Genetic diversity of a <Emphasis Type="Italic">Coffea</Emphasis> Germplasm Collection assessed by RAPD markers

Genetic diversity and relationships within and among nine species of Coffea, one species of Psilanthus and the Piatã hybrid from the Coffee Germplasm Collection of Instituto Agronômico de Campinas (IAC), Brazil were assessed using RAPD markers. Genetic diversity and relationships were evaluated by proportion of polymorphic loci (P), Shannon’s genetic index (H′ and G′_ST) and clustering analysis. The overall RAPD variation among all accessions was mostly partitioned between rather than within species. However, C. canephora and C. liberica showed a high genetic diversity within the species (\({\underline{\hbox{H}'}} \) _sp = 0.414 and \({\underline{\hbox{H}'}} \) _sp = 0.380, respectively) and this was highly structured (high \({\underline{\hbox{G}'}} \) _ST). Genetic diversity from C. congensis and C. arabica was also structured, but with lower levels of genetic diversity (\({\underline{\hbox{H}'}} \) _sp = 0.218 and \({\underline{\hbox{H}'}} \) _sp = 0.126, respectively). The results were consistent with agronomic and molecular studies and demonstrated that the IAC Coffea Collection is representative of the phylogenetic structure observed in the genera. This study devises sampling strategies for coffee germplasm collections and provides genetic diversity parameters for future comparisons among them.     

Bayesian Analysis of $$^{}$$Pb Dating

In studies of environmental change of the past few centuries, \(^{210}\)Pb dating is often used to obtain chronologies for sedimentary sequences. One of the most commonly used approaches to estimate the age of material at different depths in a sequence is to assume a constant rate of supply (CRS) or influx of ‘unsupported’ \(^{210}\)Pb from the atmosphere, together with a constant or varying amount of ‘supported’ \(^{210}\)Pb. Current \(^{210}\)Pb dating models do not use a proper statistical framework and provide poor estimates of the uncertainties. Here, we develop a new model for \(^{210}\)Pb dating, where ages and values of supported and unsupported \(^{210}\)Pb form part of the parameters. We apply our model to a case study from Canada as well as to some simulated examples. Our model can extend beyond the current CRS approach, deal with asymmetric errors and mix \(^{210}\)Pb with other types of dating, thus obtaining more robust, realistic and statistically better defined age estimates.     

Oxygen Transfer Numerical Investigation Using Intermittent Aeration Technology Under Regular Waves

Based on a combination of Reynolds-Averaged Navier-Stokes equations, standard k-ε equations, and VOF technique, a 2-D dissolved oxygen transport mathematical model was conducted to investigate oxygen-supply characteristics for regular waves with a given still water depth d and various hydrodynamic parameters (incident wave height H and wave period T equivalent to incident wave length L) and intermittent aeration parameters (air flow rate per unit width q, aeration period T_a, aeration depth d_a and air source area A_a). A series of experiments were conducted to validate the mathematical model, and they agreed well with each other. In addition, a series of dimensionless parameters were conducted to assess their relationships with oxygen transfer coefficient respectively. It was found that oxygen transfer coefficient increased slightly with the increase of \( q/{g}^2{T}_a^3 \). With the increasing \( {d}_a^2/{A}_a \), oxygen transfer coefficient increased obviously for the small \( {d}_a^2/{A}_a \) scenarios; however, it increased slightly for the high \( {d}_a^2/{A}_a \) scenarios. With increasing HL/d², a linear increase tendency of oxygen transfer coefficient appeared approximately. Furthermore, a simple prediction formula for oxygen transport coefficient was conducted using the numerical data, the dimensional analysis, and the least squares method, and it was validated well with the related experimental data.     

