Pre-Breeding helps to develop new genetic resources using genomic tools to predict the effect of introducing different genes from wild relatives into cultivated varieties.

1. PRE-BREEDING AND POPULATION IMPROVEMENT IN
VEGETABLES WITH SPECIAL REFERENCE TO HOT PEPPER
COMIENZO AGRI SCEIENCE LIMITED, RAIPUR
2nd ANNUAL R&D MEETING 2nd-4th November 2019
NAGARAJU MADALA
Jr. Breeder
HOT PEPPER & WATERMELON

2. “Agene lost is lost forever and not
possible resynthesize, hence collect,
evaluate, conserve and utilize for
nutritivefood security to ensure
peace on the only livingglobe"
[AbdulGHAFOOR]

3. What is Pre-Breeding ?
 Pre-breeding refers to all the activities designed to identify desirable characteristics and or
genes from unadapted (exotic/ semi-exotic /indigenous) materials, including those that,
although adapted, have not been subjected to any kind of selection for improvement.
 It is an essential part of germplasm diversification strategies.
 The most promising alternative to link genetic resources and breeding programmes.
The distinct uses of genetic enhancement (through pre-breeding)
1. The first is to prevent genetic uniformity and consequent genetic vulnerability.
2. Genetic enhancement through pre-breeding has a second important purpose that of raising yield
levels to new heights. This goal is more often hoped for than achieved, but it is true that most
breakthrough cultivars have highly diverse parentage.
3.Wild species and crop wild relatives are the reservoir of the gene for cope with the changing
climate, identification of this important gene and moving them from wild species into breeding
population when this appears to be most effective strategy!

4. Role of Plant breeding
 Induced evolution for the benefit of mankind using
gene/alleles.
 Pre breeding!
Un-adapted PGR not used directly, to transfer these traits, an
intermediate set of materials is used to develop new varieties.
“Linking genetic variability to utilization” use of diversity arising
from landraces and other unimproved materials.

6. Why Pre-breeding?
 Limited progress due lack of diversity: Current limited genetic
base of agriculture is apparently a threat to a food security.
 Reduction of biodiversity: Uniform modern varieties are replacing
the diverse local cultivars and landraces in traditional agro-
ecosystems.
 Genetic uniformity: Increase vulnerability for stresses.
 Effects of climate change: Search for new genes/traits for
better adaptation.
 New pest and pathogen : Motivating plant breeders to look for new
sources of resistance in genebanks.
 “Decision of pre-breeding is based on the expected
efficiency of target traits into cultivars and source of desired
gene(s)”

7. Unlocking genetic potential of landraces
and CWR for benefit of the society
1. Diversity assessment
2. Somatic Hybridization
3. Anther culture
4. Embryo rescue
5. Marker assisted breeding
6. Mapping of quantitative trait loci (QTL)
7. Introgression libraries
8. Association studies
9. Genetic transformation
10.Genome editing
11.Nutritious food security

8. PGR
Cultivated
Wild
Landraces
Pre-breeding
Evaluation, identifying of donor
Hybridization
Development of pre-breeding populations
Crop improvement
Working collections
Development of cultivars
Pre-breeding (6-8 years)
Breeding (8-10 years)

9. Applications of pre-breeding in
crop improvement
1. Broadening the genetic base, to reduce vulnerability.
2. Identifying traits in wild relatives and transferring genes into
material are more readily utilized by breeders.
3. Genes from wild species into in-between populations to
create effective breeding program.
4. Identification and transfer of novel genes from
unrelated species using novel techniques.
5. Non-GMO novel diversity.
Adoption of pre-breeding facilitates the efficiency and effectiveness of
crop improvement by enabling increased access to, and use of, genetic
variations conserved in gene banks

10. 1. PRE-BREEDING: A NEW REQUIREMENT IN PLANT BREEDING
 Factors responsible for the low utilisation of PGR
 Lack of documentation,
 Adequate description of collections,
 Lack of the desired information by breeders,
 Accessions with restricted adaptability, insufficient plant breeders, and lack of
collection evaluations.
 Low seed availability due to inadequate seed regeneration programmes is another
barrier to their use.
 Furthermore, breeder-to-breeder exchange of materials is very common and
constitutes a reasonable alternative to extend genetic variability in breeding
programmes.

