meaning ,definition of genome ,genomics ,tools of genomics ,what is genome sequencing ,methods of genome sequencingand genome mapping ,advantage of genomics over traditional breeding program, examples of some crops whose genome has been sequenced, important points about genomics, work in the field of genomics ,applications of genomics .classification of genomics .different Omics in genomics like Proteomics ,Transcriptomics ,Metabolomics ,Need of genome sequencing
A new era of genomics for plant science research has opened due the complete genome sequencing projects of Arabidopsis thaliana and rice. The sequence information available in public database has highlighted the need to develop genome scale reverse genetic strategies for functional analysis (Till et al., 2003). As most of the phenotypes are obscure, the forward genetics can hardly meet the demand of a high throughput and large-scale survey of gene functions. Targeting Induced Local Lesions in Genome TILLING is a general reverse genetic technique that combines chemical mutagenesis with PCR based screening to identity point mutations in regions of interest (McCallum et al., 2000). This strategy works with a mismatch-specific endonuclease to detect induced or natural DNA polymorphisms in genes of interest. A newly developed general reverse genetic strategy helps to locate an allelic series of induced point mutations in genes of interest. It allows the rapid and inexpensive detection of induced point mutations in populations of physically or chemically mutagenized individuals. To create an induced population with the use of physical/chemical mutagens is the first prerequisite for TILLING approach. Most of the plant species are compatible with this technique due to their self-fertilized nature and the seeds produced by these plants can be stored for long periods of time (Borevitz et al., 2003). The seeds are treated with mutagens and raised to harvest M1 plants, which are consequently, self-fertilized to raise the M2 population. DNA extracted from M2 plants is used in mutational screening (Colbert et al., 2001). To avoid mixing of the same mutation only one M2 plant from each M1 is used for DNA extraction (Till et al., 2007). The M3 seeds produce by selfing the M2 progeny can be well preserved for long term storage. Ethyl methane sulfonate (EMS) has been extensively used as a chemical mutagen in TILLING studies in plants to generate mutant populations, although other mutagens can be effective. EMS produces transitional mutations (G/C, A/T) by alkylating G residues which pairs with T instead of the conservative base pairing with C (Nagy et al., 2003). It is a constructive approach for users to attempt a range of chemical mutagens to assess the lethality and sterility on germinal tissue before creating large mutant populations.
'Genomics' is nothing but the study of entire genetic compliment of an organism. Plant genomics is study of plant genome. This is my topic of M.Sc. course 'Plant biotechnology'.
Introduction:
Proposed by Meuwissen et al. (2001)
GS is a specialized form of MAS, in which information from genotype data on marker alleles covering the entire genome forms the basis of selection.
The effects associated with all the marker loci, irrespective of whether the effects are significant or not, covering the entire genome are estimated.
The marker effect estimates are used to calculate the genomic estimated breeding values (GEBVs) of different individuals/lines, which form the basis of selection.
Why to go for genomic selection:
Marker-assisted selection (MAS) is well-suited for handling oligogenes and quantitative trait loci (QTLs) with large effects but not for minor QTLs.
MARS attempts to take into account small effect QTLs by combining trait phenotype data with marker genotype data into a combined selection index.
Based on markers showing significant association with the trait(s) and for this reason has been criticized as inefficient
The genomic selection (GS) scheme was to rectify the deficiency of MAS and MARS schemes. The GS scheme utilizes information from genome-wide marker data whether or not their associations with the concerned trait(s) are significant.
GEBV: GenomicEstimated Breeding Values-
The sum total of effects associated with all the marker alleles present in the individual and included in the GS model applied to the population under selection
Calculated on a single individual basis
Gene-assisted genomic selection:
A GS model that uses information about prior known QTLs, the targeted QTLs were accumulated in much higher frequencies than when the standard ridge regression was used
The sum total of effects associated with all the marker alleles present in the individual and included in the GS model applied to the population under selection
Calculated on a single individual basis
Population used:
Training population: used for training of the GS model and for obtaining estimates of the marker-associated effects needed for estimation of GEBVs of individuals/lines in the breeding population.
Breeding population: the population subjected to GS for achieving the desired improvement and isolation of superior lines for use as new varieties/parents of new improved hybrids.
