breeding of rice

1. BREEDING OF RICE
MOHANAPRIYA B
2019608008

2. Breeding methods
Conventional breeding methods
• Introducton
• Pureline selection
• Recombination breeding
• Mutation breeding
• Heterosis breeding
Molecular methods
• MAS
• Transgenics

3. Introduction- oldest and simplest method
• Eg –TN1 and Taichung 65 from Taiwan
• IR8,IR20,IR36,IR50 and IR64 from philippines
Pureline slection- purification of landraces
Eg – Basmati 370, Ptb 18, Ptb 33,CO 43
Recombination breeding
Controlled crossing between parent of choice followed by
pedigree or mass selection in the segregating generation for
target traits
Generate variability selection recombine desirable
traits
Single seed decent method coupled with RGA
Well suited for breeding long duration photosensitive varieties

4. Backcross breeding
Transfer genes for specific characteristics, such
as
 Disease
 Insect resistance or
 Dwarfing genes,
into otherwise desirable varieties
Xa 4 and Xa 21 into Pusa44 for BLB resistance

6. Heterosis breeding
 Heterosis in rice was reported by Jones in USA (1926) and Ramaiah (1933).
 The research work on hybrid rice was initiated in 1964, in China by Yuan
Long Ping (Father of hybrid Rice).
 The identification of ‘Wild Abortive’ or ‘WA’ type cytoplasmic male sterility
in 1970 was a breakthrough in hybrid rice breeding
New sources of male sterile cytoplasm : GA (Gambiaca), Di (Disi), DA (Dwarf
wild rice), BTC (Chinsurah Boro II) and IP (Ido Paddy 6).
The crosses showing heterosis in descending order are
• indica × japonica > indica × javanica > japonica × javanica > indica × indica
> japonica × japonica > javanica × javanica.
• Three line breeding-CGMS
• Two line breeding- PGMS and TGMS/ CHA’S
• One line breeding - Apomixis

7. Mutation breeding
LD50 for various characteristics has been shown to vary from 10 to 50 KR for
gamma rays .

8. a) Spontaneous mutation
• GEB 24 - From Athur Kichili Samba known as KONAMANI,
• ADT 41 - Dwarf mutant of Basmati 370.
b) Induced mutation :
• Jagannath rice from Orissa. Semi dwarf.
• Parbhani - from Maharastra
• Satari - Short duration, gamma irradiated
• AU 1 - from Tamil Nadu.

9. EMS Induced Mutants of Upland Rice Variety Nagina22: Generation and
Characterization
Generation and initial characterization of a large set of Ethyl Methane
Sulphonate (EMS) induced mutants in the upland rice variety Nagina22
National Initiative involving six Research Institutes namely
1.National Research Centre on Plant Biotechnology, New Delhi; 2.Indian
Agricultural Research Institute, New Delhi;
3.Tamil Nadu Agricultural University, Coimbatore;
4.Directorate of Rice Research, Hyderabad;
5.University of Agricultural Sciences, Bangalore and
6.Punjab Agricultural University, Ludhiana,
Funded by the Department of Biotechnology (DBT), Government of India.

10. Classification of the 548 EMS mutants currently maintained in
the mutant garden under different traits
 Plant growth and
architecture,
 flowering,
 maturity,
 grain number, Shape and
size,
 yield,
 phosphorus use
efficiency,
 resistance to blast and
bacterial leaf blight
diseases,
 tolerance to drought,
 salinity and
 herbicide

11. N – Nagina22; M – Mutant. a – dwarf mutant; b - dwarf mutant; c – Chlorophyll mutant
striata; d – Narrow leaf mutant; e – Mutant with shoot regeneration from panicle parts; f
– bacterial leaf blight resistant mutant; g – Mutant with a single crown root; h – A
representative variation in panicle architecture in Nagina22 panicle mutants
Representative
variation for different
traits in the
mutagenized
population of Nagina
22.
Phenotypic
Characterization of
the Mutants

12. Marker Assisted Breeding (MAS)
Marker assisted
selection is not a
time reducing tool
but a accuracy and
efficiency tool
Green revolution
Gene revolution

