Assessment of genetic diversity among African cassava Manihot esculenta Grantz accessions resistant to the cassava mosaic virus disease using SSR markers

A study was conducted to determine the extent of genetic diversity among African cassava (Manihot esculenta Crantz) accessions resistant to the cassava mosaic virus disease (CMD), using simple sequence repeat (SSR) markers. The accessions included a breeding stock (clone 58308), five improved lines, 62 CMD resistant and 10 CMD susceptible landraces. Genetic diversity was assessed among accessions in five cluster groups derived from UPGMA analysis on data from 18 SSR primer pairs. Average gene diversity, He, was high in all cluster groups, with an average heterozygosity of 0.591 ± 0.061. The estimator of inbreeding Fis revealed a low level of inbreeding within groups and averaged −0.262 ± 0.142. Gene diversity among all accessions was 51.4% and gene diversity within cluster groups was 46.6%, while 4.8% was due to diversity between the different cluster groups. The amount of genetic differentiation measured by Gst and Fst were 9.6% and 12.1% respectively, indicating a weak genetic structure.     

Determination of the conjugated linoleic acids in cow's milk fat by Fourier transform Raman spectroscopy

The collective term "conjugated linoleic acid" or "CLA" generally refers to a mixture of conjugated positional and geometric isomers of linoleic (cis-9,cis-12-octodecadienoic) acid. In nature, these isomers are mainly formed in the rumen by biohydrogenation of polyunsaturated fatty acids. This study concerns a first trial of CLA determination in cow's milk fat by Raman spectroscopy. The spectra of pure cis-9-oleic, cis-9,cis-12-linoleic, cis-9,trans-11-linoleic, and trans-10,cis-12-linoleic acids have been examined in comparison with the spectra of selected milk-fat samples containing between 0 and 3% of CLA. The trial of CLA determination by Raman spectroscopy on cow milk fat has reached its objective with the two following results. First, the examination of the Raman spectra allows to identify three specific Raman signals of the chemical bonds associated to the cis,trans conjugated C=C in the rumenic and trans-10,cis-12-octodecadienoic acids at 1652, 1438, and 3006 cm(-1). Second, the calibration of Raman spectrometer for the CLA determination has indicated that these three specific signals suit very well for the accurate and reliable measurement of CLA concentration in milk fat. To our knowledge, the present study is the first successful attempt to determine the CLA content of milk fat by a spectrophotometric method.     

Reactions of anthocyanins and tannins in model solutions

The reaction between procyanidin dimer Ec-EcG (B2 3'-O-gallate) and malvidin 3-O-glucoside (Mv3glc) was studied in a model solution system at two different pH values, 2.0 and 3.8. Disappearance of both species was much faster at pH 3.8 than at pH 2.0. That of Mv3glc was increased in the presence of Ec-EcG, whereas that of Ec-EcG was the same in the presence or absence of the anthocyanin. Values of absorbance at 520 nm measured at pH 2.0 were correlated with the amount of residual Mv3glc. Those measured at pH 3.8 hardly changed during the incubation, but absorbance values at 420 and 620 nm as well as resistance to sulfite bleaching were much increased, confirming that Mv3glc was converted to other pigments. Anthocyanin-flavanol adducts were observed at both pH values, but their structures were different. At pH 2.0, cleavage of the procyanidin linkage followed by nucleophilic addition of flavanol or anthocyanin moieties led to (Ec)(n)-EcG and (Ec)(n)-Mv3glc, respectively. At pH 3.8, nucleophilic addition of Ec-EcG onto the anthocyanin yielded Mv3glc-(Ec-EcG).     

Blind inlets: conservation practices to reduce herbicide losses from closed depressional areas

Purpose

In a 6-year study, we investigated the effectiveness of blind inlets as a conservation practice in reducing pesticide losses compared to tile risers from two closed farmed depressional areas (potholes) in the US Midwest under a 4-year cropping rotation.

Materials and methods

In two adjacent potholes within the same farm and having similar soils, a conventional tile riser and blind inlet were installed. Each draining practice could be operated independent of each other in order to drain and monitor each depression with either practice. Sampling events (runoff events) were collected from the potholes from 2008 to 2013 using autosamplers. The samples were analyzed for atrazine, metolachlor, 2,4-D, glyphosate, and deethylatrazine.

