The present investigation was carried out to study the genetic diversity among the eleven different traditional varieties of rice from southern states of Tamilnadu. High quality DNA was extracted from the seed material by Doyle and Doyle protocol with slight modifications. RAPD profile of eleven rice varieties was generated using 8 primers OP-13, 16, 17, 18 and OP – 8, 11, 17, 18 showed 98 Fragments generated. Out of which, 98 bands were polymorphic in nature and remaining were monomorphic. In dendrogram, Vellai Chittiraikar traditional rice variety was only variety which was not at all closely related to all other varieties. The seeds of these varieties have been passed on to farmers over the generations. Maximum variability of 66% between these varieties at genetic level indicated that the traditional varieties have a wider genetic base. This will enrich the rice germplasm of our nation for use in future breeding programmes. In conclusion, RAPD has high potential and remarkable quality for assessment of genetic populations. It is also evident that RAPD offer several advantages over traditional phenotypic markers as they provide data that can be analyzed objectively. This gives new dimensions to breeding especially with respect to time required for developing new and improved crop varieties.

1. STUDIES ON GENETIC DIVERSITY AND
PHYLOGENETIC RELATIONSHIP AMONG
ELEVEN TRADITIONAL VARIETIES OF
ORYZA SATIVA L. USING RAPD MARKERS
Under the guidance of Dr. R. Ravindhran
Nitu Sinha
M.Phil Scholar
12/MBT/002

2. Content
 Introduction
Why crop Improvement
Solutions
Objective
Materials and Methods
Results
Conclusion and future prospective

3. Introduction
Agriculture is the art or
science of production of
crops and livestock on
farm.
Wheat, maize and rice
-world wide cultivated
Rice - Oryza sativa and O.
glaberrima
Typical Rice Monocot
plant with leafs, stem and
panicles

4. Why Crop Improvement ..???? ..
Overpopulations and
Pollution
Natural calamities
Green Revolution
traditional varieties
diagrammatical presentation of ten various crops in 1903 and 1983.

5. Solutions
Integrated Biotechnology – Traditional Varieties
conventional biotechnology and molecular
biology integrates with field farmers plus
potential biotechnology companies
Characterizations – Molecular
marker

6. Objective
To analyze the genetic variation of traditional
rice varieties using RAPD markers.
To establish the phylogenetic relationship of the
collected traditional rice varieties.

7. Seeds of Traditional Rice varieties
a
d
b
e
c
f
(a) - Varakkal, (b) - Kuzhiyadichan, (c) – Kundhali, (d) - Varappu
kudainchan (e) – Thooyamallee and (f) – Ramakuruvikar

8. Seeds of Traditional Rice varieties
g
i
h
j
k
(g) - Kattu samba, (h)- Villai Chittiraikar, (i) – Vellai kattai,
(j) - Seeraga samba and (k) - Rajamannar

9. Materials and Methods
Doyle Doyle with little modification.
RAPD primer
(OPA – 13,16,17 and18 and OPB - 8, 11, 17 and 18)
RAPDistance package Software Version 1.04
Numerical taxonomy and Multivariate Analysis System
Unweighted Pair-group Method of Arithmetic (UPGMA)

10. RESULTS
RAPD amplification products generated from eleven traditional varieties of Oryza sativa L. using Primer (a) OPA 13 and (b) OPA
16 (M – Lamda DNA/ Hind III plus (300bp – 23130bp), 1 - Varakkal, 2 – Kuzhiyadichan, 3 – Kunthali, 4 – Varappu kudainchan, 5
– Thooyamallee, 6 – Ramakuruvikar, 7 – Kattu samba, 8 – Villai Chittiraikar, 9 – Vellai kattai, 10 - Seeraga samba, 11 – Raja
mannar
23130 bp
9416 bp
2322 bp
2027 bp
1500 bp
M
1
2
3
4
5
6
7
8
9
10
11
1
2
3
4
5
6
7
8
9
10
11
1000 bp
564 bp
a
23130 bp
9416 bp
M
2322 bp
2027 bp
1500 bp
1000 bp
564 bp
b

11. RAPD amplification products generated from eleven traditional varieties of Oryza sativa L. using Primer
(a) OPA 17 and (b) OPA 18 (M – Lamda DNA/ Hind III plus (300bp – 23130bp), 1 - Varakkal,
2 – Kuzhiyadichan, 3 – Kunthali, 4 – Varappu kudainchan, 5 – Thooyamallee, 6 – Ramakuruvikar,
7 – Kattu samba, 8 – Villai Chittiraikar, 9 – Vellai kattai, 10 - Seeraga samba, 11 – Raja mannar
M
1
2
3
4
5
6
7
8
9
10
11
1
2
3
4
5
6
7
8
9
10
11
23130 bp
9416 bp
2322 bp
2027 bp
1500 bp
1000 bp
564 bp
.
a
23130 bp
9416 bp
2322 bp
2027 bp
1500 bp
M
1000 bp
564 bp
b

12. RAPD amplification products generated from eleven traditional varieties of Oryza sativa L. using Primer
(a) OPB 8 and (b) OPB 11 (M – Lamda DNA/ Hind III plus (300bp – 23130bp), 1 - Varakkal,
2 – Kuzhiyadichan, 3 – Kunthali, 4 – Varappu kudainchan, 5 – Thooyamallee, 6 – Ramakuruvikar,
7 – Kattu samba, 8 – Villai Chittiraikar, 9 – Vellai kattai, 10 - Seeraga samba, 11 – Raja mannar
23130 bp
9416 bp
M
1
2
3
4
5
6
7
8
9
10
11
1
2
3
4
5
6
7
8
9
10
11
2322 bp
2027 bp
1500 bp
1000 bp
564 bp
a
M
23130 bp
9416 bp
2322 bp
2027 bp
1500 bp
1000 bp
564 bp
b

13. RAPD amplification products generated from eleven traditional varieties of Oryza sativa L. using Primer
(a) OPB 17 and (b) OPB 18 (M – Lamda DNA/ Hind III plus (300bp – 23130bp), 1 - Varakkal,
2 – Kuzhiyadichan, 3 – Kunthali, 4 – Varappu kudainchan, 5 – Thooyamallee, 6 – Ramakuruvikar,
7 – Kattu samba, 8 – Villai Chittiraikar, 9 – Vellai kattai, 10 - Seeraga samba, 11 – Raja mannar
23130 bp
9416 bp
M
1
2
3
4
5
6
7
8
9
10
1
2
3
4
5
6
7
8
9
10
11
2322 bp
2027 bp
1500 bp
1000 bp
564 bp
a
23130 bp
9416 bp
2322 bp
2027 bp
1500 bp
M
1000 bp
564 bp
b
11

14. Details of amplified fragment obtained from traditional
varieties of rice and percentage of polymorphism.

15. Similarity matrix using Jaccard’s coefficient for eleven
traditional varieties of rice based on 98 bands obtained
with 8 RAPD primers

16. NTSYS-PC Dendrogram showing the genetic diversity among 11 traditional
varieties of rice of Tamil Nadu.

17. CONCULSION
Vellai Chittiraikar traditional rice variety – non similar
striking genetic difference – 11 Traditional varieties
Maximum variability of 66% - wider genetic base.
RAPD - high potential & remarkable quality - genetic populations.
Breeding - improved crop varieties.

18. FUTURE PROSPECTIVE
Rooting for rice - saving our rice campaign tries -
traditional varieties
molecular marker (identification) – breeding
New crops - farmers - production
INDIA
Economy