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.
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.
Genomics and its application in crop improvementKhemlata20
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
Association mapping, also known as "linkage disequilibrium mapping", is a method of mapping quantitative trait loci (QTLs) that takes advantage of linkage disequilibrium to link phenotypes to genotypes.Varioius strategey involved in association mapping is discussed in this presentation
it cover almost all content in cis/intragesis, right from introduction definition, explanation, production of marker free transgenic, intragenic vector construction, regulatory guide lines, current and future status, limitation, advantage over existing technique, swot analysis etc
its very useful for your seminar and presentations. it contain lot of picture, table, figure for your easy understanding
thank you
Mahesh
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.
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.
Genomics and its application in crop improvementKhemlata20
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
Association mapping, also known as "linkage disequilibrium mapping", is a method of mapping quantitative trait loci (QTLs) that takes advantage of linkage disequilibrium to link phenotypes to genotypes.Varioius strategey involved in association mapping is discussed in this presentation
it cover almost all content in cis/intragesis, right from introduction definition, explanation, production of marker free transgenic, intragenic vector construction, regulatory guide lines, current and future status, limitation, advantage over existing technique, swot analysis etc
its very useful for your seminar and presentations. it contain lot of picture, table, figure for your easy understanding
thank you
Mahesh
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.
Quantitative trait loci (QTL) analysis and its applications in plant breedingPGS
Abstract
Many agriculturally important traits such as grain yield, protein content and relative disease resistance are controlled by many genes and are known as quantitative traits (also polygenic or complex traits). A quantitative trait depends on the cumulative actions of many genes and the environment. The genomic regions that contain genes associated with a quantitative trait are known as quantitative trait loci (QTLs). Thus, a QTL could be defined as a genomic region responsible for a part of the observed phenotypic variation for a quantitative trait. A QTL can be a single gene or a cluster of linked genes that affect the trait. The effects of individual QTLs may differ from each other and change from environment to environment. The genetics of a quantitative trait can often be deduced from the statistical analysis of several segregating populations. Recently, by using molecular markers, it is feasible to analyze quantitative traits and identify individual QTLs or genes controlling the traits of interest in breeding programs.
A concise and well fabricated presentation the current techniques used for plant genome editing including CRISPER/cas9 system, TALENS, TELES, ZINC FINGER NUCLEASES(ZFN), HEJ (homologous endjoing) and many other high throughout techniques along references.
Role of Pangenomics for crop ImprovementPatelSupriya
It describes about the role of pangenomics in the crop improvement.It includes pangenome,superpangenome,databases,tools used in pangenomics,utilisation in crop improvement
Molecular Breeding in Plants is an introduction to the fundamental techniques...UNIVERSITI MALAYSIA SABAH
This slide describe the process of molecular breeding in plants which involves the application of molecular markers for Marker Assisted Selection and Marker Assisted Breeding.
Banoth Madhu: Map based gene cloning in plant. In the process of map-based cloning, one starts with a mutant and eventually identifies the gene responsible for the altered phenotype, allowing the plant to tell you what genes are important in the physiological process of interest and using the genetic relationship between a gene and a marker as the basis for beginning a search for a gene
Gene stacking is a type of gene cloning that refers to the process of combining two or more genes of interest into a single plant. The emerging combined traits from this process are called stacked traits. A genetically engineered crop variety that bears stacked traits is called a biotech stack or simply stack.
Quantitative trait loci (QTL) analysis and its applications in plant breedingPGS
Abstract
Many agriculturally important traits such as grain yield, protein content and relative disease resistance are controlled by many genes and are known as quantitative traits (also polygenic or complex traits). A quantitative trait depends on the cumulative actions of many genes and the environment. The genomic regions that contain genes associated with a quantitative trait are known as quantitative trait loci (QTLs). Thus, a QTL could be defined as a genomic region responsible for a part of the observed phenotypic variation for a quantitative trait. A QTL can be a single gene or a cluster of linked genes that affect the trait. The effects of individual QTLs may differ from each other and change from environment to environment. The genetics of a quantitative trait can often be deduced from the statistical analysis of several segregating populations. Recently, by using molecular markers, it is feasible to analyze quantitative traits and identify individual QTLs or genes controlling the traits of interest in breeding programs.