Results and discussion

The results of this study demonstrated that the blind inlet reduced analyzed pesticide losses; however, the level of reduction was compound dependent: atrazine (57 %), 2,4-D (58 %), metolachlor (53 %), and glyphosate (11 %).

Conclusions

Results from this study corroborate previous research findings that blind inlets are an effective conservation practice to reduce discharge and pollutants, including pesticides from farmed pothole surface runoff in the US Midwest.

     

Genetic diversity in <Emphasis Type="Italic">Eremostachys superba</Emphasis> Royle ex Benth. (Lamiaceae), an endangered Himalayan species,as assessed by RAPD

Eremostachys superba Royle ex Benth. (Lamiaceae) has undergone a severe decline in population size since its discovery in the North-western Himalayas in late 19th century. One hundred and seventy-two plants from six populations in the Indian states of Uttar Pradesh and Jammu & Kashmir, located between 0.45 km and 455.72 km apart from each other were evaluated for RAPD polymorphism. Sixteen random primers generated 92 bands overall, 77 of which were polymorphic. Shannon’s index of genetic diversity within populations (H _o) ranged between 0.305 and 0.421; the average within-population diversity (H _pop) was 0.389; and the total species diversity (H _sp) was 0.478. The population from Mohand (representing the type locality) had the fewest plants, at 18, and was genetically the most depauperate. Among the other populations, ranging in size between 52 and 1,022 individuals, no relation between population size and genetic diversity was evident. It is suggested that these six populations represent relics of a larger, extended population, in which the presence of perennating rootstocks has helped preserve historic patterns of genetic diversity. AMOVA revealed that 83.01% of the variation exists within populations, which was consistent with earlier studies on the reproductive biology of E. superba, which indicated this species is predominantly allogamous. FST distances between all populations were significant, indicating geographic differentiation despite some of them being closely separated. Habitat restoration and protection from indiscriminate harvesting are proposed as primary strategies for conserving E. superba. Rejuvenation of the Mohand population through intrapopulation crossing between plants bearing diverse molecular phenotypes is also suggested.     

Development of EST-SSR in foxtail millet (<Emphasis Type="Italic">Setaria italica</Emphasis>)

The development of EST-SSR in foxtail millet (Setaria italica) for polymorphism and transferability study was reported here. From 1213 EST sequences, 30 SSRs were obtained and primers were designed for 26 SSRs. Among them, four pairs of SSR primers amplified polymorphic products in 12 foxtail millet cultivars and one accession of Setaria viridis, a wild relative of foxtail millet, with 10 alleles detected for the four loci and 2.5 alleles per locus. In addition, ten SSR markers could be transferred to other nine Gramineae species. The putative functions of 11 ESTs containing polymorphic and transferable SSRs were also identified.     

Near-infrared spectroscopy for analysis of chemical and microbiological properties of forest soil organic horizons in a heavy-metal-polluted area

In industrial areas, heavy metals may accumulate in forest soil organic horizons, affecting soil microorganisms and causing changes in the chemical composition of the accumulated organic matter. The objectives of this study were to test the ability of near-infrared spectroscopy (NIRS) to detect heavy metal effects on the chemical composition of forest soil O horizons and to test whether NIRS may be used to quantitatively determine total and exchangeable concentrations of Zn and Pb (Zn_t, Pb_t, Zn_ex, Pb_ex) and other chemical and microbial properties in forest soil O horizons polluted with heavy metals. The samples of O horizons (n = 79) were analyzed for organic C (C_org), total N and S (N_t, S_t), Zn_t, Pb_t, Zn_ex, Pb_ex, basal respiration (BR), microbial biomass (C_mic) and C_mic-to-C_org ratio. Spectra of the samples were recorded in the Vis-NIR range (400–2,500 nm). To detect heavy-metal-induced changes in the chemical composition of O horizons principal components (PC1–PC7) based on the spectral data were regressed against Zn_t + Pb_t values. A modified partial least squares method was used to develop calibration models for prediction of various chemical and microbial properties of the samples from their spectra. Regression analysis revealed a significant relationship between PC3 and PC5 (r = −0.27 and −0.34, respectively) and Zn_t + Pb_t values, indicating an effect of heavy metal pollution on the spectral properties of the O horizons and thus on their chemical composition. For quantitative estimations, the best calibration model was obtained for C_org-to-N_t ratio (r = 0.98). The models for C_org, N_t, and microbial properties were satisfactory but less accurate. NIRS failed to accurately predict S_t, C_org-to-S_t, Zn_t, Pb_t, Zn_ex, and Pb_ex.     

