Rosales sister to Fabales: towards resolving the rosid puzzle.
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Databases, Nucleic Acid↗
Biomedical subjects
Paramjit Khurana
Publications and source records attributed to Paramjit Khurana.
An early auxin-responsive Aux/IAA gene from wheat (Triticum aestivum) is induced by epibrassinolide and differentially regulated by light and calcium.
The plant hormone auxin plays a central role in regulating many aspects of plant growth and development. This largely occurs as a consequence of changes in gene expression. The Aux/IAA genes are best characterized among the early auxin-responsive genes, which encode short-lived transcriptional repressors. In most plants examined, including Arabidopsis, soybean, and rice, the Aux/IAA genes constitute a large gene family. By screening the available databases, at least 15 expressed sequence tags (ESTs) have been identified from wheat (Triticum aestivum), which exhibit high sequence identity with Aux/IAA homologues in other species. One of these Aux/IAA genes, TaIAA1, harbouring all the four conserved domains characteristic of the Aux/IAA proteins, has been characterized in detail. The expression of TaIAA1 is light-sensitive, tissue-specific, and is induced within 15-30 min of exogenous auxin application. Also, the TaIAA1 transcript levels increase in the presence of a divalent cation, Ca(2+), and this effect is reversed by the calcium-chelating agent, EGTA. The TaIAA1 gene qualifies as the primary response gene because an increase in its transcript levels by auxin is unaffected by cycloheximide. In addition to auxin, the TaIAA1 gene is also induced by brassinosteroid, providing evidence that interplay between hormones is crucial for the regulation of plant growth and development.
Blotting, Southern↗
Decoding the rice genome.
Rice cultivation is one of the most important agricultural activities on earth, with nearly 90% of it being produced in Asia. It belongs to the family of crops that includes wheat, maize and barley, and it supplies more than 50% of calories consumed by the world population. Its immense economic value and a relatively small genome size makes it a focal point for scientific investigations, so much so that four whole genome sequence drafts with varying qualities have been generated by both public and privately funded ventures. The availability of a complete and high-quality map-based sequence has provided the opportunity to study genome organization and evolution. Most importantly, the order and identity of 37,544 genes of rice have been unraveled. The sequence provides the required ingredients for functional genomics and molecular breeding programs aimed at unraveling intricate cellular processes and improving rice productivity.
Animals↗
Assessment of nematode resistance in wheat transgenic plants expressing potato proteinase inhibitor (PIN2) gene.
Serine proteinase inhibitors (IP's) are proteins found naturally in a wide range of plants with a significant role in the natural defense system of plants against herbivores. The question addressed in the present study involves assessing the ability of the serine proteinase inhibitor in combating nematode infestation. The present study involves engineering a plant serine proteinase inhibitor (pin2) gene into T. durum PDW215 by Agrobacterium-mediated transformation to combat cereal cyst nematode (Heterodera avenae) infestation. Putative T(0) transformants were screened and positive segregating lines analysed further for the study of the stable integration, expression and segregation of the genes. PCR, Southern analysis along with bar gene expression studies corroborate the stable integration pattern of the respective genes. The transformation efficiency is 3%, while the frequency of escapes was 35.71%. chi(2) analysis reveals the stable integration and segregation of the genes in both the T(1) and T(2) progeny lines. The PIN2 systemic expression confers satisfactory nematode resistance. The correlation analysis suggests that at p < 0.05 level of significance the relative proteinase inhibitor (PI) values show a direct positive correlation vis-à-vis plant height, plant seed weight and also the seed number.
Animals↗
Effect of water stress and heavy metals on induction of somatic embryogenesis in wheat leaf base cultures.
