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Anand Agricultural University, Anand
Anand Agricultural University (AAU) was established in 2004 at Anand with the support of the Government of Gujarat, Act No.(Guj 5 of 2004) dated April 29, 2004. Caved out of the erstwhile Gujarat Agricultural University (GAU), the dream institution of Sardar Vallabhbhai Patel and Dr. K. M. Munshi, the AAU was set up to provide support to the farming community in three facets namely education, research and extension activities in Agriculture, Horticulture Engineering, product Processing and Home Science. At present there seven Colleges, seventeen Research Centers and six Extension Education Institute working in nine districts of Gujarat namely Ahmedabad, Anand, Dahod, Kheda, Panchmahal, Vadodara, Mahisagar, Botad and Chhotaudepur
AAU's activities have expanded to span newer commodity sectors such as soil health card, bio-diesel, medicinal plants apart from the mandatory ones like rice, maize, tobacco, vegetable crops, fruit crops, forage crops, animal breeding, nutrition and dairy products etc. the core of AAU's operating philosophy however, continues to create the partnership between the rural people and committed academic as the basic for sustainable rural development. In pursuing its various programmes AAU's overall mission is to promote sustainable growth and economic independence in rural society. AAU aims to do this through education, research and extension education. Thus, AAU works towards the empowerment of the farmers.
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ThesisItem Open Access Transcriptome based identification and level of expression study of candidate genes related to andrographolide content and their validation in Andrographis paniculata (Burm f.) Nees.(DEPARTMENT OF AGRICULTURAL BIOTECHNOLOGY ANAND AGRICULTURAL UNIVERSITY ANAND, 2017) ANKITABAHEN ATULKUMAR PATEL; Dr. Y. M. ShuklaIn heritage, India is blessed with many medicinal and aromatic plants. Natural and ayurvedic medicines were used by old people prepared from medicinal plants for treatment of diseases. Now a days also, the importance of medicinal plants remain as such due to their efficient way of curing and researchers focus more in the field of medicinal plants. The present investigation has paid attention on one of the important medicinal plants “Andrographis paniculata (Burm. f.) Nees.”, due to presence of its valuable secondary metabolite “Andrographolide”. The common name of Andrographis paniculata is kalmegh. The present study aimed to elucidate the expression of candidate genes associated with biosynthesis pathway leading to andrographolide synthesis in different genotypes of kalmegh at particular vegetative growth stage. The validation of expressed genes was also carried out.ThesisItem Open Access MAPPING QTLs FOR IRON AND ZINC CONCENTRATIONS IN RICE (ORYZA SATIVA L.)(DEPARTMENT OF AGRICULTURAL BIOTECHNOLOGY ANAND AGRICULTURAL UNIVERSITY ANAND, 2017) DHARA K. SAVSANI; Dr. Y. M. ShuklRice (Oryza sativa L.) is nutritionally, one of the most important staple food crops for approximately half of the world population. It is rich in carbohydrate and the predominant dietary energy source for Asia, North and South America and Africa, re iterating its importance to human welfare.ThesisItem Open Access TRANSCRIPTOME ANALYSIS AND IDENTIFICATION OF DEFENCE RELATED GENES IN RESPONSE TO DOWNY MILDEW (Peronospora plantaginis) INFECTION IN ISABGOL (Plantago ovata Forsk)(AAU, Anand, 2013) KUMAR, VINAY; Shukla, Y. M.Isabgol (Plantago ovata Forsk), a member of Plantaginaceae family is a crucial medicinal emd industrial crop cultivated in India, having a good foreign exchange in world market. In spite of its immense important, it faces constraints in productivity due to the prevalence of numerous biotic and abiotic stresses, downy mildew disease caused by an obligate fvmgal pathogen, Peronospora plantaginis being a major one causing an estimated yield loss of up to 73 per cent. In order to identify the defence response involved in isabgol-downy mildew interaction, transcriptome analysis of downy mildew resistant (EC 124345) and susceptible (Niharika) genotypes under downy mildew