Analysis of rice blast resistance gene <Emphasis Type="Italic">Pi</Emphasis>-<Emphasis Type="Italic">z</Emphasis> in rice germplasm using pathogenicity assays and DNA markers

The Pi-z gene in rice confers resistance to a wide range of races of the rice blast fungus, Magnaporthe oryzae. The objective of this study was to characterize Pi-z in 111 rice germplasm accessions using DNA markers and pathogenicity assays. The existence of Pi-z in rice germplasm was detected by using four simple sequence repeat (SSR) markers (RM527, AP4791, AP5659-1, AP5659-5) closely linked to Pi-z, and was verified using pathogenicity assays with an avirulent strain (IE1k) and two virulent races (IB33 and IB49). Among 111 germplasm accessions evaluated, 73 were found to contain the Pi-z gene using both SSR markers and pathogenicity assays. The remaining 38 germplasm accessions were found to be inconsistent in their responses to the blast races IB33, IEIk and IB49 with expected SSR marker alleles, suggesting the presence of unexpected SSR alleles and additional R gene(s). These characterized germplasm can be used for genetic studies and marker-assisted breeding for improving blast resistance in rice.     

Comparing apparent electrical conductivity measurements on a paddy field under flooded and drained conditions

Every growing season, paddy fields are kept both flooded and drained for a significant period of time. As a consequence, these soils develop distinct physico-chemical characteristics. For practical reasons, these soils are mostly sampled under dry conditions, but the question arises how representative the results are for the wet growing conditions. Therefore, the apparent electrical conductivity (EC_a) of a 1.4 ha alluvial paddy field located in the Brahmaputra floodplain of Bangladesh was measured in both dry and wet conditions by a sensing system using the electromagnetic induction sensor EM38, which does not require physical contact with the soil, and compared both surveys. Due to the smooth water surface under wet conditions which ensured increased stability of the sensing platform, the results of the survey showed considerably reduced micro-scale variability of EC_a. Furthermore, the wet survey results more reliably furnished soil-related information mainly due to the absence of soil moisture dynamics. The differences between EC_a under wet and dry conditions were attributed to differences in soil texture, mainly the sand content variation having considerable effect on soil moisture differences when flooded following drainage. Accordingly, the largest differences between EC_a under wet and dry conditions were found in those parts of the field with a large sand content. Hence, the conclusion was that an EC_a survey on flooded fields has an added value to precision soil management.     

A plant based sensing method for nutrition stress monitoring

Due to economical and ecological reasons it is important to provide the necessary flexibility in fertilizer management to respond to differences in plant nutrients requirements. Plant-based sensors have potential to provide more accurate and on-line information regarding crop bio-responses to environmental stress and could overcome limitations of traditional methods which focus only on monitoring parameters of soil. Current research regarding on-line plant stress sensing techniques concentrates on spectroscopic and image processing methods. These techniques have many limitations connected with their sensitivity to environmental interferences. In recent years, impedance spectroscopy has become a well-known non-invasive tool for describing the electrical properties of many systems. The research hypothesis tested was that information provided by Electrical Impedance Spectroscopy is correlated with tomato plant stress caused by lack of mineral nutrients in the growth medium. The experiment was conducted with two sets of hydroponically-grown tomato plants (Lycopersicon esculentum Mill., cv. ‘Maliniak’). During the experiment the tomato plants were fed alternately with flow of necessary nutrients and with distilled water. The impedance spectra were measured by scanning frequencies from 100 Hz to 50 kHz to determine the most sensitive frequency. A Nutrition Index was proposed for indicating variability of mineral nutrition within plants, and its correlation with experimental plant data was tested. Data showed that the relation between the Nutrition Index and the stress caused by lack of mineral nutrients in the growing medium was a monotonic function in the case of study. The results presented in the paper support the concept that the electrical impedance spectroscopy is a non-destructive, economical and reliable measurement method, which can be utilised for plant nutrition stress monitoring.     

Application of day and night digital photographs for estimating maize biophysical characteristics

In this study, an inexpensive camera-observation system called the Crop Phenology Recording System (CPRS), which consists of a standard digital color camera (RGB cam) and a modified near-infrared (NIR) digital camera (NIR cam), was applied to estimate green leaf area index (LAI), total LAI, green leaf biomass and total dry biomass of stalks and leaves of maize. The CPRS was installed for the 2009 growing season over a rainfed maize field at the University of Nebraska-Lincoln Agricultural Research and Development Center near Mead, NE, USA. The vegetation indices called Visible Atmospherically Resistant Index (VARI) and two green–red–blue (2g–r–b) were calculated from day-time RGB images taken by the standard commercially-available camera. The other vegetation index called Night-time Relative Brightness Index in NIR (NRBI_NIR) was calculated from night-time flash NIR images taken by the modified digital camera on which a NIR band-pass filter was attached. Sampling inspections were conducted to measure bio-physical parameters of maize in the same experimental field. The vegetation indices were compared with the biophysical parameters for a whole growing season. The VARI was found to accurately estimate green LAI (R² = 0.99) and green leaf biomass (R² = 0.98), as well as track seasonal changes in maize green vegetation fraction. The 2g–r–b was able to accurately estimate total LAI (R² = 0.97). The NRBI_NIR showed the highest accuracy in estimation of the total dry biomass weight of the stalks and leaves (R² = 0.99). The results show that the camera-observation system has potential for the remote assessment of maize biophysical parameters at low cost.     

