Prashant Kale - Academia.edu (original) (raw)

Papers by Prashant Kale

List of 193 SSR loci by e-PCR. (XLSX 24 kb)

List of identified SSR and three sets of designed three sets of primers. (XLSX 5310 kb)

Blast results of identified transcriptional factors found in DEGs. (XLSX 599 kb)

Variants identified from soybean samples against reference genome of Glycine max and also annotat... more Variants identified from soybean samples against reference genome of Glycine max and also annotation of variants. (XLSX 31287 kb)

Pathways identified in differential expressed genes of soybean. (XLSX 55 kb)

BIOINFOLET - A Quarterly Journal of Life Sciences, 2013

Fruit and stem samples of brinjal (egg plant), infected with Phomopsis vexans were collected from... more Fruit and stem samples of brinjal (egg plant), infected with Phomopsis vexans were collected from six different locations of Vidharbha region of Maharashtra state and their virulence level were analyzed In vitro by pin prick method. Amongst all isolates, the cultures from Kinhi and Wardha were found more virulent. All isolates showed similar morphological growth pattern on synthetic growth media. However, variation was observed among them when evaluated for virulence test and RAPD (Random Amplified Polymorphic DNA) studies.

Rice (New York, N.Y.), 2017

Increased water and labour scarcity in major rice growing areas warrants a shift towards direct s... more Increased water and labour scarcity in major rice growing areas warrants a shift towards direct seeded rice cultivation under which management of weeds is a major issue. Use of broad spectrum non-selective herbicides is an efficient means to manage weeds. Availability of rice genotypes with complete tolerance against broad-spectrum non-selective herbicides is a pre-requisite for advocating use of such herbicides. In the present study, we developed an EMS induced rice mutant, 'HTM-N22', exhibiting tolerance to a broad spectrum herbicide, 'Imazethapyr', and identified the mutations imparting tolerance to the herbicide. We identified a stable and true breeding rice mutant, HTM-N22 (HTM), tolerant to herbicide, Imazethapyr, from an EMS-mutagenized population of approximately 100,000 M2 plants of an upland rice variety, Nagina 22 (N22). Analysis of inheritance of herbicide tolerance in a cross between Pusa 1656-10-61/HTM showed that this trait is governed by a single domi...

In vitro regeneration of tomato (Solanum lycopersicum L.) was attempted using shoot tip and hypoc... more In vitro regeneration of tomato (Solanum lycopersicum L.) was attempted using shoot tip and hypocotyl explants. The MS medium supplemented with zeatin (2 mg/l) and IAA (0.2 mg/l) was found to be effective for direct shoot induction and plantlet regeneration, with maximum number of shoots per explant. Highest shoot regeneration frequency was recorded with shoot tip explant (89.60%) followed by hypocotyl explant (88.27%). Number shoots per explant was high (7.13) in hypocotyl explant. Maximum rooting (86.64%) was observed without growth regulators.

Rice Science, 2015

This study was conducted to evaluate the effects of proline and glutamine on in vitro callus indu... more This study was conducted to evaluate the effects of proline and glutamine on in vitro callus induction and subsequent regeneration and to develop a reproducible and highly efficient plant regeneration protocol in four rice genotypes, viz. Pawana, Jaya, Indrayani and Ambemohar. Considerable variation in response to plant growth regulators and amino acid supplements used was observed in all the four genotypes. Medium supplemented with proline and glutamine was shown to be superior to medium without proline and glutamine. The best callusing from mature embryo was observed on Murashige and Skoog (MS) medium supplemented with 2.0 mg/L 2,4-dichlorophenoxyacetic acid (2,4-D), 500 mg/L proline and 500 mg/L glutamine. Shoot induction was higher in the callus obtained from medium supplemented with 500 mg/L proline and 500 mg/L glutamine. The highest shoot regeneration frequency (83.2%) was observed on MS medium with 2.0 mg/L benzylaminopurine, 0.5 mg/L 1-naphthaleneacetic acid, 500 mg/L proline, and 500 mg/L glutamine in the callus obtained from MS medium supplemented with 2.0 mg/L 2,4-D, 500 mg/L proline and 500 mg/L glutamine. Among the four genotypes, Pawana has the highest regeneration efficiency (83.2%), whereas the regeneration efficiency of the rest three rice genotypes was in the range of 32.0% to 72.3%. This optimized regeneration protocol can be efficiently used for Agrobacterium mediated genetic transformation in rice.