In vitro cultures of plant tissues are known to mimic the response of field-grown plants when subjected to stress treatments. This investigation on Triticum aestivum explores the effect of drought stress on somatic embryogenesis and endogenous proline content. Leaf bases were cultured on MS medium supplemented with 2,4-D (10 microM) and different concentrations of PEG (2.5, 5, 7.5%) or mannitol (0.25 and 0.5 M) and also subjected to different periods of aerial drying in the laminar flow for one-day and subsequently transferred to MS basal medium. PEG treatment induced a high percentage (up to 50%) of embryoid formation. However, with mannitol and aerial drying, percentage of embryoid formation decreased with increasing concentrations and duration. After ten days, the endogenous proline content of explants treated with different concentrations of PEG, mannitol and different durations of aerial drying increased with increasing concentration and increasing duration of the treatment, thus, corroborating the role of proline as an osmolyte during stress conditions. Similarly, addition of metals such as cadmium and cobalt caused a reduction in percentage explants depicting embryogenesis. However, when cadmium was employed alone, 22% explants displayed somatic embryogenesis as compared to 54% in 2,4-D treated cultures.
Adaptation, Physiological↗
Sequence analysis of the long arm of rice chromosome 11 for rice-wheat synteny.
The DNA sequence of 106 BAC/PAC clones in the minimum tiling path (MTP) of the long arm of rice chromosome 11, between map positions 57.3 and 116.2 cM, has been assembled to phase 2 or PLN level. This region has been sequenced to 10x redundancy by the Indian Initiative for Rice Genome Sequencing (IIRGS) and is now publicly available in GenBank. The region, excluding overlaps, has been predicted to contain 2,932 genes using different software. A gene-by-gene BLASTN search of the NCBI wheat EST database of over 420,000 cDNA sequences revealed that 1,143 of the predicted rice genes (38.9%) have significant homology to wheat ESTs (bit score >/= 100). Further BLASTN search of these 1,143 rice genes with the GrainGenes database of sequence contigs containing bin-mapped wheat ESTs allowed 113 of the genes to be placed in bins located on wheat chromosomes of different homoeologous groups. The largest number of genes, about one-third, mapped to the homoeologous group 4 chromosomes of wheat, suggesting a common evolutionary origin. The remaining genes were located on wheat chromosomes of different groups with significantly higher numbers for groups 3 and 5. Location of bin-mapped wheat contigs to chromosomes of all the seven homoeologous groups can be ascribed to movement of genes (transpositions) or chromosome segments (translocations) within rice or the hexaploid wheat genomes. Alternatively, it could be due to ancient duplications in the common ancestral genome of wheat and rice followed by selective elimination of genes in the wheat and rice genomes. While there exists definite conservation of gene sequences and the ancestral chromosomal identity between rice and wheat, there is no obvious conservation of the gene order at this level of resolution. Lack of extensive colinearity between rice and wheat genomes suggests that there have been many insertions, deletions, duplications and translocations that make the synteny comparisons much more complicated than earlier thought. However, enhanced resolution of comparative sequence analysis may reveal smaller conserved regions of colinearity, which will facilitate selection of markers for saturation mapping and sequencing of the gene-rich regions of the wheat genome.
Base Sequence↗
Structural and functional analysis of rice genome.
Rice is an excellent system for plant genomics as it represents a modest size genome of 430 Mb. It feeds more than half the population of the world. Draft sequences of the rice genome, derived by whole-genome shotgun approach at relatively low coverage (4-6 X), were published and the International Rice Genome Sequencing Project (IRGSP) declared high quality (>10 X), genetically anchored, phase 2 level sequence in 2002. In addition, phase 3 level finished sequence of chromosomes 1, 4 and 10 (out of 12 chromosomes of rice) has already been reported by scientists from IRGSP consortium. Various estimates of genes in rice place the number at >50,000. Already, over 28,000 full-length cDNAs have been sequenced, most of which map to genetically anchored genome sequence. Such information is very useful in revealing novel features of macro- and micro-level synteny of rice genome with other cereals. Microarray analysis is unraveling the identity of rice genes expressing in temporal and spatial manner and should help target candidate genes useful for improving traits of agronomic importance. Simultaneously, functional analysis of rice genome has been initiated by marker-based characterization of useful genes and employing functional knock-outs created by mutation or gene tagging. Integration of this enormous information is expected to catalyze tremendous activity on basic and applied aspects of rice genomics.
Chromosomes, Plant↗
Genetic transformation of Indian bread (T. aestivum) and pasta (T. durum) wheat by particle bombardment of mature embryo-derived calli.