14. BREEDING RICE FOR DROUGHT
TOLERANCE

15. Early drought Intermittent drought
Terminal drought

17. 16 QTLs, in which a single QTL
explained 9-39% of the
phenotypic variation.
These QTLs distributed on
eight chromosomes.
DTY Qtls

18. qDTY12.1 a large effect qtl
• qDTY12.1 works as a gene-complex of 10 genes
• transcription factor OsNAM is a major regulator.
candidate gene analysis has been carried out in this QTL region and several genes have
been reported as putative candidate genes, including a GRAM-domain containing
protein, an Amydohydrolase, a Nodulin MtN3, a No Apical Meristem, a Cellulose
Synthase A(CesA10) and a cytochrome P450 associated with different processes such
as root hair proliferation/elongation, pollen fertility, cell wall permeability and signal
transduction

22. Salinity symptoms in Rice
vegetative stage
• “Leaf tip burning”
• “Leaf tip burning extends toward base
through Lamina”
• “Ultimate death of leaf – from oldest to
youngest”
Reproductive stage
Spikelet Sterility papery sterile spikelets
Breeding For salinity tolerance in rice

23. 1. Restricting the entry of toxic
ions at root level -ion Exclusion
2. Transporting the toxic ions to
stem, leaf sheath or older leaves –
plant level compartmentation
4. Sequestration of the toxic ions
to vacuole or cell wall – cell level
compartmentation
3. Excretion of salt through salt
glands, salt-hairs or bladders – in
most halophytes
salt-tolerance mechanisms
Na+ Cl-

24. SALTOL
• Saltol - Major Quantitative Trait Loci (QTL) for salt
tolerance
• maintain low Na+, high K+, and Na+/ K+ homeostasis in
shoots of rice.
• traditional cultivars - Pokkali, Nona Bokra, Cheriveruppu
and Getu - saline tolerant but poor agronomic characteristics.
• Pokkali widely used donor in salt tolerance related studies.

25. Pokkali (salt tolerant) x IR29 (salt sensitive)
FL478 (IR 66946-3R-178-1-1)
(Shows high or comparable salt tolerance than Pokkali)
• Developed by Marker Assisted Backcrossing and Marker Assisted Selection
• FL478 - improved donor of Saltol QTL
• high level seedling stage salinity tolerance and photoperiod insensitive,
shorter and flowers earlier than original landrace Pokkali
• salt tolerance indica aromatic export quality rice varieties PB1121 and PB6.

26. Salt tolerant rice varieties
• Saltol is transferred into a rice varieties ADT45,CR1009, Gayatri,
MTU1010, PR114, Pusa 44 and Sarjoo 52.
• IRRI 112, IRRI 113, IRRI 124, IRRI 125, IRRI 126, IRRI 128
• CSR10, CSR13, CSR23, CSR27, CSR30(basmati type), CSR36 , CSR-49
Other varieties
• Lunishree, Vytilla 1, Vytilla 2, Vytilla 3, Vytilla 4, Panvel 1, Panvel 2, Sumati,
Usar dhan 1, 2 & 3 (India); BRRI dhan 40, BRRI dhan 41 (Bangladesh);
OM2717, OM2517, OM3242 (Vietnam)

27. Breeding rice for Submergence tolerance
 In India and Bangladesh alone, submergence destroys 4 million tons of rice each
year, enough to feed 30 million people.
 50 years ago, breeders discovered-ancient variety of rice that could withstand 2
weeks of complete submergence(Using conventional approaches).
 In 1990s, rice breeder David Mackill and graduate student Kenong Xu- mapped to
the Submergence tolerance 1 (Sub1) Quantitative trait locus(QTL)
 In 1996, Ronald began a project with Mackill and Xu, funded by the USDA, to
isolate the genes at the Sub1 locus.
 Xu identified and sequenced the Sub1 QTL genomic region, revealed that it carried
three ethylene response transcription factors (ERF) and demonstrated that one of
the ERFs, designated Sub1A, was up-regulated rapidly in response to
submergence.

28. SUB1
• Analyses of flashflood tolerance confirmed that the QTL on
chromosome 9 has the strongest effect, accounting for 69% of the
phenotypic variation.
• QTL analysis and positional cloning allowed the identification of
the Submergence1 (Sub1) locus on chromosome 9, which confers
submergence tolerance.
• In this locus, there are three similar genes that encode an ethylene
response factor (ERF)-type transcription factor domain:
Sub1A, Sub1B and Sub1C.