11.  The search for superior genotypes regarding
 Yielding ability, disease and pest resistance,
 Stress tolerance or better nutritional quality is very hard,
 Competitive and expensive.
 Breeders tend to concentrate to
 Adapted and improved materials,
 Avoiding wild parents,
 Landraces and exotics,
 Available in germplasm banks, which would require long-time,
 High financial support besides the difficulty to identify potentially useful genes.
 In this way, to develop new populations and inbred lines, commercial F1 hybrids are
being widely used, since this is a legitimate source of parental germplasm, the recurrent
use of these genotypes should increase the narrowness of the genetic base.
 Genetic vulnerability must be a constant concern in plant breeding for all species.

12. 2. SUSTAINABLE USE OF GENETIC DIVERSITY
 Gene banks have often, through necessity, focused mainly on the immediate conservation
aspects of plant genetic resource activities.
 However, there is an urgent need for active engagement with all stakeholders to enhance the
utilisation of plant genetic resources in order to assure the functionality of the entire “Genetic
resource-chain”.
 The conservation of genetic resources must be linked to their increased and sustainable use if
they are to play a key role in climate change adaptation.
 Bottlenecks that need to be addressed include lack of information on genotypic and
phenotypic level, e.g., need for evaluation for resistance to biotic and abiotic stresses of
increasing importance.
ABIOTIC STRESSES: ADAPTING TO ENVIRONMENTAL CHANGES
 Tolerance to particular abiotic stresses such as drought, cold, salinity, heat, water logging,
nutrient use efficiency and mineral toxicity has traditionally enabled vegetables crops to cope
with the prevalent local stresses with a balance of traits that were fine tuned to optimise
economic yields in their environments.
 Therefore, it is expected that the agricultural areas of India will experience enhanced or novel
abiotic stresses making it increasingly urgent to develop vegetables that can withstand such
environmental changes, in order to increase or even just to maintain current yield levels.

13. BIOTIC STRESS: COPING WITH EMERGING DISEASES
 Plant pathogens cause considerable yield losses in vegetables production, reducing crop
quality and threatening food safety.
 Disease prevention and control is a much needed for competitive vegetable production
with the breeding of genetically disease resistant crops being one of the most
environmentally and economically desirable ways to manage plant diseases.
 The prevalence of different plant diseases is changing due to changing environmental
conditions, including global climate change, but also changes in agricultural production
with trends towards larger areas planted to fewer and/or genetically more uniform
varieties.
TECHNIQUES FOR FOREIGN GENE TRANSFER
Different techniques are followed to overcome barriers to wide hybridisation and to
obtain viable hybrids to affect gene transfer:
1. Embryo rescue and in vitro techniques.
2. Involving bridge species, which are crossable with both the parental species.
3. Application of exogenous plant growth regulators at post pollination stage.
4. Backcrossing the hybrids with agronomically acceptable base as recurrent parent.
5. Chromosome doubling when genome nonhomology is present (4n or 6n pathway) and
backcrossing.

14. ALLOPLASM DEVELOPMENT
 Transfer of cytoplasm from interspecific and intergeneric origin greatly enables
the exploitation of cytoplasmic genetic male sterility system (CGMS)- male
fertility system.
 Breeders also need to search for many useful traits from exotic variation that are
not often considered in germplasm enhancement.
They are physiological traits such as
 Enhanced growth rate,
 Improved source sink,
 Stabilising high-yield potential,
 Insulating the preferred lines from environmental stresses,
 Conferring high adaptation and enhancing the quality.

15. GENETIC ENHANCEMENT:
 > 90 % untapped bio-resource
 Centuries adaptation to extreme biotic and a-biotic,
promising donor
 Modern breeding tools, a promise for utilization of untapped diversity under
ex-situ conservation [Back into the wild— Apply untapped genetic diversity
of wild relatives for crop improvement, Evolutionary Applications 2017;
10: 5–24 ]
 New and diverse sources of variation both in cultivated and wild type
germplasm to develop new pre-breeding populations
 In the past, a few promising wild type accessions have been utilized by some
researchers for the improvement of crop plants
There are 26 documents wild species of chilli and 5 varieties i,e Capsicum
annuum, Capsicum baccatum, Capsicum chinense, Capsicum frutenscens,
Capsicum pubescens.

