Molecular Studies of Cumin for Diversity and Modeling
Molecular studies of Cumin (Cuminum cyminum
L.), for diversity and modeling
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Presented By:
Dr. Sharda Choudhary
Scientist
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Seed spice crops are the commercial crops grown by the poor
farmers in the arid region of our country.
Seed Spices are annual herbs, whose dried seed or fruits are used
as spices.
These are used for color, aroma, flavor, medicinal properties etc.
It is one of the oldest and economically most important seed spice
with medicinal properties.
Cumin is the most important and
crucial, of all.
C
u
m
i
n
Cumin (Cuminum cyminum L.) is a valuable seed spice
belonging to the family Apiaceae.
It is a herbaceous, dicotyledonous annual plant, diploid (2n = 2x
= 14) belongs to the family Apiaceae.
Cumin is locally known as “Zeera” in Hindi and is believed to
be the native of the Mediterranean and near Eastern regions.
In India it is mainly cultivated in Rajasthan, Gujarat and in some
parts of Madhya Pradesh, Uttar Pradesh and Tamil Nadu as a
rabi crop.
Cumin seeds are preferred for their typical pleasant aroma due to
an aromatic alcohol (animol) and spicy taste.
It is largely used in mixed spices and curry powders.
Inspite of its immense use as seed spice in our routine cooking,
recent studies have indicated its pharmaceutical and medicinal
importance.
Any new technique for the development of these crops will go a
long way in improving the livelihood of the poor farmers and bring
wealth to the country.
Molecular markers are the
vital tool for genetic improvement of
crops specially seed spices in which traditional breeding
approaches are difficult to produce varieties resistant to various
biotic and abiotic stresses.
Seed spices remain neglected for one or other reasons, hence
limited work for variety development and quality improvement
have been done.
Marker development for economically important characters is
very important to apply biotechnological tools for improvement
of seed spices crops.
Molecular Markers
Molecular markers (identified
as genetic markers) are a
fragment of DNA that is
associated with a certain
location within the genome.
Molecular markers are used in
molecular biology and
biotechnology to identify a
particular sequence of DNA in
a pool of unknown DNA.
•
Revealing variation at a
DNA level
•
Characteristics:
–
Co-dominant expression
–
Nondestructive assay
–
Complete penetrance
–
Early onset of phenotypic
expression
–
High polymorphism
–
Random distribution
throughout the genome
–
Assay can be automated
It has various applications in agriculture including Seed
Spices:
•
Species Identification
•
Genetic variation and population structure study in
natural populations
•
Comparison between wild and modified populations
•
Assessment of demographic bottleneck in natural
population
•
Propagation assisted rehabilitation programmes.
However, there still exists some limitations
Methodology
Materials And Methods
Plant Materials and DNA isolation
New protocol for DNA isolation
PCR program
Gel electrophoresis of the amplified products
Reproducibility of amplification patterns
Scoring and Data analysis
Chromato
gram showing nucleotide sequences for
cumin
protein gq33
This graph was derived
by CROMA software to
derive the raw
sequences.
Different colors in the
graph shows 20
different amino acids.
The height of the peaks
in the graph determine
the amino acid to be
selected
For the prediction of secondary structure of protein FASTA
sequence were used and prediction was performed using
GOR IV, SOPMA, ProFunc and PDBSum.
Physiochemical properties
Secondary Structure
The physiochemical properties for gq33 cumin protein
were identified using Protparam.
The modeling of the three dimensional structure of the
protein was performed by ab-initio and threading Meta
servers.
Three Dimensional Structure
MEMSAT-SVM was used to identify a channel in fenugreek
MEMSAT-SVM
RESULTS
AND
DISCUSSION
In the present study, genetic similarity was assessed among fifty five
cumin accessions, analysis of the data using 20 RAPD primers showed
that 15 primers generated bright and reproducible amplified products
which detected polymorphism among the accessions used.
Fifteen RAPD primers showed clear bands and polymorphism on
profiling.
This indicates very low level (47%) of genetic diversity among
genotypes.
Cluster analysis based on the resulting data was performed using
UPGMA method and Dice's similarity coefficient by NTSYS software.
