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CREDIT SEMINAR - II
Presented by :
Asmat Ara
Ph. D GPB
03/AG(GPB)/2016-D
Seminar Incharge :
Dr. Kamal-ud-din
“Breeding for Abiotic Stress
Tolerance in Legumes”
stress
 “ A biological stress is an
adverse force or a condition,
which inhibits the normal
functioning and well being
of a biological system such as
plants .’’
(Lones et.al ,1989)
 It is an organism's response
to a stressor such as an
environmental condition.
DARYANTO et al,
2015 PLOS ONE
Breeding strategies
• Field based testing – Stress ecology
• Trait based phenotyping – Phenomics
• Gene/ QTL based screening- Genomics
• Expression/Interaction – Transcriptomics/
Proteomics/Metabolomics /Interactomics
• Microbial approaches – Microbiomes
• New Frontiers – CRISPR-cas Genome editing
Legume varieties bred for stress
CROP VARIETIES LEAD INSTITUTION
CHICKPEA JG-14, ICCV-37, ICCV-2, ICCV-42,
ICCV-96029, ICCV-94916-4, ICCV-
94916-8, ICCV- 94920-3, ICCV-
94924-2, ICCV-94924-3
ICRISAT
COMMON
BEAN
INTA SEQUA, BAT-477,
NAROBEAN-1, NAROBEAN-2,
NAROBEAN-3, NAROBEAN-4C,
NAROBEAN-5C
CIAT/INTA/PABRA
COWPEA IT-16, IT-18, IT-04K-321, IT-97K-
390, IT-99K-494, IT-849-2246,
BAMBEY-21, EPACE-1
IITA
GROUNDN
UT
TGX-1989-60F, TGX-1740-2F, TGX-
1937-1F
IITA
Physiological approaches
• Escape- proper timing of
lifecycle, resulting in the completion
of the most sensitive developmental
stages while water is abundant.
• Dehydration avoidance- Avoiding water-deficit stress with a root
system capable of extracting water from deep soil layers.
• Dehydration tolerance- Mechanisms such as osmotic adjustment
(OA) whereby a plant maintains cell turgor pressure under reduced
soil water potential.
Phenomics
• Plant phenomics
is the study of
plant growth,
performance and
composition. Cells
Chromosome
Nucleus
DNA
Gene
REGULATING SIGNALLING
• Osmotic/oxidative stress signalling (MAPK )
• Ca2+ dependent signalling ABA-responsive
elements (ABREs) – Leucine zippers, TF’s (DREB,
NAC, WRKY)
• Ca2+ dependent SOS signalling resulting in ion
homeostasis.
• Genes directly protect plant cells against stresses
(HSPs or chaperones, LEA proteins)
Response of different DREB genes to drought stresses
TRANSGENICS
(b)
(d)
(c)
Molecular Markers for Physiological Traits
• Assists the construction of linkage maps-exploited
for detection of chromosomal regions governing
traits
• Selection and characterization of QTLs
• The efficiency and precision of conventional
breeding can be enhanced through DNA markers
which have the potential to be used as molecular
tool for marker-assisted selection (MAS)
How linkage map
constructed?
• Production of a
mapping population
• Identification of
polymorphism
• Linkage analysis of
markers
QTL analysis
• Single-Marker analysis
• Simple Interval
mapping
• Composite Interval
mapping
Methods to detect QTLs
Common bean linkage map constructed using the AND 277 x SEA 5 RIL population. The
positions of the QTLs for drought (blue) and irrigated treatments (red) are shown
A case study:
Development of the
submergence tolerant
Swarna-Sub1 with
details of markers used
for foreground,
recombinant, and
background selection.
The numbers of plants
selected in each
generation are indicated
in parentheses.
Neeraja et al. (2007)
Genotype of the Swarna-Sub1 (BC2F2) plant that
is homozygous for the recipient genome except
for the Sub1 region on chromosome 9.
Neeraja et al. (2007
Micro-biome:
Zelicourta et al.2013
Dynamic community of
micro-organisms associated
with plant roots
Include plant-
growth promoting
bacteria (PGPB)
as well as plant-
growth promoting
fungi (PGPF)
(CRISPR)-Cas9 : Clustered Regularly
Interspaced Short Palindromic Repeat
 Genome editing tool in which sequence-specific
nucleases cause double-strand breaks (DSBs) at the
target genomic locus/loci.
