Caft Report

MAHATMA GANDHI MISSION’S
COLLEGE OF AGRICULTURAL BIOTECHNOLOGY,

GANDHELI,AURANGABAD
(Affiliated to Vasantrao Naik Marathawada Krishi Vidhyapith,Parbhnai)
National Capacity Building Training Report on

EXPLORING INTEGRATION OF MULTIOMICS AND
CONVENTIONAL BREEDING APPROACHES FOR SUSTAINABLE
LIVESTOCK PRODUCTION
Batch: 36
At
Center for Advanced Faculty Training Program, NDRI,
Karnal, Haryana
During: 1st December 2022 to 21st December 2022
Submitted by,
Mr. R.R.Tahakik
Department of Plant Biotechnology
MGM College of Agricultural Biotechnology
CAFT NDRI Report 2022-23 Page 1

GANDHELI,AURANGABAD
Approval letter

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Detail of Training Programme
Training name : Exploring integration of multiomics and conventional breeding

approaches for sustainable livestock production
Start from : Dec 01, 2022 to Dec 21, 2022
Course Director : Dr. Anupama Mukherjee
Training type : CAFT
Subject area : Not Available
Institute name : ICAR-National Dairy Research Institute (NDRI), Karnal, Haryana
CAFT Director : Dr. Archana Verma

Designation : HOD
Discipline : Animal Genetics & Breeding
Correspondence : Animal Genetics & Breeding Division ICAR-National Dairy
address Research Institute KARNAL-132001
Parmanent address : 360/13 Extension Urban Estate KARNAL-132001
Phone number : 0184-2259105
Mobile number : 09416079659
Fax Number : 0184-2250042
Email : archana.ndri@gmail.com

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Schedule
S. No. Topic of Lecture/Practical Start End Name & Designation of Faculty
Day Day
1 Molecular markers for economic traits 1 1 Dr Archana Verma (Principal Scientist)
in dairy animals ICAR-National Dairy Research Institute
(NDRI), Karnal
2 Proficiency in Colorful Chromosome 1 1 DrAnupama Mukherjee (Principal
World: An Indispensible Tool for Scientist)
Screening and Diagnosis of Genetic ICAR-National Dairy Research Institute
Disorders in Domestic Animals (NDRI), Karnal
3 Introduction to omics technology 1 1 Dr Anupama Mukherjee (Principal
Scientist)
ICAR-National Dairy Research Institute
(NDRI), Karnal
4 Animal Model with Special Reference 2 2 Dr Gopal Gowane (Senior Scientist)
to Maternal Effects in Animal ICAR-National Dairy Research Institute
Breeding (NDRI), Karnal
5 Use of different software for prediction 2 2 Dr Gopal Gowane (Senior Scientist)
of breeding value (P) ICAR-National Dairy Research Institute
(NDRI), Karnal
6 Isolation of Genomic DNA (P)and 2 2 Dr Anupama Mukherjee (Principal
Quantification and Quality checking of Scientist)
DNA and ICAR-National Dairy Research Institute
(NDRI), Karnal
7 Visit to LRC 3 3 Dr S.S.Lathwal (Principal Scientist)
System.Web.UI.WebControls.TextBox
8 Breeding techniques for breeding 4 4 Dr Gopal Gowane (Senior Scientist)
value estimation ICAR-National Dairy Research
Institute (NDRI), Karnal
9 Computational aspects of 4 4 Dr Vikas Vohra (Principal Scientist)
quantitative genetics ICAR-National Dairy Research
10 Understanding of molecular 4 4 Dr Anupama Mukherjee (Principal
genetics and QTL mapping Scientist)
ICAR-National Dairy Research
11 Characterization and Conservation 5 5 Dr Sabyasachi Mukherjee (Principal
of Animal Genetic Resources – Scientist)
Status, Challenges and Prospects ICAR-National Dairy Research
12 Management of high yielding dairy 5 5 Dr S S Lathwal (Principal Scientist)
herd for sustainable productivity ICAR-National Dairy Research
13 Hands on training “methods of 6 6 Dr Sabyasachi Mukherjee (Principal
estimation of genomic diversity (P) Scientist)
14 Statistical genetic tools in animal 6 6 Dr Ravindra Malhotra (Principal
breeding Scientist)