Training population-
large enough: must be representative of the breeding population: max. trait variance with marker : by cluster analysis
should have either equal or comparable LD, LD decay rates with breeding populations
Updated by including individuals/lines from the breeding population
Training more than one generation
Low colinearity between markers is needed since high colinearity tends to reduce prediction accuracy of certain GS models. (colinearity disturbed by recombination)
A new era of genomics for plant science research has opened due the complete genome sequencing projects of Arabidopsis thaliana and rice. The sequence information available in public database has highlighted the need to develop genome scale reverse genetic strategies for functional analysis (Till et al., 2003). As most of the phenotypes are obscure, the forward genetics can hardly meet the demand of a high throughput and large-scale survey of gene functions. Targeting Induced Local Lesions in Genome TILLING is a general reverse genetic technique that combines chemical mutagenesis with PCR based screening to identity point mutations in regions of interest (McCallum et al., 2000). This strategy works with a mismatch-specific endonuclease to detect induced or natural DNA polymorphisms in genes of interest. A newly developed general reverse genetic strategy helps to locate an allelic series of induced point mutations in genes of interest. It allows the rapid and inexpensive detection of induced point mutations in populations of physically or chemically mutagenized individuals. To create an induced population with the use of physical/chemical mutagens is the first prerequisite for TILLING approach. Most of the plant species are compatible with this technique due to their self-fertilized nature and the seeds produced by these plants can be stored for long periods of time (Borevitz et al., 2003). The seeds are treated with mutagens and raised to harvest M1 plants, which are consequently, self-fertilized to raise the M2 population. DNA extracted from M2 plants is used in mutational screening (Colbert et al., 2001). To avoid mixing of the same mutation only one M2 plant from each M1 is used for DNA extraction (Till et al., 2007). The M3 seeds produce by selfing the M2 progeny can be well preserved for long term storage. Ethyl methane sulfonate (EMS) has been extensively used as a chemical mutagen in TILLING studies in plants to generate mutant populations, although other mutagens can be effective. EMS produces transitional mutations (G/C, A/T) by alkylating G residues which pairs with T instead of the conservative base pairing with C (Nagy et al., 2003). It is a constructive approach for users to attempt a range of chemical mutagens to assess the lethality and sterility on germinal tissue before creating large mutant populations.
'Genomics' is nothing but the study of entire genetic compliment of an organism. Plant genomics is study of plant genome. This is my topic of M.Sc. course 'Plant biotechnology'.
Introduction:
Proposed by Meuwissen et al. (2001)
GS is a specialized form of MAS, in which information from genotype data on marker alleles covering the entire genome forms the basis of selection.
The effects associated with all the marker loci, irrespective of whether the effects are significant or not, covering the entire genome are estimated.
The marker effect estimates are used to calculate the genomic estimated breeding values (GEBVs) of different individuals/lines, which form the basis of selection.
Why to go for genomic selection:
Marker-assisted selection (MAS) is well-suited for handling oligogenes and quantitative trait loci (QTLs) with large effects but not for minor QTLs.
MARS attempts to take into account small effect QTLs by combining trait phenotype data with marker genotype data into a combined selection index.
Based on markers showing significant association with the trait(s) and for this reason has been criticized as inefficient
The genomic selection (GS) scheme was to rectify the deficiency of MAS and MARS schemes. The GS scheme utilizes information from genome-wide marker data whether or not their associations with the concerned trait(s) are significant.
GEBV: GenomicEstimated Breeding Values-
The sum total of effects associated with all the marker alleles present in the individual and included in the GS model applied to the population under selection
Calculated on a single individual basis
Gene-assisted genomic selection:
A GS model that uses information about prior known QTLs, the targeted QTLs were accumulated in much higher frequencies than when the standard ridge regression was used
The sum total of effects associated with all the marker alleles present in the individual and included in the GS model applied to the population under selection
Calculated on a single individual basis
Population used:
Training population: used for training of the GS model and for obtaining estimates of the marker-associated effects needed for estimation of GEBVs of individuals/lines in the breeding population.
Breeding population: the population subjected to GS for achieving the desired improvement and isolation of superior lines for use as new varieties/parents of new improved hybrids.