A concise and well fabricated presentation the current techniques used for plant genome editing including CRISPER/cas9 system, TALENS, TELES, ZINC FINGER NUCLEASES(ZFN), HEJ (homologous endjoing) and many other high throughout techniques along references.
Role of Pangenomics for crop ImprovementPatelSupriya
It describes about the role of pangenomics in the crop improvement.It includes pangenome,superpangenome,databases,tools used in pangenomics,utilisation in crop improvement
Molecular Breeding in Plants is an introduction to the fundamental techniques...UNIVERSITI MALAYSIA SABAH
This slide describe the process of molecular breeding in plants which involves the application of molecular markers for Marker Assisted Selection and Marker Assisted Breeding.
Banoth Madhu: Map based gene cloning in plant. In the process of map-based cloning, one starts with a mutant and eventually identifies the gene responsible for the altered phenotype, allowing the plant to tell you what genes are important in the physiological process of interest and using the genetic relationship between a gene and a marker as the basis for beginning a search for a gene
Gene stacking is a type of gene cloning that refers to the process of combining two or more genes of interest into a single plant. The emerging combined traits from this process are called stacked traits. A genetically engineered crop variety that bears stacked traits is called a biotech stack or simply stack.
TILLING AND ECO TILLING IN CROP IMPROVEMENT.pptxrushitahakik1
TILLING AND ECO TILLING in crop Improvement
A Reverse genetics Tool that enhences the potential to introduce specific mutation in oplants in order to improve crop diversity. i.e. Biotechnology beyound Genetically Modified crops.
CD Genomics is dedicated to providing a comprehensive list of genomics and microarray solutions for agriculture, including genome, exome, transcriptome, and metagenome sequencing, genome-wide association studies (GWAS), and targeted sequencing and genotyping that focus on a subset of regions or genes such as single nucleotide polymorphisms (SNPs). https://www.cd-genomics.com/Transcriptomics.html
Marker assisted selection or marker aided selection is an indirect selection process where a trait of interest is selected based on a marker linked to a trait of interest, rather than on the trait itself. This process has been extensively researched and proposed for plant and animal breeding.Marker-assisted breeding uses DNA markers associated with desirable traits to select a plant or animal for inclusion in a breeding program early in its development. ... This genetic test is helping breeders to select for hornless cattle, which makes it safer for the animals themselves and the people handling them.
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) ).
Process whereby a marker is used for indirect selection of a genetic determinant or determinants of a trait of interest (i.e. productivity, disease resistance, abiotic stress tolerance, and/or quality).
Trait of interest is selected not based on the trait itself but on a marker linked to it.
The assumption is that linked allele associates with the gene and/or quantitative trait locus (QTL) of interest. MAS can be useful for traits that are difficult to measure, exhibit low heritability, and/or are expressed late in development.
Pre-Requisites: Two pre-requisites for marker assisted selection are: (i) a tight linkage between molecular marker and gene of interest, and (ii) high heritability of the gene of interest.
Markers Used: The most commonly used molecular markers include amplified fragment length polymorphisms (AFLP), restriction fragment length polymorphisms (RFLP), random amplified polymorphic DNA (RAPD), simple sequence repeats (SSR) or micro satellites, single nucleotide polymorphisms (SNP), etc. The use of molecular markers differs from species to species also.
A powerful non-transgenic reverse genetics method that combines chemical mutagenesis with PCR based screening to identify point mutations in regions of interest.
EcoTILLING is a molecular technique that is similar to TILLING, except that its objective is to uncover natural genetic variation as opposed to induced mutations.