(Voytas et al, 2013)
 Used for genome editing, transcriptional regulation
or forward genetics screens for understanding the
molecular basis of abiotic stress response, which can
lead to generation of abiotic stress-tolerant crop
plants.
(A) A map of the codon optimized Glycine max Cas9 (GmCas9) gene is shown along with
surrounding components and restriction sites.
(B) A map of the guide RNA with designated restriction site in red for insertion of target
recognition sequence.
(C) MDC32/Cas9 construct used for targeted mutagenesis in Medicago truncatula.
(D)MDC32/GUS/Cas9 construct with GUS reporter used for targeted mutagenesis in soybean.
Cross talk
• Any instance of two signalling pathways from
different stressors that converge.
• Cross-talk can also occur between pathways
in different organs of the plant when a systemic
signal such as hydrogen peroxide moves from a
stimulated cell into another tissue to elicit a
response.
Crosstalk of signal transduction pathways
(Knight & knight ,2001)
signalling
component
Stimulus 1 Stimulus 2Stimulus 1
Response
X
Response
X
Response Y
• Cold Drought, salt stress
DREB1 DREB2
DRE
Signal transduction
Transcription factors
e.g. RD29A/LT178
cis element
TATA
Gene
expression
HANDLING
FIELD
DATA
YIELD BASED
INDEX
PHENOLOGY
BASED INDEX
REGRESSION
BASED INDEX
SCORE BASED
INDEX
PHENOLOGY BASED INDICES
Conclusion
• The multiple stress responses on various kinds of
genes and their transcribed products involved in a
variety of cellular functions are important in
understanding and solving the problems of
drought/salt stress tolerance.
• Dissecting complex phenotypes into their
constituting QTLs will offer a more direct access to
hit valuable genetic diversity regulating the
adaptive response to stress conditions (drought,
salinity etc.).
Contd …
• Phenomics provides the opportunity to study
previously unexplored areas of plant science, and it
provides the opportunity to bring together genetics
and physiology to reveal the molecular genetic basis
of a wide range of previously intractable plant
processes.
• Genome editing of crop plants is a rapidly
advancing technology whereby targeted mutations
can be introduced into a plant genome in a highly
specific manner and with great precision.
….Thank You
….Thank You

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Breeding for Abiotic Stress Tolerance in Legumes

  • 1. CREDIT SEMINAR - II Presented by : Asmat Ara Ph. D GPB 03/AG(GPB)/2016-D Seminar Incharge : Dr. Kamal-ud-din
  • 2. “Breeding for Abiotic Stress Tolerance in Legumes”
  • 3. stress  “ A biological stress is an adverse force or a condition, which inhibits the normal functioning and well being of a biological system such as plants .’’ (Lones et.al ,1989)  It is an organism's response to a stressor such as an environmental condition.
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  • 13. Breeding strategies • Field based testing – Stress ecology • Trait based phenotyping – Phenomics • Gene/ QTL based screening- Genomics • Expression/Interaction – Transcriptomics/ Proteomics/Metabolomics /Interactomics • Microbial approaches – Microbiomes • New Frontiers – CRISPR-cas Genome editing
  • 14. Legume varieties bred for stress CROP VARIETIES LEAD INSTITUTION CHICKPEA JG-14, ICCV-37, ICCV-2, ICCV-42, ICCV-96029, ICCV-94916-4, ICCV- 94916-8, ICCV- 94920-3, ICCV- 94924-2, ICCV-94924-3 ICRISAT COMMON BEAN INTA SEQUA, BAT-477, NAROBEAN-1, NAROBEAN-2, NAROBEAN-3, NAROBEAN-4C, NAROBEAN-5C CIAT/INTA/PABRA COWPEA IT-16, IT-18, IT-04K-321, IT-97K- 390, IT-99K-494, IT-849-2246, BAMBEY-21, EPACE-1 IITA GROUNDN UT TGX-1989-60F, TGX-1740-2F, TGX- 1937-1F IITA
  • 15. Physiological approaches • Escape- proper timing of lifecycle, resulting in the completion of the most sensitive developmental stages while water is abundant. • Dehydration avoidance- Avoiding water-deficit stress with a root system capable of extracting water from deep soil layers. • Dehydration tolerance- Mechanisms such as osmotic adjustment (OA) whereby a plant maintains cell turgor pressure under reduced soil water potential.
