Using linear-bilinear models for studying gene expression × treatment interaction in microarray experiments

In microarray experiments, the global and the specific gene expression in the two-way table of gene x treatments (or tissues) can be studied using linear-bilinear models that incorporate the main effects of genes (G), treatment (T), and gene x treatment interaction (G x T). The plot of the first two axes obtained from the singular value decomposition of the bilinear (multiplicative) term of these models (biplot) facilitates the interpretation of the gene expression patterns. In this study, two microarray datasets were used to illustrate how two linear-bilinear models, the additive main effect and multiplicative interaction (AMMI) and the treatment regression model (TREG) and their biplots can be used to determine the overall gene expression pattern across treatments (or tissues) and for specific treatments. Dataset 1 had 5,339 genes and the objective was to identify genes with modified expression during maize (Zea mays) seed development in response to different parental ploidy levels. In Dataset 2, the aim was to study gene expression in 15 tissue samples with different levels of development of breast cancer when compared with the expression of the genes in noninfected tissues. The results from the analyses of Dataset 1 showed that the biplots of the AMMI and TREG models allow identification of subsets of genes and treatments with noncrossover G x T interaction or with important levels of crossover G x T. Results from Dataset 2 showed that the TREG model and its biplot facilitates the identification of genes with high expression in all tumor cells. Also, the TREG biplots allowed identification of subsets of genes with a low level of gene x tissue crossover interaction.     

Genotype × environment interaction effects on pod yield and pod number in West African Okra

As year-to-year weather fluctuation increases, the need for better understanding of their effects on crops becomes ever more pressing. Genotype × environment (G × E) interactions for pod yield and pod number were assessed in a set of 25 West African okra genotypes that were cultivated in four successive years (otherwise called environments) through field trials, arranged in a randomized complete block design, with three replicates. Significant G × E interactions in measured traits were detected, suggesting that selection for stable genotypes, with respect to these traits must be environmental specific. Consequently, additive main effects and multiplicative interaction model was applied to dissect G × E interactions. For pod yield, the highest percentage (38.4%) of the treatment sum of square was attributable to genotypes followed by G × E interactions (36.0%) and environment (25.6%), indicating predominance of genotypic variation for this trait. Conversely, prevalence of G × E interactions was observed for pod number. The biplots of the grand mean and IPCA 1 score revealed that the environments tended to discriminate genotypes in dissimilar fashion. Rainfall, relative humidity, wind speed and soil temperature were identified as strong driving forces for development and growth, affecting pod yield. The identified genotypes could be suitable candidates for further study.     

Genotype × environment interactions for wheat grain yield and antioxidant changes in association with drought stress

The phenotypic performance of a genotype is not necessarily the same under diverse agro-ecological conditions. Two commercial wheat cultivars and 33 wheat landrace varieties were selected for screening drought tolerance and the investigation of genotype × environment interactions (GEI). The study site experiences drought stress at reproductive stages. Fully irrigated along with two drought stress trials at early heading (EHS) and 50% heading stages (HDS) were performed in 2 years. The highest antioxidant and proline contents were accumulated under EHS. Reduction in cell membrane stability in EHS was 90.9% in 2011–2012. The lowest grain yield belonged to EHS (3.2 t ha^?1) while the highest (6.8 t ha^?1) was observed in the irrigated trial. GEI analysis indicated that the Pinthus’s coefficient was not an efficient index for screening GEI. Positive correlations were found between GEI parameters such as regression deviation, Wricke’s ecovalence and Shukla’s variance. Regression coefficients over trials ranged from 0.65 to 1.42, indicating genotypes had different responses to environmental changes. Regression models, GEI variances and grain yield showed that some varieties (KC4557, KC4862, KC3891, KC4495, and KC4633) had higher stability under drought stress and fully irrigated conditions and can be involved in breeding programs for drought stress tolerance.     

