development of SSR markers is time-consuming and very expensive procedure so make use of already developed molecular markers in related species.

1. Transferability of molecular markers and
it’s significance
MUTTURAJ M D
MA1TAF0179
SEMINAR-1
9/23/2017 Department of genetics and plant breeding 1

2. Most commonly used
• RAPD
• AFLP
• RFLP
• SNP
• SSR
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Department of genetics and plant
breeding 2

3. Transferability of molecular markers
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4. WHY SSR ?
Co-dominant
High
reproducibility
High variability
Locus specificity
Polymorphic
9/23/2017 Department of genetics and plant breeding 4Ajay kumar et al. 2015

5. Locus
specificity
Polymorphic
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6. Transferability of SSR markers
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7. Scarcity of SSR Markers
Transfer of SSR Markers
Availability of Markers
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8. Development of transferable SSR
Markers
1
• Collection of SSR Markers
2
• Transfer rate of SSR Marker
3
• Polymorphic level of transferable
SSR Marker
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Ming et al. 2009

9. Collection of SSR Markers
Development of SSR markers is time consuming and
very expensive procedure.
It has been found that genetic material and its
arrangement are highly conserved among many
closely related species.
Conserved nature of flanking sequences between
closely related species.
Construction of a small DNA insert genomic library
Hybridisation with tandemly repeated oligonucleiotides
Sequencing of the candidate clones
9/23/2017 Department of genetics and plant breeding 9Ming et al. 2009

10. Transfer rate of SSR Marker
Amplify DNA fragments in the species of
Percentage of markers = interest
total number of SSR markers screened
• A set of 124 SSR markers are collected from various Brassica sp.
Such as B. nigra, B. oleracea, B. napus and B. rapa has been tested
for cross-transferability in twelve popular varieties of B. juncea.
• Individually conduct the SSR marker analysis.
• SSR marker was considered to be transferable if the amplification of
a PCR product/band of the expected size was obtained.
• Out of 124 SSR markers 81 (65.30%) markers gave successful
amplification.
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Ajay kumar et al. 2015

11. Cross-transferability of a) B. nigra- and b) B. oleracea derived SSR
markers to B.juncea cultivars
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Ajay kumar et al. 2015

12. Cross-transferability of a) B. napus- and b) B. rapa derived SSR
markers to B.juncea cultivars
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Ajay kumar et al. 2015

13. Overall cross-transferability of various Brassica species-derived
SSR markers to B. juncea cultivars
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Ajay kumar et al. 2015

14. Dendrogram
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Ajay kumar et al. 2015

15. Polymorphic level of transferable SSR
Marker
• We want to get not only high rate
transferability of markers, but also a high level
of polymorphism markers.
9/23/2017 Department of genetics and plant breeding 15Ming et al. 2009

16. Significance of transferable SSR
markers
 It considered as cost effective strategy to ensure
availability of markers in genomic resources of crop
species.
• Assessing transferability of heterologous SSR
markers to cotton genotypes.
• Collected 88 SSR markers from safflower(37) and
pulses(mungbean and urdbean)(51).
• The two cotton genotypes(DS-28 and SBYP-425) are
used , DNA was extracted using CTAB method.
9/23/2017 Department of genetics and plant breeding 16Yallappa et al. 2017

17.  PCR amplification and electrophoresis.
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18. Data scoring
• Products of PCR were scored visually based on presence or
absence of amplicon in agarose gel matrix.
• Loci were classified as monomorphic or polymorphic.
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19. Per cent transferability of heterologous
SSR markers to cotton genotypes
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Yallappa et al. 2017

20. Per cent transferability of heterologous SSR
markers from safflower to cotton by number and
nature of repeat
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Yallappa et al. 2017

21. Use of transferred markers
Assessing genetic variability
Selection of genetically diverse
parents
Enhance the efficiency of cotton
breeding.
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22. Transferability of SSR markers in
Blackgram
• Major challenge for MAS in Blackgram is the lack of
sufficient DNA markers.
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361 SSR
markers
Cowpea
(14)
Mungbean
(50)
Chickpea
(30)
Pigeonpea
(20)
Adzukibean(202) Commonbean(45)
Sanjeev gupta et al. 2013

23. Evaluated for their transferability on 24
diverse genotypes of blackgram.
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Sanjeev gupta et al. 2013

24. Percent transferability
Species Total markers
used
Amplified
markers
Transferability
(%)
Mungbean 50 46 92
Adzukibean 202 178 91
Cowpea 14 12 86
Commonbean 45 9 20
Chickpea 30 0 0
Pigeonpea 20 0 0
Total 361 245 68
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Sanjeev gupta et al. 2013

25. Results
These identified SSR markers
may be useful for genetic
analysis and marker assisted
breeding in blackgram.
Some SSR markers are showing
specific to genotypes, these can
use for species identification.
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Sanjeev gupta et al. 2013

26. Limitations to transferable SSR
markers
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A. PCR duration and Annealing temperature:
The PCR duration and annealing
temperature are standardised for each primers.
For Pulses- 53o C for 35 seconds
For Safflower- 56o C for 45 seconds
Yallappa et al. 2017

27. B. Stutter bands
Extra bands
observed on
agarose gel.
Shorter and have
weaker signal
intensity than
actual
microsatellite
bands.
Improper scoring
of bands will
affect the data
analysis.
9/23/2017 Department of genetics and plant breeding 27Ming et al. 2009

28. C. Null alleles
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Alleles at a microsatellite locus that fails to amplify.
Primer template
mismatch
Due to
Ming et al. 2009

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