The world population Data sheet indicates that world population is projected to increase from 7.8 billion in 2020 to 10 billion by 2050. Hence as population increases the food demand also increases, and due to urbanization process the per capita availability of land for agriculture also reduces. So we will reach to the situation where we have to increase the yield of crops per unit land availability. Among all the discipline, we the plant breeders mainly plays important role in increasing the yield of crops, so we need to be ready to feed uncertain future. And it will achieved by a approach called „„ANTICIPATORY PLANT BREEDING‟‟. Breeding for future needs using both conventional and contemporary approaches
12. How to combat ???
1. Increased utilization of germplasm accessions
2. Development of elite cultivar
3. Utility of MAGIC population
4. Identification of DNA sequences
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13. Breeding strategies:
1. Conventional plant breeding
2. Contemporary plant breeding
In combination
Sexual hybridization and introgression of genes
Broadening of genetic base
Mutation breeding
Others
• Cis genesis
• Gene editing
• Allele mining
• GMO
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14. HYBRIDIZATION
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Inter-varietal hybridization Distant hybridization
Simple cross
Complex cross
Inter-specific cross
Inter-generic cross
Application:
New crop
Gene / chromosome transfer
Transfer of cytoplasm
Creation of genetic variation
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Improvement of agronomic traits using traditional breeding
These methods require longer time for the development of hybrids or varieties and are
based on phenotypic selection
18. Marker Assisted Breeding
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Trait QTL and QTL Marker
FM- Functional Markers, GMM- Genic Molecular Marker, RDM- Random DNA Markers
19. Identification of markers linked/associated with trait
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LINKAGE MAPPING
Biparental/Multiparental
Mapping Population
Linkage Map
Markers-QTLs
ASSOCIATION MAPPING
Natural Population
Markers-QTLs
Validation
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Applications of markers in breeding
1.Assessing variability of genetic differences and
characteristics within a species
2.Identification and fingerprinting of genotypes
3.Estimating distances between species and offspring
4.Identifying location of QTL’s
5.Identification of DNA sequence from useful
candidate genes
27. The TILLINGMethodology
Development of mutagenized population
EMS mutagenesis
Development of M2 population
DNApreparation and pooling ofindividuals
Mutation Discovery
PCR amplification of a region of interest
Mismatched cleavage
Detection of Heteroduplexes as extra peak or band (HPLCor
Acrylamide gel)
Identification of the mutant individual
Sequencing of Mutant PCR product.
28. The TILLING population - MUTAGENESIS
Mutagenizing seed with EMS done by soaking seeds in an EMS
solution (14-18 h in a 30-100 mM (0.3%-1%) EMSsolution.
Planting the seeds in field
Mutagenized population (M1generation) is grown tomaturity
allowed to self-fertilize to produce M2seeds.
M2 seeds can be maintained as lines orbulked
If the M2 seed is bulked then lines need to be established using M3 seed. In
either case, when sampling M2 plants to establish population.
29. Arraying the population for TILLING
Allowing up to 8-fold pooling of diploid plants toincrease
TILLING throughput
Arrayed in a 96-well microtiterplate
Genomic DNAis isolated from individuals M2/M3plants
Standardized the DNAconcentration of eachsample
30. Advantages
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Its applicability to virtually anyorganism.
Its facility for high-throughput and its independence of genome size,
reproductive system or generationtime.
High degree of mutational saturation can be achieve withoutexcessive
collateral DNAdamage.
Eco- TILLING is useful for association mapping study and linkage
disequilibrium analysis.
31. Limitation
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• Development of densely mutagenized population
• Requires high quality DNA
• No general protocols
• Mutation discovery in heterozygous species
39. Concept of how plant genome editing can advance breeding targets
40. Scientists discovered base editing
Holly Rees (left), David Liu, and Nicole Gaudell (right).
In 2016, David Liu & his team at Harvard University developed the first Base Editors Using
Cytosine Deaminases.
