Genomics

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TOPICS LAST VIEWED PREVIOUS END Genomics and its Applications in Crop Improvement A.K. Chhabra Professor (Plant Breeding)

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Genomics LAST VIEWED PREVIOUS END Genomics and its Applications in Crop Improvement Introduction Types of Genomics Brief History of Genomics Crop Genomics in India Genome Sequencing in Some Organisms Estimated Genome Size of Different Crops Role of Genomics in Crop Improvement Genome Mapping Laboratories Genes to be Mapped Limitations in Genomics Research Future Thrust Areas Molecular Markers in Crop Improvement Complete Description of ……………… Complete Description of ……………… A.K. CHHABRA TOPICS

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LAST VIEWED PREVIOUS END 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 TOPICS

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LAST VIEWED PREVIOUS END 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 TOPICS

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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. It deals with sequencing of genes in an organism. It is a rapid and accurate method of gene mapping. It is more accurate than recombination mapping and deletion mapping techniques. 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 LAST VIEWED PREVIOUS END TOPICS

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TYPES OF GENOMICS LAST VIEWED PREVIOUS END TOPICS

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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. LAST VIEWED PREVIOUS END TOPICS

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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 . LAST VIEWED PREVIOUS END TOPICS

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Functional genomics assigns functions to each and every gene identified through structural genomics. Thus function genomics is more complicated that structural genomics LAST VIEWED PREVIOUS END TOPICS

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Microarray Chip Technology LAST VIEWED PREVIOUS END TOPICS

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Comparative Genomics LAST VIEWED PREVIOUS END TOPICS

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Genome sequencing in some organisms LAST VIEWED PREVIOUS END TOPICS

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After gene sequencing, function is assigned to individual gene through various molecular techniques. Assigning of function to individual gene involves following techniques. (i) Analysis of whole genome at the level of transcriptome, proteome and metabolome. (ii) Techniques of bio-informatics for analysing and presenting data in easily understandable format. (iii) The effect of each gene is correlated with phenotypic expression of the trait. (iv) Genotyping and phenotyping LAST VIEWED PREVIOUS END GENOMIOCS IN PROKARYOTES TOPICS

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The genomic research has so far been carried out mainly on prokaryotes and a very little 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. GENOMIOCS IN CROP PLANTS LAST VIEWED PREVIOUS END TOPICS

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LAST VIEWED PREVIOUS END Estimated No. of genes in various crop species TOPICS

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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. LAST VIEWED PREVIOUS END GENOME MAPPING IN INDIA Lab Setup TOPICS

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GENOME MAPPING LABORATORIES The genome mapping work is carried out by various International and National Research laboratories of public domain. The genome mapping of different animal and plant species has been carried out jointly by various organizations as discussed below: At International level, the genome mapping work is being carried out in USA, UK, China, Japan, Australia and some other countries. Genome mapping Laboratories TOPICS

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Mexico's National Laboratory of Genomics LAST VIEWED PREVIOUS END TOPICS

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Marine Genomics Lab Texas A&M University LAST VIEWED PREVIOUS END TOPICS

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ICGEB Lab, New Delhi LAST VIEWED PREVIOUS END TOPICS

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ICGEB Lab, New Delhi LAST VIEWED PREVIOUS END TOPICS

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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 LAST VIEWED PREVIOUS END TOPICS

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CCMB Lab Centre for Cellular & Molecular Biology (CCMB) LAST VIEWED PREVIOUS END TOPICS

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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 LAST VIEWED PREVIOUS END TOPICS

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Jawaharlal Nehru University New Delhi JNU Campus LAST VIEWED PREVIOUS END TOPICS

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National Botanical Research Institute, Lucknow. LAST VIEWED PREVIOUS END TOPICS

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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. LAST VIEWED PREVIOUS END Department of Biotechnology (DBT) TOPICS

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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 : LAST VIEWED PREVIOUS END TOPICS

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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 mung bean. Thus all type of characters can be mapped through genomic studies. GENES TO BE MAPPED LAST VIEWED PREVIOUS END TOPICS

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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 bacterira, the genome mapping was first completed in influeza fever causing bacterium, viz. Haemophillus injluenzae 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 LAST VIEWED PREVIOUS END TOPICS

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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 genome was completed in 2001. The genome size of human is 3200 Mb and 40,000 genes have been mapped so far. 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 LAST VIEWED PREVIOUS END TOPICS

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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 related to F2, RILs, NILs and doubled haploids need to be screened for such purpose. This limits the progress of work. LIMITATIONS LAST VIEWED PREVIOUS END TOPICS

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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 m1'1rkers are yet to be identified for such characters. LIMITATIONS LAST VIEWED PREVIOUS END TOPICS

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In the past, the studies on genomics have been confined mostly to proaryotes and a very little work has been Jone 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 prestigeous 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 divided. 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 LAST VIEWED PREVIOUS END TOPICS

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Genomics refers to the study of structure and function of entire genome of a living organism Gcnomics 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 LAST VIEWED PREVIOUS END TOPICS

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The genome mapping work is carried out through International collaboration. Now international consortia are available for such expensive research work. The genome mapping work is being done in USA, UK, China, Japan, Australia. In India, genome mapping work is being done at NRC PB, New Delhi, ICGEB, New Delhi, JNU, New Delhi and NBRI, Lucknow. The genome mapping is possible for both qualitative and quantitative characters. The genome mapping work has been completed in a variety of organisms such as bacteria, mycoplasma, yeasts, nematodes, fruit fly, human and crop plants. In crop plants, genome mapping has been completed in two species viz. Arabidopsis thaliana and rice. Now genome mapping work has been initiated in several crops such as wheat, barley, maize, sorghum, chick pea, pigeon pea, field pea, soybean, Brassica, Tomato, etc. The genome mapping work has some limitations. It is very expensive, requires high technical skill and is a laborius work. Availability of limited number of genes and promoters and lack of proper markers limit the scope of genome mapping work. Adequate funding, proper training facilities and sharing of material is essential for promoting genomic research. Future thrust areas have been indicated. SUMMARY LAST VIEWED PREVIOUS END TOPICS

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LAST VIEWED PREVIOUS END Genomics and its Applications in Crop Improvement THANKS A.K. CHHABRA TOPICS

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LAST VIEWED PREVIOUS END Genomics and its Applications in Crop Improvement TOPICS A.K. CHHABRA TOPICS