BACKGROUND: Particle bombardment has been successfully employed for obtaining transgenics in cereals in general and wheat in particular. Most of these procedures employ immature embryos which are not available throughout the year. The present investigation utilizes mature seeds as the starting material and the calli raised from the hexaploid Triticum aestivum and tetraploid Triticum durum display a high regeneration response and were therefore used as the target tissue for genetic transformation by the biolistic approach. RESULTS: Mature embryo-derived calli of bread wheat (Triticum aestivum, cv. CPAN1676) and durum wheat (T. durum, cv. PDW215) were double bombarded with 1.1 gold microprojectiles coated with pDM302 and pAct1-F at a target distance of 6 cm. Southern analysis using the bar gene as a probe revealed the integration of transgenes in the T0 transformants. The bar gene was active in both T0 and T1 generations as evidenced by phosphinothricin leaf paint assay. Approximately 30% and 33% primary transformants of T. aestivum and T. durum, respectively, were fertile. The transmission of bar gene to T1 progeny was demonstrated by PCR analysis of germinated seedlings with primers specific to the bar gene. CONCLUSIONS: The transformation frequency obtained was 8.56% with T. aestivum and 10% with T. durum. The optimized protocol was subsequently used for the introduction of the barley gene encoding a late embryogenesis abundant protein (HVA1) in T. aestivum and T. durum. The presence of the HVA1 transgene was confirmed by Southern analysis in the T0 generation in case of Triticum aestivum, and T0 and T1 generation in Triticum durum.
Acetyltransferases↗
Evaluation of parameters for high efficiency gene transfer via particle bombardment in Indian mulberry.
Particle bombardment is a popular method of direct gene delivery into cell, tissue and organs since it requires minimum pre- and post-bombardment manipulation. In addition, this technique is much easier and fast to perform with intact tissue/organ and reduces the period of in vitro culture. Genetic transformation of mulberry, Morus indica cv. K2 was attempted by particle bombardment using hypocotyl, cotyledon, leaf and leaf callus explants. The effect of various physical and biological parameters during bombardment were studied by the histochemical localization of GUS reporter gene following two days of bombardment and by assessing the number of blue spots per explant. p35SGUSINT was used for optimization of different parameters. The percentage of GUS positive explants was very low with tungsten (20%) as compared to gold particles (36%) indicating tungsten toxicity to the tissue. Maximum GUS activity was observed at 1100 psi helium pressure and 9 cm target distance for hypocotyl, cotyledon and leaf. Double bombardment of explants with 10 microg of DNA loaded on macrocarriers clearly yielded a better (up to 56%) result as compared to a single bombardment (30%). Amongst the various plasmids tested, pBI221 gave the highest (100%) GUS positive explants in the leaf callus.
Biolistics↗
Regeneration from mature and immature embryos and transient gene expression via Agrobacterium-mediated transformation in emmer wheat (Triticum dicoccum Schuble).
The present study establishes a regeneration protocol and optimizes conditions for Agrobacterium-mediated transformation of the tetraploid emmer wheat, Triticum dicoccum. Regeneration from mature and immature embryos was accomplished as a two-step process involving callus induction in the presence of 2,4-D followed by regeneration on a 2,4-D free, cytokinin-containing medium (RM1). Higher concentrations of 2,4-D (4 mg/l) though conducive for callusing (89.39% in mature embryos and 96% in immature embryos) proved detrimental for further regeneration. At lower 2,4-D (1 mg/ml) although callusing was suboptimal, (56.8% and 84% from mature and immature embryos, respectively) the regeneration response was the highest on RM1 medium (64.4% and 56.6% from mature and immature embryos, respectively). Overall, the regeneration response of immature embryos was lower than the mature embryos by 10-12%. Due to the ease of availability of mature embryos the mature embryo-derived calli were chosen as the target tissue for Agrobacterium-mediated transformation in the two Indian varieties DDK1001 and DDK1009. Histochemical GUS expression revealed the suitability of the mature embryo-derived calli for such investigations. Of the CaMV35S and Act1 promoters employed, the monocot promoter Act1 displayed higher GUS gene activity in the mature embryo derived calli when co-cultivated with LBA4404 (pBI101::Act1).
2,4-Dichlorophenoxyacetic Acid↗