The document discusses using omics approaches to improve crop productivity and quality. It covers various omics fields including genomics, epigenomics, transcriptomics, proteomics, metabolomics, and phenomics. Examples are provided on applying these approaches in crops like rice, tomato, groundnut, and brassica to traits such as drought tolerance, nutrient enrichment, and reduced anti-nutrients. A case study on analyzing protein abundance changes in wheat cultivars under drought stress using proteomics is also mentioned.
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.
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
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.
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
Presentation delivered by Dr. Jesse Poland (Kansas State University, USA) at Borlaug Summit on Wheat for Food Security. March 25 - 28, 2014, Ciudad Obregon, Mexico.
http://www.borlaug100.org
Association genetics‟ or ‟association studies,” or ‟linkage disequilibrium mapping”.
Tool to resolve complex trait variation down to the sequence level by exploiting historical and evolutionary recombination events at the population level.
Natural population surveyed to determine MTA using LD.
Association mapping approaches for tagging quality traits in maizeSenthil Natesan
Association mapping has been widely used to study the genetic basis of complex traits in human and animal systems and is a very efficient and effective method for confirming candidate genes or for identifying new genes (Altshuler et al., 2008). Association mapping is now being increasingly used in a wide range of plants (Rafalski, 2010), where it appears to be more powerful than in humans or animals (Zhu et al., 2008). Unlike linkage mapping, association mapping can explore all the recombination events and mutations in a given population and with a higher resolution (Yu and Buckler, 2006). However, association mapping has a lower power to detect rare alleles in a population, even those with large effects, than linkage mapping (Hill et al., 2008). Yan et al., (2010) demonstrated that the gene encoding β-carotene hydroxylase 1 (crtRB1) underlies a principal quantitative trait locus associated with β-carotene concentration and conversion in maize kernels has been identified through candidate gene strategy of association mapping.
Marker Assisted Gene Pyramiding for Disease Resistance in RiceIndrapratap1
Why marker assisted gene pyramiding?
For traits that are simply inherited, but that are difficult or expensive to measure phenotypically, and/or that do not have a consistent phenotypic expression under specific selection conditions, marker-based selection is more effective than phenotypic selection.
Traits which are traditionally regarded as quantitative and not targeted by gene pyramiding program can be improved using gene pyramiding if major genes affecting the traits are identified.
Genes with very similar phenotypic effects, which are impossible or difficult to combine in single genotype using phenotypic selection, can be pyramided through marker assisted selection.
Markers provides a more effective option to control linkage drag and make the use of genes contained in unadapted resources easier.
Pyramiding is possible through conventional breeding but is extremely difficult or impossible at early generations..
DNA markers may facilitate selection because DNA marker assays are non destructive and markers for multiple specific genes/QTLs can be tested using a single DNA sample without phenotyping.
CONCLUSION:
• Molecular marker offer great scope for improving the efficiency of conventional plant breeding.
• Gene pyramiding may not be the most suitable strategy when many QTL with small effects control the trait and other methods such as marker-assisted recurrent selection should be considered.
• With MAS based gene pyramiding, it is now possible for breeder to conduct many rounds of selections in a year.
• Gene pyramiding with marker technology can integrate into existing plant breeding program all over the world to allow researchers to access, transfer and combine genes at a rate and with precision not previously possible.
• This will help breeders get around problems related to larger breeding populations, replications in diverse environments, and speed up the development of advance lines.
For further queries please contact at isag2010@gmail.com
OMICS is the comprehensive analysis of the biological system. The technologies which made a revolution such as Genomics, Transcriptomics, Proteomics, Metabolomics and Phenomics, in screening traits and develop novel improved organisms are mentioned here. The presentation gives a brief idea about various OMICS technology used in crop improvement, their steps, techniques used, applications, scope, advantages and disadvantages.
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.
