Genomics and its Applications in Crop Improvement

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Genomics and its Applications in Crop Improvement AK CHHABRA AND Ashish jain

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1910 – to identify and map genes in organisms of interest. Mapping of genes – Identification of mutations. Linkage analysis & linkage maps. Physical maps of genes. Drawback: one mutation for each gene in the genome. Mutation must produce a phenotypic effect. But mutations are lethal, so not possible to map the mutated gene. Mid 1980’s-rDNA technology for genetic analysis. Genomic library is established.

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The term genome (derived from the words genes and chromosomes) was first used by Winkler to signify the complete set of chromosomes and their genes Genome refers to the basic set of chromosome. In a genome each type of chromosome is represented only once. Genome H. Winkler 2n = 2x = 1x…………. Haploid……..GENOME 2n = 6x = 1x………..Monoploid…….GENOME

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The term genomics was first used by Thomas Roderick in 1986. It refers to the study of structure and function of entire genome of a living organism. Genomics Structure of Chromosome Function of all the genes Genomics

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Now genomics is being developed as a sub-discipline of genetics which is devoted to the mapping, sequencing and functional analysis of genomes. Main points related to genomics are given below: It is a computer aided study of structure and function of entire genome of an organism. It deals with mapping of genes on the chromosomes, functioning of genes and metabolic pathways in an organism. It deals with sequencing of genes in an organism. It is a rapid and accurate method of gene mapping. The genomic techniques are highly powerful, efficient and effective in solving complex genetic problems. Now the use of genomic techniques has become indispensable in plant breeding and genetics. Genomics

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TYPES OF GENOMICS

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TYPES OF GENOMICS Structural Genomics: It deals with the study of the structure of entire genome of an organism. In other words, it deals with the study of the genetic structure of the each chromosome of the genome. It determines size of the genome of a species in Megabases (Mb) and also the number of genes present in the entire genome of a species.

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TYPES OF GENOMICS STRUCTURAL GENOMICS: it involves High resolution genetic and physical maps. Sequencing Complete set of proteins in an organism Often, three-dimensional structure of the concerned protein.

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TYPES OF GENOMICS Functional Genomics: It deals with the study of function of all genes found in the entire genome of a living organism. deals with transcriptome and proteome. The transcriptome refers to complete set of RNAs transcribed from a genome and proteome refers to complete set of proteins encoded by a genome. genomics can be classified based on the experimental material used and type of analysis carried out . Functional genomics assigns functions to each and every gene identified through structural genomics. Thus functional genomics is more complicated that structural genomics

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Tool Used in Genomics: Molecular Marker Technology Microarray Chip Technology Comparative Genomics

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Microarray Chip Technology

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Comparative Genomics Computer Software Technology

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The discipline of genomics is of recent origin. The genome mapping was first completed in a free living bacterium Haemophillus influenzae in 1995. Later on work on genome mapping was intensified both in prokaryotes and eukaryotes. The genome sequence work has been completed in 165 species of bacteria and 20 species of eukaryotes so far. In plants genome mapping work has been completed in two species viz., Arabidopsis thaliana (a weedy relative of mustard) and rice (Oryza sativa). Arabidopsis thaliana Oryza sativa Haemophillus influenzae Yeast

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D. melanogaster Genome sequencing in some organisms Nemotode (C. elegans)

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The fragments aligned into contigs. Also called as the directed sequencing of the BAC contigs. BAC clones(80-100 kb long DNA fragment) arranged in contigs. Fragments used to create the cosmid and plasmid clones. Clones arranged in contigs and then sequenced. Randomly selected clones are sequenced until all clones in the genomic library are analyzed. Assembler software's organizes the nucleotide sequence information into a genome sequence. It works very well with prokaryotic genomes. Overlapping fragments are aligned either into contigs(Clone-by-clone) or into a sequence for the concerned region (shot-gun method). The genome is sequenced more than once ,to ensure that genome is complete and error free. e.g. P. aeruginosa (7 times) The draft of human genome is over, however correcting errors, filling gaps, and then sequencing the remaining genome that contains the heterochromatin.

