Analysis of nucleotide diversity in Coffea spp. (W153)

Marker-assisted selection becomes a reality for many crops; in perennial crops, the utilization of molecular markers in breeding programs can speed up genotype selection. However, the most important commercial coffee species - allotetraploid C. arabica - has a restrict number of available polymorphic markers, which is a consequence of the narrow genetic basis and low molecular variability among cultivars. In order to study the nucleotide diversity in C. arabica, as well in other diploid Coffea relatives, we sequenced PCR amplified fragments of nine genes in 20 Coffea genotypes: twelve C. arabica, including eight wild genotypes and four commercial cultivars; and eight C. canephora genotypes. Genotypes of C. eugenioides, C. racemosa and Psylanthus bengalensis were also included in this analysis. From a total of 9 Kb analyzed, we found 573 polymorphisms: 500 SNPs; 39 INDELs and 34 SSRs. In C. canephora genotypes, we detected 188 polymorphisms (frequency of 2.09/100bp). For C. arabica we obtained similar results: 144 polymorphism (frequency of 2.13/100bp). Most of the polymorphism found in C. arabica only reflected the differences between ancestral homeologs, and they were monomorphic among different genotypes. However, 19 % of these polymorphisms (27 SNPs) were interespecific for C. arabica, and 13 of them were fixed among genotypes. The strategy of this work reflects the importance in using a more diverse panel of genotypes in order to identify SNPs in C. arabica, pointing out that the exploitation of wild germplasm will be an important source of genetic variability. (Résumé d'auteur

Genetic diversity and distance among Iranian and European alfalfa (Medicago sativa L.) genotypes

Alfalfa is the best known fodder crop with high ability of biological nitrogen fixation and drought tolerance in dry, Pannonian region of east Austria. Different morphological and physiological characteristics of 18 alfalfa genotypes from different geographical origins, 8 Iranian ecotypes and 10 European cultivars were evaluated under irrigated and rainfed conditions during 2006-08 cropping seasons. The objectives of this study were to measure genetic distance and divergence among genotypes and to classify them based on morphological and physiological characters. Cluster analysis differentiated Iranian ecotypes and European cultivars from each other under irrigated condition, and when data averaged across two environments (irrigated and rainfed). However, under rainfed conditions small changes occurred in grouping of genotypes due mainly to differential responses of the genotypes to rainfed condition. Considerable genetic distance observed between Iranian and European genotypes. Different crossing programs are recommended between Iranian and European genotypes to develop new alfalfa cultivars

Characterization of water deficit tolerance of Poncirus trifoliata genotypes related to diversity

Rootstock provides better adaptation to biotic and abiotic constraints. Poncirus and its hybrids are widely used since they are tolerant to Citrus Tristeza Virus. However, when grafted, most of them are considered to be sensitive to salinity and water deficit. Diversity does exist within the Poncirus trifoliata specie but little is known regarding the behaviour variability of genotypes to abiotic constraints. The citrus diversity of 72 P. trifoliata genotypes was investigated using SSR markers. Two mayor genetic groups were clearly identified. Five genotypes, belonging to each genetic group, were then selected to investigate their properties of tolerance to water deficit. Water deficit was applied by withdrawing irrigation for 4 weeks. Physiological parameters such leaf stomatal conductance and quantum yield of PSII electron transport, soil water potential, leaf osmotic pressure and transpiration were estimated. Among genotypes, we observed that some genotypes such as' Rubidoux' were clearly more tolerant to water deficit than others such as 'Pomeroy'. Interestingly, the genotypes that were sensitive belonged to one genetic group and the tolerant ones belonged to the other group. Therefore, it sounds that among the Poncirus genus, it is possible to select genotypes as parent in breeding programs, which are more tolerant to water deficit. (Résumé d'auteur

Past and future of a century old Citrus tristeza virus collection: a California citrus germplasm tale.