Nutraceutical market, scope and growth: Herbal drug technologyLokesh Patil
As consumer awareness of health and wellness rises, the nutraceutical market—which includes goods like functional meals, drinks, and dietary supplements that provide health advantages beyond basic nutrition—is growing significantly. As healthcare expenses rise, the population ages, and people want natural and preventative health solutions more and more, this industry is increasing quickly. Further driving market expansion are product formulation innovations and the use of cutting-edge technology for customized nutrition. With its worldwide reach, the nutraceutical industry is expected to keep growing and provide significant chances for research and investment in a number of categories, including vitamins, minerals, probiotics, and herbal supplements.
Richard's aventures in two entangled wonderlandsRichard Gill
Since the loophole-free Bell experiments of 2020 and the Nobel prizes in physics of 2022, critics of Bell's work have retreated to the fortress of super-determinism. Now, super-determinism is a derogatory word - it just means "determinism". Palmer, Hance and Hossenfelder argue that quantum mechanics and determinism are not incompatible, using a sophisticated mathematical construction based on a subtle thinning of allowed states and measurements in quantum mechanics, such that what is left appears to make Bell's argument fail, without altering the empirical predictions of quantum mechanics. I think however that it is a smoke screen, and the slogan "lost in math" comes to my mind. I will discuss some other recent disproofs of Bell's theorem using the language of causality based on causal graphs. Causal thinking is also central to law and justice. I will mention surprising connections to my work on serial killer nurse cases, in particular the Dutch case of Lucia de Berk and the current UK case of Lucy Letby.
The ability to recreate computational results with minimal effort and actionable metrics provides a solid foundation for scientific research and software development. When people can replicate an analysis at the touch of a button using open-source software, open data, and methods to assess and compare proposals, it significantly eases verification of results, engagement with a diverse range of contributors, and progress. However, we have yet to fully achieve this; there are still many sociotechnical frictions.
Inspired by David Donoho's vision, this talk aims to revisit the three crucial pillars of frictionless reproducibility (data sharing, code sharing, and competitive challenges) with the perspective of deep software variability.
Our observation is that multiple layers — hardware, operating systems, third-party libraries, software versions, input data, compile-time options, and parameters — are subject to variability that exacerbates frictions but is also essential for achieving robust, generalizable results and fostering innovation. I will first review the literature, providing evidence of how the complex variability interactions across these layers affect qualitative and quantitative software properties, thereby complicating the reproduction and replication of scientific studies in various fields.
I will then present some software engineering and AI techniques that can support the strategic exploration of variability spaces. These include the use of abstractions and models (e.g., feature models), sampling strategies (e.g., uniform, random), cost-effective measurements (e.g., incremental build of software configurations), and dimensionality reduction methods (e.g., transfer learning, feature selection, software debloating).
I will finally argue that deep variability is both the problem and solution of frictionless reproducibility, calling the software science community to develop new methods and tools to manage variability and foster reproducibility in software systems.
Exposé invité Journées Nationales du GDR GPL 2024
Remote Sensing and Computational, Evolutionary, Supercomputing, and Intellige...University of Maribor
Slides from talk:
Aleš Zamuda: Remote Sensing and Computational, Evolutionary, Supercomputing, and Intelligent Systems.
11th International Conference on Electrical, Electronics and Computer Engineering (IcETRAN), Niš, 3-6 June 2024
Inter-Society Networking Panel GRSS/MTT-S/CIS Panel Session: Promoting Connection and Cooperation
https://www.etran.rs/2024/en/home-english/
ISI 2024: Application Form (Extended), Exam Date (Out), EligibilitySciAstra
The Indian Statistical Institute (ISI) has extended its application deadline for 2024 admissions to April 2. Known for its excellence in statistics and related fields, ISI offers a range of programs from Bachelor's to Junior Research Fellowships. The admission test is scheduled for May 12, 2024. Eligibility varies by program, generally requiring a background in Mathematics and English for undergraduate courses and specific degrees for postgraduate and research positions. Application fees are ₹1500 for male general category applicants and ₹1000 for females. Applications are open to Indian and OCI candidates.