Color analysis of storage roots from the USDA,ARS sweetpotato (<Emphasis Type="Italic">Ipomoea batatas</Emphasis>) germplasm collection

The United States Department of Agriculture (USDA), Agricultural Research Service (ARS), Plant Genetic Resources Conservation Unit in Griffin, GA maintains the United States germplasm collection for Ipomoea spp. (Convolvulaceae). During 2012–2014, 737 sweetpotato, Ipomoea batatas (L.) Lam., plant introductions (PI) were acquired as tissue-culture plantlets and then acclimated to greenhouse conditions at the USDA, ARS, U. S. Vegetable Laboratory (USVL), Charleston, SC. Single plants were transferred to plastic-covered plant beds to produce cuttings for replicated field trials. Storage roots were harvested from 690 PIs grown in the field and 695 PIs grown in pots. Color coordinates were obtained for each PI using a tristimulus colorimeter. Hue angle values (h*) ranged from 8.2° to 88.3° (\( \bar{x} \) = 54.9°) for the periderm (peel or skin) of field-grown storage roots (n = 690 PIs) and ? 9.4° (= 350.6°) to 96.2° (\( \bar{x} \) = 51.3°) for pot-grown roots (n = 695 PIs). The red–green coordinate (a*) ranged from 0.8 to 30.7 (\( \bar{x} \) = 12.8) for the periderm of field-grown roots and ? 2.0 to 44.9 (\( \bar{x} \) = 16.1) for pot-grown roots. The yellow–blue coordinate (b*) ranged from 2.8 to 33.1 (\( \bar{x} \) = 19.4) for the periderm of field-grown roots and ? 7.4 to 38.1 (\( \bar{x} \) = 19.3) for pot-grown roots. Color saturation (chroma, C*) ranged from 13.7 to 35.8 (\( \bar{x} \) = 24.9) for the periderm of field-grown roots and 14.9–45.5 (\( \bar{x} \) = 29.3) for pot-grown roots. Lightness (white–black, L*) ranged from 32.6 to 81.7 (\( \bar{x} \) = 54.6) for the periderm of field-grown roots and 32.1–88.2 (\( \bar{x} \) = 64.0) for pot-grown roots. Hue angles ranged from ? 13.1° (= 346.9°) to 100.9° (\( \bar{x} \) = 80.9°) for the stele (flesh) of field-grown storage roots (n = 672 PIs) and ? 29.9° to 103.5° (\( \bar{x} \) = 81.6°) for pot-grown roots (n = 676 PIs); a* ranged from ? 5.6 to 35.0 (\( \bar{x} \) = 8.0) for the stele of field-grown roots and ? 6.0 to 41.0 (\( \bar{x} \) = 7.6) for pot-grown roots; and b* ranged from ? 7.7 to 56.1 (\( \bar{x} \) = 34.6) for the stele of field-grown roots and ? 12.6 to 56.1 (\( \bar{x} \) = 31.8) for pot-grown roots. C* ranged from 12.7 to 65.8 (\( \bar{x} \) = 37.2) for the stele of field-grown roots and 8.9–65.7 (\( \bar{x} \) = 34.5) for pot-grown roots; and L* ranged from 27.8 to 91.1 (\( \bar{x} \) = 77.7) for the stele of field-grown roots and 28.2–91.9 (\( \bar{x} \) = 80.4) for pot-grown roots. There were significant relationships between stele color (h*) and percent dry matter, with orange stele having a significantly lower % dry matter (\( \bar{x} \) = 25.6%, n = 183) compared with roots with cream/white stele (\( \bar{x} \) = 30.8%, n = 373). There appears to be wide genetic diversity for root color characteristics for the United States sweetpotato germplasm collection.     

Vis/NIR Chemical Imaging Technique for Predicting Sodium Humate Contents in Aquaculture Environment

This study aimed to develop a visible and near-infrared (Vis/NIR) chemical imaging (400–1000 nm) technique to provide rapid prediction of the contents of sodium humate dissolved in aquaculture environment. Gray reference image with 5% reflectance value was first used to correct the obtained raw images in order to promote the reflectance values as compared to that with 99% reflectance for further spectral analysis. Successive projection algorithm (SPA) was introduced to extract four optimal wavelengths, which were then used for the establishment of back-propagation artificial neural network (BP-ANN) models. The results revealed that the BP-ANN model based on the selected four optimal wavelengths better performed (\( {R}_C^2 \) = 0.986, \( {R}_{CV}^2 \) = 0.985, \( {R}_P^2 \) = 0.993, RMSEC = 0.329 mg/L, RMSECV = 0.433, RMSEP = 0.734 mg/L) than that based on the whole 381 wavelengths (\( {R}_C^2 \) = 0.978, \( {R}_{CV}^2 \) = 0.996, \( {R}_P^2 \) = 0.977, RMSEC = 0.388 mg/L, RMSECV = 0.625, RMSEP = 0.734 mg/L). Finally, a series of chemical images were developed to clearly display the concentration distribution of the sodium humate dissolved in water, demonstrating that Vis/NIR chemical imaging technique was feasible to quantify the contents of sodium humate in the aquatic environment and could be further used for real-time monitoring the quality of aquaculture water.     

