Detecting epistatic effects associated with cotton traits by a modified MDR approach

Genetic expression of a trait is complicated and it is usually associated with many genes including their interactions (epistasis) and genotype-by-environment interactions. Genetic mapping currently focuses primarily on additive models or marginal genetic effects due to the complexity of epistatic effects. Thus, there exists a need to appropriately identify favorable epistatic effects for important biological traits. Several multifactor dimensionality reduction (MDR) based methods are important resources to identify high-order gene–gene interactions. These methods are mainly focused on human genetic studies. Many traits in plant systems are not only quantitatively inherited but also are often measured in repeated field plots under multiple environments. In this study, we proposed a mixed model based MDR approach, which is suitable for inclusion of various fixed and random effects. This approach was used to analyze a cotton data set that included eight agronomic and fiber traits and 20 DNA markers. The results revealed high order epistatic effects were detected for most of these traits using this modified MDR approach.     

Water yam (Dioscorea alata L.) diversity pattern in Brazil: an analysis with SSR and morphological markers

Substantial progress was made in the last decade in understanding the diversity in Dioscorea species. However, most of the studies so far concentrated in the ‘yam belt in Africa’. We present a genetic diversity and structure analysis among commercial and local varieties of water yam (Dioscorea alata L.) in Brazil using microsatellite and morphological markers. Twelve microsatellite primers were used to generate DNA profiles of 72 local varieties and 17 commercial accessions of water yam collected in four different regions in Brazil. Also, four morphological traits were evaluated on individual plants under field conditions. The morphological characterization showed considerable diversity. High polymorphism was found with 100 % polymorphism observed for 11 primers and a discriminating power value of 0.92, on average. We did not observe a strong population structure among sampling regions, while most of the genetic diversity was concentrated within regions (95.9 %). Analysis of the relationship between accessions did not clearly separate the local and commercial genotypes. However, the molecular analyses of D. alata showed high intraspecific diversity in local accessions from different regions in Brazil, with the highest Shannon index value (H′ = 0.41) for the Southeast region. These results confirmed an admixture of accessions in all sampling regions, consistent with the lack of a significant correlation between geographic and genetic distances, suggesting that farmers exchanged water yam materials extensively. The genetic diversity can be explained by the result of a continuous exchange of accessions by farmers throughout Brazil.     

Assessment of sediment connectivity from vegetation cover and topography using remotely sensed data in a dryland catchment in the Spanish Pyrenees

Purpose

Many Mediterranean drylands are characterized by strong erosion in headwater catchments, where connectivity processes play an important role in the redistribution of water and sediments. Sediment connectivity describes the ease with which sediment can move through a catchment. The spatial and temporal characterization of connectivity patterns in a catchment enables the estimation of sediment contribution and transfer paths. Apart from topography, vegetation cover is one of the main factors driving sediment connectivity. This is particularly true for the patchy vegetation cover typical of many dryland environments. Several connectivity measures have been developed in the last few years. At the same time, advances in remote sensing have enabled an improved catchment-wide estimation of ground cover at the subpixel level using hyperspectral imagery.

Materials and methods

The objective of this study was to assess the sediment connectivity for two adjacent subcatchments (~70 km²) of the Isábena River in the Spanish Pyrenees in contrasting seasons using a quantitative connectivity index based on fractional vegetation cover and topography data. The fractional cover of green vegetation, non-photosynthetic vegetation, bare soil and rock were derived by applying a multiple endmember spectral mixture analysis approach to the hyperspectral image data. Sediment connectivity was mapped using the index of connectivity, in which the effect of land cover on runoff and sediment fluxes is expressed by a spatially distributed weighting factor. In this study, the cover and management factor (C factor) of the Revised Universal Soil Loss Equation (RUSLE) was used as a weighting factor. Bi-temporal C factor maps were derived by linking the spatially explicit fractional ground cover and vegetation height obtained from the airborne data to the variables of the RUSLE subfactors.

Results and discussion

The resulting connectivity maps show that areas behave very differently with regard to connectivity, depending on the land cover and on the spatial distribution of vegetation abundances and topographic barriers. Most parts of the catchment show higher connectivity values in August as compared to April. The two subcatchments show a slightly different connectivity behaviour that reflects the different land cover proportions and their spatial configuration.

Conclusions

The connectivity estimation can support a better understanding of processes controlling the redistribution of water and sediments from the hillslopes to the channel network at a scale appropriate for land management. It allows hot spot areas of erosion to be identified and the effects of erosion control measures, as well as different land management scenarios, to be studied.     

