The document outlines strategies for developing drought-smart future crops. It discusses omics tools like genomics, transcriptomics, proteomics, and metabolomics that can be used to identify genes and pathways related to drought tolerance. Transgenic approaches like genetic engineering can introduce drought tolerance genes. Conventional breeding and speed breeding can combine traits from parental lines. Integrating these modern techniques with traditional methods like agronomic practices can help develop crops with improved drought resistance and yield stability under water scarcity. A case study identifies genomic loci, genes and transcription factors in maize affecting seminal root length under drought. Future work may combine genome editing, phenomics and speed breeding to rapidly deliver climate-smart crops.
2. 1. WHAT IS DROUGHT STRESS ?
2. WHY DO WE NEED DROUGHT-SMART FUTURE CROPS ?
3. WHAT ARE THE DIFFERENT KINDS OF CROPS RESPONSE TO
DROUGHT-STRESS?
4. HOW DROUGHT-STRESS TO DROUGHT-SMART CROPS
5. CASE STUDY
6. CONCLUSION
7. FUTURE OUTLOOK
8. REFRENCES
OUTLINE
3. DROUGHT STRESS(DS): “Drought stress is a condition in which
a prolonged or severe deficiency of water (moisture) limits the
normal growth, development, and productivity of plants,
ecosystems, or agricultural systems”.
(Ansari et al., 2019)
DROUGHT-SMART FUTURE CROPS: They are the plant varieties
that have been obtained by combination of advanced phenotyping,
molecular breeding and genetic engineering approaches which exhibits
enhanced tolerance or resistance to drought conditions.
(Cheng et al., 2021)
WHAT IS DROUGHT STRESS
4. READY-TO-GROW FUTURE CROP:
where crops are designed or engineered to be more resilient,
productive, and adaptable to changing environmental conditions,
thus being "ready to grow" in various circumstances and future
agricultural challenges.
(Raza et al., 2023)
6. ABIOTIC
STRESS
• Drought (water
stress)
• Water logging(excessive
watering)
• Extreme temperature
• Salinity and mineral
toxicity
BIOTIC
STRESS
• Bacteria
• Virus
• Fungi
• Nematodes
• Weeds
• Insects etc.
WHAT ARE THE DIFFERENT TYPES OF STRESS ?
7. Plant
species
Stress condition Experiment
al condition
Effect References
GROWTH
Barley 40% water
holding
capacity(WHC);
6month
Field Average plant height
reduced by 20%
Hellal et al.,
(2019)
Chickpea 70% field
capacity;30 days
Field Reduced germination
rate by 40%
Mahmood et
al ., (2019)
wheat 25% field
capacity; 21day
Pot Reduced shoot &
grain mass by 30-40%
Mickky et
al.,(2020)
Tomato 33% field
capacity; 4month
Field Reduced average fruit
weight by 78%
Cui et al.,
(2020)
Rice 30% field
capacity; 4-5
month
Pot Reduced plant height
by 26%
Tefera et al.,
(2021)
Maize 50% field
capacity
Pot Reduced plant height
by 38%
Shemi et al .,
(2021)
Table 1 : Growth reduction in various crop plants under drought stress
8. Plant
species
Stress condition Experiment
al condition
Effect References
YIELD
Maize 50% field
capacity; 15days
Greenhouse Reduced 100-kernel
weight and yield by
85%
Hussain et
al., (2019)
Rice Withholding
water; 60days
Field Reduced plant yield by
28%
Yang et al .,
(2019)
Rice Withholding
water; 14days
Field Reduced plant yield by
~50%
Melandri et
al.,(2020)
Potato PEG8000; 21days Growth
room
Reduced average plant
yield by 90-95%
Handayani
et al., (2020)
wheat Aminoacid at 3 ml
/L; 7days
Field trial Reduced grain yield by
3.4%
Haider et al.,
(2021)
Maize 50% field
capacity; 10-
20days
Pot
experiment
Reduced grain yield by
30%
Shemi et al
., (2021)
Table 2 : Yield reduction in various crop plants under drought stress
9. MORPHO-
PHYSIOLOGICAL
CHANGES
Reduced leaf
surface area
Reduction in plant
height
Reduced
chlorophyll
Low stomatal
conductance
Low transpiration
and low biomass
Loss in fresh or dry
biomass
ROOT ARCHITECTURE
ADJUSTMENT
Changes in root length
More root surface area
Narrowing of root angle
Greater root density
WHAT ARE THE DIFFERENT KINDS OF CROPS RESPONS TO
DROUGHT-STRESS?
OXIDATIVE
DAMAGE
• Accumulation of
free radicals/
reactive oxygen
species(ROS)
• Synthesis of
enzymes such as
gluthione
reductase
• Oxidation of
lipids, DNA, RNA
10. WHAT ARE THE DIFFERENT KINDS OF CROPS RESPONSE
TO DROUGHT-STRESS?
