In silico analysis of carotenoid biosynthesis pathway in cassava (Manihot esculenta Crantz).

The apocarotenoids play a vital role in plant growth and development process, especially strigolactones, which can induce rooting and help in the interaction with symbiotic microbes in plants. They also act as colorants, antioxidants, hormones, signalling components, scent/aroma constituents and chromophores. In silico approaches are valuable in reducing the complexity regarding gene networks in plants that help to develop new biotechnological and bioinformatics tactics in crop improvement programmes. An in silico comparative genomic analysis of the key enzymes encoding genes involved in apocarotenoid biosynthesis in cassava was carried out using template plants such as arabidopsis, tomato, potato and sweet potato. Forty carotenoid genes were identified, and the nucleotide sequences were subjected to various regulatory sequence analyses such as transcription factor prediction, CpG island analysis, microRNA regulatory analysis and promotor sequence analysis. The corresponding protein sequences were subjected to domain/motif analysis and phylogenetic analysis. The expression profile of apocarotenoid genes in cassava were generated and subcellular localization prediction was done to identify the distribution of the proteins. The results indicated that the apocarotenoid protein domains were conserved in template plants and cassava. Eighteen transcription factors like MYB, BBR-BPC, bHLH and NAC were associated with the identified carotenoid genes in cassava. The apocarotenoid genes were found to be expressed in all the major parts of the plants. These genes were distributed in 17 of 18 cassava chromosomes and the third one contained maximum number of genes. MiRNA regulatory analysis identified three microRNAs, namely miR159a, miR171b and miR396a which were significantly associated with carotenoid biosynthesis in cassava and the pathway was reconstructed by incorporating the above information. A better understanding of the genes and pathway associated with carotenoid biosynthesis in cassava would be helpful in the breeding programme to develop improved carotenoid rich varieties.

Association mapping of drought tolerance and agronomic traits in rice (Oryza sativa L.) landraces.

BACKGROUND: Asian cultivars were predominantly represented in global rice panel selected for sequencing and to identify novel alleles for drought tolerance. Diverse genetic resources adapted to Indian subcontinent were not represented much in spite harboring useful alleles that could improve agronomic traits, stress resilience and productivity. These rice accessions are valuable genetic resource in developing rice varieties suited to different rice ecosystem that experiences varying drought stress level, and at different crop stages. A core collection of rice germplasm adapted to Southwestern Indian peninsular genotyped using SSR markers and characterized by contrasting water regimes to associate genomic regions for physiological, root traits and yield related traits. Genotyping-By-Sequencing of selected accessions within the diverse panel revealed haplotype variation in genic content within genomic regions mapped for physiological, morphological and root traits. RESULTS: Diverse rice panel (99 accessions) were evaluated in field and measurements on plant physiological, root traits and yield related traits were made over five different seasons experiencing varying drought stress intensity at different crop stages. Traits like chlorophyll stability index, leaf rolling, days to 50% flowering, chlorophyll content, root volume and root biomass were identified as best predictors of grain yield under stress. Association mapping revealed genetic variation among accessions and revealed 14 genomic targets associated with different physiological, root and plant production traits. Certain accessions were found to have beneficial allele to improve traits, plant height, root length and spikelet fertility, that contribute to the grain yield under stress. Genomic characterization of eleven accessions revealed haplotype variation within key genomic targets on chromosomes 1, 4, 6 and 11 for potential use as molecular markers to combine drought avoidance and tolerance traits. Genes mined within the genomic QTL intervals identified were prioritized based on tissue specific expression level in publicly available rice transcriptome data. CONCLUSION: The genetic and genomic resources identified will enable combining traits with agronomic value to optimize yield under stress and hasten trait introgression into elite cultivars. Alleles associated with plant height, specific leaf area, root length from PTB8 and spikelet fertility and grain weight from PTB26 can be harnessed in future rice breeding program.

Comparative Study on the Chemical Structure and In Vitro Antiproliferative Activity of Anthocyanins in Purple Root Tubers and Leaves of Sweet Potato ( Ipomoea batatas).

The structure and in vitro antiproliferative activity of anthocyanins in the root tubers of a sweet potato variety cv. Bhu Krishna and the purple leaves of a promising accession S-1467 were studied with the objectives of understanding the structure-activity relationship and comparing the leaf and tuber anthocyanins. The chemical structure of anthocyanins was determined by high-resolution electrospray ionization mass spectrometry analysis. A fluorescence-resonance-energy-transfer-based caspase sensor probe had been used to study the antiproliferative property, and analysis of the cell cycle was performed after staining with propidium iodide and subsequent fluorescence-activated cell sorting. Structurally, the anthocyanins in root tubers were identical to those in leaves, but there was a difference in the proportion of various aglycones present in both. This has led to distinguishable differences in the antiproliferative activity of leaf and tuber anthocyanins to various cancer cells. All nine anthocyanins were found in acylated forms in both tubers and leaves. However, peonidin derivatives were major anthocyanins in tubers (33.98 ± 1.41 mg) as well as leaves (27.68 ± 1.07 mg). The cyanidin derivatives were comparatively higher in leaves (20.55 ± 0.91 mg) than tubers (9.44 ± 0.94 mg). The tuber and leaf anthocyanins exhibited potential antiproliferative properties to MCF-7, HCT-116, and HeLa cancer cells, and the structure of anthocyanins had a critical role in it. The leaf anthocyanins exhibited significantly higher activity against colon and cervical cancer cells, whereas tuber anthocyanins had a slightly greater effect against breast cancer cells.

