Omics related approaches for higher productivity and improved quality.

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

2. Genomics
Epigenomics
Transcriptomics
Proteomics
Metabolomics
Phenomics
Introduction
Omics
Approaches and applications
Case studies
Conclusion
Future prospects
Flow of seminar

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Impact of climate change on major crops

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5. Introduction
F2
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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
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7. GENOMICS
EPIGENOMICS
TRANSCRIPTOMICS
PROTEOMICS
METABOLOMICS
PHENOMICS
OMICS
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Keiichi Mochida et al,.2011

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
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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
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Guotian Li et al 2017

10. Human Genome Sequencing project
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NHGRI

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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
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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
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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
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o psy (phytoene synthase)
o crtl (carotene desaturase)
Waxy gene
OsMYB3
Beta carotene
Glycaemic index
Anthocyanin
Jie Zheng et al,2021

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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

17. Groundnut aflatoxin management
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Ojiewo et al.2020

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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

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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

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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

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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

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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

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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

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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).

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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).

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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

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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.

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Sajad majeed et al.,2015

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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

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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.

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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

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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).

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Proteome analysis

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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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Muthamilarasan, M., Singh, N. K., and Prasad, M. (2019). Multi-omics approaches for strategic improvement of stress tolerance in underutilized crop
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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
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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
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