Molecular diversity of Egyptian cotton (<Emphasis Type="Italic">Gossypium barbadense</Emphasis> L.) and its relation to varietal development

Twenty-eight Egyptian cotton (Gossypium barbadense L.) genotypes (varieties and hybrids) were used for analysis of genetic diversity using DNA based markers (ISSR, SSR, and EST) and to study varietal development of cotton. The ISSR markers gave the highest percentage of polymorphic bands as well as polymorphic information content compared with the other molecular markers (i.e. EST and SSR markers). Using clustering analysis, no general clustering according to the pedigree history of the genotypes was observed. Using principal coordinate analysis (PCOORDA), cotton genotypes were separated by the first three principal coordinates (PC1, PC2, and PC3) accounting for 11.5, 8.6, and 7.2% of the total genetic variance, respectively. The cotton genotypes were distributed into three parts based on the first PC, each part containing a group of varieties having a common ancestor. ‘Giza 12’ variety was the common ancestor for the varieties included in the first part and ‘Ashmouni’ variety was the common ancestor for the varieties included in the second part, while both ‘Sakha 3’ and ‘Sakha 4’ varieties were common ancestors for the varieties included in the third part. The results of the PCOORDA also showed better resolution of the genetic diversity than cluster analysis especially in the illustration of the varietal development of cotton. That means that principal coordinate analysis can be strongly used either alone or in combination with cluster analysis to discuss both genetic diversity and varietal development in the cotton genotypes.     

Identification and characterization of EST-SSRs in finger millet (<Emphasis Type="Italic">Eleusine coracana</Emphasis> (L.) Gaertn.)

In recent years, microsatellites have become the most used markers for studying population genetic diversity. The increased availability of the DNA sequences has given the possibility to develop EST-derived SSR markers. A total of 1,927 ESTs of Eleusine coracana available in the NCBI database were mined for SSRs. Di-nucleotides are the most occurring motifs accounting for more than 50% of the repeats, of which GA was the most abundant motif and tetra-nucleotides are the least occurring motifs. Of the 132 markers identified, 30 primer pairs based were synthesized. SSR markers were used for variety discrimination and genetic assessment in 15 finger millet accessions; 20 primers showed polymorphism and 13 primers were identified as having a PIC value above 0.5. On the basis of the distribution of these polymorphic alleles, the 15 accessions were classified into two groups. This study has demonstrated the potential of EST-derived SSR primer pairs in finger millet. These primers will serve as valuable source for further breeding programs.     

Regeneration in sugarcane via somatic embryogenesis and genomic instability in regenerated plants

In the present study, embryogenic calli of sugarcane variety BL4 were induced using 2,4-dichlorophenoxyacetic acid (2,4-D) and kinetin in different concentrations and combinations. In contrast to earlier studies, embryogenic callus sectors were identified and isolated microscopically within 1–2 weeks. Subsequently, 51 media formulations were used for regeneration of proliferated embryogenic callus, using MS medium supplemented with three different cytokinins [kinetin, 6-Benzylamino purine (BAP), and thidiazuron (TDZ)] and auxins (IAA/NAA and IBA) in different combination and concentrations. After acclimatization, the genomic DNA of regenerated plants was studied to explore the insertion polymorphism of transposable elements in order to ascertain the variation among somaclones. Though low concentration of kinetin with 2,4-D was found supportive to embryogenic callus development, the highest number of regenerated plantlets was observed using BAP (1 μM), however the plantlets had very low fresh weight (2.2 g). Conversely, TDZ alone supported a significant increase in the number of plantlets regenerated (38–40) with higher fresh weight. The somaclones generated during this study showed considerable positional polymorphism of activator-like transposable elements possibly due to the stress associated with in vitro culture. This study provides a procedure to produce regenerated sugarcane plants from embryogenic callus in a relatively short time.     