16. CHALLENGES IN ADOPTING PRE-BREEDING
 Pre-breeding is the playing key role in crop improvement, there are several factors
a) Lack of characterization and evaluation data
b) Knowledge of inter and intra-specific diversity
c) Inter and intra-species relationship
d) Funding sources?
e) Research infrastructure
 Use of genebank accessions in breeding program is limited by the high complexity of
traits, time-duration, linkage of desirable genes with undesirable ones
NEW TOOLS TO ADDRESS THE CHALLENGES
The recent progress in biotechnology has opened up enormous possibilities, both for
introgression of specific traits and for base broadening in pre-breeding.
1. Molecular techniques and Bioinformatics allow more prefer, faster selection and handle
complicated traits efficiently.
2. Molecular genotyping are constantly decreasing and methods becoming more efficient,
reliable and precise phenotyping are costly, time consuming and an increasing challenge.
3.The strategy for the future should contain a broad knowledge and access to modern
technology, and combining the application of new tools and techniques with traditional and
efficient plant breeding methods to achieve final goal rapidly.

17. Future Prospects
 Urgent need to collect, characterize and document landraces.
 There is emerging demand for novel genes for biotic & abiotic
stresses, quality and bio-fortification.
 Genome mapping and synteny of the genes sequenced from chilli and
tomato could be assigned to encoding abiotic stress tolerance and can
be utilized for crop improvement.
 Potential of genetic transformation form the tertiary gene pool and/or
beyond.
 New breeding strategies and bioinformatics tools are required to use
the information from genomics for complex traits more effectively.

18.  Limited genetic variability in cultivated germplasm blazed pre-
breeding in most crop improvement programs
 New gene pools, useful genes, wider adaptability, broader
genetic base for agronomic and nutrition-related traits, as well
as for resistance/tolerance to important biotic/abiotic stresses
 Phenotyping and genotyping in identifying the lines with
enhanced genetic base and minimum linkage drag for use in
future breeding programs, as well as to find out the markers
associated with traits of interest
 Initiatives and Hope for Enriching Cultivated Gene Pool
Through Genomics-Assisted Pre-Breeding
Pre-Breeding: Present Status and Future

19. CONCLUSION
 Pre-breeding is an essential part of germplasm diversification strategies. It is the
most promising alternative to link genetic resources and breeding programmes.
 By exercising the pre-breeding procedure in crop improvement programme, the
genetic vulnerability due to uniformity can be avoided in the population.
 Useful variability for breeding pipeline to develop new high-yielding cultivars,
resistant to stresses and broad genetic base
 Genetic resources, the bio-treasurers, make substantial long term investment for
exploiting its full potential.
 Intelligent and judicious use of PGR: according to needs not desires.
 Molecular markers– strong tool for PGR utilization through pre-breeding.
 Pre-breeding useful for un-adapted materials, ‘captures’, and incorporates into a
usable form employing different techniques.

20. POPULATION IMPROVEMENT
Accumulation of desirable alleles in a population through various breeding
techniques is known as population improvement
 In self-pollinated crops, selection is employed to isolate plants with superior
genotypes; these plants are then used to establish separate pure lines or their seeds
are bulked to produce a mixture of pure lines.
 In contrast, cross-pollinated crops generally show moderate-to-severe inbreeding
depression. Consequently,
a) inbreeding must be avoided or kept to a minimum in cross-pollinated species.
b) individual plants from such crops are highly heterozygous; the progeny from
such plants would be heterogeneous and usually different from the parent plant
due to segregation and recombination.
c) The breeder, therefore, aims at increasing the frequency of desirable alleles in the
populations.
d) This would result in an increase in the frequency of desirable gene combinations
or genotypes. As a result, the phenotype of the population would be favourably
changed.

21. METHODS OF POPULATION IMPROVEMENT
The various breeding methods used for population improvement may be
grouped into the following two general classes:
(1) Methods without progeny testing.
(2) Methods with progeny testing.
1.BREEDING METHODS WITHOUT PROGENY TESTING
 In breeding methods belonging to this group, plants are selected on the
basis of their phenotype, and no progeny test is carried out,
e.g., Mass selection
2.BREEDING METHODS WITH PROGENY TESTING
 In most breeding methods, however, plants are initially selected on the
basis of their phenotype, but the final selection of plants that contribute
to the next generation is based on a progeny test. This class is population
improvement methods include progeny selection or ear-to-row method,
and recurrent selection.