Advances in Genomics Research and Molecular Breeding in Dryland Crops through...apaari
Advances in Genomics Research and Molecular Breeding in Dryland Crops through Partnership for Achieving Food and Nutritional Security by Rajeev Varshney, ICRISAT, India
Presentation delivered by Dr. Jesse Poland (Kansas State University, USA) at Borlaug Summit on Wheat for Food Security. March 25 - 28, 2014, Ciudad Obregon, Mexico.
http://www.borlaug100.org
Association genetics‟ or ‟association studies,” or ‟linkage disequilibrium mapping”.
Tool to resolve complex trait variation down to the sequence level by exploiting historical and evolutionary recombination events at the population level.
Natural population surveyed to determine MTA using LD.
Association mapping approaches for tagging quality traits in maizeSenthil Natesan
Association mapping has been widely used to study the genetic basis of complex traits in human and animal systems and is a very efficient and effective method for confirming candidate genes or for identifying new genes (Altshuler et al., 2008). Association mapping is now being increasingly used in a wide range of plants (Rafalski, 2010), where it appears to be more powerful than in humans or animals (Zhu et al., 2008). Unlike linkage mapping, association mapping can explore all the recombination events and mutations in a given population and with a higher resolution (Yu and Buckler, 2006). However, association mapping has a lower power to detect rare alleles in a population, even those with large effects, than linkage mapping (Hill et al., 2008). Yan et al., (2010) demonstrated that the gene encoding β-carotene hydroxylase 1 (crtRB1) underlies a principal quantitative trait locus associated with β-carotene concentration and conversion in maize kernels has been identified through candidate gene strategy of association mapping.
Marker Assisted Gene Pyramiding for Disease Resistance in RiceIndrapratap1
Why marker assisted gene pyramiding?
For traits that are simply inherited, but that are difficult or expensive to measure phenotypically, and/or that do not have a consistent phenotypic expression under specific selection conditions, marker-based selection is more effective than phenotypic selection.
Traits which are traditionally regarded as quantitative and not targeted by gene pyramiding program can be improved using gene pyramiding if major genes affecting the traits are identified.
Genes with very similar phenotypic effects, which are impossible or difficult to combine in single genotype using phenotypic selection, can be pyramided through marker assisted selection.
Markers provides a more effective option to control linkage drag and make the use of genes contained in unadapted resources easier.
Pyramiding is possible through conventional breeding but is extremely difficult or impossible at early generations..
DNA markers may facilitate selection because DNA marker assays are non destructive and markers for multiple specific genes/QTLs can be tested using a single DNA sample without phenotyping.
CONCLUSION:
• Molecular marker offer great scope for improving the efficiency of conventional plant breeding.
• Gene pyramiding may not be the most suitable strategy when many QTL with small effects control the trait and other methods such as marker-assisted recurrent selection should be considered.
• With MAS based gene pyramiding, it is now possible for breeder to conduct many rounds of selections in a year.
• Gene pyramiding with marker technology can integrate into existing plant breeding program all over the world to allow researchers to access, transfer and combine genes at a rate and with precision not previously possible.
• This will help breeders get around problems related to larger breeding populations, replications in diverse environments, and speed up the development of advance lines.
For further queries please contact at isag2010@gmail.com
OMICS is the comprehensive analysis of the biological system. The technologies which made a revolution such as Genomics, Transcriptomics, Proteomics, Metabolomics and Phenomics, in screening traits and develop novel improved organisms are mentioned here. The presentation gives a brief idea about various OMICS technology used in crop improvement, their steps, techniques used, applications, scope, advantages and disadvantages.
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.
Advances in Genomics Research and Molecular Breeding in Dryland Crops through...apaari
Advances in Genomics Research and Molecular Breeding in Dryland Crops through Partnership for Achieving Food and Nutritional Security by Rajeev Varshney, ICRISAT, India
High-value pleiotropic genes for developing multiple stress-tolerant biofort...PABOLU TEJASREE
Modern agriculture confronts multifaceted challenges, encompassing biotic and abiotic stresses alongside malnutrition. Biofortified crops emerge as a pivotal solution, augmenting nutritional quality during plant growth. By harnessing specific genes with pleiotropic effects for stress tolerance, these crops exhibit heightened yields, resilience against pests and diseases, and adaptability to environmental stressors. This innovation not only secures food safety and nutrition but also fosters the development of "high-value farms," ensuring sustainable escalation in global food productivity and stable food prices.
