Assignment

Topic :
what is omics especially the role of GWAS and Bioinformatics tools for the betterment
of livestock population
Subject: Genetics
Group Members:
1. Ali Akbar (2021-zgy-037)
2. Muhmmad Sohail (2021-zgy-020)
3. Muhmmad Bilal (2021-zgy-041)
4. Muhmmad Junaid (2021-zgy-052)

What is Omics?
In biology the word omics refers to the sum of constituents within a cell. The omics
sciences share the overarching aim of identifying, describing, and quantifying the
biomolecules and molecular processes that contribute to the form and function of cells
and tissues.

Role of GWAS in livestock population

Genome-wide association studies help scientists identify genes associated with a
particular disease. This method studies the entire set of DNA of a large group of people,
searching for small variations, called single nucleotide polymorphisms or SNPs.
A genome-wide association study (GWAS) is an approach to compare the genomes from
many different people to find genetic markers associated with a particular phenotype or
risk of disease.
Briefly, this method scans the genome for SNPs, and can analyze hundreds or even
thousands of SNPs simultaneously.

GWAS typically compare the DNA of two groups of patients:

(1) patients who exhibit the disease (cases)
(2) subjects who do no exhibit the disease (controls).

More information might be obtained by analyzing GWAS using a polygenic model, which
allows for the possibility that thousands of genetic variants could impact disease.
Furthermore, there may exist common polygenic effects between potentially related
phenotypes (e.g., prostate and breast cancer).

Bioinformatics tools in livestock population

Bioinformatics tools play a crucial role in improving livestock populations by analyzing
and interpreting large datasets related to genetics, genomics, and breeding. Some key
bioinformatics tools for the betterment of livestock populations include:

1. Genomic selection tools: Like GenSel, BayesR, and GCTA, which predict breeding
values and identify superior animals.
2. Genome assembly and annotation tools: Like SPAdes, Canu, and NCBI's Prokaryotic
Genome Annotation Pipeline, which help assemble and interpret genome sequences.
3. Variant analysis tools: Like BWA, Bowtie, and SAMtools, which identify genetic
variations associated with desirable traits.
4. Gene expression analysis tools: Like RNA-seq, DESeq2, and EdgeR, which study gene
expression patterns and identify key genes regulating important traits.
5. Phylogenetic analysis tools: Like RAxML, Phyrex, and FigTree, which reconstruct
evolutionary relationships and identify genetic lineages.
6. Breeding program optimization tools: Like EVA, Breedplan, and SELVi, which optimize
breeding strategies and predict outcomes.
7. Machine learning and predictive modeling tools: Like TensorFlow, scikit-learn, and R's
caret package, which develop predictive models for breeding and management
decisions.
8. Data visualization tools: Like Circos, Plotly, and ggplot2, which help visualize complex
data and facilitate insights.
9. Database management tools: Like MySQL, PostgreSQL, and MongoDB, which store
and manage large datasets.
10. Cloud computing platforms: Like AWS, Google Cloud, and Azure, which provide
scalable computing resources for demanding analyses.

These bioinformatics tools enable researchers and breeders to:

- Identify genetic markers associated with desirable traits

- Develop more accurate breeding programs
- Improve disease resistance and overall health
- Enhance productivity and efficiency
- Make informed decisions based on data-driven insights

By leveraging these tools, the livestock industry can become more sustainable, efficient,
and productive, ultimately leading to better animal welfare and improved food security.