Dendogram showing Cluster analysis
(a) 3D Plot (b) Line Graph, showing cluster analysis conducted by the software NTSYS-pc
version 2.00
Thank You
Cumin (Cuminum cyminum L.) is a valuable seed spice with medicinal properties, belonging to the Apiaceae family. This herbaceous plant is locally known as Zeera and cultivated mainly in India. Molecular studies, using markers for genetic improvement, are crucial for enhancing the quality and variety of seed spices, benefiting farmers economically and pharmaceutically.
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Presentation Transcript
Molecular studies of Cumin ( Molecular studies of Cumin (Cuminum L.), for diversity and modeling L.), for diversity and modeling Cuminum cyminum cyminum National Research Centre on Seed Spices, Tabiji, Ajmer, Rajsthan-305206 Presented By: Dr. Sharda Choudhary Scientist
Introduction Introduction Seed spice crops are the commercial crops grown by the poor farmers in the arid region of our country. Seed Spices are annual herbs, whose dried seed or fruits are used as spices. These are used for color, aroma, flavor, medicinal properties etc. It is one of the oldest and economically most important seed spice with medicinal properties. Cumin is the most important and crucial, of all.
Cumin Cumin Cumin (Cuminum cyminum L.) is a valuable seed spice belonging to the family Apiaceae. It is a herbaceous, dicotyledonous annual plant, diploid (2n = 2x = 14) belongs to the family Apiaceae. Cumin is locally known as Zeera in Hindi and is believed to be the native of the Mediterranean and near Eastern regions. In India it is mainly cultivated in Rajasthan, Gujarat and in some parts of Madhya Pradesh, Uttar Pradesh and Tamil Nadu as a rabi crop.
Cumin seeds are preferred for their typical pleasant aroma due to an aromatic alcohol (animol) and spicy taste. It is largely used in mixed spices and curry powders. Inspite of its immense use as seed spice in our routine cooking, recent studies have indicated its pharmaceutical and medicinal importance. Any new technique for the development of these crops will go a long way in improving the livelihood of the poor farmers and bring wealth to the country.
Molecular markers are the vital tool for genetic improvement of crops specially seed spices in which traditional breeding approaches are difficult to produce varieties resistant to various biotic and abiotic stresses. Seed spices remain neglected for one or other reasons, hence limited work for variety development and quality improvement have been done. Marker development for economically important characters is very important to apply biotechnological tools for improvement of seed spices crops.
Molecular Markers Revealing variation at a DNA level Characteristics: Co-dominant expression Nondestructive assay Complete penetrance Early onset of phenotypic expression High polymorphism Random distribution throughout the genome Assay can be automated Molecular markers (identified as genetic markers) are a fragment of DNA that is associated with a certain location within the genome. Molecular markers are used in molecular biology biotechnology to identify a particular sequence of DNA in a pool of unknown DNA. and
It has various applications in agriculture including Seed Spices: Species Identification Genetic variation and population structure study in natural populations Comparison between wild and modified populations Assessment of demographic bottleneck in natural population Propagation assisted rehabilitation programmes. However, there still exists some limitations
Materials And Methods Plant Materials and DNA isolation New protocol for DNA isolation PCR program Gel electrophoresis of the amplified products Reproducibility of amplification patterns Scoring and Data analysis
This graph was derived by CROMA software to derive the sequences. raw Different colors in the graph shows different amino acids. 20 The height of the peaks in the graph determine the amino acid to be selected Chromatogram showing nucleotide sequences for cumin protein gq33
Physiochemical properties The physiochemical properties for gq33 cumin protein were identified using Protparam. Secondary Structure For the prediction of secondary structure of protein FASTA sequence were used and prediction was performed using GOR IV, SOPMA, ProFunc and PDBSum.
Three Dimensional Structure The modeling of the three dimensional structure of the protein was performed by ab-initio and threading Meta servers. MEMSAT-SVM MEMSAT-SVM was used to identify a channel in fenugreek
RESULTS AND DISCUSSION
In the present study, genetic similarity was assessed among fifty five cumin accessions, analysis of the data using 20 RAPD primers showed that 15 primers generated bright and reproducible amplified products which detected polymorphism among the accessions used. Fifteen RAPD primers showed clear bands and polymorphism on profiling. This indicates very low level (47%) of genetic diversity among genotypes. Cluster analysis based on the resulting data was performed using UPGMA method and Dice's similarity coefficient by NTSYS software.
(a) 3D Plot (b) Line Graph, showing cluster analysis conducted by the software NTSYS-pc version 2.00