Conclusion: Integrating diverse transgenes and gene editing with omics approaches enhances stress tolerance and nutritional content in biofortified crops. This holistic strategy enables precise modifications to crop genomes and comprehensive insights into stress responses and nutrient metabolism, ensuring sustainable food production and nutrition security.
Flow Cytometric Analysis for Ploidy and DNA Content of Banana Variants Induce...paperpublications3
Abstract: Nuclear DNA content of mutated banana plants was determined by using flow cytometric techniques. It is a powerful tool for large scale screening of ploidy levels. Nuclei were isolated from young leaves from (banana mutants & Glycine plants) supplemented with Propidium- iodide (PI) and RNAse. "Glycine max" used as internal reference standard for identifying the nuclear DNA content by FCM. For ploidy estimation DAPI was used. The results showed differences in DNA content between variants indicating the effect of gamma-irradiation on the genotype of these plants. Variants of short plant stature or stunted growth showed great differences in DNA content compared to control (non-irradiated). The phenotypic variations observed at high doses were likely due to changes in the DNA sequences at the chromosomal level. Nuclear DNA contents decreased with an increase of gamma-dose from 20 Gy to 60 Gy. However, there were no significant differences between DNA content at 20 Gy and 30 Gy and also between 40 Gy and 60 Gy, while they were differed significantly from the control. The results showed no significant differences in ploidy level between all samples used (3n); while all selected mutants (variants) showed differences in DNA content.
Optimization of experimental protocols for cellular lysisExpedeon
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DOI:10.21276/ijlssr.2016.2.4.11
ABSTRACT- Every year more than 13 million deaths worldwide are due to environmental pollutants, and
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measures. Out of all these environmental chemicals, effects of air pollution is responsible for death of 3.3 million people
prematurely worldwide - a figure that could double by 2050 if emissions continue to rise at the current rate. Increasing
number of evidences has linked environmental pollutants with epigenetic variations, including changes in DNA
methylation status, histone modifications and other factors like incorporation of miRNAs, nucleosome remodeling, etc.
These entire mechanisms are likely to play important roles in disease aetiology, and their modifications, thus providing
further understanding of disease aetiology, as well as biomarkers for these exposures to environmental chemicals and/or
prediction of the risk for the disease. In this, we had tried to summarize the different epigenetic alterations related to
environmental chemical exposures, and propose the probable mechanisms of action behind such epigenetic changes. We
will also focus onopportunities, challenges and further directions for future epidemiology research in environmental
epigenomics. Further studies are needed in this regard to solve methodological and practical challenges, including
uncertainties about stability over time of epigenomic changes induced by the environment, tissue specificity of epigenetic
alterations, validation of laboratory methods, and adaptation of bioinformatic and biostatistical methods to
high-throughput epigenomics. Moreover, there are several reports of epigenetic modifications arising from environmental
chemical exposures, but most have not been directly linked to disease endpoints. Key-words- Environmental chemicals, Epigenetics, Disease susceptibility
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The Roman Empire, a vast and enduring power, stands as one of history's most remarkable civilizations, leaving an indelible imprint on the world. It emerged from the Roman Republic, transitioning into an imperial powerhouse under the leadership of Augustus Caesar in 27 BCE. This transformation marked the beginning of an era defined by unprecedented territorial expansion, architectural marvels, and profound cultural influence.
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Cambridge International AS A Level Biology Coursebook - EBook (MaryFosbery J...
