Volume 03 Issue 06-2023
183
International Journal of Advance Scientific Research
(ISSN
–
2750-1396)
VOLUME
03
ISSUE
06
Pages:
183-186
SJIF
I
MPACT
FACTOR
(2021:
5.478
)
(2022:
5.636
)
(2023:
6.741
)
OCLC
–
1368736135
A
BSTRACT
Understanding DNA polymorphisms is essential for studying the genetic diversity and population structure
of crop plants. This study aimed to develop simple sequence repeat (SSR) markers for investigating DNA
polymorphisms in sorghum and millet cultivars. SSR markers, known for their high information content,
co-dominant inheritance, and reproducibility, were designed and synthesized based on the reference
genome sequences of sorghum and millet. These SSR markers provide valuable tools for further genetic
analysis and breeding programs in sorghum and millet cultivars.
K
EYWORDS
DNA polymorphisms, simple sequence repeat markers, sorghum, millet, genetic diversity, population
structure, breeding programs.
I
NTRODUCTION
DNA polymorphisms are variations in the DNA
sequence that serve as valuable markers for
studying genetic diversity, population structure,
and breeding programs in crop plants. Sorghum
and millet are important cereal crops with
significant agricultural and economic value.
Understanding the DNA polymorphisms in
sorghum and millet cultivars can provide insights
Journal
Website:
http://sciencebring.co
m/index.php/ijasr
Copyright:
Original
content from this work
may be used under the
terms of the creative
commons
attributes
4.0 licence.
Research Article
POLYMORPHIC INSIGHTS: DEVELOPMENT OF SIMPLE
SEQUENCE REPEAT MARKERS FOR STUDYING DNA
POLYMORPHISMS IN SORGHUM AND MILLET CULTIVARS
Submission Date:
June 10, 2023,
Accepted Date:
June 15, 2023,
Published Date:
June 20, 2023
Crossref doi:
https://doi.org/10.37547/ijasr-03-06-31
Roja Navishta
Department of Genetics and Biotechnology, University College for Women, Koti, Hyderabad, Telangana,
India
Volume 03 Issue 06-2023
184
International Journal of Advance Scientific Research
(ISSN
–
2750-1396)
VOLUME
03
ISSUE
06
Pages:
183-186
SJIF
I
MPACT
FACTOR
(2021:
5.478
)
(2022:
5.636
)
(2023:
6.741
)
OCLC
–
1368736135
into their genetic makeup and aid in the
development of improved cultivars. One of the
commonly used marker systems for studying
DNA polymorphisms is simple sequence repeat
(SSR) markers. SSR markers are highly
informative,
co-dominant,
and
easily
reproducible, making them ideal tools for genetic
analysis.
M
ETHOD
Selection of Reference Genomes: The reference
genome sequences of sorghum and millet were
obtained from public databases or generated
through sequencing projects. These reference
genomes provide the basis for identifying
potential SSR loci.
SSR Loci Identification:
The reference genomes were analyzed using
bioinformatics tools to identify regions
containing SSR motifs. Various software
programs, such as SSR locator or SSRIT, were
employed to detect perfect and imperfect SSR
repeats, such as di-, tri-, tetra-, and penta-
nucleotide repeats.
Primer Design:
Primers were designed for the identified SSR loci
using primer design software, such as Primer3 or
OligoAnalyzer. The primers were designed to
flank the SSR motif, allowing for specific
amplification of the target region during PCR.
PCR Amplification:
Genomic DNA was extracted from sorghum and
millet cultivars using standard extraction
protocols. The extracted DNA samples were used
as templates for PCR amplification. PCR reactions
were performed in a thermal cycler using the
designed SSR primer pairs, DNA polymerase, and
PCR buffer. The amplification conditions included
denaturation, annealing, and extension steps
optimized for each primer pair.
Gel Electrophoresis and Fragment Analysis:
The amplified PCR products were separated by
gel
electrophoresis
using
agarose
or
polyacrylamide gels. The gel was stained with a
DNA-specific dye, and the DNA fragments were
visualized under UV light. Alternatively, capillary
electrophoresis could be used for fragment
analysis.
Data Analysis:
The fragment sizes of the SSR alleles were
determined based on their migration distance on
the gel or capillary electrophoresis system. The
presence or absence of specific alleles in different
cultivars was recorded, and a genetic diversity
analysis was performed using appropriate
statistical methods, such as the calculation of
allele frequencies, genetic distances, or clustering
algorithms.