Origin of rice (<Emphasis Type="Italic">Oryza sativa</Emphasis> L.) domestication genes

A number of genes that contribute to the domestication traits of cultivated rice have been identified. These include Sh4, Rc, PROG1 and LABA1, which are associated with non-shattering rachis, white pericarp, erect growth and barbless awns, respectively. The mutations giving rise to the “domestication alleles” of these genes are either invariable in cultivated rice, or have variability that is strictly associated with the phenotypic trait. This observation forms the basis to those current rice domestication models that envisage a single origin for the domesticated phenotype. Such models assume that the domestication alleles are absent or rare in wild rice, emerged under cultivation and spread across all rice groups by introgressive hybridization. We examined whole-genome sequencing datasets for wild and cultivated rice to test the former two assumptions. We found that the rc and laba1 alleles occur in wild rice with broad geographical distribution, and reach frequencies as high as 13 and 15%, respectively. These results are in agreement with previous observations of the prog1 and sh4 domestication alleles in wild populations. We also show that the diversity of the genomic regions surrounding the rc, laba1, prog1 and sh4 alleles in wild accessions is greater than that in cultivated rice, suggesting that these alleles emerged prior to domestication. Our findings indicate that the possibility that independent rice groups obtained identical domestication alleles directly from the wild population needs to be considered.     

Hazard Function Models to Estimate Mortality Rates Affecting Fish Populations with Application to the Sea Mullet (<Emphasis Type="BoldItalic">Mugil cephalus</Emphasis>) Fishery on the Queensland Coast (Australia)

Fisheries management agencies around the world collect age data for the purpose of assessing the status of natural resources in their jurisdiction. Estimates of mortality rates represent a key information to assess the sustainability of fish stocks exploitation. Contrary to medical research or manufacturing where survival analysis is routinely applied to estimate failure rates, survival analysis has seldom been applied in fisheries stock assessment despite similar purposes between these fields of applied statistics. In this paper, we developed hazard functions to model the dynamic of an exploited fish population. These functions were used to estimate all parameters necessary for stock assessment (including natural and fishing mortality rates as well as gear selectivity) by maximum likelihood using age data from a sample of catch. This novel application of survival analysis to fisheries stock assessment was tested by Monte Carlo simulations to assert that it provided unbiased estimations of relevant quantities. The method was applied to the data from the Queensland (Australia) sea mullet (Mugil cephalus) commercial fishery collected between 2007 and 2014. It provided, for the first time, an estimate of natural mortality affecting this stock: \(0.22 \pm 0.08\)  year\(^{-1}\).     

Diversity and differentiation of <Emphasis Type="Italic">Oryza sativa</Emphasis> and <Emphasis Type="Italic">O. rufipogon</Emphasis> in Indonesia

Analysis of the genetic structure of Indonesian Oryza sativa and O. rufipogon using neighbour-joining trees based on single nucleotide polymorphism (SNP) and simple sequence repeat (SSR) markers revealed that O. sativa in Indonesia is separated from O. rufipogon. Accessions of O. sativa in this study were differentiated into two major groups, indica and tropical japonica, excluding some varieties. SSR and SNP markers revealed the high value of differentiation (F _ST) and genetic distance (D) between indica and tropical japonica and we discovered four loci by SNP markers and one locus by SSR markers that play a role in differentiation between indica and tropical japonica. Interestingly, genetic diversity (H) in O. rufipogon was lower than that in O. sativa, however H in O. rufipogon was the highest and H in tropical japonica was the lowest when O. sativa was divided into two groups. Inbreeding coefficient (Fst) showed evidences that gene flow (Nm) between species and within species might be one of the mechanisms related to the diversification and differentiation of Indonesian rice germplasm by asymmetric pattern between species and within O. sativa as revealed by SSR and SNP markers. In addition, we found evidences on stabilizing selection in Indonesian rice germplasm and they might be the reasons why Indonesian rice germplasm did not differentiate due to source location of landrace. However, we found a weak relation between SSR and SNP markers probably due to highly polymorphic in SSR and the different properties of both markers.     