The use of Nauplii and metanauplii artemia in aquaculture (brine shrimp).pptxMAGOTI ERNEST
Although Artemia has been known to man for centuries, its use as a food for the culture of larval organisms apparently began only in the 1930s, when several investigators found that it made an excellent food for newly hatched fish larvae (Litvinenko et al., 2023). As aquaculture developed in the 1960s and ‘70s, the use of Artemia also became more widespread, due both to its convenience and to its nutritional value for larval organisms (Arenas-Pardo et al., 2024). The fact that Artemia dormant cysts can be stored for long periods in cans, and then used as an off-the-shelf food requiring only 24 h of incubation makes them the most convenient, least labor-intensive, live food available for aquaculture (Sorgeloos & Roubach, 2021). The nutritional value of Artemia, especially for marine organisms, is not constant, but varies both geographically and temporally. During the last decade, however, both the causes of Artemia nutritional variability and methods to improve poorquality Artemia have been identified (Loufi et al., 2024).
Brine shrimp (Artemia spp.) are used in marine aquaculture worldwide. Annually, more than 2,000 metric tons of dry cysts are used for cultivation of fish, crustacean, and shellfish larva. Brine shrimp are important to aquaculture because newly hatched brine shrimp nauplii (larvae) provide a food source for many fish fry (Mozanzadeh et al., 2021). Culture and harvesting of brine shrimp eggs represents another aspect of the aquaculture industry. Nauplii and metanauplii of Artemia, commonly known as brine shrimp, play a crucial role in aquaculture due to their nutritional value and suitability as live feed for many aquatic species, particularly in larval stages (Sorgeloos & Roubach, 2021).
What is greenhouse gasses and how many gasses are there to affect the Earth.moosaasad1975
What are greenhouse gasses how they affect the earth and its environment what is the future of the environment and earth how the weather and the climate effects.
DERIVATION OF MODIFIED BERNOULLI EQUATION WITH VISCOUS EFFECTS AND TERMINAL V...Wasswaderrick3
In this book, we use conservation of energy techniques on a fluid element to derive the Modified Bernoulli equation of flow with viscous or friction effects. We derive the general equation of flow/ velocity and then from this we derive the Pouiselle flow equation, the transition flow equation and the turbulent flow equation. In the situations where there are no viscous effects , the equation reduces to the Bernoulli equation. From experimental results, we are able to include other terms in the Bernoulli equation. We also look at cases where pressure gradients exist. We use the Modified Bernoulli equation to derive equations of flow rate for pipes of different cross sectional areas connected together. We also extend our techniques of energy conservation to a sphere falling in a viscous medium under the effect of gravity. We demonstrate Stokes equation of terminal velocity and turbulent flow equation. We look at a way of calculating the time taken for a body to fall in a viscous medium. We also look at the general equation of terminal velocity.
Observation of Io’s Resurfacing via Plume Deposition Using Ground-based Adapt...Sérgio Sacani
Since volcanic activity was first discovered on Io from Voyager images in 1979, changes
on Io’s surface have been monitored from both spacecraft and ground-based telescopes.
Here, we present the highest spatial resolution images of Io ever obtained from a groundbased telescope. These images, acquired by the SHARK-VIS instrument on the Large
Binocular Telescope, show evidence of a major resurfacing event on Io’s trailing hemisphere. When compared to the most recent spacecraft images, the SHARK-VIS images
show that a plume deposit from a powerful eruption at Pillan Patera has covered part
of the long-lived Pele plume deposit. Although this type of resurfacing event may be common on Io, few have been detected due to the rarity of spacecraft visits and the previously low spatial resolution available from Earth-based telescopes. The SHARK-VIS instrument ushers in a new era of high resolution imaging of Io’s surface using adaptive
optics at visible wavelengths.
2. Introduction:
• Green revolution enabled India to achieve self suffiency in
food production, but still there is a continuous challenge to
futher increase agricultural production to feed the growing
population of India.