OSMOTIC
ADJUSTMENTS
• Increase in total
sugar content
• Synthesis of
osmolytes, such
as proline,
betaines, sugar
alcohols,
organic acids
YIELD LOSS
Decreased grain
fillings(cereals)/po
ds(soya bean)
Poorly developed
pods(soya bean)
Reduced seed
weight
Reduced seed
number
Decline in seed
quality
14. • Genomic-Assisted Breeding (GAB), also known as Genomic
Selection (GS), that integrates genomics and genetics.
• Trait Identification- through genome-wide association studies
(GWAS) or Quantitative trait loci (QTL) mapping.
• QTL mapping offers genetic insight into physiological and agronomic
traits in the biparental population under drought stress.
• Genome-wide association studies (GWAS) can identify contributory
alleles for specific traits that can be used to develop DS-tolerant crop
plants.
A. GENOMIC-ASSISTED BREEDING (GAB) FOR DROUGHT
TOLERANCE
16. • Transcriptomics is the study of the transcriptome. It involves
techniques to identify, quantify, and analyze the RNA molecules
expressed under different conditions.
• Transcriptomics study for drought tolerance involves sample collections
-under well-defined drought stress conditions. mRNA is extracted from
the collected plant samples and subjected to mRNA sequencing.
• In data analysis, Differential expression analysis compares gene
expression levels between upregulated or downregulated in response to
drought stress and identifying the candidate gene.
B. TRANSCRIPTOMICS
18. • Proteomics is the study of the proteome, encompassing the
identification, quantification, and functional characterization of
proteins. It aims to understand how the expression and activity
of proteins change in response to stressors like drought.
• The extracted protein is analyzed in mass spectrometer. It
identifies which proteins are upregulated or downregulated
during drought , specific proteins that act as biomarkers for
drought stress, and researchers can target specific proteins or
pathways for genetic manipulation, breeding,
C. PROTEOMICS
20. • Metabolomics has largely focused on the organic molecular
compounds (metabolites) and the related biochemical changes
found in or produced by organisms and their tissues and cells .
• It is provides an insights into the metabolic pathways and
compounds involved in the drought adoption.
• Various techniques are used to analyze the metabolites which
includes mass spectrometry, nuclear magnetic resonance etc.,
then data analysis and validation of specific metabolites.
D. METABOLOMICS
21. • The metabolome data can be used in future studies such as
Quantitative Trait Locus (QTL) or Genome-Wide Association
Studies (GWAS) to discover genetic loci or specific genes linked to
these metabolic traits, facilitating the development of gene-specific
markers for crop improvement
22. • Epigenetics is a branch of genetics that studies heritable changes in
gene expression or cellular phenotype caused by mechanisms other
than alterations in the DNA sequence.
• Various techniques employed to analyze the epigenetic changes
associated with DS, which involve DNA methylation, histone
modifications et.,
E. EPIGENETICS
25. • Transgenic breeding, also known as genetic engineering,
involves the introduction of specific genes from one organism
into the genome of another organism to confer a desirable
traits.
• Gain of function and gene-knock-down approaches, such as
RNAi and CRISPR/cas9, have yielded valuable information on
how complex gene networks regulate dehydration stress
physiology.
2. TRANSGENIC APPROACHES
27. • Conventional breeding generally takes 8–10 year to generate
a new variety.
• Speed breeding (SB) techniques which allow breeders to
advance the crop generation in a shorter period of time
(Samantara et al., 2022)
3. SPEED BREEDING:
30. • Conventional breeding identifies parental lines with desirable
traits to generate a favorable combination of the new line for
the next generation.
• Comparing a large set of cultivars makes identifying the best
ones with desirable traits under water-scarce conditions easier
than using a small set.
• However, breeding for drought tolerance mainly depends on
the yield potential of parental lines rather than tolerance-
related traits.
4. CONVENTIONAL BREEDING
31. • Phytohormones including
auxins, gibberellic acid,
cytokines, ABA, ethylene,
jasmonic acid (JA),
strigolactones, and
brassinosteroids are signal
molecules and essential
components for regulating
plant growth under DS.
a. Phytohormone applications
5. BIOCHEMICALAND MECHANICAL OPTIONS FOR
DROUGHT MANAGEMENT
32. B. AGRONOMIC PRACTICES
• Agronomic practices, such as water management, adjusting plant density, and
nutrient management, are the backbone for increasing crop production under
seasonal DS.
• Applying gypsum is important for soils with low infiltration capacity. Other
strategies include zero tillage, mulching, intercropping, and deep plowing.
C .PLANT DENSITY AND TIME OF SOWING
• Sowing date is important for mitigating the devastating effects of DS at the
reproductive stage.
• Early sowing of maize avoids the potential drought and high temperatures in
mid-summer.
• Increasing plant density- high plant density of maize crop decreases leaf area
index, thus reducing evapotranspiration and enhancing WUE under arid
conditions.