BMC Plant Biology, 2019

Background: Soybean (Glycine max L. Merril) crop is major source of edible oil and protein for hu... more Background: Soybean (Glycine max L. Merril) crop is major source of edible oil and protein for human and animals besides its various industrial uses including biofuels. Phytoplasma induced floral bud distortion syndrome (FBD), also known as witches' broom syndrome (WBS) has been one of the major biotic stresses adversely affecting its productivity. Transcriptomic approach can be used for knowledge discovery of this disease manifestation by morpho-physiological key pathways. Results: We report transcriptomic study using Illumina HiSeq NGS data of FBD in soybean, revealing 17,454 differentially expressed genes, 5561 transcription factors, 139 pathways and 176,029 genic region putative markers single sequence repeats, single nucleotide polymorphism and Insertion Deletion. Roles of PmbA, Zn-dependent protease, SAP family and auxin responsive system are described revealing mechanism of flower bud distortion having abnormalities in pollen, stigma development. Validation of 10 randomly selected genes was done by qPCR. Our findings describe the basic mechanism of FBD disease, right from sensing of phytoplasma infection by host plant triggering molecular signalling leading to mobilization of carbohydrate and protein, phyllody, abnormal pollen development, improved colonization of insect in host plants to spread the disease. Study reveals how phytoplasma hijacks metabolic machinery of soybean manifesting FBD. Conclusions: This is the first report of transcriptomic signature of FBD or WBS disease of soybean revealing morphological and metabolic changes which attracts insect for spread of disease. All the genic region putative markers may be used as genomic resource for variety improvement and new agro-chemical development for disease control to enhance soybean productivity.

Agricultural Research, 2018

Floral bud distortion (FBD) is a peculiar disorder limiting yield of soybean in central India. In... more Floral bud distortion (FBD) is a peculiar disorder limiting yield of soybean in central India. Investigations were conducted to understand tissue-specific cytological, biochemical and molecular alterations associated with FBD. The conspicuous morphological symptom seen was extended vegetative phase, which remained green even after R7 (beginning maturity) stage of growth and failure to produce pods leading to complete yield loss in affected plants. Reduced numbers of pollen grains as well as pollens with high percent of sterility were recorded in symptomatic plants. Although the stigma was found to be receptive in the symptomatic plants, pollens showed irregular shape and had a thicker exine wall. Carbohydrate (2.21 times), protein (2.38 times) and chlorophyll (2.17 times) contents were found to be significantly higher in symptomatic plants. Tissue-specific differentially expressed TDFs (transcript-derived fragments) were generated through cDNA-RAPD using 40 primers. Seven primers were found polymorphic and size ranged from 160 to 1100 bp. Re-amplified TDFs were sequenced, and they showed partial homology with characterized (ARF, XM_003529058) and uncharacterized (LOC 100815325) transcription factors. This indicates investigating differentially expressed genes are needed to understand the insights of molecular alterations associated with floral bud distortion.

Vegetos- An International Journal of Plant Research, 2016

Genetic Diversity in Vegetable and Grain Type Soybean Genotypes Identified using Morphological De... more Genetic Diversity in Vegetable and Grain Type Soybean Genotypes Identified using Morphological Descriptor and EST-SSR Markers Thirty four soybean genotypes were evaluated for morphological, quality traits and genetic parameters. Correlation and path coefficients were studied for some traits. Analysis of variance and mean performance for various traits revealed significant differences diversity between all the genotypes for traits studied. The genetic diversity among the soybean genotypes was analyzed using ten expressed sequence tag derived simple sequence repeat (ESTSSR) markers. A total of 27 alleles were detected from 334 amplicons with an average of 2.7 alleles per locus. The polymorphism information content (PIC) values of EST-SSR markers ranged from 0.334 to 0.837 with an average of 0.559. These grain and vegetable soybean genotypes could be divided into 7 subgroups based on similarity matrix and arithmetic average (UPGMA) cluster with no correlation between genetic and morphological diversity. The analysis clearly indicated that even with the EST-SSR primers, reliable estimation of genetic diversity among the population could be obtained...

Journal of Genetics, 2016

An attempt was made to understand the 'floral bud distortion' (FBD), an unexplored disorder preva... more An attempt was made to understand the 'floral bud distortion' (FBD), an unexplored disorder prevailing in soybean. Cytological behaviour of floral reproductive organs and in silico characterization of differentially expressed transcript-derived fragments (TDFs) in symptomatic and asymptomatic soybean plants were carried out. Pollens in asymptomatic plants do not have defects in number, size, shape and function. However, in symptomatic plant, pollens were found nonviable, abnormal in shape and with reduced germination ability. Here, we employed a computational approach, exploring invaluable resources. The tissue-specific transcript profile of symptomatic and asymptomatic sources was compared to determine differentially expressed TDFs associated with FBD to improve its basic understanding. A total of 60 decamer primers produced 197 scorable amplicons, ranged 162-1130 bp, of which 171 were monomorphic and 26 were differentially regulated. Reproducible TDFs were sequenced and characterized for their homology analysis, annotation, protein-protein interaction, subcellular localization and their physical mapping. Homology-based annotation of TDFs in soybean revealed presence of two characterized and seven uncharacterized hits. Annotation of characterized sequences showed presence of genes, namely auxin response factor 9 (ARF9) and forkhead-associated (FHA) domain, which are directly involved in plant development through various pathways, such as hormonal regulation, plant morphology, embryogenesis and DNA repair.