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“SDN1 and SDN2 genome-edited products
free from exogenous introduced DNA be
exempted from biosafety assessment in
pursuance of rule 20 of the Manufacture, Use,
Import, Export and Storage of Hazardous
Microorganisms/Genetically engineered
Organisms or Cells Rules 1989,” the new rule,
issued through an office memorandum, states.
43. CISGENIC
“A cisgenic is a crop
plant that has been
genetically modified
with one or more
genes isolated from
crop plant”
Cisgenesis
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45. How cis/intragenic plants can overcome problems of
transgenic plants?
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No need sequence
information of
other species
No change
in fitness
No alter in
gene pool
No additional
traits in
recipient spp.
Transgenesis
46. Limitation of the cisgenesis
concepts
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• Traits outside the sexually compatible gene
pool cannot be introduced.
• Additional expertise and time
• Less transformation efficiency.
48. 16-05-2022 Dept. of Genetics and Plant Breeding 48
Domestication
De-domestication/
Feralization
Feralization/De-domestication
49. 16-05-2022 49
Domestication for new species has been explored in the context of performing
modern domestications of domestic species
Re-domestication is relatively unexplored for feral populations
Re-domestication
Domestication De-domestication Re-domestication
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Anticipatory resistance breeding
process of breeding for resistance to virulent pathotypes before
such pathotypes become prevalent and cause significant losses.
A program of anticipatory resistance breeding has the following
prerequisites
A knowledge of the epidemiology of the pathogen across the target
region
Relevant annual pathogen surveys aimed at detecting new
pathotypes with potential to overcome the resistance genes that are
deployed.
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A knowledge of the main resistance genes that are deployed
in current cultivars grown throughout the target region.
A well coordinated system for screening all breeding
materials with pathotypes posing the greatest threat, for
identifying new sources (genes) of resistance to those
pathotypes and prebreeding often required to have those
resistance sources available in locally adapted germplasm
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Effective ways to fight rusts in India
Survey and surveillance in Mediterranean areas on our own
or with international collaboration
Understanding of evolution of biotypes in races
Durable resistance genes are to be deployed (ACI to be
substituted with AUDPC)
Combating threat of new races
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Ug 99- The biggest threat to Indian cultivation
Ug 99 race originated in Uganda in 1999
Has potential to migrate to the Indian sub continent
Majority of the popular Indian cultivars possess gene Sr
31 gene which is susceptible to this race
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Approaches for resistance breeding
Short term goals (immediate returns)
Introgression and pyramiding of major effective genes into popular
cultivated varieties- Conventional+ MAS
Long term goals (Durable resistance)
Second step is to combine some of the APR genes like Sr2, Sr136,
Sr14, Sr22 with major genes like Sr24, Sr25, Sr26, Sr27, Sr36
(already introgressed)- Conventional + MAS
Exploring new rust resistance gene sources from wild wheat
relatives, land races and their utilization
72. Inference:
• Based on these markers without physical screening the introgressed
line were detected.
• These identified markers helps in pyramiding of genes for rust resistance .
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73. Material and method:
• They used 10 varieties and developed 40 clones of complex interspecific
potato hybrids
• Disease screening: Carried over two location under natural infection condition
• DNA extraction, quantification and further from PCR product the specific regions
are extracted for SCAR
• Correlation analysis was done
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74. • The markers used by them have been developed for late blight resistance R genes initially
characterized in four Solanum species, S. bulbocastanum, S. demissum, S. stoloniferum
and S. venturii.
• R genes mainly controlling the late blight disease were R1, R2, R3a, R3b.
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75. • R1, R2, R3a and R3b gene markers were most probably transferred from S. demissum.
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76. Inference:
• The best method of prevention of new P. infestans races emergence is preventive
breeding, i.e. development of breeding donors for late blight on the basis of interspecies
hybrids with resistance genes transferred from wild potato congeners.
• Durable resistance of these hybrids is determined by stacking several R genes
and development of interspecies donor hybrids pool with several resistance genes by
means of introgressive MAS.
