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.     

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.     

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.     

Diversity in cowpea (<Emphasis Type="Italic">Vigna unguiculata</Emphasis> (L.) Walp.) local populations from Greece

Cowpea cultivation in many countries around the Mediterranean Basin depends on a number of locally adapted populations conserved on-farm at a small scale, rather than on the use of modern varieties. Documentation, characterization and exploitation of traditional local populations could contribute to their conservation and utilization as sources of desirable characteristics. Therefore, a study was conducted to (a) characterize, (b) assess diversity and (c) classify 23 on-farm conserved local cowpea populations based on 32 agro-morphological traits. Investigations on diversity of characteristics related to seed yield, mineral and seed crude protein content as well as on correlations among them were carried out. A relatively high phenotypic diversity was observed. In particular, a high level of within population diversity was found (\( \bar{H}s \) = 0.34) exceeding that among populations’ diversity (Gst = 0.27). Principal component analysis classified the majority of local populations into two groups (mainly according to populations’ seed coat color and eye color), further divided into six subgroups regardless of the populations’ geographical origin. Significant differences were also observed among the populations studied for potassium and calcium, as well as for their seed crude protein content which ranged from 22.14 to 28.37 %. The results show appreciable levels of intra- and inter-phenotypic diversity in on-farm conserved cowpea populations, which indicates the existence of a valuable gene pool for future exploitation in breeding programs.     

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.     

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.     

Morphological and genetic diversity of shea tree (<Emphasis Type="Italic">Vitellaria paradoxa</Emphasis>) in the savannah regions of Ghana

Vitellaria paradoxa C. F. Gaertn., commonly known as shea tree or Vitellaria, is ranked the most important tree species of the savannah regions in the most African countries due to its ecological and economic importance for livelihoods and national economies. However, the savannah regions are the most vulnerable areas to the global climate change. Moreover, the Vitellaria populations on farmlands are threatened by the dominance of old trees with low or lack of regeneration. In this study both morphological and genetic diversity were assessed using several phenotypic traits and 10 microsatellite markers, respectively, to assess the impact of land use and agro-ecozone types on Vitellaria in Ghana. The land use types were forests and farmlands, and the agro-ecozone types included the Transitional, Guinea, and Sudan savannah zones. The mean values of morphological traits, such as diameter at breast height (DBH) and canopy diameter (CD), were statistically different between forest (DBH = 22.20, CD = 5.37) and farmland (DBH = 39.85 CD = 7.49) populations (P < 0.00001). The Sudan savannah zone with mean petiole length of 4.96 cm showed significant difference from the other zones, likely as a result of adaptation to drier climate conditions. Genetic data analysis was based on 10 microsatellite markers and revealed high genetic diversity of Vitellaria in Ghana: mean expected heterozygosity, H _e was 0.667, and allelic richness, measured as number of effective alleles A _e , was 4.066. Both farmlands and forests were very diverse indicating lack of negative influence of farmer’s selection on genetic diversity. Fixation index was positive for all populations (mean F _IS = 0.136) with farmlands recording relatively higher values than forests in all ecological zone types studied, probably indicating less gene flow in the farmlands. Moderate differentiation (F′ _ST = 0.113) was comparable to other similar tree species. Both land use and ecological zone types influenced genetic differentiation of Vitellaria at varying levels. The species was spatially structured across three ecozones and following climatic gradient. The forest reserves are used in situ conservation for Vitellaria in Ghana. High diversity observed in the most arid zones provides opportunity to find and use appropriate plant materials for breeding climate change resilient trees.     

Geographical distribution of wild <Emphasis Type="Italic">Daucus</Emphasis> species in the natural grasslands of the Argentinian pampas

Three wild carrot species have been reported in the argentinian flora: Daucus montanus Humb. et Bonpl. ex Schult., D. montevidensis Link ex Sprengel and D. pusillus Michx. There is a discrepancy among authors about the distinctive morphological traits of the last two species; thus, it is difficult to ascertain if they are truly two distinct taxa. Based on the available literature and in the search of a paradigmatic site, four collection trips were carried out in 2004 and 2005 in Buenos Aires and Southern Entre Ríos provinces. Populations were sampled at 30 sites, and local environmental parameters and associated plant species were recorded. Morphological observations and chromosome counts were carried out on 10 plants/population. Three morphological phenotypes were distinguished: one in 18 populations, all with 2n = 2x = 18, and two in the remaining 12, with 2n = 2x = 22 or aneusomaty (2n = 2x = 20, 22). Populations of the first phenotype were assigned to wild D. carota and the rest, tentatively, to D. pusillus (D. montevidensis?), till further evaluations are carried out in test sites to verify this tentative conclusion.     