Characterization of American hazelnut (Corylus americana) accessions and Corylus americana?×?Corylus avellana hybrids using microsatellite markers

The American hazelnut (Corylus americana Marshall) is native to the eastern United States and Southern Canada. In the early decades of the last century, breeding work by several individuals attempted to combine the cold hardiness and disease resistance of the American hazelnut with the larger nut size of the European hazelnut (C. avellana L.). Many hybrid selections grown today trace back to these early efforts. Over the past three decades, representatives of C. americana were collected and are preserved in Corvallis, Oregon. Seeds were collected along roadsides, in hedgerows, in woodland clearings, and in gardens. The seeds were germinated and the best of the resulting seedlings were preserved for later use. In this study, genetic diversity was studied in 87 American and 67 hybrid hazelnut selections using 21 microsatellite loci. The total number of alleles was 266 in the 162 accessions examined, of which 229 were present in C. americana accessions, but only 168 in the Arbor Day Farm hybrids, and 116 in the hybrids of C. americana ‘Rush’. In the American accessions, a high level of genetic diversity was observed (H _e ?=?0.74, H _o ?=?0.68). A genetic similarity matrix of the American and hybrid accessions, and a few European cultivars, was constructed and the resulting dendrogram revealed seven major groups: European cultivars and ‘Rush’ hybrids, two groups of Arbor Day Farm hybrids, three groups of C. americana accessions, and a mixed group of hybrid and American accessions. Analysis confirmed the reported parentage of 10 hybrids. The genetic diversity among the American hazelnut accessions, untapped to date, will be useful in breeding hybrids that will allow expansion of hazelnut production into eastern North America.     

Vegetative Growth,Yield and Leaf Mineral Composition in Strawberry (Fragaria × Ananassa DUCH. CV. Pajaro) as Influenced using Nickel Sulfate and Urea Sprays

In this study, interactions of nickel sulfate and urea sprays on vegetative growth, yield and leaf mineral contents in strawberry were investigated. Rooted Pajaro strawberry plants were potted in 3 liter pots filled with soil, leaf mold and sand (1:1:1, v/v/v). Established plants were foliar sprayed with nickel sulfate at 0, 150, 300 and 450 mg L^?1 and urea 0 and 2 g L^?1 concentrations. Results indicated that nickel (Ni; 300 mg L^?1) plus urea (2 g L^?1) significantly increased the yield and runner numbers. Nickel sulfate at the rate of 300 and 150 mg L^?1and urea (2 g L^?1) significantly increased the crown numbers. The greatest root fresh and dry weights were obtained from untreated plants. Urea at 2 g L^?1 without nickel significantly increased shoot fresh and dry weights. Nickel at 450 mg L^?1 without urea significantly increased Ni concentration in leaves. Overall, nickel sulfate at 150 and 300 mg L^?1 along with urea at 2 g L^?1 were the best treatments.     

Regulation of macro,micro, and toxic element uptake by <Emphasis Type="Italic">Salix</Emphasis> × <Emphasis Type="Italic">smithiana</Emphasis> using liming of heavily contaminated soils

Purpose

Willow cultivation in soils heavily contaminated by risk elements is a challenging issue due to phytotoxic effects that restrict plant growth. Liming reduces the mobility of some risk elements in contaminated soils and therefore can be a suitable measure for contaminated soils but can also affect availability of nutrients for planted willows. We investigate how liming affects concentrations of macro, micro, and toxic elements in the organs of willows planted in contaminated soils.

Materials and methods

We established a 3-year pot experiment with Salix × smithiana planted in weakly acid and alkaline soils anthropogenically seriously contaminated by As, Cd, Pb, and Zn. Soils were both untreated and treated with two doses of lime and dolomite in the first year before planting. We determined biomass production, mortality, and the concentration of macro- and micronutrients and toxic elements in the willows’ aboveground organs.

Results and discussion

Lime application increased biomass production in both soils; dose of lime played an important role for its increase only in alkaline soil. Lime in a higher dose was incompatible with the vitality of just-planted willows in both soils. Doses of dolomite significantly affected the biomass production and mortality of willows, where lower doses caused a permanent decrease of biomass production and mortality in weakly acid soil. The toxicity of Cd and Zn in leaves was recorded in both untreated soils; the latent deficiency of P and deficiency of Fe in leaves was only recorded in weakly acid untreated soil.

Conclusions

Lime application irrespective of dose with foliar Fe application seemed to be the most suitable measure for increasing biomass production and decreasing toxic elements, especially Cd and Zn, without decreasing the macro- and micronutrients in the aboveground organs of willows in weakly acid soil. In alkaline soil, only higher doses of lime had a positive effect on the studied parameters. Dolomite application is not a suitable measure for planting willows in both contaminated soils. Dolomite in a lower dose impairs the growth of willows in weakly acid soil.