In-depth characterization of apple genetic resources is a prerequisite for genetic improvement and for germplasm management. In this study, we fingerprinted a very large French collection of 2163 accessions with 24 SSR markers in order to evaluate its genetic diversity, population structure, and genetic relationships, to link these features with cultivar selection date or usage (old or modern, dessert or cider cultivars), and to construct core collections. Most markers were highly discriminating and powerful for varietal identification, with a probability of identity P (ID) over the 21 retained SSR loci close to 10 −28. Pairwise comparisons revealed 34 % redundancy and 18.5 % putative triploids. The results showed that the germplasm is highly diverse with an expected heterozygosity H e of 0.82 and observed heterozygosity H o of 0.83. A Bayesian model-based clustering approach revealed a weak but significant structure in three subgroups (F ST = 0.014-0.048) corresponding, albeit approximately, to the three subpopulations defined beforehand (Old Dessert, Old Cider, and Modern Cultivars). Parentage analyses established already known and yet unknown relationships, notably between old cultivars, with the frequent occurrence of cultivars such as BKing of Pippin^and BCalville Rouge d'Hiver^as founders. Finally, core collections based on allelic diversity were constructed. A large dessert core collection of 278 cultivars contained 90 % of the total dessert allelic diversity, whereas a dessert subcore collection of 48 cultivars contained 71 % of diversity. For cider apples, a 48-cultivar core collection contained 83 % of the total cider allelic diversity.

a b s t r a c tA stumbling block to the adoption of silvoarable agroforestry systems is the lack of quantitative knowledge on the performance of different crops when competing for resources with trees. In North-Western Europe, light is likely to be the principal limiting resource for understorey crops, and most agronomic studies show a systematic reduction of final yield as shade increases. However the intensity of the crop response depends on both the environmental conditions and the shade characteristics. This study addressed the issue by monitoring winter wheat (Triticum aestivum L.) growth, productivity and quality under artificial shade provided by military camouflage shade-netting, and using the Hi-sAFe model to relate the artificial shade conditions to those applying in agroforestry systems.The field experiment was carried out over two consecutive years (2013-14 and 2014-15) on the experimental farm of Gembloux Agro-Bio Tech, Belgium. The shade structures recreated two shade conditions: periodic shade (PS) and continuous shade (CS), with the former using overlapping military camouflage netting to provide discontinuous light through the day, and the latter using conventional shade cloth. The experiment simulated shading from a canopy of late-flushing hybrid walnut leaves above winter wheat. Shading was imposed 16 (2013-14) and 10 (2014-15) days before flowering and retained until harvest. The crop experienced full light conditions until the maximum leaf area index stage (LAI max ) had been reached. In both years, LAI followed the same dynamics between the different treatments, but in 2013-2014 an attack of the take-all disease (Gaeumannomyces graminis var. tritici) reduced yields overall and prevented significant treatment effects. In season 2014-15 the decrease in global radiation reaching the crop during a period of 66 days (CS: -61% and PS: -43%) significantly affected final yield (CS: -45% and PS: -25%), mainly through a reduction of the average grain weight and the number of grain per m 2 . Grain protein content increased by up to 45% under the CS treatment in 2015. Nevertheless, at the plot scale, protein yield (t/ha) did not compensate for the final grain yield decrease.The Hi-sAFe model was used to simulate an agroforestry plot with two lines of walnut trees running either north-south or east-west. The levels of artificial shade levels applied in this experiment were compared to those predicted beneath trees growing with similar climatic conditions in Belgium. The levels used in the CS treatment are only likely to occur real agroforestry conditions on 10% of the cropped area until the trees are 30 years old and only with east-west tree row orientation.

