Mining Sorghum bicolor genes for stress mediated response

SUBMITTED TO

SAVITRIBAI PHULE PUNE UNIVERSITY, PUNE.

In partial fulfilment for the award of the degree of

BACHELOR OF SCIENCE IN BIOTECHNOLOGY

(2023-2024)

SUBMITTED BY

Ms. Akanksha Londhe

UNDER THE GUIDANCE OF

Dr. Monica Jamla

AT

DEPARTMENT OF BIOTECHNOLOGYMODERN COLLEGE OF ARTS,

COMMERECE AND SCIENCE (AUTONOMOUS) GANESHKHIND, PUNE-411016

2023-2024
 PROGRESSIVE EDUCATION SOCIETY
MODERN COLLEGE OF ARTS, SCIENCE AND COMMERCE (AUTONOMOUS)
GANESHKHIND, PUNE-411016

DEPARTMENT OF BIOTECHNOLOGY

(Department supported under DBT-BUILDER, DST-FIST & DBT-STAR College scheme)

CERTIFICATE
This is to certify that Ms. Akanksha Londhe, Exam seat no.________ (Roll No.233231015),
has submitted project formulation “Mining Sorghum bicolour genes for stress mediated
response” as a part of the Bachelors in Biotechnology curriculum under the guidance of Dr.
Monica Jamala, Modern College of Arts, Science and Commerce (Autonomous), Ganeshkhind,
Pune-411016, as laid down by the Savitribai Phule Pune University for the academic year 2023-
2024.

Project Guide Head of Department External Examiner

Title of the project:

Mining Sorghum bicolor genes for stress mediated responses

Rationale and significance of the studies:

Millets are resilient cereals that can provide an affordable and nutritious option and help
guarantee food security. Millets can grow in both low and high altitudes and across a wide
latitudinal range, on arid lands, under non-irrigated conditions, in very low rainfall regimes,
and have a low water footprint. They are very tolerant of heat (up to 64 degrees Celsius),
drought and flood and it makes the crop an obvious choice for farmers in an era of climate
change and depleting natural resources.

Survey of the research done in the area:

Sorghum bicolor
Sorghum bicolor Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta;
Spermatophyta; Magnoliopsida; Liliopsida; Poales; Poaceae; PACMAD clade; Panicoideae;
Andropogonodae; Andropogoneae; Sorghinae; Sorghum.

The origins of sorghum cultivation were found in the eastern Sudanese savannah. Today,
Nigeria, the United States of America and Sudan are the largest producers of sorghum
globally. Sorghum is high in copper, magnesium, phosphorus and selenium, and is a source of
iron, zinc, thiamin, niacin, pantothenic acid and vitamin B6. Sorghum is an economically
important and a staple food crop for over half a billion people in developing countries, mostly
in arid and semi-arid regions where drought stress is a major limiting factor. Although
sorghum is generally considered tolerant, drought stress still significantly hampers its
productivity and nutritional quality across its major cultivation areas. Hence, understanding
both the effects of the stress and plant response is indispensable for improving drought
tolerance of the crop. Mechanisms of sorghum response to drought-stress involving
morphological, physiological, and molecular alterations are presented. we discussed
interactions of drought with other abiotic stresses and biotic factors, which may increase the
vulnerability of the crop or enhance its tolerance to drought stress. The genetic diversity of
millets offers a myriad of opportunities for economic development through income-generating
activities in the food sector. Millet value chains can be strengthened through mechanization,
digital tools and technologies. Sorghum is also a cheap source of energy, protein, Fe, and Zn,
the cost difference is high when sorghum and pearl millet are compared with fruits,
vegetables, meal. These crops possess high nutritive and fodder value and are primarily
consumed by their producers. On the supply side, there has been a large shift in the area under
cultivation to rice and wheat and other commercial crops. On the demand side, the
distribution of rice and wheat at subsidized prices through the public distribution system has
led to a fall in the consumption of sorghum and millets. The decline in cultivated area could
result in a problem for the livestock sector in many regions. It is crucial that the sorghum and
millet sector be supported by strong government policies and programmes for food, fodder,
and better nutrition through value addition and demand creation. It is thought that sorghum
plants are well tolerant to drought conditions not only because of the special cuticular wax
metabolism but, more importantly, because of the coordination between root-to-shoot water
use efficiency and a number of dynamic physiological adjustments to cope with drought
conditions.