35. • The goal of there study was to identify genomic loci and
candidate genes affecting SRL under drought conditions for
improving drought tolerance breeding in maize.
• Plant materials and growth conditions: A natural population
including 209 diverse accessions of maize inbred lines was
used for measuring the shoot dry weight (SDW), primary root
length (PRL), seminal root length (SRL), and seminal root
number (SRN) under well-watered (WW) and water-stressed
(WS) conditions.
MATERIALS AND METHODS
36. • Phenotypic identification and statistical analysis:
• RNA sequencing and data analysis:
• Genome-wide association study:
• Quantitative real-time PCR:
37.
38.
39. Differentially expressed genes (DEGs) in eight genotypes in response to drought stress.
The number of upregulated, downregulated and TF-coded DEGs of the eight genotypes are given.
40.
41.
42. • Identifying new key genes and QTL, metabolites, and proteins related to
DS-responsive mechanisms can be a potential candidate for CRISPR/Cas-
mediated genome editing, combined with speed breeding could be used to
develop new DS-tolerant cultivars.
• to achieve ‘zero hunger’ goal and feed the growing population.
• Combining a variety of traditional and modern biotechnological techniques
will significantly improve our current understanding of DS responses and
tolerance mechanisms in crop plants.
CONCLUSION
43. • Millets can be crops of choice to transfer the
beneficial attributes to other crop relatives..
• The deployment of genome editing with speed
breeding and phenomics can help in fast-track crop
breeding.
• The advent of high-throughput genomics and
phenomics- producing climate-smart crops to
overcome food security challenges in the future.
FUTURE OUTLOOK
44. 1. Ansari, F. A., & Ahmad, I. (2019). Isolation, functional characterization and efficacy
of biofilm-forming rhizobacteria under abiotic stress conditions. Antonie Van
Leeuwenhoek, 112, 1827-1839.
2. Raza, A., Mubarik, M. S., Sharif, R., Habib, M., Jabeen, W., Zhang, C., ... &
Varshney, R. K. (2023). Developing drought‐smart, ready‐to‐grow future crops. The
Plant Genome, 16(1), e20279.
3. Xu, K., Zhao, Y., Zhao, Y., Feng, C., Zhang, Y., Wang, F., ... & Li, H. (2022).
Soybean F-box-like protein GmFBL144 interacts with small heat shock protein and
negatively regulates plant drought stress tolerance. Frontiers in plant science, 13,
823529.
4. Guo, J., Li, C., Zhang, X., Li, Y., Zhang, D., Shi, Y., ... & Wang, T. (2020).
Transcriptome and GWAS analyses reveal candidate gene for seminal root length of
maize seedlings under drought stress. Plant Science, 292, 110380.
5. Samantara, K., Bohra, A., Mohapatra, S. R., Prihatini, R., Asibe, F., Singh, L., ... &
Varshney, R. K. (2022). Breeding more crops in less time: A perspective on speed
breeding. Biology, 11(2), 275.
6. Saeed, F., Chaudhry, U. K., Bakhsh, A., Raza, A., Saeed, Y., Bohra, A., & Varshney,
R. K. (2022). Moving beyond DNA sequence to improve plant stress
responses. Frontiers in Genetics, 13, 874648.
References
Editor's Notes
Drought is a key threat for plant production around the world, due to insufficient rainfall or a lack of availability of irrigation water [86]. Globally, one-third of total agricultural land is arid or semi-arid, due to insufficient water [87]. Thus, drought stress, together with other climatic changes, causes a significant loss of crop yield [88]. According to previous reports, the global temperature increased by 1.2 °C in the last century and was expected to have increased an additional 3 °C by 2010. The development of crop plants with improved performance under drought stress is therefore a major breeding objective for scientists
CONVENTIONAL APPROACHES
use of genomics-assisted breeding following funnel mating design to assemble the targated QTL/genes to develop multi-stress-tolerant homozygous breeding lines suitable for direct-seeded cultivation conditions.
Epigenetics refers to the study of heritable changes in gene expression or cellular phenotype that do not involve changes in the underlying DNA sequence. These changes can be influenced by various factors, including environmental conditions, lifestyle, and developmental stages.
These examples suggest that epigenetics or epigenomics play a vital role in understanding the DS responses and tolerance mechanisms at epigenetics level.
Mechanisms underlying epigenetic memory in plants during stress. Plants’ epigenetic memory helps protect them from different stresses. Whenever a plant faces stress regardless of its biotic or abiotic nature, it starts recovery against stress, and the plant epigenetic stress memory stores that information. Due to this stored memory, stress does not affect the plant on subsequent exposures.
Overexpression of several drought-responsive genes and transcription factors increases the accumulation of signaling molecules and metabolic compounds and enhances drought tolerance in plants
Flexibility in SB protocols allows them to align and integrate with diverse research purposes including population development, genomic selection, phenotyping, and genomic editing.
However, breeding for drought tolerance mainly depends on the yield potential of parental lines rather than tolerance-related traits