stress as well as control conditions was executed through 454 GS FLX Titanium Pyrosequencing, yielding 600.81 Mb data with an average read length of 434 bp. De novo transcriptome assembly of four samples viz. resistant inoculated; control and susceptible inoculated; control was performed using CLC Genomics Workbench producing 7246, 7650, 7390 and 9278 unigenes respectively. The Guanine: cytosine (GC) content in isabgol transcriptome varied from 51-52%. The unigenes were annotated to identify putative gene fimctions with the different databases like non redundant protein database. KEGG and IntreProscan and the highest GO terms were obtained from UniprotKB databases. The homology of isabgol tmigenes with the model plant species revealed the highest hits with Vitis vinifera followed by Glycine max, Populus trichocarpa, Medicago truncatula and Arabidopsis thaliana. Gene Ontology enrichment analyses revealed the over and under representation of GO terms by the up and down regulation of associated genes respectively. The genes encoding various types of enzymes and/or protein associated with the defence or stress related responses included pathogenesis related (PR) proteins, such as (PR-9) peroxidase, (PR-5) thaumatin like proteins, (PR-3, 4, 8, 11) a group of chitinases or endochitinases, (PR-2), P- 1, 3-glucanases, (PR-10) ribonuclease, (PR-13) thiordne, (PR-6) proteinase inhibitors and (PR-12), resistance genes NBS-LRR, CC-NBS-LRR, ser/threonine receptors kinase, LRR repeat type, MLO and Cf9 types of R genes were also foxmd. Transcription factors families viz. WRKY, zinc finger, leucine zipper, chitin-inducible gibberellin-responsive protein 1-like, dna binding, g-boxbinding factor 4, homeobox leucine zipper protein, myb family, nac domain containing, ERF were identified from the isabgol downy mildew interaction. The pathogenesis and defence related genes identified in isabgoldowny mildew interaction were validated through Real time quantitative PCR. In order to identify the most stable reference genes during downy mildew pathogen infection, the expression stabilities of the reference genes viz. elongation factor a, actin, tubulin, glyceraldehyde 3 phosphate dehydrogenase and 60S ribosomal protein were examined by the five algorithms and EF1a and ACT 7 were found to be the most stable reference genes. A total of 18 PR proteins, defence related enzymes/genes were used for validation through Real time-qPCR. The expression of peroxidase, spermine synthase, chitinases, ADP ribosylation factors, mitogen activated protein kinase kinase, 4-coumarate ligase and resistance gene CC-NBS-LRR were prominentiy enhanced in resistant inoculated samples suggesting that the defence related genes were induced during isabgol downy mildew interaction. Photosynthesis related genes like chlorophyll a-b binding protein, 14-3-3 were down regulated during downy mildew disease. The transcriptome data was mined for EST-SSR and identified the first set of genie SSRs markers. A total of 1440, and 1824 microsatellite repeats were identified from the EC 124345 and Niharika genotypes, respectively. The most frequently occurring di-nucleotide motifs were AG/CT followed by GA/TC and CA/TG and among the tri- nucleotide motifs, AGC/CTG was abundantiy present closely followed by AAG/CTT. The tri-nucleotide motifs coding for serine was highest (12%) followed by leucine (9%), while the methionine were least present (1%). A set of 34 EST-SSR was selected for validation on Plantago ovata genotypes. Out of the 34 primers, 28 primers (82%) produced their specific amplicon and four primers viz. ECSSR 4, ECSSR 9, ECSSR 14, ECSSR 31 were polymorphic within P. ovata genotypes. For cross species transferability, 24 primers out of 28 (85%) produced amplification in any of the six species tested viz. Plantago coronopus, P. lanceolata, P. indica, P. arenaria, P. syllium and P. serrena. The transcriptome data would serve as a resource for genomic studies such as identification and isolation of genes of economically important traits and disease resistance in isabgol. The newly developed first set of EST-SSR markers could be useful in identification of gene based or trait linked SSR markers for improvement of isabgol though conventional or molecular breeding approaches like marker- aided selection (MAS). This study generated for the very first time genomic resources for a highly valued medicinal plant using high throughput next generation sequencing approach and is expected to accelerate the field of functional genomics of isabgolThesisItem Open Access Transcriptome based identification of genes imparting bacterial leaf blight (Xanthomonas oryzae) resistance in rice (Oryza sativa L.)