  • 16. Phenomics • Plant phenomics is the study of plant growth, performance and composition. Cells Chromosome Nucleus DNA Gene
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  • 20. REGULATING SIGNALLING • Osmotic/oxidative stress signalling (MAPK ) • Ca2+ dependent signalling ABA-responsive elements (ABREs) – Leucine zippers, TF’s (DREB, NAC, WRKY) • Ca2+ dependent SOS signalling resulting in ion homeostasis. • Genes directly protect plant cells against stresses (HSPs or chaperones, LEA proteins)
  • 21. Response of different DREB genes to drought stresses
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  • 28. Molecular Markers for Physiological Traits • Assists the construction of linkage maps-exploited for detection of chromosomal regions governing traits • Selection and characterization of QTLs • The efficiency and precision of conventional breeding can be enhanced through DNA markers which have the potential to be used as molecular tool for marker-assisted selection (MAS)
  • 29. How linkage map constructed? • Production of a mapping population • Identification of polymorphism • Linkage analysis of markers
  • 30. QTL analysis • Single-Marker analysis • Simple Interval mapping • Composite Interval mapping Methods to detect QTLs
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  • 36. Common bean linkage map constructed using the AND 277 x SEA 5 RIL population. The positions of the QTLs for drought (blue) and irrigated treatments (red) are shown
  • 37. A case study: Development of the submergence tolerant Swarna-Sub1 with details of markers used for foreground, recombinant, and background selection. The numbers of plants selected in each generation are indicated in parentheses. Neeraja et al. (2007)
  • 38. Genotype of the Swarna-Sub1 (BC2F2) plant that is homozygous for the recipient genome except for the Sub1 region on chromosome 9. Neeraja et al. (2007
  • 39. Micro-biome: Zelicourta et al.2013 Dynamic community of micro-organisms associated with plant roots Include plant- growth promoting bacteria (PGPB) as well as plant- growth promoting fungi (PGPF)
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  • 43. (CRISPR)-Cas9 : Clustered Regularly Interspaced Short Palindromic Repeat  Genome editing tool in which sequence-specific nucleases cause double-strand breaks (DSBs) at the target genomic locus/loci. (Voytas et al, 2013)  Used for genome editing, transcriptional regulation or forward genetics screens for understanding the molecular basis of abiotic stress response, which can lead to generation of abiotic stress-tolerant crop plants.
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  • 46. (A) A map of the codon optimized Glycine max Cas9 (GmCas9) gene is shown along with surrounding components and restriction sites. (B) A map of the guide RNA with designated restriction site in red for insertion of target recognition sequence. (C) MDC32/Cas9 construct used for targeted mutagenesis in Medicago truncatula. (D)MDC32/GUS/Cas9 construct with GUS reporter used for targeted mutagenesis in soybean.
  • 47. Cross talk • Any instance of two signalling pathways from different stressors that converge. • Cross-talk can also occur between pathways in different organs of the plant when a systemic signal such as hydrogen peroxide moves from a stimulated cell into another tissue to elicit a response.
  • 48. Crosstalk of signal transduction pathways (Knight & knight ,2001) signalling component Stimulus 1 Stimulus 2Stimulus 1 Response X Response X Response Y
  • 49. • Cold Drought, salt stress DREB1 DREB2 DRE Signal transduction Transcription factors e.g. RD29A/LT178 cis element TATA Gene expression
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  • 55. Conclusion • The multiple stress responses on various kinds of genes and their transcribed products involved in a variety of cellular functions are important in understanding and solving the problems of drought/salt stress tolerance. • Dissecting complex phenotypes into their constituting QTLs will offer a more direct access to hit valuable genetic diversity regulating the adaptive response to stress conditions (drought, salinity etc.).
  • 56. Contd … • Phenomics provides the opportunity to study previously unexplored areas of plant science, and it provides the opportunity to bring together genetics and physiology to reveal the molecular genetic basis of a wide range of previously intractable plant processes. • Genome editing of crop plants is a rapidly advancing technology whereby targeted mutations can be introduced into a plant genome in a highly specific manner and with great precision.