The antagonistic activity of two yeast strains (Pichia anomala (E.C. Hansen) Kurtzman, strain K and Candida oleophila Montrocher, strain O) against the parasitic complex responsible for banana crown rot was evaluated. The strains were applied at three different concentrations (10 6 , 10 7 , 10 8 cfu/ml) and their efficacy tested in vivo on three separate fungi (Colletotrichum musae (Berk. & Curt.) Arx, Fusarium moniliforme Sheldon, and Cephalosporium sp.) and on a parasitic complex formed by association of these three fungi. At the concentrations used C. musae appeared to be the most pathogenic. The complex showed intermediate aggressiveness between C. musae and both other fungi.Statistically significant antagonistic effects were observed on C. musae, F. moniliforme, and the fungal complex. The highest protection level (54.4%) was observed with strain O added at 10 8 cfu/ml on crowns previously inoculated with the fungal complex. The level was lower when the fungi were inoculated separately.Furthermore, the antagonistic effect was strongly reinforced when strain O at 10 8 cfu/ml was applied 24 h before fungal complex inoculation (59.9%), as compared to its application 15 min (24.3%) or 3 h (27.3%) after fungal complex inoculation. Bananas showed increased susceptibility to the fungal complex from March to June, and this influenced the level of protection by yeast, which decreased over the same period. A strict negative correlation (R 2 = 0.83) was highlighted between susceptibility of banana to crown rot and protection provided by yeast.

The RADseq technology allows researchers to efficiently develop thousands of polymorphic loci across multiple individuals with little or no prior information on the genome. However, many questions remain about the biases inherent to this technology. Notably, sequence misalignments arising from paralogy may affect the development of single nucleotide polymorphism (SNP) markers and the estimation of genetic diversity. We evaluated the impact of putative paralog loci on genetic diversity estimation during the development of SNPs from a RADseq dataset for the nonmodel tree species Robinia pseudoacacia L. We sequenced nine genotypes and analyzed the frequency of putative paralogous RAD loci as a function of both the depth of coverage and the mismatch threshold allowed between loci. Putative paralogy was detected in a very variable number of loci, from 1% to more than 20%, with the depth of coverage having a major influence on the result. Putative paralogy artificially increased the observed degree of polymorphism and resulting estimates of diversity. The choice of the depth of coverage also affected diversity estimation and SNP validation: A low threshold decreased the chances of detecting minor alleles while a high threshold increased allelic dropout. SNP validation was better for the low threshold (4×) than for the high threshold (18×) we tested. Using the strategy developed here, we were able to validate more than 80% of the SNPs tested by means of individual genotyping, resulting in a readily usable set of 330 SNPs, suitable for use in population genetics applications.

Crown rot is a complex disease that affects export bananas in all banana-producing countries. Usually invisible when the fruits are packed for transportation from tropical countries to distant destinations, disease symptoms occur during shipment, ripening, and storage. This disease, characterized by rot and necrosis, affects tissues joining the fingers with each other, called the crown. It may reach the pedicel and even the banana pulp when crown rot is severe. Losses from 10 to 86% have been recorded for treated and untreated bananas, respectively. In this paper, we summarize the current knowledge on crown rot disease and associated control measures that must be considered throughout the production channel in order to be effective. We suggest a new approach to this postharvest disease of bananas: that of considering fruit quality potential in the field. This new concept of preharvest quality potential is a key factor to understanding crown rot development. Fruit quality potential depends on both a physiological and a parasitic component, both of which depend on agrotechnic and pedoclimatic factors of the crop production area. The physiological component is defined as the sensitivity of the fruits to crown rot, and the parasitic component reflects the capacity of the parasitic complex to induce a level of disease. The content of this review is divided into two parts. First, the fruit quality potential at field level is addressed, with special emphasis on its physiological and parasitic components. Second, the control methods are examined at different steps of the channel, in order to give an overview of a possible integrated control strategy.