• Recent developments in the field of Omics technologies hold
immense potential to reshape India agriculture through green
revolution.
• 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.
3.
4. Genomics
• The comprehensive study of whole sets of genes and their
interactions
• It investigates the variation in genes and how it affects
protein structure and function throughout the life of a cell.
• Genomics is the sub disciplines of genetics devoted to
i. mapping,
ii. sequencing and
iii. functional analysis of genomes
5. From Classical genetics to genomics
Classical genetics
Phenotypic ratio= 3: 1 Genotypic ratio = 1: 2: 1
Drawbacks:
• Linkage between
different genes are not
known.
• Location of genes
unknown
• Simple and qualitative
characters
• Requires more time
because of
morphological selection
• Environmental influences
6.
7. Phenotypic selection vs Marker assisted selection
• Less precise and reliable,
• Time consuming
• Simpler compared to phenotypic
selection,
• Selection at seedling stage
8. Genomic selection for crop improvement
• Two primary
limitations of MAS
1) the biparental
mapping populations
used in most QTL
studies do not readily
translate to breeding
applications
2) statistical methods
used are ill-suited to
the traits polygenic
nature
Genomic selection (GS) has been proposed to address these deficiencies.
GS reduces cycle time & cost by reducing frequency of phenotyping.
10. Overview of a
crop trait
discovery
pipeline
generating a
genome sequence
from fragmented
sequencing reads
to identify the
differences between
the DNA of the
specific individuals
sequenced with the
reference genome
where genomic
sequencing of crop
populations can
allow gene-level
resolution of
agronomic variation
determines the
phenotypic effect of
altered sequences of
specific genes or
regulatory regions
11. Trait mapping using QTL and GWAS
• The QTL analysis bridging the gap between
genomics and the field.
limitations of QTL
mapping
• low resolution caused
by coarse mapping
• only allelic diversity
present in the parents
of the segregating
population can be
assayed
These limitations of QTL
mapping overcomed by
GWAS, employed to
pinpoint genomic regions
linked to traits in diverse,
unrelated populations.
12. Forward and Reverse Genetic Screening
Forward genetic screening
- improve gene cloning and
marker development
- excludes intergenic sequences
Reverse genetic screening
- Targeted Induced Local
Lesions in Genomes (TILLING),
a reverse genetic approach, can
take advantage of conventional
mutation Induction
- providing the capability of
recovering mutations from
any genetic regions and discover
novel phenotypes
13. Advantage of GS over QTL, GWAS or
Reverse genetics
QTL
GWAS
Reverse
genetics
Based on genotyed and phenotyed training
population
Calculating the genomic estimated breeding
values (GEBV) for sets of variants
overcomes inefficient translation of QTL analysis
results from biparental mapping populations
to breeding
combination of GS with automated phenotyping
techniques can further promote prediction
accuracy of GEBV, shortening the breeding cycle
Not essential for
genomics-based
breeding
Difficult to detect
targeting polygenic
agronomic traits
such as yield,
minor effect alleles
Genomic
selection
14.
15. WHAT IS COMPARATIVE GENOMICS?
Analyzing & comparing genetic material from different
species to study
evolution, gene function, and inherited disease
Understand the uniqueness between different species
16. Comparative genomics is a powerful
tool allowing us:
to link genomic changes to
environmental adaptation
to transfer knowledge from
model species to other plants
to trace structural changes
within a genome through time
17. Application of Genomics in Crop
Improvement
• It also reduces the gap between phenotype and genotype.
• It helps in assaying genetic makeup of the individual plants rapidly, so as
to select desirable genotypes in breeding populations, and to design the
superior genotypes for ‘breeding by design’ approach.
• With genomic approaches, the marker-assisted breeding or marker-
assisted selection will gradually evolve into ‘genomics-assisted breeding’
for crop improvement.
