Quick Method to Quantify the Potassium and Sodium Content Variation in Leaves of Banana Varieties.

The current study describes novel and quick methods for the quantification of K+ and Na+ in banana leaves using Horiba Laqua twin ion meters. Foliar K+ and Na+ content measured by ion meter significantly correlated with standard test values by coefficients of 0.83 and 0.46, respectively. About 48 absorbance values associated with potassium concentrations at wave numbers (1581 to 1583 and 3194 to 3410 cm-1) and 15 sodium associated wave numbers (3773 to 3996 cm-1) predicted potassium and sodium content with regression coefficients of 0.999 and 0.588, respectively. K+ and Na+ cations of fresh leaves in seven banana varieties were quantified using ion meters and new information of differences in the foliar potassium and sodium contents was found between banana varieties within the AAB group. The Rasbali (Silk subgroup) variety possessed greater potassium (5413 mg/L) and sodium (188 mg/L) ions than Amti (Mysore subgroup).

Comparative evaluation of linear and nonlinear weather-based models for coconut yield prediction in the west coast of India.

Coconut is a major plantation crop of coastal India. Accurate prediction of its yield is helpful for the farmers, industries and policymakers. Weather has profound impact on coconut fruit setting, and therefore, it greatly affects the yield. Annual coconut yield and monthly weather data for 2000-2015 were compiled for fourteen districts of the west coast of India. Weather indices were generated using monthly cumulative value for rainfall and monthly average value for other parameters like maximum and minimum temperature, relative humidity, wind speed and solar radiation. Different linear models like stepwise multiple linear regression (SMLR), principal component analysis together with SMLR (PCA-SMLR), least absolute shrinkage and selection operator (LASSO) and elastic net (ELNET) with nonlinear models namely artificial neural network (ANN) and PCA-ANN were employed to model the coconut yield using the monthly weather indices as inputs. The model's performance was evaluated using R2, root mean square error (RMSE) and absolute percentage error (APE). The R2 and RMSE of the models ranged between 0.45-0.99 and 18-3624 nuts ha-1 respectively during calibration while during validation the APE varied between 0.12 and 58.21. The overall average ranking of the models based these performance statistics were in the order of ELNET > LASSO > ANN > SMLR > PCA-SMLR > PCA-ANN. Results indicated that the ELNET model could be used for prediction of coconut yield for the region.

Tools, resources and databases for SNPs and indels in sequences: a review.

Single Nucleotide Polymorphism (SNP) is a mutation where, a single base in the DNA differs from the usual base at that position. SNPs are the marker of choice in genetic analysis and also useful in locating genes associated with diseases. SNPs are important and frequently occurring point mutations in genomes and have many practical implications. In silico methods are easy to study the SNPs that are occurring in known genomes or sequences of a species of interest during the post genomic era. There are many on-line and stand alone tools to analyse the SNPs. We intend to guide the reader with the software details such as algorithmic background, file requirements, operating system specificity and species specificity, if any, for the tools of SNPs detection in plants and animals. We also list many databases and resources available today to describe SNPs in wide range of organisms.

In Silico RAPD Priming Sites in Expressed Sequences and iSCAR Markers for Oil Palm.

RAPD is a simple dominant marker system widely used in biology. Effectiveness of RAPD can be improved by selecting and redesigning primers whose priming sites occur in target sequence(s) of gene or organism at optimum distance. We developed software that uses sequences of random decamer primers and nucleotide sequence(s) as two input files. It locates the priming sites in input sequences and generates output files listing frequency and distance between priming sites. When the priming sites of a single primer occur more than once in a sequence with a distance of 200 to 2000 bp, the software also designs pairs of iSCAR primers. An input of 387 RAPD primers and 42,432 expressed sequences of oil palm are used as test. Wet-lab PCR results from a publication that used the same set of primers were compared with software output on priming sites. In the test sequences of oil palm covering 1.4% of genome, we found that at least 60% the primers chosen using software are sure of giving PCR amplification. We designed 641 iSCAR primers suitable for amplification of oil palm DNA. The software successfully predicted 92% (67 out of 73) of published polymorphic RAPD primers in oil palm.

Mining of expressed sequence tag libraries of cacao for microsatellite markers using five computational tools.

Expressed sequence tags (ESTs) provide researchers with a quick and inexpensive route for discovering new genes, data on gene expression and regulation, and also provide genic markers that help in constructing genome maps. Cacao is an important perennial crop of humid tropics. Cacao EST sequences, as available in the public domain, were downloaded and made into contigs. Microsatellites were located in these ESTs and contigs using five softwares (MISA, TRA, TROLL, SSRIT and SSR primer). MISA gave maximum coverage of SSRs in cacao ESTs and contigs, although TRA was able to detect higher order (5-mer) repeats. The frequency of SSRs was one per 26.9 kb in the known set of ESTs. One-third of the repeats in EST-contigs were found to be trimeric. A few rare repeats like 21-mer repeat were also located. A/T repeats were most abundant among the mononucleotide repeats and the AG/GA/TC/CT type was the most frequent among dimerics. Flanking primers were designed using Primer3 program and verified experimentally for PCR amplification. The results of the study are made available freely online database (http://riju.byethost31.com/cocoa/). Seven primer pairs amplified genomic DNA isolated from leaves were used to screen a representative set of 12 accessions of cacao.

Mining for single nucleotide polymorphisms and insertions / deletions in expressed sequence tag libraries of oil palm.

The oil palm is a tropical oil bearing tree. Recently EST-derived SNPs and SSRs are a free by-product of the currently expanding EST (Expressed Sequence Tag) data bases. The development of high-throughput methods for the detection of SNPs (Single Nucleotide Polymorphism) and small indels (insertion / deletion) has led to a revolution in their use as molecular markers. Available (5452) Oil palm EST sequences were mined from dbEST of NCBI. CAP3 program was used to assemble EST sequences into contigs. Candidate SNPs and Indel polymorphisms were detected using the perl script auto_snip version 1.0 which has used 576 ESTs for detecting SNPs and Indel sites. We found 1180 SNP sites and 137 indel polymorphisms with frequency 1.36 SNPs / 100 bp. Among the six tissues from which the EST libraries had been generated, mesocarp had high frequency of 2.91 SNPs and indels per 100 bp whereas the zygotic embryos had lowest frequency of 0.15 per 100 bp. We also used the Shannon index to analyze the proportion of ten possible types of SNP/indels. ESTs from tissues of normal apex showed highest values of Shannon index (0.60) whereas abnormal apex had least value (0.02). The present report deals the use of Shannon index for comparing SNP/ indel frequencies mined from ESTlibraries and also confirm that the frequency of SNP occurrence in oil palm to use them as markers for genetic studies.