The document describes two case studies on breeding for drought resistance in rice. The first case study details a crossing program between a drought tolerant donor variety (Nagina 22) and three susceptible varieties (Swarna, IR64, MTU1010). QTL analysis identified a major QTL (qDTY1.1) on chromosome 1 that increased yield under drought stress in the progenies. The second case study describes a crossing between a susceptible (Danteshwai) and tolerant landrace (Dagaddeshi) followed by QTL mapping, which identified 20 QTL for yield under different drought conditions, with some located on chromosomes 1, 3 and 11. The identified QTL and genomic regions can help breed

1. Breedingfor Drought resistance
(Casestudy presentation.)
Presented by
Roshan Parihar
Ph.D. Scholar (GPB)
IGKV,RAIPUR,(CG)

2. Drought Tolerance Breeding
Analytical
Breeding
Empirical
Breeding
vs.
It directly selects
the breeding
material for yield
per se or for yield
components
It relies on indirect selection
for morphological,
physiological or biochemical
traits associated with yield.

3. Use of Crop Wild Relatives
• India a drought and heat tolerant variety of chickpea
(BG1103) has been released after introgression from
Cicer reticulatumLadiz. The variety showed superior
yield and pod filling under drought stress
• Oryza longistaminata was exploited in Philippines for
the development of drought tolerant rice cultivars (Brar
2004).
• Lycopersicum chilense Dunal and Lycopersicum
penellii(Corr.) D'Arcy have been used for the
introduction of drought tolerance genes in tomato
• Helianthus argophyllusTorr. & A. Gray has been
exploited for the introduction of drought tolerance
genes into cultivated sunflower.

4. The example of Synthetic Hexaploid
Wheat (SHW)
Tetraploid wheat
Triticum turgidum L.
subsp. Durum
(2n=28, AABB)
Diploid wheat relative
Aegilops tauschii
(2n=14, DD),
F1
ABD
(21)
Chromo. Doubling
with colchicine
SHW
2n=42,(AABBDD )
Elite Bread
wheat
Cultivars
Backcrossing prog.
Withelite wheat
varieties
SBL lines synthetic backcross-derived lines, with
drought resistance ,disease and other quality traits
x
x

5. Breeding Schemes
• Mass selection
The simplest selection procedure, is used to
improve the overall population by positive or
negative mass selection.
Mass selection is practiced within populations
for traits with high range of narrow sense
heritability.

6. Pure line selection
• In this drought tolerant parents are crossed
with high yielding parents to develop
segregating populations.
• New allelic combination arises due to
recombination and segregation of traits.
• Superior plants are selected in F2 population
under drought or non-stress conditions.
• Seeds of these selected plants are used to
establish plant progenies.

7. Recurrent selection
• In this visually selected individuals out of the
base population
• Individual undergo progeny testing
• Individuals selected on basis of the progeny test
data are crossed in Diallelic fashion to form the
new base population.
• The intermating of F2 plants restores
heterozygosity, creates new genetic variation in
each population, produces new recombinants
and maximizes the favourable alleles in single
genotype.
• These populations have been successful to break
gene linkage and introduce novel recombination.

8. In-Vitro selection
• Screening of germplasm for tolerance to
osmotic stress can be carried out using various
types of osmotica to reduce the water
potential of the growth media.
• Polyethylene glycol has been frequently used
for in vitro screening of germplasm for
seedling germination or growth. Seeds are
directly germinated over the agar plates
containing PEG

9. In vitro images
• In vitro
regeneration of
sunflower
(Helianthus
annuus L.) line
“B-24” in
polyethylene
glycol 6000 (50g
L-1)

10. Ex. of in vitro selection varieties
• In vitro regeneration of sunflower (Helianthus
annuus L.) line “B-24” in polyethylene glycol
6000 (50g L-1)
• Polyethylene glycol induced drought has been
used for in vitro selection of drought tolerant
somaclones. The plants regenerated from
seedling having survived on the agar plate in
presence of PEG exhibited higher yield under
drought stress and showed diversity of drought
tolerance mechanism

11. Doubled Haploids
• In vitro or in vivo screening of haploids
gametes under drought stress has been an
effective tool to increase the frequency of
homozygous drought tolerant genotypes
(Ambrus et al. 2006).
• It has been noted that 65% of the genes
responsible for cell structure and tolerance to
stresses are expressed during the
gamteophytic stage causing variation among
gametophytes for drought tolerance.

12. Embryo Rescue Technique
• It facilitated the development of drought
resistant interspecific hybrid in sunflower
(Helianthus annuus × Helianthus argophyllus;
Sauca et al. 2011),
• Wheat (Triticum durum × Aegilops tauschii;
Trethowan et al. 2014),
• Brassica (Eruca sativa × Brassica compestris;
Agnihotri et al. 1990)

13. Marker Assisted Selection for Drought
Tolerance
• Most of the economical traits including those
related with drought tolerance are quantitative
and strongly influenced by the environment.
• The term quantitative trait loci (QTL) for drought
applies to genome regions that control these
drought responsive yield enhancing traits
• MAS permits to accelerate the breeding process
with quick screening.