Keywords AbstractThe postharvest development of crown rot of bananas depends notably on the fruit susceptibility to this disease at harvest. It has been shown that fruit susceptibility to crown rot is variable and it was suggested that this depends on environmental preharvest factors. However, little is known about the preharvest factors influencing this susceptibility. The aim of this work was to evaluate the extent to which fruit filling characteristics during growth and the fruit development stage influence the banana susceptibility to crown rot. This involved evaluating the influence of (a) the fruit position at different levels of the banana bunch (hands) and (b) changing the source-sink ratio (So-Si ratio), on the fruit susceptibility to crown rot. The fruit susceptibility was determined by measuring the internal necrotic surface (INS) after artificial inoculation of Colletotrichum musae. A linear correlation (r = −0.95) was found between the hand position on the bunch and the INS. The So-Si ratio was found to influence the pomological characteristics of the fruits and their susceptibility to crown rot. Fruits of bunches from which six hands were removed (two hands remaining on the bunch) proved to be significantly less susceptible to crown rot (INS = 138.3 mm 2 ) than those from bunches with eight hands (INS = 237.9 mm 2 ). The banana susceptibility to crown rot is thus likely to be influenced by the fruit development stage and filling characteristics. The present results highlight the importance of standardising hand sampling on a bunch when testing fruit susceptibility to crown rot. They also show that hand removal in the field has advantages in the context of integrated pest management, making it possible to reduce fruit susceptibility to crown rot while increasing fruit size.

The Bioversity International Transit Center (ITC) for banana hosts more than 1500 accessions largely covering the genetic diversity of the genus Musa. Its objective is to conserve this genetic diversity and to supply plant materials to users worldwide. All the Musa accessions must be tested for virus presence and, if infected, virus elimination must be attempted, to enable the supply of virus-free plant material. An international collaborative effort launched under the auspices of Bioversity International (2007)(2008)(2009)(2010)(2011)(2012)(2013) finally led to the implementation of a two-step process to test the accessions. The first step, called pre-indexing, involved only molecular tests and was designed as a pre-screen of new germplasm lines or existing accessions to reduce the need for post-entry virus therapy and repeated virus indexing. The second step, called full indexing, was performed on either older existing accessions or newer accessions which tested negative during pre-indexing, and involved molecular tests, transmission electron microscopy (TEM) and symptom observation. In total, 270 germplasm lines (434 samples) were pre-indexed; while full indexing was carried out on 243 accessions (68 of which had been pre-indexed). A significant proportion of the samples tested during pre-indexing was infected with at least one virus (68%), showing the utility of this early pre-screening step. Banana streak OL virus and Banana mild mosaic virus were the most commonly detected viruses during both pre-and full indexing. For 22 accessions, viral particles were observed by TEM in full indexing while the molecular tests were negative, underlining the importance of combining various detection techniques. After full indexing, viruses were not detected in 166 accessions, which were then released for international distribution from the ITC. This publication exemplifies how the practical application of diagnostic protocols can raise fundamental questions related to their appropriate use in routine practice and the need for their continuous monitoring and improvement after their first publication.

Bananas that provide a staple food to the millions of people are adversely affected by several viruses such as Banana bunchy Top Virus (BBTV), Banana Streak Virus (BSV), and Cucumber Mosaic Virus (CMV). These viruses are known to have a devastating effect on crop production and constraint to the international exchange and conservation of banana germplasm-a cornerstone for breeding new cultivars. The viruses are particularly problematic in vegetative propagated crops, like bananas, because of their transmission in the planting material. Different virus eradication techniques have been developed, such as thermotherapy, chemotherapy, and meristem culture for providing virus-free planting material. Meristem culture proved to be the most effective procedure to eradicate phloem-associated viruses. This method requires isolation of meristematic dome of plant under the aseptic conditions and culture in an appropriate nutrient medium to develop new virus-free plants. Thermotherapy is another widely used virus eradication technique, which is initially carried out on in vivo or in vitro plants and eventually combined with meristem culture technique. The plantlets are initially grown at 28°C day temperature and increase it by 2°C per day until reaches 40°C and the night temperature at 28°C; maintain plants at 40°C for 4 weeks; excise meristem and culture onto the regeneration medium. In chemotherapy technique, antiviral chemical compound Virazole(®) is applied on meristem culture. Combination of these techniques is also applied to improve the eradication rate.