The Allometric Quarter-Power Scaling Model and Its Applicability to Grand Fir and <Emphasis Type="Italic">Eucalyptus</Emphasis> Trees

The use of the allometric model \(y = \beta x ^{\alpha }\) to describe the relative growth of morphological traits of trees is a source of contention in ecology. This is particularly so in a specific form, the West, Brown and Enquist model, which predicts values of \(\alpha \) that are multiples of 1/4 for various allometric relationships—the quarter-power scaling law. We use statistical techniques to test the appropriateness of the quarter-power scaling allometric model in a number of different relative growth relationships of trees. Two separate datasets are used, one of repeated measures of Abies grandis (Grand fir) trees, another of independent measures of Eucalyptus trees. Nonlinear mixed-effects modelling is used to fit allometric models to the datasets. Generalised additive models, equivalence testing and traditional significance testing are used to assess the adequacy of the allometric models fitted and the values of the estimated exponents relative to those predicted by the WBE model. In only one of the five models fitted was there empirical evidence for the WBE-predicted quarter-power exponent. However, the adequacy of the allometric models was generally supported, though a need for further analysis over a larger range of tree ages/sizes is indicated.Supplementary materials accompanying this paper appear online.     

Population genetics of traditional landraces of <Emphasis Type="Italic">Cucurbita pepo</Emphasis> L., 1753 in the cloud forest in Baja Verapaz,Guatemala

Little is known regarding the effect of fragmentation and human agricultural management on the genetic variation and gene flow of Cucurbita pepo L., 1753 in moderate fragmented areas in central Guatemala. We hypothesize that the genetic variation of C. pepo is affected by forest fragmentation and by traditional agricultural management. Therefore, we aim to determine: (1) the genetic diversity and genetic structure of C. pepo in the Cloud Forest Corridor (CFC) (2) the extent of genetic admixture between commercial variety (CV) and traditional landraces (TL) of C. pepo, (3) the effect of habitat fragmentation in the population genetics of C. pepo with a landscape approach, and (4) the potential relationship between traditional management practices and genetic diversity of C. pepo in the CFC. We detected the existence of high level of genetic diversity (AR = 3.43; He = 0.50), inbreeding (Fis = 0.25) and moderate population structure of C. pepo in the CFC (Fst = 0.16). No correlation between landscape and genetics was found. Also, we found high genetic admixture between CV and TL. It seems that human practices, mainly related with seed exchange patterns, could affect genetic diversity of C. pepo in the CFC. C. pepo populations in the CFC are structured, with inbreeding, and show admixture with the CV, an aspect that could affect its genetic diversity. The agricultural management influenced the population genetics of C. pepo in the CFC, but the landscape did not. We suggest that special efforts should be made to preserve the diversity of this important indigenous food source for Guatemalan people as well as their management practices.     

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\(^{-1}\).     

Untapped amaranth (<Emphasis Type="Italic">Amaranthus </Emphasis>spp.) genetic diversity with potential for nutritional enhancement

Significant genetic diversity was observed in 218 out of a total of 1309 accessions of amaranth (Amaranthus hypochondriacus L.) and its seven wild relatives, A. spinosus L., A. dubius Mart. ex Thell., A. hybridus L., A. tricolor L., A. cruentus L., A. caudatus L., A. retroflexus L. for 24 nutritional parameters including total oil content, fatty acid profile, total protein content and amino acid profile. Diversity for total oil content (6.42–12.53%), linoleic acid (25.68–54.34%), oleic acid (21.97–42.01%) of the total fatty acids, total protein content (7.84–18.01%), among important essential amino acids; lysine content (0.66–11.12 g/16 g N), methionine (0.35–4.80 g/16 g N) and half cystine and (0.12–8.32 g/16 g N) was reported. The un-weighted pair-group method using arithmetic average cluster analysis based on pair wise Euclidean genetic distance grouped the accessions into seven major clusters. Histidine, half cystine, tyrosine, essential amino acids, total oil content, linoleic acid and oleic acid content were the major parameters contributing significantly to genetic diversity. Present findings indicate that significant diversity exists for nutritional parameters in amaranth germplasm. The promising accessions with higher multiple nutritive traits; protein content (>16%), oil content (>11%), lysine content (>7.5 g/16 g N) and EAA higher than the FAO reported values, were identified. This is the first report on detailed nutritional analysis of diversity collected worldwide. These could be used as potential breeding material for nutritional enhancement through genetic improvement. This will help in overcoming the “triple burden” of malnourishment, hidden hunger, and obesity.     