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Results:
• The almost all clonal hybrids has possesd resistant R genes similar to S. demissum
• Some clone which showed big difference between field and laboratory results,
expected that significant activity of race non specific resistance genes.
Anticipation is the prediction of the future and in plant breeding the we will anticipate the future goals and breed towards those goals
Flow of presentation contaions
Future challenges in front of breeders
What are the breeding methods available
Some case studies regarding anticipatory plant breeding
The world population Data sheet indicates that world population is projected to increase from 7.8 billion in 2020 to 10 billion by 2050. Hence as population increases the food demand also increases, and due to urbanization process the per capita availability of land for agriculture also reduces. So we will reach to the situation where we have to increase the yield of crops per unit land availability. Among all the discipline, we the plant breeders mainly plays important role in increasing the yield of crops, so we need to be ready to feed uncertain future. And it will achieved by a approach called „„ANTICIPATORY PLANT BREEDING‟‟. Breeding for future needs using both conventional and contemporary approaches
Over hundreds of year our plant breeding is taking main part, as we all know that during 10,000BC only domestication of crops started where farmers themselves started selection of their own. Scientific way of breeding started after discovery of mendel’s laws of inheritance. Then hybrid breeding, mutation breeding started. After discovery of DNA and its structure a new era of molecular breeding started where special application of markers started.
.Presently, farmers feed 10 times more people using the same amount of land as 100 years ago and in future it need to be doubled to feed the growing population. The breeding methods are also evolving like plants. Now a days genome editing, genomic selection, speed breeding are taking major part of plant breeding through which our dream of anticipation could be overcome i.e. by “TARGETED BREEDING”
Our plant breeding process mainly depends on controlling/exploiting factors like, genotype, environment and genotype by environment interaction, i.e. P = G + E+ G*E. Where G component can be controlled according to our need but there one uncontrollable factor is there i.e. the environment factor.
So it mainly causes climate change, hence as climate changes the response of genotype to environment also changes…so future breeding programmes should be based on the climate change.
Climate change impacts our agriculture through
Excessive heat: reduces surface water and depletes aquifers, disrupts flowering and pollination of crops, increases weed, insect and disease pressures.
Loss of natural resources: Removes habitats and food for beneficial insects
dries up water sources.
Drought: causes crop failures and loss of arable land
Excessive precipitation: Increases difficulty of planting , raises flood risk, damages crops So climate change causes erratic weather patterns, extreme temperatures, threatening farmer’s ability to sustainably produce and maintain quality crops.
New pests and disease pressures: More competition for soil and water resources greater damage to crops.
How we can mitigate these climate change and other future problems using anticipatory plant breeding
By developing resource use efficient varieties
Heat tolerant varieties
Greater yield stability in erratic weather
Greater control of insects, weeds and disease through new crop protection products.
Other factors that affect our plant breeding programme are
Market preference: As we all know that farmer’s produce directly reach to the market and marketing of his produce depends on the consumer preferences.
#And some of consumer preferences like quality of produce, its appearance and taste like factors, so while breeding we need to take care of all these factors. This can be achieved by IDEOTYPE BREEDING.
#Developing country are facing malnutrition problem which can be combat by breeding for BIOFORTIFICATION.
#In order grow crops, we need to consider agronomic traits too, in agronomic traits mainly fertilizer responsiveness and conversion of unavailable nutrient form to available form. So by considering these things also we need to breed
Coming to major challenges in near future and goals to fix these problems are
we need to increase the crop diversity and production of sufficient genetic variation for traits needed to be improved
We need to reduce the time required and improve the genetic gain over time with accuracy
We need to identify the testing environments for the future climate
Ways to combat the above mentioned factors:
Increased utilization of germplasm accessions: through germplasm evaluation we can screen for our desired traits, which can be further improved through other conventional or contemporary approaches.
Development of elite cultivar: after germplasm evaluation, if we are able to get lines with desired traits we can make different cross and finally we could get cultivar with desired trait, which could be further used as directly as cultivar for cultivation or as parent in hybrid development.