• The identification of genes that control economically important traits
provide the basis for new progress in genetic improvement of crop
species, complementing traditional methods based on assisted crosses.
Thus, a genome programme can be envisioned as a highly important tool
for crop improvement.
18. The whole genome contains both the coding and non-
coding genes (that are not related to heritable
phenotypes)
The transcriptomics analysis based only on
coding genes i.e., exons are transcribed and
the translated into proteins.
Limitations of genomics over transcriptomics:
19. Epigenomics
The term epigenetics refers to heritable changes in gene
expression that does not involve changes to the underlying
DNA sequence; a change in phenotype without a change in
genotype.
An epigenome consists of a record of the chemical changes
to the DNA and histone proteins of an organism.
Changes in the epigenome can result in changes to the
structure of chromatin and changes to the function of the
genome.
20. A Lamarckian idea that the act of stretching one's neck
could lead to change in phenotype across generations.
Lamarck's mechanism for evolution is The inheritance of acquired traits.
He believed that traits altered or acquired over an individual's lifetime
could be transferred down to its offspring.
HISTORY
23. Characteristic symptoms of Foc TR4 in
susceptible and resistant banana
WT cavendish
Resistant line RGA2,
from transgenic
cavendish
•Race 1 was involved in the 1960s Panama disease
attacks members of the banana AAB genomic group.
Cavendish cultivars are resistant to Race 1.
•Race 2 infects cooking bananas with ABB genome
and the Bluggoe subgroup.
•Race 3 infecting Heliconia spp. is no longer
considered pathogenic to bananas.
•Race 4 is the causal agent of the current Panama
disease outbreak since it is pathogenic to the
currently used Cavendish cultivars (AAA genome).
Race 4 is further subdivided into Tropical Race 4
(TR4) and Subtropical Race 4 (STR4). The latter
only infects Cavendish
Fusarium oxysporum f. sp. cubense
tropical race 4
24. DNA methylation patterns of banana leaves in response to
Fusarium oxysporum f. sp. cubense tropical race 4
Pathogen infected experiment
on in vitro banana leaves at 0,
4, 12, 24 h, 3 and 6 d post
inoculation. A, mock
inoculated group. B, infected
group.
A
B
In this study, with methylation-sensitive
amplification polymorphism (MSAP) technique,
DNA methylation was compared between the leaves
inoculated with Foc TR4 and the mock-inoculated
leaves at different pathogenic stages
Arrows indicated the polymorphic
fragments of methylation.
25. (contd..)
Results:
• DNA methylation was both
changed and the average
methylated CCGG sequences were
34.81 and 29.26% for the infected
and the mock-inoculated leaves.
• DNA hypermethylation and
hypomethylation were induced by
pathogen infection during all
pathogenic stages.
This results suggest that DNA methylation plays important roles in pathogenic
response to Foc TR4 for banana.
• RT-PCR results of four genes indicated that
their expression patterns were consistent
with their methylation patterns.
26. Transcriptomics
• Transcriptomics deals with the analysis of gene expression
patterns across a wide array of cellular responses,
phenotypes and conditions.
• The identification of candidate genes influencing any
important trait can be approached through an analysis of
gene transcripts or mRNAs.
• It is possible to determine when and where a gene is turned
on or off in various types of cells and tissues by analyzing
the transcriptome.
27. Post sequencing analysis
TOPHAT2
Cufflink program
Cuffdiff program
BLAST2GO program
0
2000
4000
6000
8000
10000
12000
14000
16000
18000
Transcripts
C S vs C R UR vs C R US vs C S US vs UR
C ombination
Neutral
UP
Down
LB
hpt
expression
cassette
pCaMV35S
Musa DIR11
CDS
RB
tnos
PmlINcoI
TRANSCRIPTOMIC APPROACH FOR SIGATOKA RESISTANCE
Resistant responsive pathways
Susceptible responsive pathways
Differential Gene Expression Gene Ontology
Resistant mechanism
Sigatoka Component
R genes
1. LRR
2. LRR/serine/threonine-
protein kinase
28. Creation of simulated drought stress &
stress imposition on selected banana
cultivars
Comparative Transcriptomics
Transcriptome sequencing –Illumina
Hi-seq
162.36 million reads (CT,DT) = nr unigenes-23,096
126.58 million reads (CS,DS)= nr unigenes -23,079
Selection of putative drought
tolerance genes
Diff. gene expn.