Human-wildlife conflict in the Kingdom of Bhutan: Patterns of livestock predation by large mammalian carnivores

We examined predation activity throughout Bhutan by tiger (Panthera tigris), common leopard (Panthera pardus), snow leopard (Uncia uncia) and Himalayan black bear (Ursus thibetanus) on a variety of livestock types using data gathered over the first two years (2003-2005) of a compensation scheme for livestock losses. One thousand three hundred and seventy five kills were documented, with leopards killing significantly more livestock (70% of all kills), than tigers (19%), bears (8%) and snow leopards (2%). About 50% of livestock killing were of cattle, and about 33% were of horses, with tigers, leopards and snow leopards killing a significantly greater proportion of horses than predicted from availability. Examination of cattle kills showed that leopards killed a significantly greater proportion of smaller prey (e.g., calves), whereas tigers killed a significantly greater proportion of larger prey (e.g., bulls). Overall, livestock predation was greatest in summer and autumn which corresponded with a peak in cropping agriculture; livestock are turned out to pasture and forest during the cropping season, and subsequently, are less well guarded than at other times. Across Bhutan, high horse density and low cattle and yak density were associated with high rates of livestock attack, but no relationship was found with forest cover or human population density. Several northern districts were identified as ‘predation hotspots’, where proportions of livestock lost to predation were considerable, and the ratio of reported kills to relative abundance of livestock was high. Implications of our findings for mitigating livestock losses and for conserving large carnivores in Bhutan are discussed.     

Modeling protein functional properties from amino acid composition

Physicochemical and functional properties of proteins were modeled as a function of the contributions of each of the 20 coded amino acids to three (z-scores) or five (extended z-scores) amino acid principal properties using partial least squares regression. The five term models were in all cases stronger in both fit and prediction than the three term models, indicating that useful information is contained in the fourth and fifth property scores. Models predicting protein hydrophobicity (R = 0.932), viscosity (R = 0.737), and foam capacity (R = 0.880) from amino acid composition rather than sequence were obtained. It is likely that additional functional and physicochemical properties of proteins can be modeled in this way.     

Cytogenetic and genetic relationships between populations of Aegilops ventricosa Tausch

Summary Five samples of Aegilops ventricosa (2n=4x=28, genome formula DDNN) from different geographical origins, were crossed in a diallelic scheme. Metaphase I chromosome pairing of the hybrids, accounting for all the possible genetic combinations, was analysed. Only bivalents were formed in some hybrids, while multivalents were scored in other ones. Seed storage proteins, gliadins and albumins, were also analysed by means of polyacrylamide gel electrophoresis. Based on the presence of multivalents in hybrids, and on the differences in seed protein profiles, the samples could be grouped into two clusters. Meiosis was regular in hybrids obtained within samples of the same group, while multivalents were present in hybrids involving a sample of one group and one of the other. The evolutionary trends in Ae. ventricosa are discussed.     

Agricultural Sediment Reduction by Giant Cane and Forest Riparian Buffers

The sediment filtering capabilities of giant cane (Arundinaria gigantea (Walt.) Chapm.) and forest riparian buffers were compared in a southern Illinois, USA non tile drained agricultural watershed. Giant cane, a bamboo species, serves as important wildlife habitat throughout its native range in the southeastern and lower midwestern United States. Overland flow samples were collected at the field edge and at 3.3 m, 6.6 m, and 10.0 m within the riparian buffers during 19 precipitation events over a 1-year period. On an annual basis, significant sediment reductions occurred by 3.3 m and 6.6 m in the cane and forest buffers, respectively. The giant cane buffer reduced incoming sediment mass by 94% within the first 3.3 m, while the forest buffer reduced sediment by 86% over 6.6 m. Within 10.0 m of the field edge, the cane and forest buffers reduced sediment mass by 100% and 76%, respectively. On a seasonal basis, the cane buffer outperformed the forest buffer. During each of the four seasons, the cane buffer reduced sediment masses within 3.3 m of the field edge, while the forest buffer showed initial reductions occurring at 6.6 m during the summer, fall, and winter. No detectable reductions occurred during the spring in the forested buffer. Reductions in sediment concentrations were less evident compared to mass basis, indicating that infiltration may be a more important sediment reduction mechanism than particle settling. Both the forest and giant cane buffers had relatively high measured soil infiltration rates. Study results indicate that giant cane is an appropriate species to include in riparian buffer restoration designs for sediment control.     

Korea’s importance in the East Asiatic gene center

New evidence from archeology and human genetics provides strong support for the introduction of rice agriculture to Japan by Korean farmers. This sheds new light on the formation and further evolution of the East Asiatic gene center and stresses the importance of Korean agri- and horticulturists in Eastern Asia.     

Application of a Balanced Scorecard System for Supporting Decision-Making in Contaminated Sites Remediation

This work introduces the development and application of a multi-goal evaluation procedure for assessing sets of remedial options that have previously been found technically suitable for managing a certain contaminated site. The construction of this decision support tool, in the form of a balanced scorecard, has followed a multi-attribute conception of the contaminated sites problem, identifying the most critical aspects considered by all stakeholders involved in contaminated sites management decisions. The developed tool has been checked in its formulation and application against an export benchmark of an Austrian remediation project. The performed evaluation allowed to identify and suggest a remedial option that best fitted the expectations of all stakeholders involved in the project. Furthermore, through the accomplishment of a sensitivity analysis it has been demonstrated that the system is stable and robust in terms of the chosen elicitation schemes, and that the preferences of the different stakeholders are influencing factors on the final result. The results and conclusions of this work present the benefits of implementing the developed balanced scorecard as a tool for supporting decision making in contaminated sites remediation projects.