome structure. Here, the authors generate a BAC-based monoploid sugarcane reference sequence.

Kava (Piper methysticum) is a major cash crop in the Pacific. The aim of this study was to assess genetic variation among 103 accessions of kava using SSRs and DArTs. Genetic structure was determined using clustering analyses (WPGMA) and principal coordinate analyses (PCA). Thirteen SSR primers and 75 DArT markers were found polymorphic, and the two types of markers generated similar clustering patterns. Genetic distances ranged from 0 to 0.65 with an average of 0.24 using SSRs and from 0 to 0.64 with an average of 0.24 using DArT. Eleven genotypes were identified with SSR while 28 genotypes were identified with DArT markers. By combining the two sets of markers, a total of only 30 distinct genotypes were observed. In the Vanuatu archipelago, noble cultivars originating from different islands clustered together within a very narrow genetic base despite their diversity of morphotypes. SSR and DArT fingerprints allowed the identification of kava cultivars unsuitable for consumption, so called two-days, and clearly differentiated the wild types classified as P. methysticum var. wichmannii from the cultivars as var. methysticum. Molecular data reveals that all noble cultivars evolved by the predominance of clonal selection. Although they are represented by clearly distinct morphotypes, these cultivars are genetically vulnerable and their potential to adapt to forthcoming changes is limited. These newly developed markers provide high resolution and will be useful for kava diversity analyses and quality assessment.

Afin d'étudier les effets des facteurs date et densité de semis sur la croissance végétative et le rendement du cotonnier en culture pluviale, quatre essais ont été conduits sur deux sites au Bénin en 2002 et 2003. Un dispositif expérimental en splitsplit plot avec trois répétitions a été utilisé pour comparer 1 O variétés différentes, à trois densités de culture (42.000, 125.000, 167.000 plants.ha-1) et deux dates de semis (juin, juillet/août). La hauteur des plants, le nombre de noeuds par tige, la longueur des branches et le rendement au champ ont été évalués. La date de semis a affecté la morphologie uniquement dans les conditions hydriques limitantes (plants plus courts en semis retardé). Le semis retardé a réduit les rendements de 12% pour la variété précoce et compacte Mar 88-214; contre plus de 30% pour les variétés à fort développement végétatif. Aux fortes densités, tous les génotypes étaient plus courts avec des branches également plus courtes. En semis retardé et à forte densité, Mar 88-214 et Guazuncho 2 ont produit au moins 100 kg.ha-1 de plus que les variétés végétatives; les variétés précoces et compactes semées aux fortes densités conviennent mieux lorsque les conditions hydriques sont limitantes. La densité de semis influence plus nettement la croissance végétative et le rendement du cotonnier que la date de semis.

China is one of the largest cotton producing countries in the world thanks to high yields, on which a variety registration system has mainly focused, so that a lack of quality is nowadays acknowledged as a weak point of the cotton industry in that country. The objective of this study was to check the hypothesis that bias in cultivar selection in favor of yield has been maintained through the application of an imperfect selection index (SI), but that a better outcome is possible. Our demonstration is based on an analysis of the data from ten years of cotton variety trials using genotype-by-trait biplots, implemented both for the cultivar selection index (SI) currently applied in China and for an adjusted selection index (ASI) that more effectively took into account the antagonism between yield and quality traits. The main findings were: 1) significant negative associations between yield and fiber quality hindered their simultaneous improvement; 2) registered genotypes were mainly determined by the SI which was primarily yield-oriented; 3) no progress in fiber quality was recorded unlike yield; 4) balanced progress in yield and quality is possible through an adjusted selection index (ASI) guided by genotype-by-trait biplot analysis.

Eggplant cultivation is confronted by the bacterial wilt disease caused by the Ralstonia solanacearum species complex. Breeding resistant cultivars is the most effective strategy to control the disease but is limited by the pathogen’s extensive genetic diversity. A major QTL (ERs1) was previously mapped in a recombinant inbred lines (RIL) population from the cross of susceptible (S) MM738 × resistant (R) AG91-25 lines. ERs1 was originally found to control 3 strains from phylotype I, while being ineffective against the strain PSS4 from the same phylotype. The objectives of this thesis was to (i) clarify the position of ERs1 and define its spectrum of action, (ii) found other QTLs, promptly to control virulent strains on AG91-25 and (iii) introgress some of the QTLs into two S cultivars. For this purpose, the new doubled haploid (DH) populations MM152 (R) × MM738 (S) and EG203 (R) × MM738 (S) were created. The RIL population was phenotyped with 4 additional RSSC strains belonging to phylotypes I, IIA, IIB and III and the DH populations were phenotyped with virulent strains PSS4 and R3598. QTL mapping confirmed the existence of ERs1 (renamed EBWR9), defined its position on chromosome (chr) 9 and validated its specific control of 3 phylotype I strains. EBWR2 and EBWR14, 2 broad-spectrum resistance QTLs, were detected on chr 2 and 5. QTL analysis reveals a polygenic system of resistance in EG203. The transfer of resistance into 2 local cultivars was initiated and allowed the introgression of EBWR9 and EBWR2 QTLs through a backcross scheme. These results offer perspectives to breed broad-spectrum R cultivars., La culture de l’aubergine est confrontée au flétrissement bactérien, maladie causée par le complexe d’espèces Ralstonia solanacearum. La résistance variétale est la méthode la plus efficace pour contrôler cette maladie. Un QTL majeur (ERs1) a précédemment été cartographié dans une population de lignées recombinantes (RIL) issue du croisement aubergine sensible (S) MM738 × aubergine résistante (R) AG91-25. Initialement, ERs1 a été détecté avec 3 souches du phylotype I, alors qu’il est contourné par la souche PSS4 de ce même phylotype. Les objectifs de cette thèse étaient (i) de préciser la position d’ERs1 et de définir son spectre d’action, (ii) d’identifier d’autres QTLs contrôlant les souches virulentes sur AG91-25, et (iii) d’introgresser certains de ces QTLs dans des cultivars S. Pour cela, 2 populations d'haploïdes doublés (HD), MM152 (R) × MM738 (S) et EG203 (R) × MM738 (S), ont été créées. La population RIL a été phénotypée avec 4 souches supplémentaires appartenant aux phylotypes I, IIA, IIB et III, tandis que les populations HD l’ont été avec les souches virulentes PSS4 et R3598. Les analyses de cartographie génétique ont confirmé l’existence d’ERs1 (renommé EBWR9), défini sa position sur le chromosome (chr) 9 et validé son contrôle spécifique de 3 souches du phylotype I. EBWR2 et EBWR14, 2 autres QTLs à large spectre, ont été détectés sur les chr 2 et 5. Les analyses QTL ont mis en évidence un système de résistance de type polygénique chez EG203. Le transfert de la résistance dans 2 cultivars locaux a été initié et a permis l’introgression d’EBWR9 et d’EBWR2. Ces résultats ouvrent des perspectives quant à la création de variétés à large spectre de résistance.