Utility of MAGIC population: MAGIC (Multi-parent Advance Generation Intercross) population, where it is developed through using different parents which are contrast for traits under consideration by making different diallele crosses among selected parents and finally a heterogenous population will be developed which on later stages after stabilization could be used as cultivar. Usually eight parents are used and this is mainly used for improving qualitative traits like disease resistance.
Identification of DNA sequences: this is nothing but use of molecular markers and genome editing tools like crisper cas, RNAi techonology..etc
Ways to achieve anticipatory plant breeding:
The main two breeding strategies for achieving this is
Conventional plant breeding: Breeding a crops following laws of inheritance, selection is carried based on phenotype.
2. Contemporary plant breeding: In addition to laws of inheritance, considering the applications of marker and then improving the crop with both phenotype based selection system and marker based selection system.
But for the crop improvement as a whole we need to consider both approaches in combination so the desired goal can be achieved.
Broadening of genetic base : Usually through pre-breeding or germplasm enrichment method.
Mutation breeding: Either conventionally using mutagens or through reverse breeding approach i.e tilling and ecotilling
Other approaches:
o Cis genesis
o Gene editing
o Allele mining
o GMO
Hence, the approaches could be:
Sexual hybridization and introgression of genes: Through intra- or inter- varietal hybridization and selection using different breeding approach we can able to get desired cultivar, but here conventional breeding and advance breeding i.e use of markers both in combination the goal could be achieved, Ex: MABC. Introgression of gene from different source can be done through inter-varietal hybridization approach Ex: Alien addition or substitution.
Some of applications of wide hybridization:
New crop
Gene / chromosome transfer
Transfer of cytoplasm
Creation of genetic variation
Conventional breeding methods like pedigree, bulk or single seed descent methods.
The conventional pedigree method requires atleast 12-13 years to produce a variety and mutation breeding requires a minimum of 9 years. These methods require longer time for the development of hybrids or varieties and are based on phenotypic selection.
To overcome this demerit a new era of marker came into existence.
In genetics, a molecular marker or genetic marker is a fragment of DNA that is associated with a certain location within the genome. Molecular markers are used in molecular biology and biotechnology to identify a particular sequence of DNA in a pool of unknown DNA. Molecular mapping aids in identifying the location of particular markers within the genome.
There are two types of maps that may be created for analysis of genetic material.
First, is a physical map, that helps identify the location of where you are on a chromosome as well as which chromosome you are on. Secondly there is a linkage map that identifies how particular genes are linked to other genes on a chromosome.
This linkage map may identify distances from other genes using (cM) centiMorgans as a unit of measurement. Codominant markers can be used in mapping, to identify particular locations within a genome and can represent differences in phenotype.
Linkage of markers can help identify particular polymorphisms within the genome. These polymorphisms indicate slight changes within the genome that may present nucleotide substitutions or rearrangement of sequence.
When developing a map it is beneficial to identify several polymorphic distinctions between two species as well as identify similar sequence between two species.
One of the application of marker system in breeding is MABC (Marker Assisted Backcross)
Mainly shortens the breeding cycle and also reduces use of resources
Through wide hybridization we can transfer gene from distant related or unrelated species either through development of alien addition or alien substitution lines.
Alien addition lines: Carries one chromosome pair from a different species in addition to somatic chromosome complement. These could be developed through development of MAALs (Monosomic alien addition lines) and DAALs (Disomic alien addition lines) Eg - Disease resistance in Wheat, oats, tobacco
Alien substitution lines: Replacement of one chromosome pair of cultivated species with the chromosome pair of wild donor species. These lines developed through development of CSSLs (Chromosome Segment Substitution Lines)
Development of crops over time,
strong selection pressure acted as a genetic bottleneck on the diversity available in our modern crops. including the loss of the diversity through the genetic bottlenecks of domestication, selection of landraces and modern plant breeding
Current limited genetic base of agriculture today is apparent a threat to food security. Reduction of Biodiversity: genetically uniform modern varieties are replacing the highly diverse local cultivars and landraces in traditional agro-ecosystems.