<Emphasis Type="Italic">p</Emphasis>-Coumaric can alter the composition of cucumber rhizosphere microbial communities and induce negative plant-microbial interactions

Phenolics from root exudates or decaying residues are usually referred as autotoxins of several plant species. However, how phenolics affect soil microbial communities and their functional significances are poorly understood. Rhizosphere bacterial and fungal communities from cucumber (Cucumis sativus L.) seedlings treated with p-coumaric acid, an autotoxin of cucumber, were analyzed by high-throughput sequencing of 16S rRNA gene and internal transcribed spacer amplicons. Then, feedback effects of the rhizosphere biota on cucumber seedlings were evaluated by inoculating non-sterilized and sterilized rhizosphere soils to sterilized background soils. p-Coumaric acid decreased the bacterial diversity of rhizosphere but increased fungal diversity and altered the compositions of both the bacterial and fungal communities. p-Coumaric acid increased the relative abundances of microbial taxa with phenol-degrading capability (such as Chaetomium, Humicola, and Mortierella spp.) and microbial taxa which contained plant pathogens (such as Fusarium spp.). However, p-coumaric acid inhibited the relative abundances of Lysobacter, Haliangium, and Gymnoascus spp., whose species can have pathogen-antagonistic and/or plant-growth-promoting effects. The positive effect of cucumber rhizosphere microbiota on cucumber seedling growth was reduced by p-coumaric acid. Overall, our results showed that, besides its direct phytotoxicity, p-coumaric acid can inhibit cucumber seedling growth through generating negative plant-soil microbial interactions.     

Predicting soil loss in central and south Italy with a single USLE-MM model

Purpose

The USLE-MM estimates event normalized plot soil loss, A_e,N, by an erosivity term given by the runoff coefficient, Q_R, times the single-storm erosion index, EI₃₀, raised to an exponent b₁?>?1. This modeling scheme is based on an expected power relationship, with an exponent greater than one, between event sediment concentration, C_e, and the EI₃₀/P_e (P_e = rainfall depth) term. In this investigation, carried out at the three experimental sites of Bagnara, Masse, and Sparacia, in Italy; the soundness of the USLE-MM scheme was tested.

Materials and methods

A total of 1192 (A_e,N, Q_REI₃₀) data pairs were used to parameterize the model both locally and considering all sites simultaneously. The performances of the fitted models were established by considering all erosive events and also by distinguishing between events of different severity.

Results and discussion

The b₁ exponent varied widely among the three sites (1.05–1.44) but using a common exponent (1.18) for these sites was possible. The A_e,N prediction accuracy increased in the passage from the smallest erosion events (A_e,N?≤?1 Mg ha^?1, median error =?3.35) to the largest ones (A_e,N?>?10 Mg ha^?1, median error =?1.72). The Q_REI₃₀ term was found to be usable to predict both A_e,N and the expected maximum uncertainty of this prediction. Soil erodibility was found to be mainly controlled by the largest erosion events.

Conclusions

Development of a single USLE-MM model appears possible. Sampling other sites is advisable to develop a single USLE-MM model for a general use.

     

Polymorphism of <Emphasis Type="Italic">Got2</Emphasis> DNA sequences sheds light on <Emphasis Type="Italic">Aegilops tauschii</Emphasis> Coss. intraspecies divergence and origin of <Emphasis Type="Italic">Triticum aestivum</Emphasis> L.