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15 Advancement and future prospects 7 7 Dr Satish Kumar (Principal Scientist)
for production of the transgenic ICAR-National Dairy Research
and genome edited farm animals Institute (NDRI), Karnal
16 Quality check and genomic 8 8 Dr Anupama Mukherjee (Principal
inbreeding from SNP array data Scientist)
andUse of various softwares for QC ICAR-National Dairy Research
and estimation of genomic Institute (NDRI), Karnal
inbreeding (P)
17 Breeding value estimation based on 8 8 Dr Gopal Gowane (Senior Scientist)
genotypic and phenotypic data ICAR-National Dairy Research
18 Transcriptomics data analysis in 9 9 Dr Rani Alex (Scientist)
livestock farm speices ICAR-National Dairy Research
19 Transcriptome Analysis 9 9 Dr Suneel Onteru (Principal Scientist)
20 DNA based Genetic disorders in 10 10 Dr S K Niranjan (Principal Scientist)
dairy cattle: New genomic ICAR-NBAGR, Karnal
approaches for their identification
21 Whole genome sequencing of farm 10 10 Dr Sabyasachi Mukherjee (Principal
animal species Scientist)
22 Genomic selection a tool for 11 11 Dr G.K.Gour (Principal Scientist)
sustainable livestock production IVRI, Izatnagar
system for small herd size
23 Molecular approach in 12 12 Dr Rubina Baithalu (Senior Scientist)
augmentation of reproduction ICAR-National Dairy Research
24 Genomic diversity in cattle breeds 12 12 Dr S.P.Dixit (Principal Scientist)
of India ICAR-National Dairy Research
25 Array based selection signature in 13 13 Dr Suneel Onteru (Principal Scientist)
livestock species ICAR-National Dairy Research
26 Animal cloning: hope for future 13 13 Dr M K Singh (Senior Scientist)
quality livestock production ICAR-National Dairy Research
27 Hands on practical on quality 14 14 Dr Anupama Mukherjee (Principal
control of genomic data Scientist)
28 Nutrigenomics and its role in 14 14 Dr Gautam Mondal (Principal
sustainable productivity in farm Scientist)
animals ICAR-National Dairy Research
29 Micro RNA and its application in 15 15 Dr Rani Alex (Scientist)

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improving fertility of farm animals ICAR-National Dairy Research

30 Hands on practical on 15 15 Dr Rani Alex (Scientist)
transcriptome data analysis ICAR-National Dairy Research
31 Precision breeding based on image 15 15 Dr Indu devi (Scientist)
analysis using machine alogrithm ICAR-National Dairy Research
32 Genomic DNA processing for next 16 16 Dr Sudarshan Kumar (Senior
generation sequencing Scientist)
33 Precision in livestock farming using 16 16 Dr T K Mohanty (Principal Scientist)
sensors and artificial intelligence ICAR-NDRI
34 Systems Biology Using 16 16 Dr Ravi Kumar (Principal Scientist)
Transcriptome analysis System.Web.UI.WebControls.TextBox
35 Latest trends in livestock farm 17 17 Dr S S Lathwal (Principal Scientist)
management practices ICAR-National Dairy Research
43 Visualization and graphics of 20 20 Dr Vikas Vohra (Principal Scientist)
results obtained from various ICAR-National Dairy Research
software Institute (NDRI), Karnal
44 Hands on practical and feedback 20 20 Dr Anupama Mukherjee (Principal
from the participants Scientist)
45 Cytogenetic techniques in farm 20 20 Dr Archana Verma (HOD)
animals ICAR-National Dairy Research
46 Hands on practical on various 21 21 Dr Gopal Gowane (Senior Scientist)
software ICAR-National Dairy Research
47 Valedictary remark and 21 21 Dr Archana Verma (HOD)
distribution of certificate ICAR-National Dairy Research