Diverse morphological and cytogenetic variation and differentiation of the two subspecies in <Emphasis Type="Italic">Aegilops geniculata</Emphasis> Roth,a wild relative of wheat

Aegilops geniculata Roth, a wild relative of wheat (2n = 4x = 28, genome UUMM), is distributed over the Mediterranean basin and nearby areas. The species consists of two subspecies, subsp. geniculata and subsp. gibberosa (Zhuk.) Hammer. The former is distributed over the whole species area and has been genetically analyzed, and the latter is endemic to Spain and North Africa and has not been genetically evaluated. In this study, to clarify the genetic variation and delineation of the two subspecies from a biosystematic viewpoint, morphological variation among 23 accessions of subsp. geniculata and three of subsp. gibberosa and chromosome pairing at meiosis and fertility in their intra- and inter-subspecific F₁ hybrids were examined. A principal component analysis based on the 11 spike characteristics clearly divided the 26 accessions into two groups representing the two subspecies. The inter-subspecific F₁ hybrids showed significantly lower frequencies of chromosome pairing, significantly higher frequencies of multivalents, and significantly lower fertilities relative to those of the intra-subspecific F₁ hybrids. It was concluded that wide-ranging cytogenetic variation is included in subsp. geniculata, that subsp. gibberosa, the intra-subspecific variation of which is small, is morphologically and cytogenetically differentiated from subsp. geniculata beyond the range of the intra-subspecific variation of subsp. geniculata, and that the two subspecies are effectively isolated reproductively by hybrid sterility. The results strongly suggested that western North Africa is one of the important diversity centers of Ae. geniculata, where two subspecies were differentiated in the past and grow together in the present.     

An overlooked nitrogen loss linked to anaerobic ammonium oxidation in estuarine sediments in China

Purpose

Despite its importance, anammox (anaerobic ammonium oxidation) in estuarine sediment systems remains poorly understood, particularly at the continental scale. This study aimed to understand the abundance, diversity, and activity of anammox bacteria and to determine the main factors influencing the anammox process in estuarine sediments in China.

Materials and methods

Estuarine sediments were collected from 18 estuaries spanning over 4000 km. Experiments using an ¹⁵ N–tracer, quantitative PCR, and clone library construction were used to determine the activity, abundance, and diversity of anammox bacteria. The impact of environmental factors on anammox processes was also determined.

Results and discussion

The abundance of the anammox-specific hydrazine synthase (hzsB) gene ranged from 1.8 × 10⁵ ± 3.4 × 10⁴ to 3.6 × 10⁸ ± 7.5 × 10⁷ copies g^?1 dw. Candidatus Scalindua, Brocadia, Kuenenia, Jettenia, and two novel unidentified clusters were detected, with Scalindua dominating the anammox population. Additionally, the abundances of Scalindua, Kuenenia, and Brocadia were found to be significantly correlated with latitude. The anammox rates ranged from 0.29 ± 0.15 to 13.68 ± 3.98 nmol N g^?1 dw h^?1 and contributed to 2.39–82.61% of total N₂ production. Pearson correlation analysis revealed that the anammox rate was positively correlated with total nitrogen, total carbon, and temperature, and was negatively correlated with dissolved oxygen (DO). The key factors influencing the hzsB gene abundance were ammonium concentration, salinity, and DO. Ammonium concentration, pH, temperature, and latitude were main variables shaping the anammox-associated bacterial community.

Conclusions

Our results suggested that anammox bacteria are ubiquitous in coastal estuaries in China and underline the importance of anammox resulting in N loss at a continental scale.

     

High Zn concentration does not impair biomass,cutting radial growth,and photosynthetic activity traits in <Emphasis Type="Italic">Populus alba</Emphasis> L.

Purpose

Evaluate the efficiency of Populus alba clone Villafranca in the uptake and translocation of Zn from contaminated soils.

Materials and methods

The effects of 48 days of zinc treatment (Zn _t ) on the growth and the photosynthetic activities of P. alba L. clone Villafranca were studied using ZnSO₄ (375 ppm per unit of soil dry weight) added in sand and peat moss substrate at the beginning of the treatment (T ₀) and again after 30 days (T ₁) in order to reach a target Zn concentration of 375 ppm at T ₀ and 750 ppm at T ₁ per unit of soil dry weight.