DNA sequences of nuclear gene Got2 was studied in 60 accessions of Aegilops tauschii, 29 of subsp. tauschii and 31 of subsp. strangulata. It was found that Got2 allozyme polymorphism in Ae. tauschii is due to a single, unique, mutation which led to replacement of glutamic acid by isoleucine in residue 256 of the enzyme molecule, encoded by Got2. As revealed by Got2 DNA sequences variation, initially in its history Ae. tauschii was presented by subsp. strangulata, and among phylogenetic lineages of subsp. strangulata, the lineage “t-9¹s” (TauL3) is the most ancient, a relict one. Subspecies tauschii is relatively “young”. Initially it was presented by the lineage marked by combination of allozyme alleles Got2 ¹⁰⁵ and Acph1 ¹⁰⁰. In the past it inhabited the Continental area from Caucasia to Pakistan, but later on it was forced out by newly originated, now—a major lineage of subsp. tauschii, marked by Got2 ¹⁰⁰. This lineage extended the Continental area of the species up to Kirgizstan, but actually failed to penetrate into pre-Caspian area, occupied by subsp. strangulata. These results essentially differ from those obtained previously, using chloroplast DNA (cpDNA) sequences polymorphism. As revealed by cpDNA, the major, “usual”, subsp. strangulata (TauL2) is “younger” than subsp. tauschii, which resided on phylogenetic tree between relict lineage “t-9¹s”of subsp. strangulata—and major subsp. strangulata. But both cpDNA and Got2 DNA sequences indicate that the level of genetic variation in subsp. tauschii is much lower than in subsp. strangulata. According to Got2 DNA sequences variation, it was Ae. tauschii subsp. strangulata lineage “k-109″ which donated genome D to Triticum aestivum L. This lineage includes accessions: k-109 from South-Eastern Precaspian Azerbaijan; KU-2105, KU-2159 from Western Precaspian Iran; KU-2080 from Eastern Precaspian Iran.     

Optimal Estimation Versus MCMC for $$\mathrm{{CO}}_{2}$$ Retrievals

The Orbiting Carbon Observatory-2 (OCO-2) collects infrared spectra from which atmospheric properties are retrieved. OCO-2 operational data processing uses optimal estimation (OE), a state-of-the-art approach to inference of atmospheric properties from satellite measurements. One of the main advantages of the OE approach is computational efficiency, but it only characterizes the first two moments of the posterior distribution of interest. Here we obtain samples from the posterior using a Markov Chain Monte Carlo (MCMC) algorithm and compare this empirical estimate of the true posterior to the OE results. We focus on 600 simulated soundings that represent the variability of physical conditions encountered by OCO-2 between November 2014 and January 2016. We treat the two retrieval methods as ensemble and density probabilistic forecasts, where the MCMC yields an ensemble from the posterior and the OE retrieval result provide the first two moments of a normal distribution. To compare these methods, we apply both univariate and multivariate diagnostic tools and proper scoring rules. The general impression from our study is that when compared to MCMC, the OE retrieval performs reasonably well for the main quantity of interest, the column-averaged \(\mathrm{{CO}}_{2}\) concentration \(X_{\mathrm{{CO}}_{2}}\), but not for the full state vector \(\mathbf {X}\) which includes a profile of \(\mathrm{{CO}}_{2}\) concentrations over 20 pressure levels, as well as several other atmospheric properties.Supplementary materials accompanying this paper appear on-line.     

Soil pre-fumigation could effectively improve the disease suppressiveness of biofertilizer to banana <Emphasis Type="Italic">Fusarium</Emphasis> wilt disease by reshaping the soil microbiome

Two seasonal pot experiments were conducted to investigate the effect of biofertilizer application after mixture of lime and ammonium bicarbonate (LA) fumigation, on banana Fusarium wilt disease suppression and soil microbial community composition. Biofertilizer application after LA fumigation decreased 80% of disease incidence compared to control of biofertilizer application to non-fumigated soil. Biofertilizer application after fumigation clearly manipulated soil microbial community composition as revealed by non-metric multidimensional scaling and Venn diagram. LA fumigation significantly reduced the abundance of F. oxysporum while biofertilizer application after fumigation could further decrease it. Furthermore, indigenous microbes, e.g., Bacillus, Pseudomonas, and Mortierella, were associated with disease suppression. Biofertilizer application after fumigation significantly (p?<?0.05) increased the soil pH and content of soil total C and available P and K, and this probably reshaped soil microbial community as revealed by redundancy analysis and variance partitioning analysis. The observed disease suppression due to biofertilizer application after soil fumigation can be attributed to the reduced abundance of F. oxysporum by general suppression resulting from manipulated soil properties and recovered soil microbiome.     