Training population-
large enough: must be representative of the breeding population: max. trait variance with marker : by cluster analysis
should have either equal or comparable LD, LD decay rates with breeding populations
Updated by including individuals/lines from the breeding population
Training more than one generation
Low colinearity between markers is needed since high colinearity tends to reduce prediction accuracy of certain GS models. (colinearity disturbed by recombination)
Genomics, proteomics and metabolomics are the three core omics technologies, which respectively deal with the analysis of genome, proteome and metabolome of cells and tissues of an organism.
Introduction
Transcriptome analysis
Goal of functional genomics
Why we need functional genomics
Technique
1. At DNA level
2.At RNA level
3. At protein level
4. loss of function
5. functional genomic and bioinformatics
Application
Latest research and reviews
Websites of functional genomics
Conclusions
Reference
Molecular Marker and It's ApplicationsSuresh Antre
Molecular (DNA) markers are segments of DNA that can be detected through specific laboratory techniques. With the advent of marker-assisted selection (MAS), a new breeding tool is now available to make more accurate and useful selections in breeding populations.
Marker Assisted Selection in Crop BreedingPawan Chauhan
Marker Assisted Selection is a value addition to conventional methods of Crop Breeding. It has been gaining importance in plant breeding with new generation of plant breeders and to get accurate and fast desired result from plant breeding.
Access to large-scale omics datasets i.e. genomics, transcriptomics, proteomics, metabolomics, phenomics, etc. has revolutionized biology and led to the emergence of systems approaches to advance our understanding of biological processes. With decreasing time and cost to generate these datasets, omics data integration has created both exciting opportunities and immense challenges for biologists, computational biologists, biostatisticians and biomathematicians. Genomics, transcriptomics, proteomics, and metabolomics together they help to bring out the best of characters in plants.
I would like to share this presentation file.
Some basics information regarding to molecular plant breeding, hope this help the beginner who start working in this field.
Thanks for many original source of information (mainly from slideshare.net, IRRI, CIMMYT and any paper received from professor and some over the internet)
Genotyping by Sequencing is a robust,fast and cheap approach for high throughput marker discovery.It has applications in crop improvement programs by enhancing identification of superior genotypes.
Genome Mapping And Biological Resources Slides.pptxAqsaZakaria
Genome Mapping is the process of determining the precise sequence of DNA nucleotides that make up an organism's genome.In rapidly evolving fields of Bioinformatics genome mapping & Biological resources interwine enabling groundbreaking discoveries in biological research. It helps in understanding life intricacies, paving a way for innovative applications in different fields.It helps in understanding the structure and function of genes, identifying genetic variations, and studying the genetic basis of diseases. Techniques like DNA sequencing and genetic markers are used for genome mapping.
In summery, Genome mapping provides critical insights into genetic makeup of biological resources ,enpowering researchers and stakeholders to utlilize these resources in different fields.
Genomics, proteomics and metabolomics are the three core omics technologies, which respectively deal with the analysis of genome, proteome and metabolome of cells and tissues of an organism.
Introduction
Transcriptome analysis
Goal of functional genomics
Why we need functional genomics
Technique
1. At DNA level
2.At RNA level
3. At protein level
4. loss of function
5. functional genomic and bioinformatics
Application
Latest research and reviews
Websites of functional genomics
Conclusions
Reference
Molecular Marker and It's ApplicationsSuresh Antre
Molecular (DNA) markers are segments of DNA that can be detected through specific laboratory techniques. With the advent of marker-assisted selection (MAS), a new breeding tool is now available to make more accurate and useful selections in breeding populations.
Marker Assisted Selection in Crop BreedingPawan Chauhan
Marker Assisted Selection is a value addition to conventional methods of Crop Breeding. It has been gaining importance in plant breeding with new generation of plant breeders and to get accurate and fast desired result from plant breeding.
Access to large-scale omics datasets i.e. genomics, transcriptomics, proteomics, metabolomics, phenomics, etc. has revolutionized biology and led to the emergence of systems approaches to advance our understanding of biological processes. With decreasing time and cost to generate these datasets, omics data integration has created both exciting opportunities and immense challenges for biologists, computational biologists, biostatisticians and biomathematicians. Genomics, transcriptomics, proteomics, and metabolomics together they help to bring out the best of characters in plants.