Results and discussion

Zn uptake in the different organs was analyzed after 30 (T ₁) and 48 days (T ₂) from the beginning of treatment, showing the following order: root ? leaves ≥ woody cutting = stem. The leaf area increased by 12 % in comparison to control plants at the end of second treatment (48 days). Cutting radial growth showed a high synchronicity in the growth rate fluctuation among control and Zn _t plants, but a higher increase in radial diameter of Zn _t cutting was observed starting from day 38 (after 8 days of second Zn _t ) reaching after 48 days 38 % higher than control plants.

Conclusions

Although our data of leaf Zn concentration were in the range usually reported as toxic for plants, Villafranca clone in Zn _t substrate were unaffected in terms of net CO₂ assimilation and stomatal conductance to water vapor.

     

C-banded karyotype of <Emphasis Type="Italic">Thinopyrum bessarabicum</Emphasis> and identification of its chromosomes in wheat background

C-banded pattern in two accessions of Thinopyrum bessarabicum (Save ex Rayss) A. Löve (2n = 2x = 14, E^bE^b) and their idiogram was established. C-banding analysis was further used to identify the chromosomes of Tritipyrum amphiploid (2n = 6x = 42, AABBE^bE^b) and a BC₁F₂ genotype from wheat and Tritipyrum. Two 18S-26S rDNA loci were detected on Th. bessarabicum chromosomes by in situ hybridization using an 18S-26S rDNA probe. E^b chromosomes in Tritipyrum generally were identified by their distinctive C-banding patterns which reflected heterochromatin regions. C-banding procedure resulted in sharp and distinct bands in one or both ends of E^b chromosomes without interval bands. Observed C-bands in E^b genome mainly reflected the telomeric and subtelomeric sequences which also showed more strong signals in genomic in situ hybridization. Results showed the importance of the C-banding technique as a screening tool in identification of addition and substitution lines in the progenies of wheat and Tritipyrum crosses during segregating generations.     

Geographic distance and amorphous iron affect the abundance and distribution of <Emphasis Type="Italic">Geobacteraceae</Emphasis> in paddy soils in China

Purpose

Geobacteraceae are important dissimilatory Fe (III)-reducing microorganisms, influencing the cycling of metals, nutrients as well as the degradation of organic contaminants. However, little is known about their distribution, diversity, and abundance of Geobacteraceae and the effects of environment factors and geographic distance on the distribution and diversity of Geobacteraceae in paddy soils remain unclear. Therefore, the objectives of this study were to investigate the distribution, diversity, and abundance of Geobacteraceae in paddy soils and to determine key factors in shaping the Geobacteraceae distribution, environmental factors, geographic distance, or both and to quantify their contribution to Geobacteraceae variation.

Materials and methods

Illumina sequencing and quantitative real-time PCR using a primer set targeting 16S rRNA genes of bacteria affiliated with the family Geobacteraceae were employed to measure the community composition, diversity, and abundance patterns of 16S rRNA genes of Geobacteraceae in 16 samples collected from north to south of China. MRT, Mantel test, and VPA were used to analyze the relationship between communities of Geobacteraceae and environmental factors and geographic distance.

Results and discussion

Quantitative PCR showed that the abundance of 16S rRNA genes of Geobacteraceae ranged from (1.20?±?0.18)?×?10⁸ to 1.13?×?10⁹?±?2.25?×?10⁸ copies per gram of soil (dry weight) across different types of soils. Illumina sequencing results showed Geobacter was the dominant genus within the family of Geobacteraceae. Multivariate regression tree (MRT) analysis showed that soil amorphous iron contributed more (22.46 %) to the variation of dominant species of Geobacteraceae than other examined soil chemical factors such as pH (14.52 %), ammonium (5.12 %), and dissolved organic carbon (4.74 %). Additionally, more geographically distant sites harbored less similar communities. Variance partitioning analysis (VPA) showed that geographic distance contributed more to the variation of Geobacteraceae than any other factor, although the environmental factors explained more variation when combined. So, we detected the uneven distribution of Geobacteraceae in paddy soils of China and demonstrated that Geobacteraceae community composition was strongly associated with geographic distance and soil chemical factors including aFe, pH, Fe, DOC, C:N, and NO₃ ^?-N. These results greatly expand the knowledge of the distribution of Geobacteraceae in environments, particularly in terrestrial ecosystems.

Conclusions

Our results showed that geographic distance and amorphous iron played important roles in shaping Geobacteraceae community composition and revealed that both geographic distance and soil properties governed Geobacteraceae biogeography in paddy soils. Our findings will be critical in facilitating the prediction of element cycling by incorporating information on functional microbial communities into current biogeochemical models.