29. SNORKEL
• Under deepwater conditions, ethylene accumulates in the plant and induces expression
of these two genes. The products of SNORKEL1 and SNORKEL2 then trigger remarkable
internode elongation via gibberellin
• T65/C9285, to detected three major QTLs for deepwater response on chromosomes 1,
3 and 12 and also detected these QTLs in the same chromosome regions in different
populations. Among these, the QTL on chromosome 12 was the most effective for
deepwater response.

31. Varieties released with sub 1
• Swarna Sub1
• CR1009 Sub1
• CO 43 Sub1
• IR64 Sub1

33. BREEDING RICE FOR HERBICIDE TOLERANCE
Acetolactate synthase (ALS) / Acetohydroxy acid synthase, (AHAS) - branched-chain
amino acids (valine, leucine, and isoleucine)
Sulfonylureas (SUs)
imidazolinones (IMIs)
triazolopyrimidines (TPs)
 pyrimidinyl oxybenzoates (POBs)
sulfonylamino carbonyl triazolinones (SCTs)
Point mutation in this gene – conferred resistance to herbicide

34. • EMS mutagenesis - Nagina22- Robin mutant
• Resistant to herbicide – Imazethapyr
• RM6844
Shoba et al. Rice (2017)

35. BREEDING FOR LODGING RESISTANCE
Culm Diameter (mm)
Culm thickness (mm)
Culm strength
Bending Strength
Per cent of Lodging

36. QTLs for STRONG CULM
QTL Population
SCM1
SCM2
Habataki/ Sansanishiki
SCM3
SCM4
Chukogu/koshihikari
K. HIRANO, R. L. ORDONIO and M. MATSUOKA
(2017)
Nomura et al., 2019

37. BPH resistance

39. Transgenic Rice
• Rice resistant to herbicides, diseases, and pests, increasing nutritional value,
eliminating rice allergies, producing human blood protein, increasing yield;
improving tolerance to drought and salinity; and enhancing nitrogen use
efficiency.
• In 2000, the first two GM rice varieties both with herbicide-resistance, called
LLRice60 and LLRice62, were approved in the United States.

41. Reference
 Waziri, A., et al. (2016). "Saltol QTL and their role in salinity tolerance in rice." Austin Journal
of Biotechnology & Bioengineering 3: 1-5.
 Y. Hattori, K. Nagai, S. Furukawa, X.J. Song, R. Kawano, H. Sakakibara, Jianzhong Wu,
Takashi Matsumoto, Atsushi Yoshimura, Hidemi Kitano, Makoto Matsuoka, Hitoshi Mori,
Motoyuki Ashikari. The ethylene response factors SNORKEL1 and SNORKEL2 allow rice
to adapt to deep water. Nature. 2009; 460, 1026-1030
 Fukao, T., & Bailey-Serres, J. (2008). Submergence tolerance conferred by Sub1A is mediated
by SLR1 and SLRL1 restriction of gibberellin responses in rice. Proceedings of the National
Academy of Sciences of the United States of America, 105(43), 16814–16819.
doi:10.1073/pnas.0807821105
 Hirano, K., Ordonio, R. L., & Matsuoka, M. (2017). Engineering the lodging resistance
mechanism of post-Green Revolution rice to meet future demands. Proceedings of the Japan
Academy. Series B, Physical and biological sciences, 93(4), 220–233. doi:10.2183/pjab.93.014

42.  K.S. Fischer, R. Lafitte, S. Fukai,G. Atlin, and B. Hardy , Breeding Rice for Drought-
Prone Environments ,IRRI,2003
 Nitika Sandhu and Arvind Kumar , Bridging the Rice Yield Gaps under Drought:
QTLs,Genes, and Their Use in Breeding Programs ,MDPI.2017.
 Vikram et al, qDTY1.1, a major QTL for rice grain yield under reproductive-stage
drought stress with a consistent effect in multiple elite genetic backgrounds. BMC
Genetics 2011, 12:89
 Mishra et al, qDTY12.1: a locus with a consistent effect on grain yield under
drought in rice. BMC Genetics 2013, 14:12