CT vs. DT, CS vs. DS
NCBI- SRP087441
Validation of some of the genes
by 2 D PAGE for Proteins (43)
q RT-PCR Validation for sel.
Candidate genes (6 DEGs)
Long non-coding RNAs
(lncRNAs)- 905
Full length gene isolation
Protein coding genes/mRNAs
2268 (T) and 2963 (S)
A.TIP3-1
B. GST
C. Wax syn
D. CUT-1
E. HSP
F. ABC I-17
Eval. of genetically transformed
plants for drought tolerance
Development of transgene
construct
pBM GF-DC-34
11730 bp
NPTII (Becks)
APsy2a
Left border 1
Left Border 2
Right Border
pVS1 sta
pBR322 bom
Nos promoter
Maize Ubiquitin Promoter
pBR322 ori
pVS1 rep
Nos Terminator
nos terminator
SmaI (6976)
XmaI (6974)
XmnI (5539)
EcoRI (3455)
HindIII (6943)
StuI (4200)
StuI (6989)
BamHI (4934)BamHI (6955)
KpnI (6941)
KpnI (6953)
Tolerant cv. Saba (ABB) ;
Sensitive cv. Grand Naine
(AAA)
Identification of Molecular targets for Drought Tolerance
Comparative
Proteomics
Drought Component
30. Limitations of transcriptomics over proteomics:
• All the transcribed mRNA are not translated into proteins
because of transcriptional gene silencing, RNA interference,
transposon gene silencing.
• This caused the RNA unable to make protein during
translation.
31. Proteomics
• The study of proteome, the structure and function of
complete set of protein in a cell at a given time.
• It is used to know plant-insect interactions that help identify
candidate genes involved in the defensive response of plants
to herbivore.
32.
33. Studies on molecular basis of somatic embryogenesis
and its manipulation in recalcitrant banana cultivars
34. Methodology
Different Stages of SE
SDS- PAGE
2DE
MALDI-TOF MS/MS
Annotation
RNA
qRT-PCR
Gene expression
Phytohormone Analysis Proteomic Analysis
TranscriptAnalysis
Antioxidantenzyme
Assay
POX
CAT
SOD
Media
Manipulation
1
23
4
5
ResultAnalysis
36. Results
Spot
No
Protein Cultivar Triggering
component
20
9
Indole-3-pyruvate
monooxygenase
Glutathione S-
transferase
Grand
Naine
Rasthali
*Tryptophan
*Increased conc.
of IAA
16 adenylate
isopentenyltransfe
rase
Grand
Naine
*Applying
cytokinins like
BAP and Kinetin.