Inverse Estimation of the Hydrodispersive Properties of Unsaturated Soil Using Complex-Variable-Differentiation Method under Field Experiments Conditions

Because soil hydraulic properties are indispensable for determining soil water retention and soil solute movement, their input for simulation models is essential. Many of these parameters cannot be estimated directly at the scale of interest, but can only be derived through inverse modeling. During this process, the parameters are generally adjusted using least-squares approach with Levenberg–Marquardt (LM) algorithms in which numerically simulated models are fitted to measured data. In this study we used a new inverse method to estimate the unsaturated soil hydro-dispersive properties from in-situ experiments. The method employs complex-variable-differentiation method (CVDM) to accurately predict of the hydraulic properties of the van Genuchten–Mualem models (θ_r, θ_s, α, k_s, n). To the knowledge of the authors, it is first study use CVDM in soil physics. The optimization procedure was performed by using a continuous data set of daily in situ soil water content and bromide concentration measurements. Estimated parameters during the inversion showed high correlation (R² = 0.88, RMSE = 0.013 and the model efficiency CE = 0.77) by using the CVDM-methods with the actual field measurements, compared with the traditional LM-algorithm (R² = 0.81, RMSE = 0.021 and CE = 0.626). The results show that the new inverse analysis in the present work has the high accuracy, validity, uniqueness, and higher inversion efficiency. Meanwhile, the convergence and stability of the modified LM-algorithm are improved. Overall, it was concluded that the CVDM is promising method to estimate hydro-dispersive parameters in soil physics.     

Estimation of natural outcrossing rate and genetic diversity in Lima bean (<Emphasis Type="Italic">Phaseolus lunatus</Emphasis> L. var. <Emphasis Type="Italic">lunatus</Emphasis>) from Brazil using SSR markers: implications for conservation and breeding

Lima bean (Phaseolus lunatus L.) is an important food source in Brazil, especially in the northeast region, where its production and consumption are high. The goals of the present study were to estimate natural outcrossing rates and genetic diversity levels of Lima bean from Brazil, using ten microsatellite loci to obtain information for their conservation and breeding. Fourteen accessions were selected from an experiment in field with open-pollinated and with the presence of pollinating insects. Twelve seeds of each of the 14 selected accessions were grown in screenhouse for tissue harvest and DNA extraction. The multilocus model was used to determine the reproductive system. The outcrossing rate was 38.1 % (t_m = 0.381; t_s = 0.078), and the results indicated a mixed mating system with a predominance of selfing (1 ? t_m = 61.9 %). The biparental inbreeding rate was high (t _m  ? t _s  = 0.303) and the multilocus correlated paternity was quite high (r _p(m) = 0.889), indicating that the progeny was mostly composed of full sibs. The average effective number of pollen donors per maternal plant (N _ep ) was low (1.12), and the fixation index for maternal genotypes (F _m ) was 0.945, indicating that most genitors resulted from inbreeding. The studied families presented considerable genetic variability: A = 6.10;  %P = 30; H _e  = 0.60 and H _o  = 0.077. Total diversity was high (H _T = 0.596), and a portion was distributed within families (H _S = 0.058). In addition, diversity was higher between families (D _ST = 0.538), and genetic differentiation was high (G _ST = 0.902). The results presented here can be used in the implementation of Lima bean conservation and breeding programs in Brazil.     