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About CAFT Programme
The ICAR policy of capacity building stipulates that the training of researchers and
teachers of National Agricultural Research and Education System (NARES) shall continue to
take cognisance of changes and shall be regularly exposed to innovations in their profession. The
basic objective in the competency framework is that professionals of NARES not only have the
required competencies for the job but are also able to promote development and delivery of need
based research and educational programmes that would enhance the livelihood security and build
up an easy, accessible and cost effective knowledge intensive information system. Career
progression of scientists/teachers is also linked with periodic exposure to capacity building
programmes. The capacity building in deficient areas of contemporary relevance and anticipated
future is addressed by ICAR by sponsoring Summer-Winter Schools (SWS) (21 d duration and
short courses (10 d duration) and also through its scheme on Centre for Advanced Faculty
Training (CAFT). The programmes under CAFT have been supporting the faculty and scientists
of NARES in the cutting edge areas of agriculture and allied sciences to meet capacity building
demands in terms of teaching, research, training and extension. There are 31 such centres
established all over the country to build the teaching, research, training and extension
competencies of professionals of NARES. During the XI plan period, ICAR sponsored 588 SWS
and CAFTs benefitting about 11,000 scientists/ faculty members of NARES.

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About Training Center
ICAR-National Dairy Research Institute is the premier research institution that undertakes
research, teaching, and extension activities towards dairy developments in the country. Being the
national institute, it conducts basic and applied research aiming to enhance animal productivity
and to develop cost-effective technologies for the benefit of dairy farmers. Further, the institute
provides high-quality manpower to meet the human resource requirements for the overall dairy
development in the country. Over the last several decades, the institute has been continuously
working to develop its R&D and HRD programmes to better serve the nation in terms of food
security, human resource generations, technology translation, and economic prosperity to dairy
farmers.

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Introduction
“Exploring integration of multiomics and conventional breeding approaches for

sustainable livestock production” was conducted during 01 to 21st December, 2022 under the
aegis of Centre of Advanced Faculty Training (AG&B) at Animal Genetics & Breeding
Division, ICAR-National Dairy Research Institute, Karnal (Haryana).
India has diverse animal genetic resources of farm livestock species and breeds. India
occupies first rank in global milk production, but their productivity and sustainability is low.
Conventional animal selection and breeding methods were based on the phenotypic performance
and is not precise in prediction the genetic worth. The advent of high-throughput omics
techniques makes it feasible to estimate the actual genetic potential of the animals. It has now
become possible to collect and access large and complex datasets comprising different genomics,
transcriptomics, proteomics, metabolomics, and phonemics data as well as animal-level data that
provide new opportunities to better understand the mechanisms regulating animals’ actual
performance. The implementation of advanced genomic technologies for production and
reproduction traits has shown to enhance genetic gain as compared to traditional approaches. The
proposed National Training programme plans to address application of quantitative and
population genetic tools for improving the productivity and welfare of farm animals for
developing effective breeding strategies for livestock improvement in India.

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Course Content & Experienced Gained
Abstract: Enhancing productivity of Indigenous cattle and buffaloes; Marker Assisted