Statement of aim:

This project will explain the use of bioinformatics for checking the factors that help millets
(sorghum bicolor) to grow in biotic and abiotic stress.

Objectives:

1. To understand gene expressed in stress responses in sorghum bicolor.

2. And to conduct functional enrichment analysis of gene expression and identification of
stress responsive modules in sorghum bicolor.

Methodology:

The National Center for Biotechnology Information (NCBI, http://www.ncbi.nlm.nih.gov)

provides analysis and retrieval resources for the data in GenBank and other biological data
made available through the NCBI web site. NCBI resources include Entrez, the Entrez
Programming Utilities, MyNCBI, PubMed, PubMed Central, Gene, the NCBI Taxonomy
Browser, BLAST, BLAST Link (BLink), Primer-BLAST, COBALT, Splign, RefSeq,
UniGene, HomoloGene, ProtEST, dbMHC, dbSNP, dbVar, Epigenomics, the Genetic Testing
Registry, Genome and related tools, the Map Viewer, Model Maker, Evidence Viewer, Trace
Archive, Sequence Read Archive, BioProject, BioSample, Retroviral Genotyping Tools, HIV-
1/Human Protein Interaction Database, Gene Expression Omnibus, Probe, Online Mendelian
Inheritance in Animals, the Molecular Modeling Database, the Conserved Domain Database,
the Conserved Domain Architecture Retrieval Tool, Biosystems, Protein Clusters and the
PubChem suite of small molecule databases.

NCBI maintains a diverse set of 35 databases that together contain 3.6 billion records most of
which are available through the Entrez retrieval system at
https://www.ncbi.nlm.nih.gov/search/.

 And we will be using following databases, Nucleotide database is a collection of

sequences from several sources, including GenBank, RefSeq, TPA and PDB. Genome,
gene and transcript sequence data provide the foundation for biomedical research and
discovery.
  The Gene database integrates information from a wide range of species. A record may
include nomenclature, Reference Sequences (RefSeqs), maps, pathways, variations,
phenotypes, and links to genome-, phenotype-, and locus-specific resources
worldwide.

 The Protein database is a collection of sequences from several sources, including

translations from annotated coding regions in GenBank, RefSeq and TPA, as well as
records from SwissProt, PIR, PRF, and PDB. Protein sequences are the fundamental
determinants of biological structure and function.

 Conserved Domain Database (CDD)

A collection of sequence alignments and profiles representing protein domains

conserved in molecular evolution. It also includes alignments of the domains to known 3-
dimensional protein structures in the MMDB database.

 Database of Genomic Structural Variation (dbVar)

The dbVar database has been developed to archive information associated with large
scale genomic variation, including large insertions, deletions, translocations and inversions. In
addition to archiving variation discovery, dbVar also stores associations of defined variants
with phenotype information.

 Database of Genotypes and Phenotypes (dbGaP)

An archive and distribution center for the description and results of studies which
investigate the interaction of genotype and phenotype. These studies include genome-wide
association (GWAS), medical resequencing, molecular diagnostic assays, as well as
association between genotype and non-clinical traits.

 Database of Short Genetic Variations (dbSNP)

Includes single nucleotide variations, microsatellites, and small-scale insertions and

deletions. dbSNP contains population-specific frequency and genotype data, experimental
conditions, molecular context, and mapping information for both neutral variations and
clinical mutations.

 PubMed

A database of citations and abstracts for biomedical literature from MEDLINE and
additional life science journals. Links are provided when full text versions of the articles are
available via PubMed Central (described below) or other websites.
  PubMed Central (PMC)

A digital archive of full-text biomedical and life sciences journal literature, including
clinical medicine and public health.

