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Saminathan T.,West Virginia State University | Bodunrin A.,West Virginia State University | Singh N.V.,National Research Center on Pomegranate | Devarajan R.,ICAR Indian Institute of Oil Palm Research | And 4 more authors.
BMC Plant Biology | Year: 2016

Background: MicroRNAs (miRNAs), a class of small non-coding endogenous RNAs that regulate gene expression post-transcriptionally, play multiple key roles in plant growth and development and in biotic and abiotic stress response. Knowledge and roles of miRNAs in pomegranate fruit development have not been explored. Results: Pomegranate, which accumulates a large amount of anthocyanins in skin and arils, is valuable to human health, mainly because of its antioxidant properties. In this study, we developed a small RNA library from pooled RNA samples from young seedlings to mature fruits and identified both conserved and pomegranate-specific miRNA from 29,948,480 high-quality reads. For the pool of 15- to 30-nt small RNAs, ~50 % were 24 nt. The miR157 family was the most abundant, followed by miR156, miR166, and miR168, with variants within each family. The base bias at the first position from the 5' end had a strong preference for U for most 18- to 26-nt sRNAs but a preference for A for 18-nt sRNAs. In addition, for all 24-nt sRNAs, the nucleotide U was preferred (97 %) in the first position. Stem-loop RT-qPCR was used to validate the expression of the predominant miRNAs and novel miRNAs in leaves, male and female flowers, and multiple fruit developmental stages; miR156, miR156a, miR159a, miR159b, and miR319b were upregulated during the later stages of fruit development. Higher expression of miR156 in later fruit developmental may positively regulate anthocyanin biosynthesis by reducing SPL transcription factor. Novel miRNAs showed variation in expression among different tissues. These novel miRNAs targeted different transcription factors and hormone related regulators. Gene ontology and KEGG pathway analyses revealed predominant metabolic processes and catalytic activities, important for fruit development. In addition, KEGG pathway analyses revealed the involvement of miRNAs in ascorbate and linolenic acid, starch and sucrose metabolism; RNA transport; plant hormone signaling pathways; and circadian clock. Conclusion: Our first and preliminary report of miRNAs will provide information on the synthesis of biochemical compounds of pomegranate for future research. The functions of the targets of the novel miRNAs need further investigation. © 2016 The Author(s). Source

Singh N.V.,National Research Center on Pomegranate | Abburi V.L.,West Virginia State University | Ramajayam D.,ICAR Indian Institute of Oil Palm Research | Kumar R.,Icar Sugarcane Breeding Institutes Regional Center | And 11 more authors.
Molecular Genetics and Genomics | Year: 2015

This genetic diversity study aimed to estimate the population structure and explore the use of association mapping strategies to identify linked markers for bacterial resistance, growth and fruit quality in pomegranate collections from India. In total, 88 accessions including 37 cultivated types were investigated. A total of 112 alleles were amplified by use of 44 publicly available microsatellites for estimating molecular genetic diversity and population structure. Neighbor-joining analysis, model-based population structure and principal component analysis corroborated the genetic relationships among wild-type and cultivated pomegranate collections from India. Our study placed all 88 germplasm into four clusters. We identified a cultivated clade of pomegranates in close proximity to Daru types of wild-type pomegranates that grow naturally near the foothills of the Himalayas. Admixture analysis sorted various lineages of cultivated pomegranates to their respective ancestral forms. We identified four linked markers for fruit weight, titratable acidity and bacterial blight severity. PGCT001 was found associated with both fruit weight and bacterial blight, and the association with fruit weight during both seasons analyzed was significant after Bonferroni correction. This research demonstrates effectiveness of microsatellites to resolve population structure among the wild and cultivar collection of pomegranates and future use for association mapping studies. © 2015, Springer-Verlag Berlin Heidelberg. Source

Sunil Kumar K.,ICAR Indian Institute of Oil Palm Research | Mathur R.K.,ICAR Indian Institute of Oil Palm Research | Sparjanbabu D.S.,ICAR Indian Institute of Oil Palm Research
Indian Journal of Agricultural Research | Year: 2015