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The genomic research has so far been carried out mainly on prokaryotes and also work has been done on crop plants. In crop plants, the genome mapping has been completed in two species, viz. Arabidopsis thaliana (a weedy relative of mustard) and rice (Oriza sativa). Now the work on genome mapping has been initiated in several field crops and fruit crops by the Indian Council of Agricultural Research, New Delhi. The estimated genome size of some crop plants is presented on next slide. GENOMICS IN CROP PLANTS

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Estimated No. of genes in various crop species

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The Arabidopsis genome sequence was completed in 2000. This has led to a great increase in our understanding of the molecular basis of both plant development and the response to environmental stimuli. Having the genome sequence has enabled genomics approaches which aim to assign a function to each of the predicted 26,000 genes. Knockout mutations generated by insertional mutagenesis or gene silencing with RNAi methodology suggest a function for a gene if the mutants can be linked to a phenotype. Oligonucleotides corresponding to each of the predicted genes can be spotted on a microarray which can be used to determine the pattern of expression of each of the genes, again, suggesting a function. The knowledge of gene function is deepening our understanding of development in Arabidopsis, and importantly, it is enabling Arabidopsis to be a platform into similar levels of understanding in our major crop plants.

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The genome mapping is a very costly affair because it requires specialized technical skill, sophisticated Laboratory, costly equipments, chemicals and glass wares. Thus main or basic requirements of genome mapping are listed below: High or specialized technical skill Sophisticated Laboratory facilities Costly equipments and Instruments Costly chemicals Costly glass wares Such very expensive projects are taken up through International Collaboration. Now intentional Consortia are available to take up such research work. GENOME MAPPING IN INDIA Lab Setup

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ROLE OF GENOMICS IN CROP IMPROVEMENT Genomics has various practical applications in crop improvement. The genome mapping is useful in the following ways:

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In the genomic research, both types of genes viz. major genes and minor genes can be easily mapped. In other words, both oligogenic and polygenic traits can be mapped. The mapping of Quantitative Trait Loci is possible by genome mapping techniques which is not possible by conventional gene mapping methods: viz. recombination and deletion techniques. Thus genomics permits mapping of genes for all types of traits. Generally, the genome mapping is done for following type of characters. Morphological Characters: It includes highly heritable characters such as shape, size, colour of leaf, flower, calyx., corolla etc. It also includes surface of leaf and stem (hail or smooth). Yield and yield contributing characters. Genes controlling resistance to biotic and abiotic stresses. Biotic stresses include insects, diseases and parasitic weeds. Abiotic stresses include, drought, soil salinity, soil alkalinity, soil acidity, heat, frost, water logging, cold, etc. Genes controlling quality characters. It includes keeping quality as well as market quality. Genes controlling toxic substances. Genes controlling male sterility and self incompatibility in crop plants. Genes controlling fertility restoration. Apomictic genes especially in fruit crops. Genes controlling adaptation to various agroclimatic conditions. Gene controlling photo and thermo-insensitivity. Genes controlling agronomic characters such as earliness, plant height, plant type, elc. Gene controlling non shattering habit in pulses viz., mung bean. Thus all type of characters can be mapped through genomic studies. GENES TO BE MAPPED

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ACHIEVEMENTS Limited progress has been made so far in the field of genomic research related to both animals and crop plants. Important achievements of genomic research are briefly presented below: 1. Bacteria In bacteria, the genome mapping was first completed in influenza fever causing bacterium, viz. Haemophilus influenzae in 1995. This was the first case of genome mapping in micro-organisms or prokaryotes. Since then genome mapping has been completed in 165 species of bacteria. 2. Mycoplasma In Mycoplasma, the genome mapping was first completed again in 1995 in Mycoplasma genetalium. The genome size of this organism is 0.58 Mb and number of genes are 500. In other words, 500 genes have been mapped in the genome of this species. 3. Yeast In yeast, the genome mapping was first completed in 1996. The genome size of yeast is 12 Mb and 5,800 genes have been mapped so far. ACHIEVEMENTS

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5. Fruit Fly (Drosophila Melanogaster) In fruit fly, the genome mapping was first completed in 2000. The genome size of fruit fly is 180 Mb and 13,600 genes have been mapped so far. 6. Human (Homo sapiens) The Human genomes working draft published (90% genome sequenced) on June 26, 2001. The genome size of human is 3200 Mb and 40,000 genes have been mapped so far. IHGSC announced that reference human genome (99.99% accuracy) had been completed in 2003. 7. Crop Plants In crop plants, genome mapping has been completed in two species, viz. Arabidopsis thaliana (a weedy relative of mustard) and rice. ACHIEVEMENTS