Omics related approaches for higher productivity and improved quality.pptx
1. Omics enabled approaches for achieving high productivity and improved
quality in crops
Master’s Seminar (GPB 591)
on
Course instructors:
Dr. Sweta Mishra
Dr. M.K. Singh
Mr. Aman Tigga
Anirudh T V
M.Sc.(Ag.) 2nd Year
Roll no.-2103205002
Department of GPB
PGCA
Dr. Rajendra Prasad Central Agriculture University, Pusa -848 125,
Samastipur, Bihar, India
6. The term Omics derived from Latin “ome” – mass or many.
In biological context, Omics refers to study of large sets of biological
molecules (Smith et al.,2005).
The realization that DNA is not alone can regulate complex biological
processes (as a result of HGP 2001), triggered the rapid development of
several fields in molecular biology that together are described with the term
OMICS.
PHENOMIC
S
METABOLOM
ICS
PROTEOMI
CS
TRANSCRIP
TOMICS
EPIGENOMI
CS
GENOMICS
2/11/2023 DEPT OF GPB 6
8. GENOMICS
Genomics term given by Thomas Roderick 1986
It refers to study of structure and function of entire genome of a living organism
Genomics is the sub discipline of genetics devoted to
• Mapping
• Sequencing
• Functional analysis of genome
Aim
• Identify and annotate the complete set of genes encoded within a
genome
• Understand the genetic basis of the phenotypic differences between
individuals and species
• Understand how the gene expression takes place
2/11/2023 DEPT OF GPB 8
9. Structural
• Sequence organization
• It determines size of
genome of a species in
Mb and also the number
of genes present in the
entire genome of a
species
Functional
• It is a high throughput
approach for
understanding the
genome
• Studies how the genes
and other sequences of
DNA act in relation to
the entire organism
Comparative
• Analysing DNA
sequences patterns of
different organisms side
by side to identify genes
and determine functions
• Looking for similar genes
in different species to
determine possible
relationships and genomic
variations
Types of Genomics
2/11/2023 DEPT OF GPB 9
Guotian Li et al 2017
11. 2/11/2023 DEPT OF GPB 11
EVENTS YEAR
1st sequenced ɸX174 1977
Human genome project proposed 1986
Human genome project initiated 1990
Haemophilus influenza genome sequenced 1995
E.coli genome sequenced 1997
Yeast (saccharomyces cerevisiae) genome sequenced 1999
Round worm ( Caenorhabditis elegans ) genome
sequenced
1999
Arabidopsis thaliana genome sequenced 2000
Rice genome sequenced (Monsanto) 2000
Human genome working draft published(90% of
genome)
2001
Finished version of human genome sequence completed 2003
12. Sequencing methods
First generation method
Third generation
method
Sanger chain
termination
Maxam gilbert chemical
degradation
Helicos
Oxford Nanopore
Pac Bio SMAT
Roch-454
Ion torrent
Illumina Solexa
SOLiD
Second generation
/NGS method
2/11/2023 DEPT OF GPB 12
13. GWAS ( Genome Wide Association Study)
Whole genome association study
Phenotyping is done first and validating with the genotyping data
Identify which genes or SNPs in the genome are associated with trait
of interest
(ex: Abiotic or biotic stress related traits)
Mapping of trait linked markers (SNP)
Genomic selection
GS –New form of MAS
Decreased genotyping cost and new statistical methods
enable simultaneous estimation of all marker effects
Genome wide markers used to predict GEBVs
(Genomic Estimated Breeding values)
Selects superior genotypes
2/11/2023 DEPT OF GPB 13
14. Implementation of genomics in different crops
RICE
Information derived from genomics on complex metabolic and nutritional
pathways can be used to tailor or value addition of commercial rice
varieties with vast health benefiting properties
Incorporate
into
commercial
rice
variety
Nutrient enriched
2/11/2023 DEPT OF GPB 14
o psy (phytoene synthase)
o crtl (carotene desaturase)
Waxy gene
OsMYB3
Beta carotene
Glycaemic index
Anthocyanin
Jie Zheng et al,2021
16. 2/11/2023 DEPT OF GPB 16
Crop Gene /QTL Function References
Rice Glutamate receptor-like Drought tolerance Lu G et al., 2014
Rac1 Resistance against blast
fungus
Kim SH et al.,2012
Nicotianamine synthase 2 Zinc accumulation in
seeds
Lee s et al.,2012
Yellow stripe1-like16 Enhanced Iron efficiency Lee S, Ryoo N
,2012
Tomato ant1 Increased Anthocyanin Mathews H et
al.,2003
18. 2/11/2023 DEPT OF GPB 18
EPIGENOMICS
Epigenetic process
Mechanism other than changes in DNA sequence that
cause effect in gene transcription and gene silencing.