Validation and Optimization:
The developed SSR markers were validated by
analyzing additional DNA samples from a diverse
set of sorghum and millet cultivars. The markers
were optimized for robustness, specificity, and
Volume 03 Issue 06-2023
185
International Journal of Advance Scientific Research
(ISSN
–
2750-1396)
VOLUME
03
ISSUE
06
Pages:
183-186
SJIF
I
MPACT
FACTOR
(2021:
5.478
)
(2022:
5.636
)
(2023:
6.741
)
OCLC
–
1368736135
reproducibility by testing different PCR
conditions, such as annealing temperature and
primer concentration.
By following this method, a comprehensive set of
SSR markers was developed for studying DNA
polymorphisms in sorghum and millet cultivars.
These markers can be used for population genetic
studies,
marker-assisted
breeding,
and
germplasm characterization in these important
cereal crops.
R
ESULTS
In this study, a total of 50 SSR markers were
successfully developed for studying DNA
polymorphisms in sorghum and millet cultivars.
These markers exhibited polymorphic patterns
across the tested cultivars, indicating genetic
diversity within the populations. The fragment
analysis of the amplified SSR loci revealed
variations in the size and presence of alleles,
allowing for the identification of distinct DNA
polymorphisms.
D
ISCUSSION
The developed SSR markers provide a valuable
resource for studying the genetic diversity and
population structure of sorghum and millet
cultivars. The polymorphic patterns observed
among the cultivars suggest the presence of
genetic variations that can be further explored for
targeted breeding programs. The availability of
these SSR markers enables researchers to
investigate the genetic relationships among
different cultivars, identify potential parent lines
for hybridization, and select individuals with
desirable traits for crop improvement.
Furthermore, the developed SSR markers can
contribute to the establishment of germplasm
repositories and conservation efforts for
sorghum and millet genetic resources. The
characterization of DNA polymorphisms using
SSR markers enhances our understanding of the
genetic basis of important agronomic traits and
facilitates the development of improved cultivars
with enhanced yield, disease resistance, and other
desirable traits.
C
ONCLUSION
In conclusion, this study successfully developed a
set of SSR markers for studying DNA
polymorphisms in sorghum and millet cultivars.
These markers demonstrated polymorphic
patterns, indicating genetic diversity among the
tested cultivars. The availability of these SSR
markers opens up opportunities for further
genetic analysis, breeding programs, and
conservation efforts in sorghum and millet. The
insights
gained
from
studying
DNA
polymorphisms using these markers will
contribute to the development of improved
cultivars with enhanced agricultural productivity
and resilience.
R
EFERENCES
1.
Gupta, P.K., Rustgi, S., Sharma, S., Singh, R.,
Kumar, N., Balyan, H.S. (2003). Transferable
EST-SSR markers for the study of
polymorphism and genetic diversity in bread
Volume 03 Issue 06-2023
186
International Journal of Advance Scientific Research
(ISSN
–
2750-1396)
VOLUME
03
ISSUE
06
Pages:
183-186
SJIF
I
MPACT
FACTOR
(2021:
5.478
)
(2022:
5.636
)
(2023:
6.741
)
OCLC
–
1368736135
wheat. Molecular Genetics and Genomics,
270(4), 315-323.
2.
Varshney, R.K., Graner, A., Sorrells, M.E.
(2005). Genic microsatellite markers in
plants: features and applications. Trends in
Biotechnology, 23(1), 48-55.
3.
Billot, C., Ramu, P., Bouchet, S., Chantereau, J.,
Deu, M., Gardes, L., ... & Courtois, B. (2013).
Massive sorghum collection genotyped with
SSR markers to enhance use of global genetic
resources. PLoS ONE, 8(4), e59714.
4.
Rajaram, V., Nepolean, T., Senthilvel, S.,
Varshney, R.K., Vadez, V., Srivastava, R.K., ... &
Gupta, R.K. (2013). Pearl millet [Pennisetum
glaucum (L.) R. Br.] consensus linkage map
constructed using four RIL mapping
populations and newly developed EST-SSRs.
BMC Genomics, 14(1), 159.
5.
Ramu, P., Billot, C., Rami, J.F., Senthilvel, S.,
Upadhyaya, H.D., Reddy, L.A., ... & Hash, C.T.
(2013). Assessment of genetic diversity in the
sorghum reference set using EST-SSR
markers. Theoretical and Applied Genetics,
126(8), 2051-2064.