 RefSeqGene

A collection of human gene-specific reference genomic sequences. RefSeq gene is a

subset of NCBI’s RefSeq database, and are defined based on review from curators of locus-
specific databases and the genetic testing community. They form a stable foundation for
reporting mutations, for establishing consistent intron and exon numbering conventions, and
for defining the coordinates of other biologically significant variation. RefSeqGene is a part
of the Locus Reference Genomic (LRG) Collaboration.

 Reference Sequence (RefSeq)

A collection of curated, non-redundant genomic DNA, transcript (RNA), and protein

sequences produced by NCBI. RefSeqs provide a stable reference for genome annotation,
gene identification and characterization, mutation and polymorphism analysis, expression
studies, and comparative analyses. The RefSeq collection is accessed through the Nucleotide
and Protein databases.

 Conserved Domain Search Service (CD Search)

Identifies the conserved domains present in a protein sequence. CD-Search uses RPS-
BLAST (Reverse Position-Specific BLAST) to compare a query sequence against position-
specific score matrices that have been prepared from conserved domain alignments present in
the Conserved Domain Database (CDD).

 E-Utilities

Tools that provide access to data within NCBI's Entrez system outside of the regular
web query interface. They provide a method of automating Entrez tasks within software
applications. Each utility performs a specialized retrieval task, and can be used simply by
writing a specially formatted URL.
NCBI receives data from three sources: direct submissions from external investigators;
national and international collaborations or agreements with data providers and research
consortia; and internal curation efforts. All of these resources can be accessed through the
NCBI home page.

Plan of work:

 To collect data from NCBI, (national center for biotechnology information), gene,
nucleotide and protein database.
 And retrieve the data from the database and study the genes expressed in the sorghum
bicolor in stress (drought, temperature) conditions.

Expected outcome:

Sorghum bicolor Genes expressed in the stress conditions.

References:

1. Bayat A. Science, medicine, and the future: Bioinformatics. BMJ. 2002 Apr
27;324(7344):1018-22. doi: 10.1136/bmj.324.7344.1018. PMID: 11976246;
PMCID: PMC1122955.
doi: 10.1136/bmj.324.7344.1018

2. NAGARAJ, N., BASAVARAJ, G., RAO, P. P., BANTILAN, C., & HALDAR, S.
(2013). Sorghum and Pearl Millet Economy of India: Future Outlook and Options.
Economic and Political Weekly, 48(52), 74–81.
http://www.jstor.org/stable/24477899

3. Numan, M., Serba, D. D., & Ligaba-Osena, A. (2021). Alternative Strategies for
Multi-Stress Tolerance and Yield Improvement in Millets. Genes, 12(5), 739.
doi: 10.3390/genes12050739

4. Kadier, Y., Zu, Y. Y., Dai, Q. M., Song, G., Lin, S. W., Sun, Q. P., ... & Lu, M.
(2017). Genome-wide identification, classification and expression analysis of
NAC family of genes in sorghum [Sorghum bicolor (L.) Moench]. Plant Growth
Regulation, 83, 301-312.
https://doi.org/10.1007/s10725-017-0295-y
5. Chen, D., Wang, W., Wu, Y., Xie, H., Zhao, L., Zeng, Q., & Zhan, Y. (2019).
Expression and distribution of the auxin response factors in Sorghum bicolor during
development and temperature stress. International Journal of
MolecularSciences, 20(19),4816. https://doi.org/10.3390/ijms20194816

6. Watts‐Williams, S. J., Emmett, B. D., Levesque‐Tremblay, V., MacLean, A.M.,

Sun, X., Satterlee, J. W., ... & Harrison, M. J. (2019). Diverse Sorghum bicolor
accessions show marked variation in growth and transcriptional responses to
arbuscular mycorrhizal fungi. Plant, Cell Environment, 42(5),1758-1774.
https://doi.org/10.1111/pce.13509