Two mechanisms
1. DNA methylation
2. Histone modification-
A change in phenotype without a change in genotype
Genetic change Epigenetic change
Normal DNA AAGTCCGAGCCT
Mutated DNA AAGTCCTAGCCT
AAGTCCTAGCCT Unmethylated DNA
AAGTCCTAGCCT Methylated DNA
Me Me
19. 2/11/2023 DEPT OF GPB 19
Crop Activity Function Refences
Maize Histone Acetylation at the
C4-PEPC Promoter
Photosynthesis in
Maize
Offermann et al.,
2006
Tomato DNA methylation at gene
locus Cnr
Ripening of Tomato
fruits
Zhong et al., 2013
Rice Histone H3K4-tri-
methylation
Drought stress
tolerance
Zong et al.,2013
20. 20
2/11/2023 DEPT OF GPB
TRANSCRIPTOMICS
o Study of Set of all RNA molecules including mRNA ,rRNA ,tRNA and
other non-coding RNA produced in one or a population of cells.
o Possible to determine when and where a gene is turned on or off in
various types of cells and tissues by analysing the transcriptome.
WHY ?
Expressed sequences and genes of a genome
Gene regulation and regulatory sequences
Functional pathways
Identification of candidate genes for any given process or diseases
21. 2/11/2023 DEPT OF GPB 21
Transcriptome study
Hybridization based- Microarray
DNA chip
probes
Prior genome sequence information is needed
Costly chip designing
Sequence based- RNA seq
No prior genome sequence information
Non model organisms
Low cost
22. 2/11/2023 DEPT OF GPB 22
RNA i
• Co-suppression or post transcriptional gene silencing
(PTGS) in plants
• RNA interference (RNAi) is a mechanism that inhibits
gene expression at the stage of translation or by
hindering the transcription of specific genes.
• Testing hypothesis of gene function
• Target validation
• Gene redundancy
• Functional screening
23. 2/11/2023 DEPT OF GPB 23
RICE
OsBADH2 by RNA interference leads to significantly
increased 2-acetyl-1-pyrroline production.
It is found that altered expression levels of OsBADH2
gene influence aroma accumulation, and the prevalent
aromatic allele probably has a single evolutionary
origin.
Niu et al.,2008
25. 2/11/2023 DEPT OF GPB 25
Low glucosinolate in brassica
Targeted silencing of BjMYB28 homologs provide
significant reduction, without altering the desirable
nonaliphatic glucosinolate pool, both in leaves and seeds
of transgenic plants
DET1 suppression in B.napus can increase the levels of
carotenoids and reduce the levels of sinapate esters
simultaneously in the seeds, thus enhancing their overall
nutritious value (Wei et al., 2009).
26. 2/11/2023 DEPT OF GPB 26
Cotton
The silencing of ghSAD-1 and/or ghFAD2-1 to various
degrees enable the development of cottonseed oils having
novel combinations of palmitic , steric , oleic and linoleic
contents (Liu et al., 2002).
27. 2/11/2023 DEPT OF GPB 27
PROTEOMICS
Term proteome -Marc Wilkins 1994
The study of proteome, the structure and function of complete set of proteins in a
cell at a given time
Classification
Structural proteomics- goal to map the 3D structure of proteins
Functional proteomics-study of protein –protein interaction
Expression proteomics-quantitative study of protein expression
AIM
1. 2-D electrophoresis
2. Mass spectrometry
28. 2/11/2023 DEPT OF GPB 28
Why
Field that promises to bridge a gap between
genome sequence and cellular behaviour
Applications Challenges
• Disease mechanism
• Signal transduction
• Drug discovery
• Medical microbiology
• Complexity- some proteins have ≥1000
variants
• Limited throughput of todays proteome
platform.