Selection; Genomic selection; Field Progeny Testing of Breeding Bulls; Linear Models in
Animal Breeding; Prediction of breeding values using BLUP; Estimation of genetic trends;
Principal component analysis; Linear Discriminant analysis; Statistical packages LSML, SAS,
WOMBAT; Univariate and multivariate animal models; Random regression model; Bayesian
approaches for genetic parameter estimation; Artificial Neural Network models for analysis.
Molecular Cytogenetics; PCR and its variants; Real Time PCR based expression analysis; SNP
genotyping; Evolution of Animal Breeding and Prospects of Genomic Selection in Livestock,
Next generation sequencing data and Genome assembly; Quality control of SNP chip data; RNA
Seq/ Differential Gene expression/Transcriptome Analysis; Genome Editing and CRISPER
Technology; Whole genome sequencing and Genome-Wide Association study; High through put
phenotyping a new dimension to genomics; Landscape genomics for identifying selection
signature Precision breeding based on image analysis using machine algorithm; Gene annotation
and network analysis of genomic data; Genomic approach in conservation of livestock species;
Molecular approaches for augmenting reproduction, Prioritization of Livestock breeds for
conservation; Role of sire and its fertility in overall productivity of animals.
In the view of above the major objectives of the CAFT Training were centered around to
understand different omics approaches in order to cope up with the simultaneously challenges in
agriculture and life sciences areas. In this 21 days National Training Programme.
 Analysis of large amounts of omics (Genomics, Proteomics, Transcriptomics, and
Metabolomics) data of Animal Breeds through big data analysis computational tools.
 Introduces fundamental and applied bioinformatics research in the field of life sciences.
 Highlights relevant databases, softwares, tools and web resources developed till date to
make ease of access for researchers working to decipher plant responses towards stresses.
 Molecular modeling and docking studies for Characterisation of the binding behaviour
which plays an important role in rational design of drugs as well as to elucidate
fundamental biochemical processes.
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Molecular and Structure biology

Studying the architecture, shape, and dynamics of biological micro/macromolecules is
paramount for understanding the basic mechanisms that drive the essential processes of all life.
Macromolecules such as proteins and nucleic acids carry out most of the functions of a cell, and
are able to perform these functions by adopting assemblies of structures under native state
conditions. Structural biology is concerned with the driving forces and interactions that
determine the threedimensional shapes and dynamics of bio-molecules.
Big data analysis
All organisms operate through activating and repressing genes in a coordinated and timely
manner between biological conditions. Gene or protein cannot work in isolation. Understanding
how interactions are formed and activated at specific time points or conditions is a central part of
understanding how specific cells work. With the increase of high-throughput methods it is
possible to obtain large amount of data to study a cellular system from complementary aspects
more easily. The vast quantity of data produced also enables data re-use and provokes new
methods for integration of heterogeneous data.
NGS Analysis
Intervention and application of NGS data analysis and sequencing technologies in the plant
biology by study of different file formats and databases for pre-processing of raw reads and
quality control and important role of Transcriptome/Genome/GBS data in Plant & Animal
systems biology for betterment of agriculture sector
First day of Training, Dr. Dheer Singh, Director, NDRI, Dr. Archana Verma, Director
CAFT Center, Dr, Ashish Kumar Singh, Joint Director, Dr. Anupanma Mukherjee, course Co-
coordinator inaugurates the training programme with a very informative lecture and said that of
NDRI, Karnal maintain top position in the frontier area of Animal genetics and Breeding,
Nutrition, Extension, Biotechnology. White revolution has been successfully initiated by its
tireless efforts. He said that the Institution is doing well not only in the area of Animal & Dairy
Sciences but also advanced area of Life Sciences including Biotechnology, Bioinformatics,
Microbiology and Nano-Technology. He describe that future increase in agriculture production

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in wake of growing demand has to come through mainly productivity enhancements with
nutritional security and for that first of all identify hub network of all the genes responsible for
important traits and use that network level information for agriculture and animal productivity.
These efforts provide help in the development of newer disease resistant, high yielding varieties
and application of emerging technologies such as hybrid technology, genetic modification, and
computational approaches are certainly the viable options to raise production. Prof.Dr. A.K.
Singh, a renowned scientist from, National Bureau of Animal Genetic Resources recognized as
eminent researcher in the field of Genomics and Biotechnology was the Guest of Honor. Dr.
Khan delivered a very fruitful lecture talk on “OMICS to Systems Biology: A way to address
health challenges” on 36th National Training Programme and highlighted the importance of
throughput genomics of animal genome. He described briefly about the mechanism of drug
resistance and target identification for various diseases by using different systems biology
approaches. He described about the era of proteomics and suggested that it is the next step in the
study of biological systems. It is more complicated than genomics because an organism's genome
is more or less constant, whereas the proteome differs from cell to cell as well as time to time.
Distinct genes are expressed in different cell types, which mean that even the basic set of
proteins that are produced in a cell needs to be identified. The proteome is the entire set of
proteins that are produced or modified by an organism or system. Proteomics has enabled the
identification of ever increasing numbers of protein. Proteomics confirms the presence of the
protein and provides a direct measure of the quantity present. System biology based approach
has been emerged as a most decent approach to investigate the target protein to its functional or
phenotypic level. Systems biology is the computational and mathematical modeling of complex
biological systems. It is a biology-based interdisciplinary field of study that focuses on complex
interactions within biological systems, using a holistic approach to biological research. Systems
biology has been responsible for some of the most important developments in the science of
human health and environmental sustainability. It is a holistic approach to deciphering the
complexity of biological systems that starts from the understanding that the networks that form
the whole of living organisms are more than the sum of their parts. It is collaborative, integrating
many scientific disciplines – biology, computer science, engineering, bioinformatics, physics and