Citrus tristeza virus (CTV) isolates collected from citrus germplasm, dooryard and field trees in California from 1914 have been maintained in planta under quarantine in the Citrus Clonal Protection Program (CCPP), Riverside, California. This collection, therefore, represents populations of CTV isolates obtained over time and space in California. To determine CTV genetic diversity in this context, genotypes of CTV isolates from the CCPP collection were characterized using multiple molecular markers (MMM). Genotypes T30, VT, and T36 were found at high frequencies with T30 and T30+VT genotypes being the most abundant. The MMM analysis did not identify T3 and B165/T68 genotypes; however, biological and phylogenetic analysis suggested some relationships of CCPP CTV isolates with these two genotypes. Phylogenetic analysis of the CTV coat protein (CP) gene sequences classified the tested isolates into seven distinct clades. Five clades were in association with the standard CTV genotypes T30, T36, T3, VT, and B165/T68. The remaining two identified clades were not related to any standard CTV genotypes. Spatiotemporal analysis indicated a trend of reduced genotype and phylogenetic diversity as well as virulence from southern California (SC) at early (1907-1957) in comparison to that of central California (CC) isolates collected from later (1957-2009) time periods. CTV biological characterization also indicated a reduced number and less virulent stem pitting (SP) CTV isolates compared to seedling yellows isolates introduced to California. This data provides a historical insight of the introduction, movement, and genetic diversity of CTV in California and provides genetic and biological information useful for CTV quarantine, eradication, and disease management strategies such as CTV-SP cross protection

Genetic diverstiy of Sugarcane yellow leaf virus in a sugarcane selection plot in Guadeloupe (FWI)

THE GENETIC diversity of Sugarcane yellow leaf virus (SCYLV) was investigated in a sugarcane selection plot in Guadeloupe to determine the incidence of the different known virus genotypes (BRA-PER, CUB and REU) in a breeding progeny. Four F1 leaves were randomly collected from each of 154 sugarcane clones and tested for the presence of SCYLV by tissue blot immunoassay (TBIA). The leaf samples were stored at ¿80°C until total RNA was extracted from SCYLV-infected leaves. The virus genotypes were determined by RT-PCR and primer pairs specific to each virus genotype. Eighty-two percent of the tested leaves were infected by SCYLV and all known virus genotypes occurred in the selection plot. The majority of plants were infected by genotypes CUB or REU, or by a mixture of these two genotypes. This situation was completely different from the situation observed in commercial fields in Guadeloupe where the incidence of SCYLV is much lower and where most plants are infected by genotype REU. The significance of this striking situation will be further investigated. (Résumé d'auteur

Field Screening of Lentil Genotypes Against Aphid Infestation in Inner Tarai of Nepal

Twenty lentil (Lens culinaris Medik) genotypes received from Grain Legumes Research Program, Khajura, Banke were screened for relative tolerance against aphid (Aphis craccivora Koch.) at the research field of National Maize Research Program, Rampur, Chitwan during winter seasons of two consecutive years 2016 and 2017. The design of the experiment was Randomized Complete Block having three replications. The unit plot size was 4m × 1 m with 25cm row to row spacing and continue plant to plant spacing was maintained and net harvested plot was 4 square meters. The recommended dose of fertilizer was 20:40:20 N:P2O5:K2O kg/ha and seed rate 30 kg/ha. Insect data were collected based on aphid population found at apical twigs (10 cm) per plant and scoring was done during flowering and pod formation stage. The grain yield was recorded. All screened genotypes differed significantly (p<0.05) on aphid population and grain yield.  Genotypes, ILL 9924, RL 83, ILL 10856, ILL 6458 and RL 67 were less susceptible with higher grain yield. These results have important implications for the development of aphid tolerant high yielding lentil variety in inner Tarai of Nepal

Microsatellite typing of avian clinical and environmental isolates of Aspergillus fumigatus