30. 2/11/2023 DEPT OF GPB 30
METABOLOMICS
Study of metabolome, collection of all metabolites in a cell, tissue, organs or
organism
Metabolome consists of small molecules (e.g. lipids or vitamins) that are also
known as metabolites ( claudino et al., 2007)
They determine the flavour, aroma, colour and texture of crops ,their storge
properties and performance in field( Memelink, 2005)
Wen et al.,2015
31. 2/11/2023 DEPT OF GPB 31
Metabolomics for improvement of fruits
Kiwifruit gained popularity due to distinct appearance and health
benefiting nutrients such as vitamin c and fibre
Application of Synthetic cytokinin's N-(2-chloro-4pyridyl) affects
ripening process by altering the accumulation pattern of metabolite
i.e. sugars, organic acids etc.
32. 2/11/2023 DEPT OF GPB 32
PHENOMICS
Phenomics refers to sum total of phenotypes at various levels ranging from
molecules to organs and the whole organism
Study of plant growth, architecture, performance and composition using high
throughput methods of data acquisition and analysis.
Spectroscope MRI
Lidar Infra Red camera
33. 2/11/2023 DEPT OF GPB 33
Case Study -1
Objective:- To study the quantitative changes in protein abundance of three Australian
bread wheat cultivars (Triticum aestivum L.) in response to a drought stress.
Materials and methods:-
Kukri (intolerant), Excalibur (tolerant), and RAC875 (tolerant)-bread wheat cultivars
Protein concentrations were estimated using the Bradford assay
Shotgun proteomics study using iTRAQ ( Isobaric tags for relative and absolute
quantitation approach).
35. 2/11/2023 DEPT OF GPB 35
Protein changes during drought stress
Completion of the drought regime RAC 875 (tolerant) had the most number of protein changes
(206) with Excalibur (tolerant) intermediate (177) and Kukri (intolerant; 168) the least.
RAC875 has highest capacity among the three cultivars for a cellular protein response to
drought.
Known drought responsive proteins, including dehydrins, were also significantly up-regulated.
This highlights the importance of proteomics as a complementary tool for identifying candidate
genes in abiotic stress tolerance in cereals.
Results
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Case Study -2
Objective: To investigate salt tolerance properties through integrative analysis of
transcriptomics and metabolomics
Materials:
Foxtail millet cultivar's of Tugu2 and An04
150mM Nacl solution used for salt stress treatment
30/25 ℃ day/night cycle with 14 hr photoperiod for 7 days, the roots were sampled
after been treated for 24 hr and 48 hr.
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Methods :
Transcriptomics-
RNA library construction and sequencing
Validation of DEGs using qRT-PCR.
Metabolomics analysis-
LC-MS
Histochemical detection of H2O2 and O2, antioxidant enzyme activity
Results:
• In the transcriptomics results ,8887 and12,249 DEGs were identified in Yugu2
and An04 in response to salinity respectively ,and 3,149 of which were
overlapped between two verities.
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The salinity responsive genes identified that ion transport, redox homeostasis,
phytohormone metabolism, signalling and secondary metabolism were enriched in
Yugu2 (using GO and KEGG analyses).
The integrative omics analysis implied that flavonoid and lignin biosynthesis
pathways, and Lys phospholipids were vital in determining the foxtail millets salinity
tolerance.
Based on the phenotypic alteration and physiological indexes Yugu2 was defined as
salt tolerant variety and An04 as salt sensitive.
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Future prospects
Reduction in cost of technology usage
Development of bioinformatics tools for data analysis and storage of database
Human resource development for an overall purview of technology to apply in
crop breeding
Capacity building of young scientists is required in breeding to handle, analyse
and interpret the enormous data sets from omics
Use of high throughput methods that enable comprehensive profiling of entire
organism.