(AAU, Anand, 2017) DESAI AMRUTA S.; Dr. Subhash N.Rice is one of the most important staple foods for a larger part of the world’s population. It is a rich source of carbohydrates, energy, thiamine, pantothenic acid and folic acid. Because world-wide rice production has been severely affected by one of the major disease referred to as bacterial leaf blight caused by Xanthomonas oryzae pv. oryzae (Xoo), early efforts has been focusing on cloning and utilizing of disease resistance (R) genes in rice for resistance breeding. In the present study, thirty day old seedlings of BB resistant (IR 64) and susceptible (GR 11) genotypes were inoculated with and without BB (4 x l04 cells /ml). The seedlings were harvested 36 hours post inoculation for transcriptome sequencing employing the Miseq Illumina NGS sequencer after assaying the normal range for quantity and quality of total RNA, mRNA and cDNA. Transcriptome sequencing yielded 19311304 bp data with an average read length of 150 bp and constituted of 18440773 high quality reads which were assembled employing Trinity assembler for functional annotation. Trinity assembler gave assembly matrix (N50 of 2,453), proteome coverage and read alignment (90%) resulting in 30,000 contigs and 2,35,433 singletons/transcripts which were subjected to gene ontology (GO) following functional annotation. ii The maximum number of gene ontology was ascribed to cellular components, molecular function and biological processes showed that the maximum transcripts belonged to plastid, mitochondria and plasma membrane; nucleotide binding, kinase activity, DNA binding; cellular protein modification response to abiotic stress and biotic stress, respectively. Rice transcripts showed highest homology to Setaria italica and maximum blast hits with Hordeum vulgare. The maximum number of annotated transcripts was ascribed to transferase, hydrolase and oxidoreductase class of enzymes. The highly represented transcripts included disease resistance genes, pathogenesis related proteins, transcription factors (MYB, WRKY), signaling molecules (MAPK), enzymes of oxidative burst and LRR domain. These proteins were assumed to be involved in signaling networks induced in rice during BB infection. The transcripts were further subjected to confer their metabolic involvement through biochemical pathway through Kyoto encyclopedia of genes and genomes. Total 118 metabolic pathways were identified in rice transcriptome. Metabolic pathway enrichment ascribed the maximum number of transcripts in Glutathione metabolism leading to activation of defence responses called systemic acquired resistance (SAR). Metabolic pathway for purine metabolism, phenylalanine metabolism and starch and sucrose metabolism were prominently present. Transcriptomes of resistant and susceptible rice genotypes (with and without inoculum) were further screened for differential gene expression analysis by mapping individual reads to the assembly. Among the resistant and susceptible genotypes (with and without inoculum), 1314 transcripts were either up regulated or down regulated. The number of differentially expressed transcripts between the samples resistant inoculated and susceptible inoculated was 154. Further confirmation and validation was carried out through quantitative real time PCR. iii Relative quantification of defence related transcripts by quantitative real time PCR was performed using a-tubulin as endogeneous control. The relative expression of defence related genes associated with BB disease MYB, bZIP; defence related enzymes including lipoxygenase (LOX), phenylalanine ammonia lyase (PAL), respiratory burst oxidase (RBO), beta glucanase (BGLUC), Ribonuclease (RNase), Endo chitinase (CHI), signaling molecules, MAPK and CDPK showed up regulation in resistant inoculated than susceptible inoculated. Overall results of transcriptome study generated the information on involvement of MYB, WRKY, mitogen activated protein kinases, cellular ATPases, calcium dependent protein kinase and phenylalanine ammonia lyase transcription factors and the genes associated with resistance involved R genes homologous with the cell wall degrading enzymes like chitinase, 3-1,3 glucanases and metabolic pathway coding enymes polygalacturonase inhibiting proteins (PGIPs), cysteine proteases in the process of BB resistance. It could be inferred that defence responses associated with BB in rice were activated by hypersensitive response arising due to gene to gene interaction and systemic acquired resistance associated with pathogenesis related proteins, transcription factors, signaling molecules and enzyme related to glutathione pathwayThesisItem Open Access CHARACTERIZATION AND EXPRESSION STUDIES FOR IRON TRANSPORTER AND STORAGE GENES IN KODO MILLET (Paspalum scrobiculatum L.)(AAU, Anand, 2016) PRAJAPATI VIJAYKUMAR ISHWARBHAI; Dr. J. G. TalatiKodo millet is a balanced and staple food of tribal and economically poor section of the population. The grains of kodo millet possess excellent storage properties and are known for health benefits. It is highly nutritious food crop with higher fiber content along with quality protein and mineral composition, which can serve as excellent dietary source for these elements. Poor nutritional quality of cereals is the primary cause of disorders related to nutritional imbalance among the population having cereal-based diet, especially those belonging to underdeveloped or developing counties. The present study was carried out with an aim to study the relative importance of nutritional quality, molecular diversity existing in kodo millet and to study genes responsible for the iron transport and storage at three developmental stages (10 DAS, 20 DAS and 30 DAS). A wide variation for the micronutrient content was observed in grains of twenty kodo millet genotypes under study. Iron and zinc concentrations ranged from 17.1 to 66.4 ppm and 18.3 to 29.0 ppm respectively. The highest iron content was found to be in KAVT-13, whereas zinc in PSC-1. The observed values were higher than the average iron content present in major cereal crops such as rice, wheat, maize, etc. The protein content ranged from 6.86 to 10.36 %, which is equivalent to protein content of other cereals. The percent oil content of different genotypes varied from 1.60 to 3.13, carbohydrates 70.54 to 76.04 and starch percent content from 59.51 to 68.63. It also showed higher crude fiber content, ranging from 13.15 to 15.57%. Phenolic acids from defatted grains of kodo millet genotypes were analysed by UPLC method. Among all the phenolic acids, the salicylic acid was found to be highest in kodo millet. The phenolic acid content was found to differ from genotype to genotype. The highest content for different phenolic acids such as proto-catechuic acid (KAVT-25), p-Hydroxybenzoic acid (PSC-1), Chlorogenic acid (JK-48), Caffeic acid (CO-2), Syringic acid (KAVT-13), p-Coumaric acid (KAVT-13), Ferulic acid (DK-127), Vanilllic acid (KAVT-30), Sinapic acid (JK-41) and Cinnamic acid (KAVT-13) were observed in different genotypes. In SDS-PAGE protein profiling of kodo millet grains revealed 20.54 to 104.93 kDa protein. There is little variation in the SDS-PAGE electrophoretic patterns of the twenty genotypes of kodo millet. Iron content specific thirteen SSR markers were utilized in this study, which generated 302 scorable bands. The average number of alleles per locus was found to be 2.69. The highest PIC value of YS4 indicated that it would be a very useful SSR marker for diversity analysis of kodo millet genotypes. The candidate gene markers of NRAMP family, NRAMP1 and NRAMP3 can be useful to discriminate high and low iron-containing genotypes. The candidate gene specific markers viz., YS1, IRT1, ZIP3 and Ferritin were found to discriminate high iron genotypes and the marker YS12 for low iron containing genotypes. The relative gene expression profiling of seven iron