Aspergillosis is one of the most common causes of death in captive birds. Aspergillosis in birds is mainly caused by Aspergillus fumigatus, a ubiquitous and opportunistic saprophyte. Currently it is not known whether there is a link between the environmental isolates and/or human isolates of A. fumigatus and those responsible for aspergillosis in birds. Microsatellite typing was used to analyse 65 clinical avian isolates and 23 environmental isolates of A. fumigatus. The 78 genotypes that were obtained were compared with a database containing genotypes of 2514 isolates from human clinical samples and from the environment. There appeared to be no specific association between the observed genotypes and the origin of the isolates (environment, human or bird). Eight genotypes obtained from isolates of diseased birds were also found in human clinical samples. These results indicate that avian isolates of A. fumigatus may cause infection in humans

Iron and zinc grain density in common wheat grown in Central Asia

Sixty-six spring and winter common wheat genotypes from Central Asian breeding programs were evaluated for grain concentrations of iron (Fe) and zinc (Zn). Iron showed large variation among genotypes, ranging from 25 mg kg1 to 56 mg kg1 (mean 38 mg kg1). Similarly, Zn concentration varied among genotypes, ranging between 20 mg kg1 and 39 mg kg1 (mean 28 mg kg1). Spring wheat cultivars possessed higher Fe-grain concentrations than winter wheats. By contrast, winter wheats showed higher Zn-grain concentrations than spring genotypes. Within spring wheat, a strongly significant positive correlation was found between Fe and Zn. Grain protein content was also significantly (P < 0.001) correlated with grain Zn and Fe content. There were strong significantly negative correlations between Fe and plant height, and Fe and glutenin content. Similar correlation coefficients were found for Zn. In winter wheat, significant positive correlations were found between Fe and Zn, and between Zn and sulfur (S). Manganese (Mn) and phosphorus (P) were negatively correlated with both Fe and Zn. The additive main effects and multiplicative interactions (AMMI) analysis of genotype × environment interactions for grain Fe and Zn concentrations showed that genotype effects largely controlled Fe concentration, whereas Zn concentration was almost totally dependent on location effects. Spring wheat genotypes Lutescens 574, and Eritrospermum 78; and winter wheat genotypes Navruz, NA160/HEINEVII/BUC/3/F59.71//GHK, Tacika, DUCULA//VEE/MYNA, and JUP/4/CLLF/3/II14.53/ODIN//CI13431/WA00477, are promising materials for increasing Fe and Zn concentrations in the grain, as well as enhancing the concentration of promoters of Zn bioavailability, such as S-containing amino acids

Splitting pairs and the number of clusters generated by random pair incompatibilities

We consider a random fitness landscape on the space of haploid diallelic genotypes with n genetic loci, where each genotype is considered either inviable or viable depending on whether or not there are any incompatibilities among its allele pairs. We suppose that each allele pair in the set of all possible allele pairs on the n loci is independently incompatible with probability p=c/(2n). We examine the connectivity of the viable genotypes under single locus mutations and show that, for 0<c<1, the number of clusters of viable genotypes in this landscape converges weakly (in n) to N=2^{Psi} where Psi is Poisson distributed; while for c>1, there are no viable genotypes with probability converging to one. The genotype space is equivalent to the n-dimensional hypercube and the viable genotypes are solutions to a random 2-SAT problem, so the same result holds for the connectivity of solutions in the hypercube to a random 2-SAT problem.Comment: 13 pages, 1 figur

In vitro screening of four genotypes of citrus for salt tolerance : S08P07

Soil and water salinity is an important abiotic stress that can affect both production and quality of citrus. The use of tolerant rootstocks in these conditions would be the solution the most used. The objective of this study was to compare in vitro behavior of four citrus genotypes in terms of tolerance to salinity. The genotypes used were 'Cleopatra' mandarin, 'Chios' mandarin, 'Shamouti' orange and 'Star Ruby' grapefruit. Salt tolerance was evaluated by determination of callus and suspension cells growth, the fresh and dry weight, water content and chloride ion content after one month of culture in solid and liquid media supplemented with NaCl at different concentrations: 50, 100, 150 and 200 mM. At 0 mM NaCl, the results revealed that callus of the four genotypes tested have a similar behavior in term of tolerance to salinity as the suspension cells. However, a differential behavior was observed at high salt concentrations depending on genotypes and the nature of medium. (Texte intégral