37 calcium-binding
mitochondrial
carrier protein
Rasthali *Increased
concentration of
Calcium chloride
7 calcium-dependent
protein kinase
Rasthali *Increased
concentration of
Calcium chloride
Spot No Protein Cultivar Triggering
component
1 and 13 SAUR-like auxin-
responsive family
protein
Grand
Naine
NAA
13 and 55 Glutaredoxin Rasthali NAA
9 Glutathione S
transferase
Rasthali NAA , ethryl, cold
treatment
19, 61 and
67
Ethylene responsive
transcription factor
Rasthali Methionine, Ethryl
56 Calcium dependent
protein kinase
Rasthali CaCl2, cold
treatment
63 methylthioalkyl
malate synthase
Rasthali Methionine
27 and 28 cysteine proteinase
inhibitor
Grand
Naine
cold treatment
3 3-ketoacyl-CoA
synthase 11
Grand
Naine
cold treatment
8 Oleosin 18.5 kDa Grand
Naine
cold treatment
Stimulation of highly expressed proteins via exogenous application Induction of highly expressed proteins via exogenous application
37. Establishment of ECS in Recalcitrant banana cultivarsGrandNaineRedBananaMonthanNeyPoovanKarpuravalliSabri
Cultivar Media
Augmentation
Improved EC
induction
(%) over
control
Grand
Naine
IAA (11.41
µM)
> 200
Red
Banana
Tryptophan
(2.32 µM )
> 250
Monthan Tryptophan
(489.64 µM)
> 200
Ney
Poovan
Tryptophan
(489.64 µM)
> 300
Karpurav
alli
CaCl2 (10
mM)
> 400
Sabri IAA (11.41
µM)
>700
Flower Buds Embryogenic callus Cells with starch Cells with Nucleus ECS
38. Effect of Cold treatment @ 4 ˚C for 24 hr on Germination
Modified germination
medium
Shooting medium
Well Rooted plants
Primary hardening
Secondary hardening
Genetic fidelity
cv. Ney Poovan cv. Red Banana cv. Sabri
39. Application of Proteomics
• In Arabidopsis, while studying the role of GAs during
initial stages of seed germination, and the impact of
scarification on seed germination, application of
proteome analysis resulted in better understanding of the
complex cellular events.
• Similarly, in barley, the proteome analysis revealed new
insights into cellular mechanisms underlying seed
development during grain filling and seed maturation
phases.
40. Contd..
• In rice, proteome studies have helped in detecting novel
traits useful for breeding.
• Both abiotic and biotic stresses can bring about
dramatic changes to the plant proteome, andthese are
manifested as the up- or down- regulation of proteins,
or their post translation modification.
41. Metabolomics
• Study of metabolome, collection of all metabolites in a cell,
tissue, organ or organism.
• The metabolites determine the flavour, aroma, colour and
texture of crops, their storage properties and performance in
field (Memelink, 2005).
42. Global metabolomics analysis reveals distinct tolerance
mechanism of different plant organs of lentils
(Skliros et al., 2018)
Varieties used:
• F-56, a Greek variety
from Samos island,
• LC-960254, a variety
originating from the
U.S.A.)
Studied differences in their global
metabolite profile
• using gradual or initial application of
salt stress,
• between leaves and roots and
• between the varieties.
Experimental designs:
• For the purpose of gradually acclimation
(GA), 50 mM NaCl (GA 50) and 75 mM
NaCl (GA 75).
• For the initial application (IA) treatment, 25
mM NaCl (IA 25), 50 mM NaCl (IA 50) and
75 mM NaCl (IA 75)
Results:
• Demonstrated the driver of
deleterious Cl− accumulation in
leaves, a defensive mechanism for
withstanding salinity stress in plants.
• Finally, a model is suggested of how
legumes upregulate a metabolic
pathway, which involves purines
catabolism in order to assimilate
carbon and nitrogen, which are
limited during salinity stress.
43. . (A) Plant figure
shows the
compartmentalizati
on of deleterious
ions in vacuole of
leaf cells.
(B) Heat maps
represent
comparative
metabolic response
of L-asparagine, D-
trehalose and
Lactobionic acid in
roots and putative
osmoprotectants in
leaves for each
variety and
treatment (GA
stands for gradual
acclimation; IA for
initial application)
separately.
(C) Increase of salinity stress, oxidative stress and purine catabolism and
decrease of respiration and photosynthetic carbon accumulation over time
is shown as well. (D) Part of the purine catabolism pathway in the root cells
is shown
44. Applications of metabolomics
• Characterization of metabolism
• Identification of regulated key sites in network
• Biofortification and genetic modification
• Investigation of gene function under stress
conditions
47. Future concerns
• Reduction in cost of technology usage.
• Development of bioinformatic tools for data
analysis and storage of databases.
• Human resource development for an overall
purview of technology to apply in crop breeding.