AGRICULTURE UPDATE, 2017

Molecular alterations of symptomatic and asymptomatic soybean plants in response to floral bud di... more Molecular alterations of symptomatic and asymptomatic soybean plants in response to floral bud distortion (FBD) are not completely understood yet. Oilgo-dT anchoredcDNA-RAPD and cDNA-SCoT markers were exploited to determine differentially expressed genes in response to FBD. Differential transcriptome analysis using cDNA based oligo-decamer profiling was executed to identify differentially expressed TDFs. The TDFs were further analyzed using computational tools viz., BLAST homology, protein interactome, virtual karyotyping, sub-cellular localization, neighbor joining placement.The in-silico studies were used for annotation, structural, functional characterization and protein interaction of TDFs. Differential expression studies (cDNA-RAPD) produced transcript derived fragments (TDFs) in all tissues (leaf bud and node) of symptomatic and asymptomatic plant. Out of 197, only 26 TDFs were found differentially regulated. Amongst them 15 were found completely polymorphic and 11 showed differences in their amplicon intensity. Similarly cDNA-SCoTit revealed that total of 36 primers amplified 86 fragments between 200 bp to 1800 bp in length. Amongst them, nine differentially expressed fragments (DEFs) were re-amplified and sequenced. Sequence based studies of DEFs revealed their homology to five known genes; which were functionally involved in DNA repair mechanism, apoptopic, autophagy and pathogen responsive mechanisms in soybean. However, four fragments encode un-clarified proteins with unknown functions. The possible role of unknown genes, along with protein-protein interactome, physical karyotyping and cellular localization were predicted using in silico analysis. This study suggests that oligo-dT anchoredcDNA-RAPD, cDNA-SCoT differential display approach is a useful tool to serve as initial step for understanding alterations involved in upcoming malady and provide valuable information for further studies.

3 Biotech, 2016

Shoot regeneration in safflower (Carthamus tinctorius 'AKS 207' and 'PKV Pink') genetically trans... more Shoot regeneration in safflower (Carthamus tinctorius 'AKS 207' and 'PKV Pink') genetically transformed using Agrobacterium was used for assessing various constraints to the efficiency of transformation including infection period, virulence induction medium, co-cultivation period, bacterial titre, selection regime, and the natural phenolic compound acetosyringone. Transformation frequency was promising with 8-10-day-old cotyledonary leaf explants. Therefore, explants of that age cultured on Agrobacterium minimal medium (AB) containing 100 lM acetosyringone were infected with Agrobacterium (cell titre 0.5 OD 600nm) for 15 min followed by 48 h of co-cultivation on kanamycin-enriched medium (50 mg/L). Transformation of the shoots was confirmed using b-glucuronidase (GUS) histochemical assay and polymerase chain reaction (PCR). With the transformation protocol thus optimized, the transformation frequency as determined using GUS assays was 54.0 % for AKS 207 and 47.6 % for PKV Pink. The corresponding figures using PCR were 27.0 and 33.3 %. The transformed shoots required 10-14 weeks of culture initiation but produced very few roots. Keywords Indirect regeneration Á Agrobacterium tumefaciens Á GUS histochemical assay Á Carthamus tinctorius L. Á Oilseed Electronic supplementary material The online version of this article (

Vegetos- An International Journal of Plant Research, 2013

ABSTRACT An efficient and reproducible plant regeneration procedure is essential for introducing ... more ABSTRACT An efficient and reproducible plant regeneration procedure is essential for introducing genes of interest in important crops through genetic transformation. However, some crops, such as soybean [Glycine max (L.) Merrill), are difficult to manipulate in vitro, often depending on their genotype, and the reproduction of the established protocols is not always possible. The purpose of this paper is the optimization of a regeneration protocol for soybean shoots of the Indian variety JS-335 to enable its reproduction. Four explants viz, Cotyledonary node, embryo, half seed and hypocotyl were tested using various combinations and concentrations of growth hormones. The effect of several concentrations of 2,4-D and BAP was effective in initiating Callogenesis in three types of explants though concentration varied widely. The highest callogenesis of 82.93% were recorded on 14th day using half seed explant. However, the highest shoot induction of 93.79% with multiple numbers of shoots was recorded using cotyledonary node explant inoculated on the medium fortified with 5.0 mg.L−1 BAP.

Egyptian Journal of Biology, 2013

We describe a peculiar and often harmful budding disorder in soybean, leading to huge yield loss ... more We describe a peculiar and often harmful budding disorder in soybean, leading to huge yield loss in India. To determine the prevalence of floral distortion in soybean, an extensive random roving survey was undertaken in the soybean-growing regions of Madhya Pradesh, Maharashtra and the adjoining part of Karnataka states during two successive seasons of kharif (monsoon-planted) crops-Oct 2010 and Sept 2011. The average rate of the disorder ranged from 8.0% to 14.6% and severity from 2.0 to 90.0% during 2010 and 2011, respectively. Affected plants were found to have either no or deformed pods and distorted flowers, and they remained green after maturity. All the soybean varieties grown in the surveyed region (i.e. JS 335, JS 93-05, JS 73-23, JS 95-60, AMS-MB-5-19, CO-2, Bragg, JS 10-44, Samrat) were affected by the disorder. The PCR-based diagnosis revealed the absence of phytoplasma in symptomatic soybean samples.