Effects of ectomycorrhizal fungus <Emphasis Type="Italic">Boletus edulis</Emphasis> and mycorrhiza helper <Emphasis Type="Italic">Bacillus cereus</Emphasis> on the growth and nutrient uptake by <Emphasis Type="Italic">Pinus thunbergii</Emphasis>

The present greenhouse study was undertaken to evaluate the effects of co-inoculating the ectomycorrhizal (ECM) fungus Boletus edulis with the mycorrhiza helper bacterium Bacillus cereus HB12 or HB59 on the growth and nutrient uptake of Pinus thunbergii. The inoculation with mycorrhiza helper bacterium significantly (P?≤?0.05) increased the ectomycorrhizal colonization. Treatments with dual inoculum (the mycorrhiza helper bacterium plus mycorrhiza) significantly (P?≤?0.05) increased the P. thunbergii growth. Bacteria–mycorrhizae interactions resulted in a great utilization of phosphate and potassium. The single inoculation resulted in a higher root activity than the control while the co-inoculation led to the highest root activity. The 6-CFDA staining assay showed that B. cereus enhanced fungal activity in ectomycorrhizal symbiosis. The results conclusively suggest that B. cereus isolated from the rhizosphere of P. thunbergii can potentially be used as individual inoculant or co-inoculated with ECM fungi to increase the production in sustainable ecological systems. These results support the potential use of B. cereus (HB12 or HB59) and B. edulis as mixed inoculants stimulating growth of P. thunbergii.     

Remarks on genetic diversity and relationship of <Emphasis Type="Italic">Punica protopunica</Emphasis> and <Emphasis Type="Italic">P. granatum</Emphasis> assessed by molecular analyses

Here, two Punica species, viz., P. protopunica Balf. fil., reported as native to Socotra, and P. granatum L., were compared for the first time. Analysis of one P. protopunica and eleven P. granatum accessions was performed using three molecular markers, i.e., sequence related amplified polymorphism (SRAP), target region amplification polymorphism (TRAP), and intron targeted amplified polymorphism (ITAP), along with analysis of pgWD40 sequences, a gene involved in anthocyanin biosynthesis. All markers revealed the relationship between the two species and placed them at 33% similarity. SRAP, TRAP, and ITAP generated a total of 299, 260, and 160 bands, respectively. Of these, 78, 74, and 41 bands were specific for P. protopunica, and 92, 85, and 57 bands, respectively, were shared between both species. Sequence analysis of pgWD40~870 bp amplicons exhibited 100% identity among P. granatum accessions and 98% identity to that of P. protopunica. Phylogenetic analysis of WD40 sequences from monocot and dicot species, including both Punica species confirmed the relation between P. protopunica and P. granatum, supporting earlier reports that P. protopunica could be an ancestral species of P. granatum. Furthermore, the genetic diversity among and within P. granatum accessions from Egypt (3), Mexico (5), and Yemen (3) was assessed. Molecular marker-based relationships among region-bulked accessions was approximately the same (~90% similarity), whereas the degree of genetic variation was altered within each region. Specific bands (alleles) for accessions of each region along with those shared among them were identified. Thus, these bands could be used for pomegranate genotyping and breeding programs.     

Genetic diversity and relationships of wild and cultivated <Emphasis Type="Italic">Zanthoxylum</Emphasis> germplasms based on sequence-related amplified polymorphism (SRAP) markers

The genus Zanthoxylum, belonging to Rutaceae, has a long history of cultivation both for economic and chemical values in China. To effectively conserve and sustainably utilize this genus resource, a study on genetic diversity and relationships of Zanthoxylum germplasms was carried out by employing SRAP markers. We used 16 primer combinations to assess genetic variations and relationships among 175 accessions from eight cultivated provenances, including Shandong, Henan, Shanxi, Shaanxi, Gansu, Sichuan, Guizhou and Yunnan. A total of 145 clear repetitive and intense bands were yielded, and the percentage of polymorphic bands was 100 % for per primer combination, indicating a relatively high diversity among Zanthoxylum germplasms. From a geographic perspective, the highest genetic diversity level was observed within Guizhou provenance (N _a  = 1.97, Ne = 1.52, H = 0.31, I = 0.46) while Henan provenance had the lowest genetic diversity (N _a  = 1.68, Ne = 1.45, H = 0.25, I = 0.37). Based on AMOVA results, the abundant genetic variation was mainly caused by variation of intra-provenances (84.96 %), rather than among provenances (15.038 %). The results indicated low genetic differentiation (G _st  = 0.133) and high gene flow (N _m  = 3.2605) among provenances. The neighbor-joining tree revealed that the 175 accessions could be divided into four groups, and groupings indicated a divergence between the cultivated accessions of Zanthoxylum bungeanum Maxim. and Z. armatum DC. Moreover, three accessions of Z. piperitum DC. var. inerme without prickles introduced from Japan gathered one cluster. Cluster IV is composed of accessions of different geographical origin, including 11 wild species and 10 cultivated accessions of Z. bungeanum. The cluster analysis also reflected a relatively close relationship between the geographical origins and the classification of accessions in cluster I. Structure analysis indicated that collected Zanthoxylum accessions could be divided into two major groups. The information obtained from our research would benefit to make use of Zanthoxylum germplasms and assist the management of a Zanthoxylum germplasms collection.     