I would like to share this presentation file.
Some basics information regarding to molecular plant breeding, hope this help the beginner who start working in this field.
Thanks for many original source of information (mainly from slideshare.net, IRRI, CIMMYT and any paper received from professor and some over the internet)
Genotyping by Sequencing is a robust,fast and cheap approach for high throughput marker discovery.It has applications in crop improvement programs by enhancing identification of superior genotypes.
Genome Mapping And Biological Resources Slides.pptxAqsaZakaria
Genome Mapping is the process of determining the precise sequence of DNA nucleotides that make up an organism's genome.In rapidly evolving fields of Bioinformatics genome mapping & Biological resources interwine enabling groundbreaking discoveries in biological research. It helps in understanding life intricacies, paving a way for innovative applications in different fields.It helps in understanding the structure and function of genes, identifying genetic variations, and studying the genetic basis of diseases. Techniques like DNA sequencing and genetic markers are used for genome mapping.
In summery, Genome mapping provides critical insights into genetic makeup of biological resources ,enpowering researchers and stakeholders to utlilize these resources in different fields.
Genomic aided selection for crop improvementtanvic2
In last Several years novel genetic and genomics approaches are expended. Genetics and genomics have greatly enhanced our understanding of the structural and functional aspects of plant genomes.
Molecular Markers: Indispensable Tools for Genetic Diversity Analysis and Cro...Premier Publishers
Recent progress in molecular biology has led to the development of new molecular tools that offer the promise of making plant breeding faster. Molecular markers are segments of DNA associated with agronomically important traits and can be used by plant breeders as selection tools. Breeders can use marker-assisted selection (MAS) to bypass the traditional phenotype-based selection methods in order to improve crop varieties with pyramiding the desirable traits within short time. Various molecular markers such as RAPD, SSR, ISSR, RFLP, AFLP, SNP, SCAR, CAPS, etc. are extensively used for plant genetic diversity studies and crop improvement biotechnology. These markers are different in characteristic properties, applicability to various plants, unique in the resolving power and also have own advantages and disadvantages. This review article provides a valuable insight into different molecular marker techniques, classification, their advantages, disadvantages, ways of actions, uses of molecular markers in plant genetic diversity analysis and quantitative trait loci (QTL) mapping. It could be helpful for plant scientists and breeders in MAS breeding and crop improvement biotechnology in the post-genomic era.
This topic explains genomics and proteomics and types of genomics and proteoics and explains about positional cloning,microsatellites,SNP,VNTRS,HUMAN GENOME PRPJECT
Functional genomics is a general approach toward understanding how the genes of an organism work together by assigning new functions to unknown genes. Information about the hypothesized function of an unknown gene may be deduced from its sequence structure using already known functions of similar genes as the basis for comparison. Gene function analysis therefore necessitates the analysis of temporal and spatial gene expression patterns (Yunbi Xu et al , Plant Molecular Biology (2005) ).
Role of Marker Assisted Selection in Plant Resistance RandeepChoudhary2
Topic Role of Marker Assisted Selection in Plant Resistance is described in detail including some case studies.
Types of markers used in genetic engineering and biotechnology are described in detail.
Marker assisted selection is a process whereby a marker (morphological, biochemical or one
based on DNA/RNA variation) is used for indirect selection of a genetic determinant of a trait
of interest. Since the first reported linkage of an agronomically important trait (a quantitative
trait locus affecting seed weight) to a simply controlled gene (seed colour) in common bean by
Sax (1923), it has taken more than 60 years for genetic markers to become a qualified tool for
plant breeding programs. In rice, the Xieyou 218 hybrid was the first to be developed through
MAS to select individuals carrying a bacterial blight-resistant gene. Marker-assisted selection
(MAS) can be applied at the seedling stage, with high precision and reductions in cost. Genetic
mapping of major genes and quantitative traits loci (QTLs) for agricultural traits is increasing
the integration of biotechnology with the conventional breeding process. Traits related to
disease resistance to pathogens and to the quality of some crop products are offering some
important examples of a possible routinary application of MAS. For more complex traits, like
yield and abiotic stress tolerance, a number of constraints have severe limitations on an efficient
utilization of MAS in plant breeding. However, the economic and biological constraints such
as a low return of investment in small-grain cereal breeding, lack of diagnostic markers, and
the prevalence of QTL-background effects hinder the broad implementation of MAS but over
the past 2 decades, a number of R-genes conferring resistance to a diverse range of pathogens
have been mapped in many crops using molecular markers.