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The genome mapping of crop plants is gaining increasing importance these days. It has several useful applications. However, there are some limitations of genome mapping which are briefly presented below : 1. Very Expensive The genomic research requires well equipped sophisticated laboratory. The chemicals, equipments and glass wares used for such work are very expensive. Thus lot of funds are required for carrying out genomic research. Lack of adequate funds sometimes becomes limiting factor in the progress of such project. 2. Technical Skill The genome mapping work requires high technical skill. It requires training of the scientists in the specialized field of genomics. It also requires International collaboration with other leading genome research laboratories which sometimes becomes limiting factor. The international collaboration is possible if the crop on which genomic research work is to be carried out is of global significance. 3. Laborious Work The genome mapping requires detection of various DNA markers (RFLP, AFLP, SSR, RAPD etc.) which is a laborious and time consuming work. Huge populations need to be screened for such purposes. This limits the progress of work. LIMITATIONS

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4. Limited Genes Available Firstly limited number of genes and promoters are available for development of transgenics. Secondly such genes are protected under IPR and therefore, can not be used for developing transgenic plants. 5. Lack of Proper Markers Most of the useful agronomic traits are governed by polygenes and are complex in nature. Tightly linked DNA markers are yet to be identified for such characters. LIMITATIONS Bt Gene Cry gene series Antisense RNA technology for tomato Terminator gene Beta Carotene gene in rice

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In the past, the studies on genomics have been confined mostly to prokaryotes and also work has been done on crop plants. In future, the genome research work needs to be directed towards the following thrust areas. Funding. Since genome mapping projects are very costly, there is need of international collaboration for supporting such prestigious projects. Training. Some Laboratories are well equipped for genomic research. Such organizations should impart training to scientist from various countries to develop large number of skilled manpower in genome mapping. Material Sharing. The leading laboratories should develop and distribute frame work DNA markers to various other research laboratories for their use and further research. Research Priorities. The research priorities should be defined. In order to get International collaboration areas of common interest/global significance should be identified for genomic research work. Important Traits. In genome mapping, the major emphasis needs to be given on characters of economic importance such as productivity, quality and resistance to biotic and abiotic stresses. Species. In the past genome mapping has been done mostly on micro-organisms. In plants, such studies have been carried out with two species, viz. Arbidopsis and rice. In future genome mapping needs to be carried out with almost all important field, vegetable and fruit crops. The experienced gained in genome mapping of one species may be helpful in the study of related species. FUTURE THRUST

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Genomics refers to the study of structure and function of entire genome of a living organism, Genomics is of two types, viz. (i) structural genomics and (ii) functional genomics. The former deals with the study of the structure of entire genome, whereas the latter deals with the study of the function of all genes found in the entire genome of a living organism. Genomics has several practical applications in crop improvement. Genomics is useful in determining (i) genome size, (ii) gene number in the genome, (tii) gene mapping, (iv) gene sequencing, (v) tracing evolution of crops plants, (vi) gene cloning, (vii) identification of DNA markers, (viii) marker assisted selection, (ix) transgenic breeding, (x) construction of linkage maps, and (xi) QTL mapping. SUMMARY

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Genome mapping Laboratories

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ICGEB Lab, New Delhi

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Bioinformatics Centre Dept. of Microbiology and Biotechnology Centre, M.S.University of Baroda, Baroda, India 390002 Phone:91-0265-2794396 , Fax: 91-265-2792508

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CCMB Lab Centre for Cellular & Molecular Biology (CCMB)

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National Research Centre for Plant Biotechnology IARI New Delhi The National Research Centre on Plant Biotechnology was established in 1985 to undertake research, teaching and training personnel in the modern areas of Molecular Biology and Biotechnology. Since its inception, the Centre has grown and has acquired high degree of scientific competence and established excellent research facilities. The Centre is working towards achieving the national priorities of increased agricultural productivity and sustainability

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National Institute of Plant Genome Research

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Jawaharlal Nehru University New Delhi JNU Campus

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National Botanical Research Institute, Lucknow.

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Now functional genomic projects are being initiated by the Department of Biotechnology (DBT) and ICAR. The DBT has initiated such work on Rice and ICAR has taken up genome sequencing work on several crops such as Rice, Wheat, Maize, Chickpea, banana, Tomato, Brassica, etc. The ICAR has created genome sequencing facilities for rice at NRCPB, IARI, New Delhi. Facilities for genome mapping of other crops are also being created. Department of Biotechnology (DBT)

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Mexico's National Laboratory of Genomics

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Marine Genomics Lab Texas A&M University

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Thanks for kind attention