Spatial patterns of diversity and genetic erosion of traditional cassava (<Emphasis Type="Italic">Manihot esculenta</Emphasis> Crantz) in the Peruvian Amazon: An evaluation of socio-economic and environmental indicators

This study evaluates quantitatively the suitability of the use of site-specific socio-economic and environmental data as indicators to rapidly assess patterns of diversity and genetic erosion risk in cassava. Socio-economic data as well as farmers’ estimation of genetic erosion were collected in the study area, the Ucayali region of the Peruvian Amazon, through interviews with 285 cassava farmers in 50 communities, while diversity was assessed based on agromorphological characterization of 295 cassava accessions. Using multivariate regression analyses, 50 and 45% of the variation in respectively diversity and genetic erosion estimation could be explained by a selected set of socio-economic and environmental indicators. In both regression models four out of the total of 38 variables proved to contribute significantly (at p < 0.10 level). Additionally, the study revealed that farmers are a good direct source of information on the diversity present at community level, which can contribute to the development of methodologies to assess diversity more rapidly. The results of this study are valuable for the development of models to rapidly assess diversity dynamics in large areas.     

Genetic diversity of potato landraces from northwestern Argentina assessed with simple sequence repeats (SSRs)

Andean potato varieties are cultivated in the northwest of Argentina and constitute the most important staple food for the local farmers. The genetic diversity of 155 accessions conserved at the Genebank of Balcarce (INTA) was tested using four microsatellites. Three commercial potato varieties of Tuberosum group and one accession of Curtilobum group were used as outgroups. The presence of bands was scored for each microsatellite and for each accession and the data were analysed by principal coordinate analysis. The polymorphism information content was obtained for each molecular marker from banding patterns. Analysis of molecular variance was carried out with a variable number of accessions for each landrace, from different departments and sites within departments. More than one genotype was detected in the majority of the potato landraces. Some accessions within each landrace did not differentiate. AMOVA revealed that most of the genetic variation occurred among sites within departments and among local varieties. These findings are discussed considering the agricultural practices carried out in the Andean farming system.     

Diversity among landraces of Indian snapmelon (<Emphasis Type="Italic">Cucumis melo</Emphasis> var. <Emphasis Type="Italic">momordica</Emphasis>)

Diversity among 36 snapmelon landraces, collected from 2 agro-ecological regions of India (9 agro-climatic sub-regions), was assayed using RAPD primers, morphological traits of plant habit and fruit, 2 yield-associated traits, pest and disease resistance and biochemical composition (TSS, ascorbic acid, titrable acidity). Typical differences among accessions were observed in plant and fruit characteristics and snapmelon germplasm with high titrable acidity and possessing resistance to downy mildew, Cucumber mosaic virus, Zucchini yellow mosaic virus, Papaya ringspot virus, Aphis gossypii and Meloidogyne incognita was noticed in the collection. RAPD based grouping analysis revealed that Indian snapmelon was rich in genetic variation and region and sub-region approach should be followed across India for acquisition of additional melon landraces. Accessions of var. agrestis and var. momordica clustered together and there was a separate cluster of the accessions of var. reticulatus. Comparative analysis of the genetic variability among Indian snapmelons and an array of previously characterized reference accessions of melon from Spain, Israel, Korea, Japan, Maldives, Iraq, Pakistan and India using SSRs showed that Indian snapmelon germplasm contained a high degree of unique genetic variability which was needed to be preserved to broaden the genetic base of melon germplasm available with the scientific community. N. P. S. Dhillon and Ranjana contributed equally to this work and are considered the first authors.