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others – to predict how these systems change over time and under varying conditions, and to
develop solutions to the world’s most pressing health and environmental issues. Network-based
approaches for analyzing high dimensional genomic data sets uch as; weighted correlation
network analysis is often used for identifying clusters, modeling the relationship between
clusters, calculating fuzzy measures of cluster (module) membership, identifying intra-modular
hubs, and for studying cluster preservation in other data sets. Pathway-based methods for omics
data analysis and these approaches have to identify and score pathways with differential activity
of their gene, protein, or metabolite members.
In the afternoon session Dr. S.K Niranjana presented a very informative lecture related to Hi-
throughput Omics data analysis by utilizing the power of Bioinformatics and Systems Biology
Tools” and provided a fundamental concepts of Omics technology, computational tools for
experimentation and interpretation of the biological data in context of farm animals. He also
discussed about key concepts of Omics for better understanding of biological systems with
respect to biotechnological research for improving agricultural productivity. Next Day, Dr.
Archana verma delivered lecture and hands on experience on Molecular markers for economic
traits analysis, she explain design of molecular markers on basic of QTL based approach for
identification of economic trait, use of genomic data for trait selection and designing of
molecular markers. In Afternoon session Prof. Sabyasachi Mukharjee, explains molecular
characterization of animal genetic resources over the last two decades and prospects for the
future is followed by a section that provides practical advice for researchers who wish to
undertake a characterization study. Emphasis is given to the importance of obtaining high-quality
and representative biological samples, yielding standardized data that may be integrated into
analyses on an international scale. Appendices provide a g lossary of technical terms; examples
of questionnaires; an example of a simple material transfer agreement; a summary of software
that can be used to analyse molecular data; and the standard International Society for Animal
Genetics–FAO Advisory Group panels of microsatellite markers for nine common livestock
species. In Evening Session Dr. Anupama Mukharjee Explains while performing Genomic
Analysis or Transcriptomics Analysis we should review Accuracy of the data and review suspect
portion from data. This can be achieved by Quality Check, SNP Array data which is handled by

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PLINK software, she demonstrated the entire protocol for analyses the SNP data and Quality
Check by following Keywords SNP Call Rate, Individual Call Rate, Minor Allele Frequency,
and Hardy Weinberg Distribution (Fig.1) .
Fig. 1 Quality Control Analysis for Automated Sequence data
In her extended session she also explain Inbreeding analysis and Runs of Homozygosity data on
PLINK softwares. In this practical we will analyse a simulated dataset using PLINK
15 single nucleotide polymorphisms, in a candidate gene region spanning ~30kbCase/control
design: 1000 cases and 1000 controls, Specifically, we will examine the format of the raw data
(PED and MAP files)perform an initial association analysis for each SNP perform basic QC
steps, including tests for HWE and looking at genotyping rate statistic srepeat the association
analysis consider genotypic as well as allelic testsperform sex-specific testsperform conditional