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Goh, H. H. (2018). “Integrative multi-omics through bioinformatics,” in Omics Applications for Systems Biology. Advances in Experimental Medicine
and Biology, eds W. Aizat, H. H. Goh, and S. Baharum (Cham: Springer), 69–80.
Gupta, B., Saha, J., Sengupta, A., and Gupta, K. (2013). Plant abiotic stress: ‘omics’ approach. J. Plant Biochem. Physiol. 1:3.
Muthamilarasan, M., Singh, N. K., and Prasad, M. (2019). Multi-omics approaches for strategic improvement of stress tolerance in underutilized crop
species: a climate change perspective. Adv. Genet. 103, 1–38.
Yang Y, Saand MA, Huang L, Abdelaal WB, Zhang J, Wu Y, Li J, Sirohi MH and Wang F (2021) Applications of Multi-Omics Technologies for Crop
Improvement. Front. Plant Sci. 12:563953
Keiichi Mochida, Kazuo Shinozaki, Advances in Omics and Bioinformatics Tools for Systems Analyses of Plant Functions, Plant and Cell Physiology,
Volume 52, Issue 12, December 2011, Pages 2017–2038, https://doi.org/10.1093/pcp/pcr153
Li, G., Jain, R., Chern, M., Pham, N. T., Martin, J. A., Wei, T., Schackwitz, W. S., Lipzen, A. M., Duong, P. Q., Jones, K. C., Jiang, L., Ruan, D., Bauer,
D., Peng, Y., Barry, K. W., Schmutz, J., & Ronald, P. C. (2017). The Sequences of 1504 Mutants in the Model Rice Variety Kitaake Facilitate
Rapid Functional Genomic Studies. The Plant cell, 29(6), 1218–1231. https://doi.org/10.1105/tpc.17.00154
Chris O. Ojiewo et al., 2020 ,Advances in Crop Improvement and Delivery Research for Nutritional Quality and Health Benefits of Groundnut (Arachis
hypogaea L.) https://www.frontiersin.org/articles/10.3389/fpls.2020.00029.
Gil-Humanes, J., Pistón, F., Tollefsen, S., Sollid, L. M., & Barro, F. (2010). Effective shutdown in the expression of celiac disease-related wheat gliadin
T-cell epitopes by RNA interference. Proceedings of the National Academy of Sciences of the United States of America, 107(39), 17023–17028.
https://doi.org/10.1073/pnas.1007773107
References
Editor's Notes
Genome is entire genetic complement of an organism
Psy –daffodil
Crtl- soil bacterium (Erwinia uredovora)
Selection for low GI based on amylose content is practised and screening the genotypes for low GI.
Low GI – whole grain basmati rice,
High Vit A-Golden rice
Anthocyanin –Purple rice.
Histone modifications include –acetylation, methylation ,phosphorylation
Recently RNA i has acquired considerable attention
2-d for separation of complex protein mixtures
Mass spectroscopy for identification and structural analysis
Earlier The behaviour of gene products is difficult or impossible to predict from genome sequence,
Now with vast availability of proteome database, most accurate protein structure and functions can be known for a query sequence.
Since metabolome is closely tied to phenotype of organism
Application-1) investigation of gene function under stress conditions
2) Biofortification and genetic modification
High throughput phenotyping-process of phenotyping which is automated, simultaneous and non –destructive, which analyses the plant growth, morphology and physiology
Peptides were analyzed via electrospray ionization (ESI)
Peak lists from the MS/MS spectra were made using Protein Pilot software version 2.01. The peak lists were searched against a six-frame translation of the Wheat Gene Index (V11.0, DFCI) using MASCOT 2.06.
WS- water stressed at 5 days; WP1, wilting point 1 for intolerant cultivar at day 14; WP2, wilting point 2 for intolerant cultivar at day 24; and RW, re-watered at day 25
In Variety Yugu2, these metabolisms are vital for salinity tolerance.
Based on the phenotypic alteration and physiological indexes Yugu2 was defined as salt tolerant variety and An04 as salt sensitive