Increase in growth,productivity and nutritional status of rice (<Emphasis Type="Italic">Oryza sativa</Emphasis> L. cv. Basmati) and enrichment in soil fertility applied with an organic matrix entrapped urea

Field experiments were conducted to evaluate the effects of eco-friendly organic matrix entrapped urea (OMEU) on growth, productivity, and yield of rice (Oryza sativa L. cv. Basmati) and soil enrichment in the paddy field at Rohtak (Haryana) located near Delhi. The OMEU prepared in granular form contained cow dung, rice bran (grain cover of Oryza sativa), powder of neem leaves (Azadirachta indica), and clay soil (diameter of particles < 0.02 mm) in 1:1:1:1 ratios and saresh (plant gum of Acacia sp.) as binder along with half of the recommended dose of commercially available soluble urea (free urea; FU). Single basal application of OMEU showed an increase in plant growth in terms of fresh and dry weights, root length, root, leaf and tiller numbers, soluble protein, total N and ammonium in leaves, productivity in terms of grain and straw yield, and nutritional and microbial activities of field soil over free form of urea and no fertilizer application. Nutritional status of rice grains was also improved over the free urea and no fertilizer controls. Our data indicate that OMEU, which is low cost and based on bio-degradable, non-toxic, and locally available agro-waste, can be attempted to replace the conventional use of soluble urea in rice.     

Prevalence and antimicrobial resistance profiles of <Emphasis Type="Italic">Salmonella enterica</Emphasis> serovars isolated from slaughtered cattle in Bahir Dar,Ethiopia

A study was undertaken from October 2006 to March 2007 to determine the prevalence and antimicrobial resistance patterns of Salmonella serovars. Liver, mesenteric lymph nodes, intestinal content, and carcass swab samples (each n?=?186) were collected from 186 apparently healthy slaughtered cattle at Bahir Dar abattoir. Bacteriological analysis was done according to the International Organization for Standardization (ISO 6579 2002). Isolates were serotyped at Agence Française de Securite Sanitaire des Aliments, Cedex, France. Twenty-eight isolates consisting of Salmonella Typhimurium, Salmonella Newport, Salmonella Haifa, Salmonella Heidelberg, Salmonella Infantis, and Salmonella Mishmarhaemek were identified. Salmonella Typhimurium and Salmonella Newport were most frequently isolated while Salmonella Heidelberg and Salmonella Mishmarhaemek were isolated least. Eleven of the 28 (39.3%) were resistant to one or more of the antimicrobials tested. Resistance was shown to ampicillin, chloramphenicol, gentamycin, norfloxacin, polymyxin-B, streptomycin, tetracycline, and trimethoprim. Four of 11 (36.4%) were multiple antimicrobial resistant. All the isolates tested were susceptible to the antimicrobial effects of gentamycin, norfloxacin, and trimethoprim. Eleven, four, and two isolates of the 28 were resistant to streptomycin, tetracycline, and ampicillin, respectively. All isolates of Salmonella Infantis, Salmonella Typhimurium (except one), and Salmonella Mishmarhaemek were susceptible to the tested antimicrobials. One Typhimurium isolate was resistant to chloramphenicol, streptomycin, and tetracycline. Salmonella Haifa was multiply antimicrobial resistant to ampicillin, tetracycline, and streptomycin. All isolates of Salmonella Heidelberg were resistant to streptomycin. Results of this study indicated high level of carcass contamination with antimicrobial-resistant Salmonella serovars which could pose public health risk; suggests need for hygienic slaughtering operations and proper cooking of meat before consumption. Further detailed studies involving different abattoirs, animal products, food items, and animals on different settings were recommended in the study area.     

Evaluation of two Indian native chicken breeds for reproduction traits and heritability of juvenile growth traits

The present study was conducted to evaluate two Indian native chicken breeds, namely, Aseel and Kadaknath for fertility, hatchability, genetic parameters of juvenile growth traits, and semen quality traits at the onset of sexual maturity. The fertility was similar in Aseel (86.96%) and Kadaknath (85.15%); however, a relatively higher hatchability was observed in Kadaknath (77.94%) than Aseel (70.74%). Heritability estimates of body weights at 4 weeks of age were almost similar in Aseel (0.37) and Kadaknath (0.39), while the estimate of body weight at 6 weeks of age was higher in Aseel (0.42) than Kadaknath (0.31). The heritability estimate of shank length at 6 weeks of age was lower in Aseel (0.16) compared to Kadaknath (0.35). The age at first egg in the flock was comparable in Aseel (148 days) and Kadaknath (150 days). Aseel breed with significantly (P ≤ 0.001) higher body weight, absolute and relative testes weights had significantly higher semen volume (P ≤ 0.05) and sperm motility (P ≤ 0.01) but had lower seminal plasma cholesterol level (P ≤ 0.05) as compared to Kadaknath. It can be concluded that there is a scope for genetic improvement of these two native breeds for juvenile growth traits since heritability estimates of these traits were relatively high.