14. Transgenic breeding examples.
• MON 87460, a transgenic variety of maize
over expressing the cold shock protein B
which has been released for cultivation in
water deficit areas of US northern Great Plains
• Tomato plants with GA methyl transferase
(ATGAMT1) increased drought tolerance by
reducing the transpiration and maintaining
water contents
• Transformation of the alfalfa with GsWRKY20
increased proline and sugar contents

15. Case study-1 :

16. Materials used
• Nagina 22 (N22), the drought-tolerant donor, is a shortduration
(90-95 days) variety developed by selection from landrace Rajbhog
from Nepal.
• Swarna (MTU 7029) is a semi-dwarf high-yielding long-duration
(140-145 days) variety for irrigated and rainfed rice ecosystems in
India, Nepal, and Bangladesh . Swarna is highly susceptible to RS .
• IR64 is a well-known semi-dwarf high-yielding medium-duration
(112-118 days) variety developed at IRRI. It is grown on large areas
in South and Southeast Asia and East Africa. IR64 is also
susceptible to RS .
• MTU1010 is a semi-dwarf high-yielding medium-duration (112-118
days) variety grown in large areas in central, southern,
• and eastern India. MTU1010 is moderately susceptible to RS .

17. Crossing & screening programme
Swarna ,IR-64,MTU-1010
(Susceptible for drought) x
Nagina 22 (N22),
drought-tolerant
donor
F1’s of all
Three crosses
F1plants are selfed
F2 –F3
Generation
SSD (Single Seed Descendent method used)
1.Seeds from each F2 plant were selected and bulked.
2.F3 seeds were grown and harvested individually
500 F3 of
Swarna plants
harvested
500 F3 of IR64
plants
harvested
500 F3 of MTU-
1010 plants
harvested
292 F3 plants are
selected and grown
on F3:4 Population
289 F3 plants are
selected and grown
on F3:4 Population
362 F3 plants are
selected and grown
on F3:4 Population
All Three F3:4 populations were used for mapping large-
effect QTLs for GY under RS
Phenotyping & Genotyping 2009,2010
With 682 SSRmarkers
BSA approach for all 3 Popu. done
Selected lines of BSA were run with 140
and 125 SSr markers .

23. Linkage map construction and QTL analysis,
• In N22/ Swarna and N22/IR64 populations, maps
were constructed for markers used on
chromosomes 1 and 3 and on chromosomes 1 and
2, respectively.
• Polymorphism of N22 with Swarna, IR64, and
MTU1010 was 43.5%, 42.5%, and 40.1%,
respectively.
• QTLs for GY, DTF, PH,HI, and BIO were identified.
Results of QTL analysis are presented in Tables 3
and 4.

24. Results:
• A major QTL for GY under RS, qDTY1.1, was identified on rice
chromosome 1 flanked by RM11943 and RM431 in all three
populations.
• In combined analysis over two years, qDTY1.1 showed an
additive effect of mean yield in N22/Swarna, N22/IR64, and
N22/MTU1010, respectively, under RS.
• However it showed a positive effect on GY in non-stress (NS)
situations in N22/Swarna, N22/IR64 over both years, and N22/
MTU1010 in DS2009.
• This experiment identified additional QTLs for GY under RS that
showed an effect against a single genetic background. qDTY2.3
in N22/IR64, qDTY3.2 in N22/ Swarna, and qDTY10.1 in
N22/MTU1010 populations were identified. qDTY3.2 had a
significant effect on GY under RS in DS2009 only,
• qDTY1.1 could be used effectively for improving the GY of
lowland rice cultivars Swarna , IR64, and MTU1010 under both
RS and NS situations.

25. Case study no. II

26. Crossing & screening programme
Danteshwai
(Susceptible for drought) x
Dagaddeshi,
drought-tolerant
donor ,Landrace
F1 & Onwards
Gen. selfed
RIL,s upto F11
generationSSD (Single Seed Descendent method used)
271 lines in F11
are selected
Genotyping of F12,13
generation for QTL
Analysis
Genotyping 2011,2012
With 162 were polymorphic markers and
molecular study conducted.
1. Lines evaluated under water stress&
irrigated condition
2. 122 lines are screened for grain yield,
leaf rolling, plant height and root pulling
resistance; highest and lowest genotypes
were selected.
122 RILs in F12-
13 gen. are
screened
This F12-13 generation grown under five
conditions for 2 years.
1.Irrigated 2. Rainfed 3 .TSD(Terminal stage
drought) 4.Direct seeded, 5.Transplanted,
Early and Late condition
The phenotypic and genotypic data was
analyzed using QTL cartographer 2.5 and QTL
IciMapping 3.2

31. Conclusion
• A total of 20 QTL were detected for grain yield under different conditions by
employing QTL cartographer 2.5 and 7 QTL by employing QTL IciMapping 3.2.
• out of which 5 QTL were common under both the software.
• Among the major QTL, QTL on chromosome 1 (qDTY1.1) under rainfed
transplanted condition between RM 3825 (143.7cM) to RM 302 (147.8cM) had
LOD score of 5.09,
• QTL on chromosome 3 (qDTY3.3) under irrigated transplanted condition
between RM 7 (64.0cM) to RM 232 (76.7cM) had LOD score of 6.59 .
• QTL on chromosome 11 (qDTY11.1) under TSD transplanted condition between
RM 21 (85.7cM) to RM 26334 (90.0cM) had LOD score of 7.39.
• This study has resulted in identification of new major QTL, one on chromosome
11 (qDTY11.1) under TSD condition, which is different than most of other QTL
reported by earlier workers.
• These QTL except qDTY 3.3, had positive additive effects, indicating that alleles
at these loci increase grain yield under different conditions and come from
tolerant parent Dagad deshi.
• Two regions of chromosome #1 and 3 had QTL for grain yield under stress as
well as non-stress conditions.
• These genomic regions associated with grain yield under different conditions
will be useful in marker assisted breeding for drought tolerance in rice.