Efficiency of SNP and SSR-based analysis of genetic diversity,population structure,and relationships among cowpea (<Emphasis Type="Italic">Vigna unguiculata</Emphasis> (L.) Walp.) germplasm from East Africa and IITA inbred lines

The extent of genetic diversity and relatedness of cowpea germplasm from East Africa are poorly understood. A set of 13 microsatellites (SSR) and 151 single nucleotide polymorphisms (SNPs) markers were applied to assess the levels of genetic diversity in a sample of 95 accessions of local cowpea germplasm and inbred lines of Vigna unguiculata. The average genetic diversity (D), as quantified by the expected heterozygosity, was higher for SSR loci (0.52) than for SNPs (0.34). The polymorphic information content was 0.48 for SSR and 0.28 for SNP while the fixation index was 0.095 for SSR and 0.15 for SNPs showing moderate differentiation and high gene flow among cowpea accessions from East African countries. The results of data analysis of both SSR and SNP markers showed similar clustering patterns suggesting a substantial degree of association between origin and genotype. Principal coordinate analysis (PCoA) with SSR and SNP markers showed that accessions were grouped into two and three broad groups across the first two axes, respectively. Our study found that SNP markers were more effective than SSR in determining the genetic relationship among East African local cowpea accessions and IITA inbred lines. Based on this analysis, five local cowpea accessions Tvu-13490, Tvu-6378, Tvu-13448, Tvu-16073, and 2305675 were identified to be tightly clustered sharing several common alleles with the drought tolerant variety Danila when analyzed with SSR and SNP markers. The findings will assist and contribute to future genetic diversity studies aimed at the genetic improvement of local Eastern Africa cowpea accessions for improved overall agronomic performance in general and breeding for drought tolerant in particular.     

Evaluation of multi-satellite precipitation products for soil loss and sediment export modeling over eastern regions of the Koshi River Basin,Nepal

Journal of Soils and Sediments - Precipitation data are an important input variable for soil loss (SL) and sediment export (SE) modeling, although they are rarely available at fine spatial and...     

Earthworm primers for DNA-based gut content analysis and their cross-reactivity in a multi-species system

Specific primers can be used in polymerase chain reactions (PCR) to amplify prey DNA from the gut content of generalist predators at high specificity and sensitivity. A prerequisite for applying this approach to field studies, however, is to confirm that primers are actually targeting specific prey species or prey groups and do not produce false positive results by amplifying DNA either from predator species or from the wide range of potential alternative prey found under natural conditions. Here, we report on a new group-specific primer pair for earthworms designed from cytochrome oxidase c subunit 1 (COI) sequences of 11 earthworm species found in Central Europe that can be used to detect consumption of earthworms by invertebrate predators. Besides inter-specific also considerable intra-specific variation was found for COI sequences among most of the earthworm species. We, therefore, combined a universal forward primer with an earthworm-specific reverse primer which amplified a 523 bp product from all 11 species tested. Earthworm DNA amplification was also successful in the presence of excess DNA of a predator species. The primer pair was tested against 82 non-target invertebrate species commonly found in the same habitats, including potential prey for generalist predators and predators themselves. The earthworm primer was highly specific: only one of the non-target species showed a product of similar length as the earthworms, whereas PCR with 12 non-target species produced amplicons whose length differed from that of earthworms. We conclude that the new primer will be a useful tool to investigate the role earthworms play as a food resource in soil food-webs. Moreover, we suggest that future studies utilizing DNA-based approaches for prey detection should select non-target species for cross-reactivity tests according to their abundance and importance rather than choosing representatives of taxonomic units; this will help validate the results achieved using species- or group-specific primers and guarantee their meaningful ecological interpretation.     

