BrAPI-an application programming interface for plant breeding applications

Motivation: Modern genomic breeding methods rely heavily on very large amounts of phenotyping and genotyping data, presenting new challenges in effective data management and integration. Recently, the size and complexity of datasets have increased significantly, with the result that data are often stored on multiple systems. As analyses of interest increasingly require aggregation of datasets from diverse sources, data exchange between disparate systems becomes a challenge. Results: To facilitate interoperability among breeding applications, we present the public plant Breeding Application Programming Interface (BrAPI). BrAPI is a standardized web service API specification. The development of BrAPI is a collaborative, community-based initiative involving a growing global community of over a hundred participants representing several dozen institutions and companies. Development of such a standard is recognized as critical to a number of important large breeding system initiatives as a foundational technology. The focus of the first version of the API is on providing services for connecting systems and retrieving basic breeding data including germplasm, study, observation, and marker data. A number of BrAPI-enabled applications, termed BrAPPs, have been written, that take advantage of the emerging support of BrAPI by many databases

Fabrication of cerium-doped LaNiO3 thin films on LaAlO3 (100) substrate by pulsed laser deposition

In this study we report the fabrication of La1-xCexNiO3 (0 <= x <= 0.4) thin films on a LaAlO3 (100) substrate by pulsed laser deposition where the cerium ions are believed to be in the Ce (IV) oxidation state. At low Ce concentrations, the films grow in the (100) direction with a pseudocubic structure and above x similar to 0.3, they exhibit a change in the crystal symmetry. Core-level photoelectron spectroscopic studies of the thin films deposited have shown that the cerium exists in the +4 oxidation state. Correspondingly, the nickel exhibits mixed valency in these thin films. Conductivity of this highly metallic system progressively decreases as more and more Ce is doped. In the range 0.3 < x < 0.4, the system undergoes a transition from metallic to semiconducting behavior. The electrical nature of La1-xCexNiO3 thin films gives clear indications of significant electron-lattice interactions present for compositions close to the transition

Fabrication of cerium-doped LaNiO<SUB>3</SUB> thin films on LaAlO<SUB>3</SUB> (100) substrate by pulsed laser deposition

In this study we report the fabrication of La<SUB>1&#8722;x</SUB>Ce<SUB>x</SUB>NiO<SUB>3</SUB> (0&#8804;x&#8804;0.4) thin films on a LaAlO<SUB>3</SUB> (100) substrate by pulsed laser deposition where the cerium ions are believed to be in the Ce (IV) oxidation state. At low Ce concentrations, the films grow in the (100) direction with a pseudocubic structure and above x~0.3, they exhibit a change in the crystal symmetry. Core-level photoelectron spectroscopic studies of the thin films deposited have shown that the cerium exists in the +4 oxidation state. Correspondingly, the nickel exhibits mixed valency in these thin films. Conductivity of this highly metallic system progressively decreases as more and more Ce is doped. In the range 0.3 &lt; x &lt; 0.4, the system undergoes a transition from metallic to semiconducting behavior. The electrical nature of La<SUB>1&#8722;x</SUB>Ce<SUB>x</SUB>NiO<SUB>3</SUB> thin films gives clear indications of significant electron-lattice interactions present for compositions close to the transition

Investigation of high-k yttrium copper titanate thin films as alternative gate dielectrics

Nearly amorphous high-k yttrium copper titanate thin films deposited by laser ablation were investigated in both metal-oxide-semiconductor (MOS) and metal-insulator-metal (MIM) junctions in order to assess the potentialities of this material as a gate oxide. The trend of dielectric parameters with film deposition shows a wide tunability for the dielectric constant and AC conductivity, with a remarkably high dielectric constant value of up to 95 for the thick films and conductivity as low as 6 x 10(-10) S cm(-1) for the thin films deposited at high oxygen pressure. The AC conductivity analysis points out a decrease in the conductivity, indicating the formation of a blocking interface layer, probably due to partial oxidation of the thin films during cool-down in an oxygen atmosphere. Topography and surface potential characterizations highlight differences in the thin film microstructure as a function of the deposition conditions; these differences seem to affect their electrical properties

Tomato Fruits Show Wide Phenomic Diversity but Fruit Developmental Genes Show Low Genomic Diversity

<div><p>Domestication of tomato has resulted in large diversity in fruit phenotypes. An intensive phenotyping of 127 tomato accessions from 20 countries revealed extensive morphological diversity in fruit traits. The diversity in fruit traits clustered the accessions into nine classes and identified certain promising lines having desirable traits pertaining to total soluble salts (TSS), carotenoids, ripening index, weight and shape. Factor analysis of the morphometric data from Tomato Analyzer showed that the fruit shape is a complex trait shared by several factors. The 100% variance between round and flat fruit shapes was explained by one discriminant function having a canonical correlation of 0.874 by stepwise discriminant analysis. A set of 10 genes (<i>ACS2</i>, <i>COP1</i>, <i>CYC-B</i>, <i>RIN</i>, <i>MSH2</i>, <i>NAC-NOR</i>, <i>PHOT1</i>, <i>PHYA</i>, <i>PHYB</i> and <i>PSY1</i>) involved in various plant developmental processes were screened for SNP polymorphism by EcoTILLING. The genetic diversity in these genes revealed a total of 36 non-synonymous and 18 synonymous changes leading to the identification of 28 haplotypes. The average frequency of polymorphism across the genes was 0.038/Kb. Significant negative Tajima’D statistic in two of the genes, <i>ACS2</i> and <i>PHOT1</i> indicated the presence of rare alleles in low frequency. Our study indicates that while there is low polymorphic diversity in the genes regulating plant development, the population shows wider phenotype diversity. Nonetheless, morphological and genetic diversity of the present collection can be further exploited as potential resources in future.</p></div

Clustering of accessions based on SNP polymorphism.

<p>The tree was made using the Neighbor-Joining method in MEGA4 taking together the sequences of all the genes. Substitutions are represented by branch lengths and the bootstrap value is indicated as numbers above the branches (10000 replicates).</p

Nucleotide polymorphism.

<p>Nucleotide polymorphism.</p

Fruit traits associated with the factors extracted from factor analysis.

<p>Fruit traits associated with the factors extracted from factor analysis.</p