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and haplotype tests, On Next day Dr.S.P Dixit, presented an informative lecture talk on “A
Journey from “Animal Physiology to Systems Biology describe that the systems biology and
present scenario, expanding our understanding for a holistic view of the functions and forms of
biological systems as an iterative process is the main objective of research on Systems Biology.
In Afternoon Session was at Department of Agricultural Statistics on Experimental Designs, Dr.
Ravindra Malhotra Explained how participants are allocated to the different groups in an
experiment. Types of design include repeated measures, independent groups, and matched pair’s
designs
Next Session lead by Dr. Vikas Vhora about R language and Principal Component Analysis
He explain that PCA is a normalized linear combination of the original predictors in a data set.
We can write the principal component in the following way:
Z¹ = Φ¹¹X¹ + Φ²¹X² + Φ³¹X³ + …. +Φp¹Xp
(Z¹ is the first principal component.
Φp¹ is the loading vector comprising of loadings (Φ¹, Φ²..) of a first principal component.
Also, the loadings are constrained to a sum of square equal to )
This is because the large size of loadings may lead to large variance. The direction of the
principal component (Z¹) which has the highest variation of data is also defined. Moreover, it
results in a line in p dimensional space which is closest to the n observations. We can measure
closeness using average squared Euclidean distance. X¹..Xp is normalized predictors. The
means of normalized predictors are equal to 0 and have a standard deviation of 1.

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We will now proceed towards implementing our own Principal Components Analysis (PCA) in
R. For carrying out this operation, we will utilise the pca() function that is provided to us by
the FactoMineR library. We will make use of the mtcars dataset which is provided to us by R.
In this dataset, there are total 11 features out of which we require 9 features as two of them are
categorical in nature.
PCA objects with the help of summary() function.
> library(FactoMineR) #Author DataFlair
> pca <- PCA(mtcars[,c(1:7,10,11)], scale. = TRUE)
> summary(pca)

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Dr. G.R. Gowne delivered a lecture talk on Next Generation Sequencing: Data analysis and
applications" and described that Genomics, the word itself drags our consciousness toward its
Greek origin “genesis” meaning a body of gene and the word “omics” meaning the study of a
field. Genomics means the branch of molecular biology concerned with the structure, function,
evolution, and mapping of genomes. Genome includes the complete set of DNA content present
within an organism. He also presented a hands-on module on "Genome sequence databases and
thheir role in data analysis. During hand-on module Dr. Ravi Gandham the Major steps of NGS
data analysis which are Pre-assembly, denovo and reference based assembly and annotation of
assembled genome Later,
Dr.Rani Alex, delivered a Hands-on module on “Transcriptome/Genome/ Proteome Sequence

homology search Using Standalone BLAST” and described about the importance of Standalone
blast for sequence analysis. Also performed practical module on Basic local alignment of high-
throughput sequencing data for mining of important genes/proteins linked with specific traits. a
very informative lecture Talk delivered by Dr.Rubina Baithhalu “Pattern Mining Approaches”

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briefly described about the different algorithms and computational languages wildly used in
systems biology. He also described about different approaches for mining of biological data and
solves biological problems using perl scripting language. After that Dr. Divya Vashitha,
Clavergene Pvt. Ltd., New Delhi deleverd a lecture talk on “Data analyzing and associating traits
with regions of genome by Genotyping by Sequencing (GBS)” and also performed a hands on
module on “GBS Data analysis”. She described the exponential reduction in sequencing costs
with advances in Next Generation Sequencing (NGS) technologies has led to rapid developments
in the field of genotyping technologies. Genome complexity reduction methods such as
Restriction Associated DNA sequencing (RAD-seq) and Genotyping by sequencing (GBS) has
emerged as powerful genotyping platform which are capable of discovering, sequencing and
genotyping not hundreds but thousands of markers across almost any genome of interest, but also
number of individuals in a population in a single and simple experiment. GBS currently usage
low coverage sequencing protocol backed by power of NGS for genotyping large populations
and more precise association of genotype and phenotype. Few potential drawbacks of GBS are
large proportion of missing data points due to low coverage of sequencing, management and
analysis of large amount of sequence data. But with further increase in sequencing output,
availability of more reference genomes and developments in field of bioinformatics will further
empower these techniques. However flexible, rapid and low cost of GBS makes it an excellent
tool for many applications and to address many questions of plant breeding and genetics. This
review summarizes the family of GBS approaches and its potential to hold a genome wide
genotyping platform. Later Dr. Dev Bukhsh Singh, Assistant Professor, Department of
Biotechnology, CSJM University, Kanpur delivered a very informative lecture Talk on
“Principles and Approaches for 3D structure Modeling and Validation” and discussed various
computational biology approaches modeling of tertiary structure of proteins and their role in
medical sciences.