Genotyping-by-sequencing reveals the origin of the Tunisian relatives of cultivated carrot (<Emphasis Type="Italic">Daucus carota</Emphasis>)

Tunisia, other countries in northwestern Africa, and the Iberian Peninsula, represent a center of diversity of Daucus. The genus traditionally has included about 20–25 species worldwide, but a recent molecular study redefined and expanded Daucus to include representatives from nine other genera. By this classification, Daucus now contains about 40 species, with some of them having winged fruits in addition to its traditionally recognized spiny fruits. The taxonomy of Daucus in Tunisia has recently been studied with morphological data, concluding that D. carota subsp. capillifolius is a subspecies that co-occurs and crosses with subsp. carota. The present study extends these findings with additional data from Genotyping-by-Sequencing (GBS) from 33 Tunisian accessions of D. carota (93 individuals with two to three replicates per accession), including the first collections of subsp. gummifer from Tunisia. Placed in the context of additional GBS data, D. carota subsp. gummifer has separate origins from other collections of subsp. carota in Tunisia and/or immediately adjacent areas to the north in Italy or its surrounding islands. Our results add support to the utility of large SNP datasets for species-level phylogenetic studies in Daucus.     

Combined bioremediation of soil co-contaminated with cadmium and endosulfan by <Emphasis Type="Italic">Pleurotus eryngii</Emphasis> and <Emphasis Type="Italic">Coprinus comatus</Emphasis>

Purpose

The subjects of this study were to investigate the remediating potential of the co-cultivation of Pleurotus eryngii and Coprinus comatus on soil that is co-contaminated with heavy metal (cadmium (Cd)) and organic pollutant (endosulfan), and the effects of the co-cultivated mushrooms on soil biochemical indicators, such as laccase enzyme activity and bacterial counts.

Materials and methods

A pot experiment was conducted to investigate the combined bioremediation effects on co-contaminated soil. After the mature fruiting bodies were harvested from each pot, the biomass of mushrooms was recorded. In addition, bacterial counts and laccase enzyme activity in soil were determined. The content of Cd in mushrooms and soil was detected by the flame atomic absorption spectrometry (FAAS), and the variations of Cd fractions in soil were determined following the modified BCR sequential extraction procedure. Besides, the residual endosulfan in soil was detected by gas chromatography-mass spectrometry (GC-MS).

Results and discussion

The results indicated that co-cultivation of P. eryngii and C. comatus exerted the best remediation effect on the co-contaminated soil. The biomass of mushroom in the co-cultivated group (T group) was 1.57–13.20 and 19.75–56.64% higher than the group individually cultivated with P. eryngii (P group) or C. comatus (C group), respectively. The concentrations of Cd in the fruiting bodies of mushrooms were 1.83–3.06, 1.04–2.28, and 0.67–2.60 mg/kg in T, P, and C groups, respectively. Besides, the removal rates of endosulfan in all treatments exceeded 87%. The best bioremediation effect in T group might be caused by the mutual promotion of these two kinds of mushrooms.

Conclusions

The biomass of mushroom, laccase activity, bacterial counts, and Cd content in mushrooms were significantly enhanced, and the dissipation effect of endosulfan was slightly higher in the co-cultivated group than in the individually cultivated groups. In this study, the effect of co-cultivated macro fungi P. eryngii and C. comatus on the remediation of Cd and endosulfan co-contaminated soil was firstly reported, and the results are important for a better understanding of the co-remediation for co-contaminated soil.