Genomics is a discipline in genetics that applies recombinant DNA, DNA sequencing methods, and bioinformatics to sequence, assemble and analyze the function and structure of genomes
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Genomics and its application in crop improvement
1. MASTER SEMINAR
ON
GENOMICS AND ITS APPLICATION IN CROP
IMPROVEMENT
DATE-24/03/2018
SPEAKER
KHEMLATA THAKUR
M.Sc. (Ag.) Previous
Dept. of Genetics & Plant Breeding
CoA, I.G.K.V, Raipur
2. CONTENTS
• Meaning of Genomics
• Types of Genomics
• Classification of Genomics
• Genome sequencing
• Genes to be Mapped
• Genome Mapping in India
• Role of Genomics in Crop Improvement
• Limitations of Genomics
3. WHAT IS GENOMICS?
• Genomics term was given by Thomas Roderick in
1986.
• Genomics = the branch of molecular biology
concerned with the structure, function, evolution and
mapping of genomes.
• Genome = the complete set of genes or genetic
material present in a cell or organism.
4. Genomics is the sub discipline of genetics
devoted to the
mapping,
sequencing ,
and functional analysis of
genome
The field includes studies of
intra-genomic phenomena
such as heterosis, epistasis,
pleiotropy and other
interactions between loci
and alleles within the genome.
6. Main points related to genomics
It is a computer aided study of structure and function of entire
genome of an organism.
It deals with mapping and sequencing of genes on the
chromosomes.
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 use of genomic techniques has become indispensable in
plant breeding and genetics.
10. GENOME SEQUENCING
Genome sequencing is figuring out the
order of DNA nucleotides, or bases, in a
genome-the order of A, C, G, and T that
make up an organism's DNA.
The human genome is made up of over 3
billion of these genetic letters.
11. Why we need to sequence genome ??
• It determines complete genetic information present in
the genome.
• It provides insights on genome organization and
evolution.
• It has opened up exciting areas for functional
genomics.
• It allows to workout the various molecular interactions.
• Information like SNPs have become available.
• It may provide an understanding of
pharmacogenomics.
• Better understanding of human genetic disease .
• Pathogenicity would be better understood.
13. ACHIEVEMENTS
EVENTS YEAR
• Discussion in scientific community for sequencing genome 1984-1990
• Human genome project proposed 1986
• Human genome project initiated Oct .1,1990
• Haemophilu influenzae genome sequenced 1995
• E.coli genome sequenced 1997
• Yeast (Saccharomyces cerevisiae) genome sequenced 1999
• Worm (Caenorhabditis elegans) genome sequenced 1999
• Arabidopsis thaliana(a weed) genome sequenced 2000
• Human genome working draft published (90% genome
sequenced)
June 26,2001
14. Genome Size and Gene Number
in some crop plants
CROPS GENOME
SIZE(Mb)
GENE
NO.
YEAR REFERENCE
1) Rice (Oryza sativa) 370 40577 2002 Goff, et al.,
2) Corn (Zea mays) 2500 >32000 2009 Schnable, P et al.
3) Sorghum
(Sorghum bicolor )
700 34496 2009 Paterson , A et al
4) Wheat
(Triticum urartu)
392 - 2013 Ling HQ et al
5) Arabidopsis
(Arabidopsis thaliana)
120 27417 2000 -
6) Soybean
(Glycine max)
950 46430 2010 Haung, et al.
7) Pigeon pea
(Cajanus cajan)
833 48680 2011 Varshney , et al,
8)Potato
(Solanum tuberosum)
844 39031 2011 PGS Constorium
9)Flax
(Linum usitatissimum)
686 43384 2012 Wang,et al
15. Gene to be mapped
Morphological Characters:
It includes highly heritable traits such as shape, size and colour of
leaf, flower ,calyx, corolla, etc. It also includes surface of leaf
and stem (hairiness and smoothness).
