Utilization of crop wild relatives and land-races in crop improvement

1. Pre-breeding in field
crops using indigenous
landraces
Abdul GHAFOOR,
ghafoor59pk@yahoo.com

2. PGR utilization

3. Overview
Longest association (GR-human beings)
World population > 7 billion (Food security is issue)
In 2100 10-14 billion (Global food production?)
Plant food consumption by developing countries (> 80%)
Consumption by developed countries (< 40%)
Converted to animal sources
Increased demand
45% by 2030 (IEA)
Energy
Water
Increased demand
30% by 2030
(IFPRI)
Food
Increased demand
50% by 2030
(FAO)
Climate
Change
1.Increasing population
2.Changing diets
3.Losing land to
urbanisation and
rising sea levels
Consumption or utilization of genetic
resources is imperative for healthy
and peace full society; Noble peace
prize for Norman Ernest
Borlaug (March 25, 1914 – September
12, 2009)

4. Crop Pakistan Worldwide
Wheat 169 > 10,000
Barley 10 > 1,200
Maize 42 > 6,500
Rice 45 > 12,000
Cotton 154 > 4,600
Sugarcane 51 -
Pulses 79 -
Oilseeds 86 -
Fodders 39 -
Vegetables 88 -
Fruits 48 -
Flowers 03 -
Total 814 -
Registered varieties

5. Crop, Characters of interest Varieties Reference
Rice Varieties (quality) Basmati 385, Kashmir Basmati
Plant type Pk–0000335
Yield potential Pk–0003358
Early ness Pk–0003058
Maize Early ness Pk–0071103, Pk–0071557, Pk–0071058 Khan et al., 2000
Wheat Drought tolerance Pak–0018170, Pk–0018188
Chickpea Yield potential Punjab 2000, Bittal, Dashat Iqbal et al., 2004; Iqbal et al.,
2005
Blight Dasht, NIFA 88, Balkasar, Wanhar,
97047, 924043
Iqbal and Ghafoor, 2005
Mungbean Yield potential NCM 209 Zubair and Ghafoor, 2001
ULCV 98-CMH-016, NM- 2, BRM- 195 Bashir et al., 2005
Black gram High yielding, resistant to
MYMV
Mash 1, Mash 2, Mash 3 Ghafoor et al., 2015
Dual season cultivar NARC Mash 2014 Ghafoor et al., 2013
Charcoal rot Pk–45718, Pk–45719, Pk–45721, Pk -
45731
Iqbal et al., 2003
ULCV VH 9440039-3, ES- 1 Bashir et al., 2005
Lentil Yield potential Pk-40688, Pk-40757, Pk-40787 Bakhsh et al., 1992
Cowpea Yield potential 27003, 27009, 27044, 27082, 27097,
27123, 27147, 27167, 27171
Iqbal et al., 2003
BICMV Pk–27168, Pk– 27192 Bashir et al., 2002
Pea Yield potential 10603, 10607, 10610, 10645, 10646 Javaid et al., 2002
Powdery mildew Pk–10603, Pk– 10628 Ahmad et al., 2001
Vigna
unguiculata
Variety Dera moth Yaqoob, 2014
Utilization of PGR in crop improvement

6. Landraces and crop improvement

7. Is definition of landraces possible?
A distinct population that lacks “formal” crop
improvement, is characterized by a specific ID with
adaptation to the area of cultivation (tolerant to the
biotic and abiotic stresses of that area), closely
associated with the traditional uses, knowledge,
habits, dialects, and celebrations of the people who
developed and continue to grow it.
A crop developed its unique characteristics
through repeated in-situ growers’ selection
and never subjected to formal plant
breeding

8.  Decrease in genetic diversity to develop
improved varieties
 Changing consumers’ demands and
environmental conditions
 New markets or environments for food
security
 Cultivars grown by farmers become
increasingly genetically homogenous
 Agro-ecosystem
 Potential innovation in sustainable agriculture
impacted
Consequences of landraces, if lost

9. On-farm management within the traditional
agricultural systems where landraces
developed their unique characteristics
In-situ and ex-situ conservation
Protected areas and national parks
National management plan for landraces
conservation
Agriculturists-taxonomists-conservationists
joint working closely together with farmers
Conservation of LR and CWR

10. Landraces
utilization in crop
improvement

11. Pre-breeding and crop improvement

12. Plant breeding
Induced evolution for the benefit of mankind using
PGRFA/gene/s as the building blocks.
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, landraces and other unimproved materials.