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 Dr. Singh described about the algorithms and software’s for protein structure modeling
and validation. He also described in detail about the protein folding and its prediction of
(tertiary, 3-dimensional) protein structure given the (primary, linear) structure defined by
the sequence of amino acids of the protein. He told that the experimental approaches for
protein structure prediction like X- Ray Crystallography and Nuclear magnetic resonance
are too costly and time taking but by the use of computational approaches it makes easy,
with no cost and time. After that Mr. Rutash Kumar (JRF) and Mr. Apoorv Tiwari (SRF)
performed Hands on Module on “Molecular Structure Prediction and described different
steps for protein structure prediction and validation through MODELLER. In This CAFT
Training, Dr. Dev Buksh Singh, presented another lecture on “Natural Product and
optimization strategies to achieve better potency”. He described that molecular docking
has become an increasingly important tool for drug discovery. He covered the brief
introduction of the available molecular docking methods, and their development and
applications in drug discovery. Natural products can be used as resource for new drugs.
Nature provides a boundless set of structurally diverse compounds that can be used as a
medicine. Natural products have made immense contribution to drug discovery over the

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many decades and remain an important source of structural and molecular diversity for
drug discovery. Large number of natural products may serve as important leads for
further drug development in many diseases. Later Mr. Rutash Kumar and Mr. Apoorv
Tiwari performed Hands on Module on “Molecular Docking”. The last lecture on “RNA
seq Analysis and Algorithms” presented by Dr. Soma S Marla, Principal Scientist,
NIPGR, New Delhi. He described that Impute genotypes
Generate a reference panel by perform low pass sequencing and estimate recombination
sites and frequencies.
The samples should be from diverse individuals.
 Using the haplotype information impute the missing genotypes in the study samples.
RNA- seq is an important transcriptome analysis technique for characterization and
understanding of variation in biology existing at molecular level. Cells during growth and
development dynamically access information from genome and translate specific instructions
through ‘gene expression’ by selectively switching on and off of a particular set of genes. Thus,
the set of RNAs transcribed in a certain condition (for example during a disease) and time
reflects the current state of a cell and can reveal plant response during pathogenesis.
Interestingly, comparative study of gene expression profiles of diseased vs. healthy plants
enables to identify genes that play a major role. He suggests some popular tools (available in
public domain) for mapping on to reference genome and alignment including BOWTIE,
TOPHAT, BFAST, MAQ, SHRIMP and SOAP etc.
Genome Editing Technology
Dr. Sudarshan Kumar Delevered Lecture on Genome editing, It is a type of genetic engineering
in which nucleotide is inserted, deleted or replaced in the host genome using engineered
nucleases or "molecular scissors”.
Impute genotypes, Generate a reference panel by perform low pass sequencing and estimate
recombination sites and frequencies. The samples should be from diverse individuals.Using the
haplotype information impute the missing genotypes in the study samples.