Productivity traits:
Such characters differ from species to species.
Resistance Traits:
Such characters include resistance to diseases, insects, drought,
soil salinity, soil alkalinity, soil acidity, heat, frost, water logging, cold, etc.
Quality Traits:
Such traits include nutritional quality, market quality and keeping quality.
Agronomic Traits:
Such traits include earliness, plant height, plant type, etc.
Special Characters:
Such characters include genes controlling male sterility, self
incompatibility, photo and thermo-insensitivity, toxic
substances, apomixes, adaptation, etc.
16. Conventional breeding to molecular
breeding
through Genomic research ?
Through conventional breeding, selection for crop
improvement is carried out on phenotypic character, which is
the result of genotypic and environmental effects.
The difficulties of phenotype based selection can be
overcome by direct selection for genotype using DNA
markers that co-segregate with the genes of interest.
Many potential genes that confer resistance have been
mapped in economical crops like rice.
17. Contd…..
In conventional breeding normally options of presence of genes can
be identified, when expression where comes during adverse
condition. By the use of genomic research now we can easily identify
the presence or absence of gene in early stage.
By the use of molecular markers exact location of particular gene on
chromosome can easily be identified.
Presence of all of the important genes and related markers will be
very much helpful to identified and development of new cultivars as
we desire - Varietal identification.
Insertion and deletions are desirable or undesirable, easily be
possible to identify with the sequencing of genome.
18.
19.
20. Genome Mapping in India:
• In India, the functional genome research projects are looked after
by the Depart of Biotechnology [DBT] and ICAR.
• The DBT has initiated such work on several crops such as rice,
wheat, maize, chick pea, banana, tomato, Brassica, etc.
• The ICAR has created genome mapping facilities for rice at
NRC-PB, IARI, New Delhi.
• In India, the genome mapping work is carried out at the following
centres.
i. National Research Centre for Plant Biotechnology, IARI, New
Delhi.
ii. International Centre for Genetic Engineering and
Biotechnology, New Delhi.
iii. Jawahar Lal Nehru University, New Delhi.
iv. National Botanical Research Institute, Lucknow.
21. Application of Genomics in Crop
Improvement
•Genome size
•Gene number
•Gene mapping
•Gene sequencing
•Evolution of crop plants
•Gene cloning
•Identification of DNA markers
•Marker assisted selection
•Transgenic breeding
•Construction of linkage maps
•QTL mapping
It is useful
and
provides
information
about
28. results
• An indica variety with small grain size was crossed to a
japonica variety with large grain size to construct a set of
recombinant inbred lines (RILs) which was used to identify
quantitative trait loci (QTLs) controlling eight grain quality
traits.
• Based on a linkage map of 185 SSR markers, a total of 16
QTLs were mapped on six chromosomes.
• A pleiotropic main effect QTL (M-QTL) flanked by RM3204
and RM16 on chromosome 3 influences the grain length (GL),
length width ratio (LWR) and head rice ratio (HRR), explaining
the phenotypic variation of 46.0, 36.1 and 29.7%, respectively.
• A total of 18 epistatic QTLs were identified for all the traits ,
distributed on all the chromosomes except chromosome 10.
29. GENOMICS STATUS at RRL,IGKV
• Almost all the facilities are available for genomics
• work on structural genomics, functional genomics, are
carried on in RRL
• All kind of markers are available in RRL like SSR. RAPD
etc. For selection, pyramiding .
• Gene mapping ,gene sequencing is done in various crops such
as vegetables, oilseeds basically in rice.
• Advance euipment’s present in RRL are PCR machine, gel
electrophoresis.
• ion torrent machine for gene sequencing
• Availabilty of Taqman based SNP Genotyping.
31. CONCLUSION
.
• Marker technology has rapidly exerted influence in plant
breeding due to advances in genomics.
• Functional markers have contributed to diagnostics technology
that enable identification of molecules or sequences that
contribute or participate during plant response to various
stresses.
• This has enabled designing of better crop/plant varieties.
• The future of food security depends on availability of funding
to improve agricultural practises for millions of people in
developing countries who depend on it as a source of income
and to ensure the worlds poor are foods secure.