     

Nuclear and cytoplasmic contributions from <Emphasis Type="Italic">Erianthus arundinaceus</Emphasis> (Retz.) Jeswiet in a sugarcane hybrid clone confirmed through genomic in situ hybridization and cytoplasmic DNA polymorphism

A hybrid between Erianthus arundinaceus (Retz.) Jeswiet and Saccharum spontaneum L. which are wild related species of sugarcane (Saccharum L., Family Poaceae), was repeatedly crossed as female parent with sugarcane commercial varieties to develop near commercial sugarcane clones. The cytoplasm type of the hybrid derivatives were confirmed to be of E. arundinaceus through the mitochondrial and chloroplast DNA polymorphism of nad 4/3-4 intron segment and psbC–trnS segment, respectively. The E. arundinaceus × S. spontaneum hybrid with somatic chromosome number 2n = 62 was confirmed to have 30 chromosomes from E. arundinaceus through genomic in situ hybridization (GISH). The (E. arundinaceus × S. spontaneum) × sugarcane hybrid (2n = 118) had 24 chromosomes from E. arundinaceus whereas its next generation hybrid with sugarcane (2n = 108) had only 12 Erianthus chromosomes. The commercial sugarcane hybrid Co 15015, which is the third generation hybrid with 2n = 106 was confirmed to have two E. arundinaceus chromosomes through GISH. It is the first report of sugarcane with both alien cytoplasm and chromosome contributions from E. arundinaceus.     

Genetic structure of Lima bean (<Emphasis Type="Italic">Phaseolus lunatus</Emphasis> L.) landraces grown in the Mayan area

Lima bean (Phaseolus lunatus L.) is an important crop in the Mayan culture. The Mayan area, considered as a main center of Mesoamerican diversity, has been divided into two subareas: the Mayan lowlands and the Mayan highlands. The Yucatan Peninsula is part of the Mayan lowlands and holds the highest number of Lima bean landraces of Mexico, but Lima beans are in high risk of genetic erosion due to intensification of the traditional Mayan agriculture. However, information on genetic diversity of Lima beans of the Mayan highlands is lacking. By using 46 landraces collected in the Mayan area (23 from each subarea) and 73 ISSR loci (inter-simple sequence repeats), we analyzed the structure, diversity and genetic relationships of Lima beans of this part of Mesoamerica. High levels of diversity (H _BAY = 0.45) and genetic structure (F _ST = 0.66) were found for the whole Mayan area. Genetic diversity in the Mayan lowlands was apparently higher than the Mayan highlands (H _BAY = 0.44 and 0.36, respectively); but differences were not statistically significant. Genetic structure between the subareas was high (AMOVA = 30% of total variation), most landraces grouping according to their geographic origin. This study shows the importance of the Mayan culture in the diversification and conservation of Lima beans. The results provide important information that should be considered when implementing strategies to collect Lima bean landraces and planning in situ and ex situ programs to conserve these landraces in the Mayan region.     

Cross-transferability of SSR markers in <Emphasis Type="Italic">Osmanthus</Emphasis>

Developing a molecular tool kit for hybrid breeding of Osmanthus species and related genera is an important step in creating a systematic breeding program for this species. To date, molecular resources have been aimed solely at Osmanthus fragrans with little work to develop markers for other species and cultivars. The objectives of this study were to (1) determine cross-transferability of O. fragrans and Chionanthus retusus derived SSRs in diverse Osmanthus taxa, (2) quantify the influence of locus-specific factors on cross-transferability, and (3) determine the genetic relationships between accessions. We tested 70 SSR markers derived from O. fragrans and C. retusus in 24 accessions of Osmanthus. Sixty-seven markers showed transfer to at least one other Osmanthus species with an overall transfer rate of 84% of loci across taxa. Genotyping with 42 microsatellite markers yielded a total of 367 loci. Number of alleles per locus ranged from 2 to 17 with a mean of 8.7 ± 4.8. Mean observed and expected heterozygosities were 0.560 ± 0.225 and 0.688 ± 0.230, respectively. Percent of polymorphic loci ranged from 40% in Osmanthus delavayi to 100% in O. fragrans. Osmanthus fragrans had the highest mean number of alleles per locus (4.2) while O. delavayi had the lowest (1.1). A reduced suite of eight-markers can distinguish between accessions with non-exclusion probabilities of identity from 3.91E?⁰⁴ to 2.90E?⁰⁷. The SSR markers described herein will be immediately useful to characterize germplasm, identify hybrids, and aid in understanding the level of genetic diversity and relationships within the cultivated germplasm.