transporter and storage related genes i.e., FRO2, IRT1, NAAT1, NAS2 and YSL2 were analyzed in roots, whereas gene NRAMP5 and Ferritin were analyzed in leaves of GK-2 (Low Fe) and GPUK-3 (High Fe) kodo millet varieties under three different stages viz., 10 DAS, 20 DAS and 30 DAS. Expression of two genes FRO2 and ITR1 which are part of strategy I iron transport, was found to be correlated to high grain Fe content in kodo millet. These genes are the part of strategy I for iron transport in plant. Expression of three genes viz., NAAT1, NAS2 and YSL2 (Strategy II iron transport) are significantly higher in GPUK-3 as compared to GK-2. It was possible due to deficient Fe content in the soil at later stages of development. The expression of NRAMP5 and ferritin in kodo millet showed differential expression in leaf at 10 to 30 days after sowing. This result indicates that kodo millet possess the Strategy II iron (Fe) uptake system in which Fe is absorbed by roots as Fe3+-phytosiderophore. However, in spite of being a Strategy II plant, kodo millet identifies Fe2+ transporter (Strategy I) genes viz., FRO2 and IRT1.ThesisItem Open Access IDENTIFICATION AND CHARACTERIZATION OF THE ZINC-REGULATED TRANSPORTERS, IRON-REGULATED TRANSPORTER –LIKE PROTEIN (ZIP) GENE FAMILY IN RICE (Oryza sativa L. ssp indica)(Anand Agricultural University, Anand, 2016) Ruchi V. Trivedi; Dr. N. SasidharanZinc (Zn) and iron (Fe) are essential micronutrients for plant growth and development, their deficiency or excess severely impaired physiological and biochemical reactions of plants. Therefore, a tightly controlled zinc and iron uptake and homeostasis network has been evolved in plants. The Zinc-regulated transporters, Iron-regulated transporter-like Proteins (ZIP) are capable of uptaking and transporting divalent metal ion and are suggested to play critical roles in balancing metal uptake and homeostasis, though a detailed analysis of ZIP gene family in Oryza sativa L. ssp indica is still lacking. Therefore, in order to identify and characterize ZIP gene family in Oryza sativa L. ssp indica we developed a BLAST based approach. By using this approach we were able to identify 21 putative ZIP transporter genes in indica genome. Phylogenetic analysis indicated that they form well-supported nine classes, which were further divided into subclasses. The distribution of OsIZIP genes was found to be random across chromosomesThesisItem Open Access “MOLECULAR AND BIOCHEMICAL EFFECTS OF ZINC AND IRON NANOPARTICLES ON RICE (Oryza sativa L.)”(Anand Agricultural University, Anand, 2016) MOUNIL C. MANKAD; Dr. R. S. FougatChanges in agricultural technology have been a major factor shaping modern agriculture. Among the latest line of technological innovations, nanotechnology occupies a prominent position in transforming agriculture and food production. The development of nanodevices and nanomaterials could open up novel applications in plant biotechnology and agriculture. Nanoparticles (NPs) interact with plants causing many morphological and physiological changes, depending on the properties of NPs. Efficacy of NPs is determined by their chemical composition, size, surface covering, reactivity, and most importantly the dose at which they are effective.ThesisItem Open Access “Comparative analysis of mitochondrial genomes of rice (Oryza sativa L. ssp. indica) Cytoplasmic Male Sterile (CMS) line and its maintainer line”(Anand Agricultural University, Anand, 2016) F.S.Patel; Dr. Subhash N.Rice (Oryza sativa L.) is one of the most important cereal crops in the world. Cytoplasmic male sterility (CMS), a maternally inherited trait failing to produce functional pollen, is a useful for production of hybrid seeds in crops. In rice (Oryza sativa L.), several types of CMS lines were defined by different sources of sterile cytoplasm with distinct genetic features have been identified. CMS-WA/Rf, have been widely used for hybrid rice seed production using the three-line (CMS, maintainer and restorer) technology. Hybrid rice varieties usually increase yields by about 20%.ThesisItem Open Access TRANSCRIPTOME ANALYSIS OF SALT STRESS INDUCED GENES IN RICE [Oryza sativa L.]”(AAU, 2012) Vala, Ashishkumar G; Dr Subhash N.