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Zinc Finger Nucleases (ZFNs)

ZFNs are dimers of a chimeric molecule consisted of DNA-binding domain and restriction
endonuclease FokI. ZFN genome editors have two basic parts:
1. FoK1 endonuclease which cuts the DNA between each FokI dimer.
2. ZFN finger domain which directs the endonuclease (FokI) to a specific DNA sequence. (Fok1
is type II restriction enzyme, found in Flavobacterium okeanokoites).
Target specificity is mediated through the Cys2-His2 residues of zinc fingers (DNA
binding domains).
 Each zinc finger (consisted of ~30aa) which bind to 3-base sequence (usually three or
four adjacent fingers can bind to 9 or 12 bases, respctively).
When both partners in pair, bind to their respective target sequence, the Fok1 cut the DNA and
create double stand break (DSBs) and these breaks are repaired by NHEJ, which cause the frame
shift mutation
Clustered Regularly Interspaced Short Palindromic Repeat (CRISPR) and CRISPR

associated gene 9 (Cas9)
 CRISPR/Cas9 system differs from the Fok1 based enzyme in which it uses RNA to
confer target specificity.
 It comprises the CRISPR RNA (crRNA) array of exogenous DNA targets (protospacers)
and direct repeat sequences, trans-activating crRNA (tracrRNA) and Cas9 gene.

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 TracrRNA facilitates the processing of crRNA array into a 20-nt guide RNA sequence
and a direct repeat sequence. The 20-base single guide RNA (sgRNA) sequence directs
the Cas9 nuclease to the target site by base pairing, where a unique proto-spacer adjacent
motif (PAM) directs the cleavage of the target site.
Designing CRISPER gRNA

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He Concluded that, transgenic and genome editing technologies have significant impact on
modification of economically important traits as well for production of therapeutic proteins for
bio-medicine. Still, transgenic efficiency is very low and needs to be improved

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Conclusion and Feedback Analysis

With response to Advertised on ICAR-CAFT Portal, Total 48 Applications from received
throughout the country. Twenty five participants were selected based on educational
qualification and experience. Out of 25 participants the CAFT Training drew 22 participants
representing academia, industry, and research organizations across India. Participants’ feedback
was also asked to judge the end result of the CAFT Training. The feedback consisted of
subdomains, starting from technical experience to learning expertise to active coaching to cordial
reception rendered. The domains included as overall CAFT Training assessment; talks on
bioinformatics, systems biology; technical acumen of trainers; active training; CAFT Training
hand-outs; CAFT Training conduct; logistics; outcome evaluation; enhancements for future
CAFT Trainings and overall impressions, comments, and suggestions. The organizers were
gratified by participants’ self-analysis of their knowledge, skills, and confidence with respect to
combining laboratory exercises with the use of different systems biology during the CAFT
Training. Thus, it was absolutely clear from the feedback analysis that the CAFT Training was a
substantial success. Gradual increase in the high-quality hi-throughput data and mathematical
modeling of biological processes by using different bioinformatics tools will lead to better
strategies to researchers for development of crop varieties for robust agricultural productivity and
sustainability. Efforts made toward enhancing our knowledge base and broadening our
knowledge towards Omics and Systems biology is ultimately aimed at improving our academic
standards and its use in the welfare of our society.

GANDHELI,AURANGABAD

GANDHELI,AURANGABAD

Caft Report

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MAHATMA GANDHI MISSION’S

COLLEGE OF AGRICULTURAL BIOTECHNOLOGY,

National Capacity Building Training Report on

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Detail of Training Programme

Training name : Exploring integration of multiomics and conventional breeding

CAFT Director : Dr. Archana Verma

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ICAR-National Dairy Research

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improving fertility of farm animals ICAR-National Dairy Research

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About CAFT Programme

CAFT NDRI Report 2022-23 Page 7

About Training Center

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“Exploring integration of multiomics and conventional breeding approaches for

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Course Content & Experienced Gained

Abstract: Enhancing productivity of Indigenous cattle and buffaloes; Marker Assisted

Molecular and Structure biology

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Fig. 1 Quality Control Analysis for Automated Sequence data

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Dr.Rani Alex, delivered a Hands-on module on “Transcriptome/Genome/ Proteome Sequence

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Zinc Finger Nucleases (ZFNs)

Clustered Regularly Interspaced Short Palindromic Repeat (CRISPR) and CRISPR

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Designing CRISPER gRNA

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Conclusion and Feedback Analysis

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