The oil palm is the richest source of vegetable oil in the world. The hybrid nature of crop necessitates artificial hybridization between proven parent palms which in turn require the pollen from male parent to be collected and stored without loss of viability for sufficiently long period. Reports suggested that pollen grains of various taxa could be successfully preserved in different organic solvents. In the present study, attempt was made to evaluate the suitability of organic solvents to store the oil palm pollen at 0 to -5°C temperature. Among the five solvents used, there was significant variation for viability and germination percentages. Viability was the maximum for pollen stored in Diethyl ether (90.45 %) as well as in n-Hexane (88.41%) after 200 days of storage. Viability of pollen stored in Chloroform and Acetone were moderate and in case of Methyl alcohol, complete loss of viability was observed. With respect to pollen germination in vitro, similar trend was observed. The trend was same at different intervals/period of storage. This was confirmed through in vivo pollination and fruits set studies. Thus, present method indicated that it is feasible to store oil palm pollen in non polar solvents beyond 200 days without considerable loss of viability or germination. Source

Murugesan P.,ICAR Indian Institute of Oil Palm Research | Ravichandran G.,ICAR Indian Institute of Oil Palm Research | Shareef M.,ICAR Indian Institute of Oil Palm Research
Indian Journal of Agricultural Sciences | Year: 2015

Seed dormancy in oil palm (Elaeis guineensis Jacq.) is considered as one of the major causes for low and erratic germination. Oil palm hybrid seeds (dura × pisifera) were subjected to heat treatment for 0, 10, 20, 30, 40, 50, 60, 70, 80 and 90 days in a heating room at 39 + 1°C and germination response, ultrastructural changes in embryo, endosperm and operculum structures were observed. The results revealed that seed heating for 50, 60 and 70 days and incubation in germination room (25 to 27 °C) resulted in germination of 90.4, 93.6 and 94.8%, respectively. Heating of seeds for 0, 10 and 20 days had no effect on germination. Structural changes of dormant and germinating seeds were investigated through microtome sectioning and Scanning Electron Microscope (SEM). Endosperm above the embryo is demarcated by several layers of small cells. During the break of seed dormancy, endosperm cleaves in the micropylar region through the small cells. Enlargement of embryo facilitates the dislocation of the operculum during the germination. It is confirmed that heat treatment for 60 to 70 days to be optimum for obtaining maximum oil palm seed germination. Nevertheless, heating oil palm seeds at 50°C is recommended for maximum germination in a short time. Source

Behera S.K.,ICAR Indian Institute of Oil Palm Research | Suresh K.,ICAR Indian Institute of Oil Palm Research | Narsimha Rao B.,ICAR Indian Institute of Oil Palm Research | Mathur R.K.,ICAR Indian Institute of Oil Palm Research | And 5 more authors.
Solid Earth | Year: 2016

Mapping spatial variability of soil properties is the key to efficient soil resource management for sustainable crop yield. Therefore, the present study was conducted to assess the spatial variability of soil properties such as acidity (pH), salinity (electrical conductivity (EC)), organic carbon, available K, available P, exchangeable Ca2+, exchangeable Mg2+, available S and hot water soluble B in surface (0-20cm) and subsurface (20-40cm) soil layers of oil palm plantations in south Goa district of Goa located in west coastal area of India. A total of 128 soil samples were collected from 64 oil palm plantations of Goa located at an approximate interval of 1-2km and analyzed. Soil was acidic to neutral in reaction. Other soil properties varied widely in both the soil layers. Correlations between soil pH and exchangeable Ca2+, between soil EC and available K, between available P and available S and between exchangeable Ca2+ and exchangeable Mg2+ in both the soil layers were found to be positive and significant (P < 0.01). Geostatistical analysis revealed a varied spatial distribution pattern for the measured soil properties. Best-fit models for measured soil properties were exponential, Gaussian, stable, K-Bessel and spherical with moderate to strong spatial dependency. The results revealed that site-specific fertilizer management options needed to be adopted in the oil palm plantations of the study area owing to variability in soil properties. © 2016 Author(s). Source

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