Woody plant diversity,structure and regeneration in the Ambo State Forest,South Gondar Zone,Northwest Ethiopia

For this study in the Ambo State Forest on woody plant diversity, structure and regeneration, 70 quadrats, each 25 m by 25 m, were selected using a systematic random sampling technique and intervals of 100 m along a transect line. For assessing seedlings and saplings,two 2 × 10 m sub quadrats were set upon opposite sides of each main quadrat. Data on species diversity, abundance,structure, basal area, density, frequency and regeneration status were collected and analyzed using standard procedures and programs. Of 58 woody plant species identified,69 % were trees, 16 % were shrubs, 12 % were tree/shrubs and 4 % were climbers. Fabaceae was the most speciesrich family comprising 17 species. The Shannon–Weiner diversity index was 2.73, and evenness was 0.67. The population structure in the cumulative diameter class frequency distribution revealed an interrupted and inverted J-shape with a very high decrease in higher diameter class.Acacia lahai(49 %) was the most important woody species with the highest importance value index. To maintain balanced structure, enhanced regeneration and protecting the forest from selective cutting are recommended.     

Development and validation of a stem volume equation for Cupressus lusitanica in Gergeda Forest,Ethiopia

Stem volume equations were fitted for Cupressus lusitanica in Gergeda Forest, Ethiopia using six different established equation forms. A total of 260 trees were measured for their diameter at breast height (D), total height (H?)and stem volume using destructive sampling methods. The data set was randomly divided into equal size for equation development and equation validation. Five fit statistics comprising of the fit index, root mean square error, bias (ē?), absolute mean deviation and coefficient of variation were used to evaluate the performance of each equation. Among the different equations, the Schumacher and Hall function of the form V = b₁D^b2H^b3 (model 5), which estimates volume (V?) using diameter at breast height and total height as predicting variables, performed best and was then fitted to the combined data set for prediction of volume over-bark of C. lusitanica in Gergeda Forest. Overall, volume equations with two independent variables (D and H?) performed better than those with only one variable (D). The equations developed in this study can provide forest managers with accurate estimations of stem volumes for C. lusitanica in Gergeda Forest.     

Yield,quality and profitability of sensor-controlled irrigation: a case study of snapdragon (<Emphasis Type="Italic">Antirrhinum majus</Emphasis> L.) production

Advanced wireless irrigation sensor networks that can monitor and control irrigation are only recently available commercially, but on-farm research has found a number of advantages compared with current irrigation practices including reduced water application, disease incidence, production time and labor, together with increased profitability. We examined the effects of wireless sensor networks to precisely control irrigation based on substrate moisture in a 0.15-ha greenhouse producing cut-flower snapdragons (Antirrhinum majus). We calculated changes in yield, production time, quality, cost, revenue and profit using grower data on production, expenditures and sales, which included 3 years of data before and after implementation of sensor irrigation networks. Sensor-based irrigation was associated with a 62 % ($65,173 or $434,487 ha^?1) increase in revenue and a 65 % ($35,327 or $325,513 ha^?1) increase in profit per year. Sensor-based irrigation was also associated with increases in the quality and the number of stems harvested per crop. The time to first harvest and time to last harvest were reduced for all cultivar groups, indicating that the plants grew faster using sensor networks. Production time per crop was decreased, allowing 2.5 additional crops per year. Electricity usage was also reduced, likely due to less frequent irrigation using sensor networks. These results are in line with other benefits we have seen by installing sensor networks in other types of ornamental operations.     

Estimation of genetic parameters for growth traits and Kleiber ratios in Boer x Central Highland goat

Tropical Animal Health and Production - Accurate performance evaluation and genetic parameters estimation are the prerequisites for any successful genetic improvement program. This study was...     

Antioxidant 1 copper chaperone gene expression and copper levels in dog osteosarcoma patients

Twenty-four dogs with OS underwent limb amputation. Serum, OS tumour, and normal bone were harvested at time of surgery. RNA was extracted and gene expression was performed using quantitative polymerase chain reaction (qPCR). Tissue and blood copper concentrations were also determined with spectrophotometry. Compared to bone, tumour samples had significantly higher expressions of antioxidant 1 copper chaperone (ATOX1, p = .0003). OS tumour copper levels were significantly higher than that of serum (p < .010) and bone (p = .038). Similar to our previous observations in mouse and human OS, dog OS demonstrates overexpression of genes that regulate copper metabolism (ATOX1), and subsequent copper levels. Dogs with OS may provide a robust comparative oncology platform for the further study of these factors, as well as potential pharmacologic interventions.