Genetic uniformity: Increases genetic vulnerability for pests and diseases.
The effects of climate change: search for new genes/traits for better adaptation. Evolving pest and pathogen populations
:motivating plant breeders to look for new sources of resistance in genebanks and widening of genetic base of the species
Broadening of genetic base: In plant breeding it can be done by pre-breeding.
Using crop wild relatives (CWR) in crop improvement is much more difficult than breeding with domesticated varieties.
Pre-breeding aims to isolate desired genetic traits (e.g. disease resistance) from unadapted material like CWR and introduce them into breeding lines that are more readily crossable with modern, elite varieties.
Pre-breeding broadens the elite genepool by recapturing lost beneficial genetic diversity.
Mutation Breeding: Mutation breeding, sometimes referred to as "variation breeding", is the process of exposing seeds to chemicals or radiation in order to generate mutants with desirable traits to be bred with other cultivars.
Plants created using mutagenesis are sometimes called mutagenic plants or mutagenic seeds. From 1930 to 2014 more than 3200 mutagenic plant varieties were released.
Crop plants account for 75% of released mutagenic species with the remaining 25% ornamentals or decorative plants.
One of the application of mutation breeding in crop improvement is through TILLING AND ECOTILLING:
Conventionally, mutagen treated material will be sown and in further generation selection will be carried and for qualitative traits usually from M2 selection is carried and for quantitative traits usually from M3 generation. And the desired cultivar with desired traits will be developed.
But conventional method is tedious so now a days a new approach is used i.e tilling and ecotiling process.
TILLING is a general reverse genetic technique that combines chemical mutagenesis with PCR based screening to identify point mutations in regions of interest.
GM crops are plants used in agriculture, the DNA of which has been modified using genetic engineering methods. Plant genomes can be engineered by physical methods or by use of Agrobacterium for the delivery of sequences hosted in TDNA binary vectors. In most cases, the aim is to introduce a new trait to the plant which does not occur naturally in the species. Examples in food crops include resistance to certain pests, diseases, environmental conditions, reduction of spoilage, resistance to chemical treatments (e.g. resistance to a herbicide), or improving the nutrient profile of the crop
Coming to the comparison of breeding methos cross breeding was taking more time…. So we evolved mutation breeding…. To over come disadvantages of mutation breeding we developed the transgene breeding and to over come disadvantages of transgene breeding now they came up with genome editing technique
Coming to disease resistance breeding
In conventional breeding we used to target the region of genome
In genetic engineering we used to transfer the gene of interest…..both these methods are random and time taking
Now they developed genome editing to target the particular gene with more precession
CRISPR–Cas9-based genome editing.
Selection of the desired genomic DNA target, and recognition of protospacer adjacent motif (PAM) sequences before 20 bp sequences. Design of the sgRNA using online bioinformatics tools.
Cloning of designed sgRNAs, and binary vector construction using promoters.
The delivery of CRISPR-Cas editing reagents into plant cells. via Agrobacterium tumefaciens, nanoparticles, biolistic bombardment, or polyethylene glycol (PEG). Alternatively, plant RNA viruses have been used to induce heritable genome editing. When the cassette harbouring the sgRNA, RNA mobile element, and tobacco rattle virus (TRV) is transformed into the Cas9 expressing plants, the systemic spread of sgRNA will introduce heritable genome editing.
Plant transformation and development of transgenic plants.
Genotyping of transgenic plants.
Transgene-free plants with the desired mutation are obtained
Coming to the next more advanced breeding method than genome editing is base editing.. Recently 3 scientists from Harvard university developed the first base editor
In genome editing we used to target the part of genome and that part was either excised from the genome or altered.