22. RECURRENT SELECTION
 Recurrent selection is a modified form of progeny selection. However, it
differs from progeny selection in two main aspects.
 First, the selected plants are self-pollinated in recurrent selection, whereas
they are open-pollinated in progeny selection.
 Second, the progeny of selected plants are intermated in all possible
combinations in this method, whereas they are open-pollinated in progeny
selection.
TYPES OF RECURRENT SELECTION
There are four types of recurrent selection.
1.Simple recurrent selection
2.Recurrent selection for general combining ability
3. Recurrent selection for specific combining ability
4.Reciprocal recurrent selection
con

23. GENETIC IMPROVEMENT IN CHILLI[CASE
STUDIES]
CASE STUDIES
 Diversity
 BITOTIC AND ABIOTIC STRESS RESISTANCE
 QUALITY
 YIELD
 MOLECULAR BREEDING
1.Diversity, Conservation, and Enhancement of Genetic Resources
 The National Bureau of Plant Genetic Resources(NBPGR), New Delhi facilitates collection,
regeneration, characterization, conservation, and distribution of chilli germplasm to
researchers in India. However, at NBPGR indigenous collection constitute only 18./. Of the
total Capsicum collections, while the majority of the accessions are exotics.
Genetic diversity of chilli(Capsicum annuum L.) genotypes of India
based on morpho-chemical traits
Vikas sing , Upadhyay and Rakesh Kr.

24. BREEDING FOR QUALITY
Effect of storage on stability of capsaicin and colour content in chilli(
Capsicum annuum L.)
J.pandey, J.Sing, R.Kumar, K.Srivastava and S.Kumar.
 Assess the stability of quality traits in stored chilli powder.
 The red ripe fruits of chilli genotypes (Capsicum annuum L.) were evaluated for quality
parameters viz. Capsaicin, as extractable colour and colour value in freshly grinded powder
as well in powder stored at ambient temperature for six months.
BREEDING FOR YIELD
Providing genomic tools to increase the efficiency of molecular breeding for complex
traits in pepper
M.Nicolai , P.Nemouchi and B.Savio.
 Molecular markers of the Quantitative Trait Loci(QTL) for yield related traits and for
model parameters are needed for phenotypes prediction.
 To improve the estimation of allelic values at QTLs, functional markers(sequence
polymorphism controlling the phenotypic variation) are expected instead of QTL flanking
markers.
 The microarray technology is widely used in gene expression studies.

25. CONCLUSION
 The various breeding methods of population improvement can be employed in breeding
programmes so as to increase the frequency of desirable alleles in the population. As a result,
the phenotype of the population would be favourably changed.
 High variability present in nature for quality and yield contributing characters.
 Characters like fruits per plant, pricap thickness, fruit size, fruit weight and oleoresin content
can be used for selection.
 Heterosis can be manifested using diverse germplasm.
 Easy and more hybrid seed production can be possible through proper exploitation of male
sterility system.
 Mutation can be employed to create new useful mutant for crop improvement.
 In vitro cloning is more successful when cotyledon leaf was used an explants.
 Abiotic stress tolerant germplasm present in nature.
 Disease resistant cultivar can be developed through crossing and back crossing with
resistance germplasm.

26. FUTURE THRUST
 Genesis of varieties with less pungency and consumer preference.
 Exploitation of male sterility and chemical hybridizing agents in developing new hybrids.
 Introduction of heat and drought tolerance germplasm as a strategy for climate change.
 Development of location specific varieties.
 To develop a varieties which can maintain and gives stable performance as such capsaicin
content even in cold periods and after a longer storage period (dry)
 Developments of varieties with higher antioxidant and oleoresin content.
 Breeding for dwarf plant type for HDP and single harvest hybrids in Chilli for mechanized
harvesting.

27. THANK YOU
ACKNOWLEDGEMENT
Very much thankful to Vijaykumar Katre-Breeder (Hot pepper &Watermelon),
Sandeep Baranwal-(R&D Head), Saurabh rathi-Director(Vachan seeds),
Aswathappa K.V , Charles Wesley and my team Prasanth &Chandrakant.