Optimization of chitosan nanoparticle synthesis and its potential application as germination elicitor of Oryza sativa L.

The worldwide rice production has been dwindling due to biotic and abiotic causes. Chitosan is a proven biofunctional material that induces many biological responses in plants. However, the growth and yield increasing properties of chitosan nanoparticles (ChNP) on rice crop are not well understood. In the present work, effect of ChNP on germination of rice has been studied. Seed toxicity of ChNP was also analyzed to ensure the safety of ChNP application. The toxicity study was done according to EPA guidelines and ChNP was found to be non-toxic. Rice seeds were treated with ChNP at different concentrations for different time periods and kept for germination. Upon complete germination, the seedlings were sown in seed trays and growth was evaluated at 21 days after sowing. All treatments showed better results than the untreated control. Treatment T22 (1 mg/ml ChNP for 120 mins) gave the highest growth rates. Therefore we could deduce that ability of ChNP to elicit growth was associated with the concentration of ChNP and soaking time. The shelf life of ChNP was studied over a period of one year by analyzing the germination eliciting capacity on rice seeds. ChNP was found to effective for seven months when stored under room temperature.

Effect of chemical modification with citric acid on the physicochemical properties and resistant starch formation in different starches.

Potato, cassava, sweet potato, banana and lentil starches were modified with citric acid (CA) with the main objective of enhancing the resistant starch (RS) and slowly digestible starch (SDS) fractions and to compare starches of diverse botanical origins. The percentage CA substitution of modified starches ranged from 3.84 to 15.06 and showed similar type of XRD patterns, but with variation in intensity and percentage crystallinity. The peaks around 1705 cm-1 and 1150 cm-1 in FT-IR spectra of modified starches confirmed the presence of CA group. Scanning electron microscopy confirmed that there were no noticeable changes in granular structure and morphology. No peaks could be observed in RVA pasting profiles of modified starches, confirming cross-linking reaction. The SDS and RS were significantly higher in modified starches of all origins and consequently there was a lower estimated glyceamic index (EGI). Modified starches were associated with lower setback viscosity indicating their lower temperature stability.

Correlated mutations via regularized multinomial regression.

BACKGROUND: In addition to sequence conservation, protein multiple sequence alignments contain evolutionary signal in the form of correlated variation among amino acid positions. This signal indicates positions in the sequence that influence each other, and can be applied for the prediction of intra- or intermolecular contacts. Although various approaches exist for the detection of such correlated mutations, in general these methods utilize only pairwise correlations. Hence, they tend to conflate direct and indirect dependencies. RESULTS: We propose RMRCM, a method for Regularized Multinomial Regression in order to obtain Correlated Mutations from protein multiple sequence alignments. Importantly, our method is not restricted to pairwise (column-column) comparisons only, but takes into account the network nature of relationships between protein residues in order to predict residue-residue contacts. The use of regularization ensures that the number of predicted links between columns in the multiple sequence alignment remains limited, preventing overprediction. Using simulated datasets we analyzed the performance of our approach in predicting residue-residue contacts, and studied how it is influenced by various types of noise. For various biological datasets, validation with protein structure data indicates a good performance of the proposed algorithm for the prediction of residue-residue contacts, in comparison to previous results. RMRCM can also be applied to predict interactions (in addition to only predicting interaction sites or contact sites), as demonstrated by predicting PDZ-peptide interactions. CONCLUSIONS: A novel method is presented, which uses regularized multinomial regression in order to obtain correlated mutations from protein multiple sequence alignments. AVAILABILITY: R-code of our implementation is available via http://www.ab.wur.nl/rmrcm.

Short-duration cassava genotypes for crop diversification in the humid tropics: growth dynamics, biomass, yield and quality.

BACKGROUND: Short-duration (6-7 months) cassava provides opportunities to smallholder farmers for effective utilisation of resources such as land, moisture and nutrients as well as diversification of enterprise and income. The variation in biomass production and partitioning, seasonal course of growth indices, yield, quality and nutrient uptake of ten short-duration/early-bulking genotypes of cassava and their impact on nutrient contents in soil in a lowland situation akin to rice fallow were examined in this study. RESULTS: Triploid 2-18 gave the highest yield (38.34 t ha(-1)), followed by triploid 4-2, Sree Vijaya, Sree Jaya and Vellayani Hraswa, which were on a par (30-32 t ha(-1)). Vellayani Hraswa, Sree Vijaya and triploid 4-2 had significantly higher tuberous root dry matter content (370-380 mg g(-1)) and fairly higher starch content (270-280 mg g(-1)). All genotypes except triploid 4-2, triploid 2-18 and H-165 had low cyanogen content (29.2-43.8 microg g(-1)), well within the tolerable limit. Tuberous root dry matter and total dry matter production, crop growth rate, tuberous root bulking rate and harvest index at the last phase, number of tuberous roots, mean weight of tuberous roots and nutrient uptake showed significant positive correlations with tuberous root yield. Principal component analysis also showed a similar trend. CONCLUSION: The diploids Sree Vijaya, Sree Jaya, Vellayani Hraswa and Kalpaka are ideal for cultivation in rice fallow for food use owing to their high yield, good cooking quality and low cyanogen content. The triploids are better suited for industrial use owing to their high tuberous root dry biomass production.