In base editing we target the particular base pair and alter it which is more precise and accurate compared to genome editing
Recently govt of India excluded the SDN1 and SDN2 genome edited products from its biosafety assessment rule 20 of the Manufacture, use and export of Genetically engineered organisms or cells rules 1989 trough its office memorandum to states….which will open the future avenues for plant breeders in this field
Cisgenic plants are made using genes found within the same species or a closely related one. Some breeders and scientists argue that cisgenic modification is useful for plants that are difficult to crossbreed by conventional means (such as potatoes), and that plants in the cisgenic category should not require the same regulatory scrutiny as transgenics. Methodology for cisgenic crop development is same as that of GMO.
Advantages of Cisgenic over introgression breeding: • Linkage drag free • Enhance the breeding speed to obtain durable multigenic resistance • Comparable with traditional introgression resistance breeding using same gene pool
Advantages of Cisgenic over transgenic breeding: No additional traits in recipient species No alter in gene pool No need sequence information of other species No change in fitness
We have seen the evolution of crop from wild to domesticated…..in future we can predict the origin of de domesticated or feral ones from the cultivated plant….Feral are the new species which are originated from the cultivated species
These ferals offers a valuable new gene pool for breeders and in future we can re domesticate them for the purpose of crop improvement
Crop domestication and breeding are critical for the survival and development of human civilization, which cost thousands of years to change the wild plants in civilization origins to modern cultivars; however, the genetic diversity, represented by different color of dots, is greatly reduced due to the intensive selection of wild plants and monoculture of elite varieties.
selecting an appropriate starting material,
establishing an efficient transformation system and an annotated reference genome,
editing of domestication-related genes followed by breeding and field evaluation, and
cultivar registration
Speed breeding is a suite of techniques that involves the manipulation of environmental conditions under which crop genotypes are grown, aiming to accelerate flowering and seed set, to advance to the next breeding generation as quickly as possible.
integrating speed breeding with other modern crop breeding technologies, including high-throughput genotyping, genome editing and genomic selection, accelerating the rate of crop improvement
Future breeding depends on big data management for genotype phenotype and environment to breeding the new climate resilient varieties
to meet the demands of an increasing population and the challenges of a changing climate. Plant phenomics has been proposed as a solution to relieve the ‘phenotyping bottleneck’ between functional genomics and plant breeding studies.
Plant phenomics is a new avenue for linking plant genomics and environmental studies, thereby improving plant breeding and management. Remote sensing techniques have improved high-throughput plant phenotyping.
Newly available technologies, genomics rapid cycling, high throughput phenotyping (HTP, phenomics) and historical descriptions of environmental relatedness (enviromics) are crucial to improving conventional breeding schemes and increasing genetic gain. Integrating these new technologies into routine breeding pipelines will support the delivery of cultivars with robust yields in the face of the expected unfavorable future environmental conditions caused by climate change and the consequently increased occurrence of biotic and abiotic stresses
Average coefficient of infection
First we need to identify the primary sources of the inoculum
Then we need to go for gene deployment along the puccinia path to manage the rusts in india
Dr. Norman Borlaug led the call for a joint effort to tackle this threat, which led to the establishment of the Borlaug Global Rust Initiative (BGRI, earlier Global Rust Initiative)
They identified the resistance stocks and they tested in kenya and maintained them at wellington
They organinzing the annual workshops to review the progress and future planning for resistance breeding
Adult plant resistant genes (even QTLs)
They identified the different resistance genes and their sources
Further they identified the markers linked to those resistance sources and these markers helps in gene pyramiding and we can screen the genotypes without the availability of inoculum of the pathogen
Then they went for gene deployment that is growing of varieties carrying diverse gene sources for resistance in a mosaic pattern.. And further crop diversification by growing dicoccum and durum in puccinia pah to reduce the disease development.
Through anticipatory breeding approach we could feed the uncertain future by developing the biotic and abiotic resistant cultivars so that climate change factor can controlled well in advance.
Maintenance of clean environment by improved nutrient use efficient and resistance to pest and disease is needed
So we the plant breeders mainly should be ready to feed uncertain future.