13. 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)

14. Why Pre-breeding?
Limited progress due lack of diversity: Current limited genetic
base of agriculture is apparently a threat to 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 and efficacy of target trait/s into cultivars and
source of desired gene(s)”

15. The Gene Pool Concept
Gene pool is the total genetic variation in the breeding
population of a species and closely related species
capable of crossing with it.
Primary gene pool: same species cultivated and wild
Secondary gene pool: different species than the
cultivated
Tertiary gene pool: more distantly related
Quaternary gene pool: unrelated plant species and/or
other organism
Introgression: Incorporation or broadening of
genetic base
Wide crosses: Synthesis of new base populations

16. 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

17. Applications of pre-breeding in crop improvement
1. Broadening the genetic base, to reduce vulnerability.
2. Identifying traits in exotic materials and transferring genes into
material more readily accessed/utilized by breeders.
3. Genes from wild species into intermediate populations to
formulate effective breeding program.
4. Identification and transfer of novel genes from unrelated
species using novel techniques.
5. Non-GMO novel diversity.
Pre-breeding facilitates the efficiency and
effectiveness of crop improvement through
increased access and use of ex-situ genetic
diversity

18. Challenges
a) Lack of characterization and evaluation data
b) Knowledge of inter and intra-specific diversity
and relationship
c) Strong breeding program and funding sources
d) Research infrastructure and HRD
Use of genebank accessions in breeding
program is limited due to high complexity
of traits, time-duration, linkage of
desirable genes with undesirable ones

19. Future Prospects
Need to collect, characterize and document
landraces.
Emerging demand for novel genes for biotic &
abiotic stresses, quality and bio-fortification.
Genome mapping be utilized for crop
improvement.
Potential of genetic transformation form the
tertiary gene pool and/or beyond.
New breeding strategies and bioinformatics
tools.

20. Application of Biotech Tools
 Exploration & Collection: Tissue culture, Molecular markers
 Conservation: Molecular markers, Tissue culture and cryo-
preservation
 Genomic resources: cloning, genetic engineering, molecular
markers
 Quarantine: Molecular markers for pathogen detection
 Utilization of germplasm: marker techniques, embryo rescue
(pre-breeding), cloning
 Diversity analysis of Germplasm: Phylogenetic relationship,
core collection, gene flow study
 DNA Fingerprinting: Germplasm identification, genetic purity,
genetic stability, identification of duplicates
 Gene discovery: Association mapping, allele mining
 Trait specific germplasm: Identification and validation

21. Use of landraces in pre-
breeding for crop
improvement

22. Use of landraces in pre-
breeding for crop
improvement

23. Identification of landraces for pre-
breeding

24. Global Genetic Bio-fortification (Plant
Breeding)
Wild wheats and spelt wheat to improve zinc and
iron. Screening of > 15,000 genotypes of wild
wheats and spelt wheat. Developed wheat high
in zinc and iron.
Indigenous wheat landraces rich in zinc and iron.
The accessions (11170, 11296, 11334,
11363, 11156, 11308, 11298, 11238,
11200, 11534, 11304, 11309, 11199,
18708, 11211, 11272, 11229, 11280)
identified better for Zn concentration
>40ppm.
Accessions (1193, 11309, 11237, 11195,
11335, 11199, 18692, 11310, 11155,
11185, 11233, 11238, 11235, 11298,
11315, 11311, 11272, 11154, 11194)
selected as high in Fe >100ppm.
Indigenousachievements

25. > 90 % untapped bio-resource
Centuries adaptation to extreme biotic and a-
biotic, promising donor
Modern breeding tools, for utilization of
untapped diversity under ex-situ conservation
New and diverse sources of variation to
develop new pre-breeding populations
Few promising wild type accessions have been
utilized for the improvement of crop plants
Pre-Breeding for Genetic Enhancement

26.  Of the eight annual wild Cicer species, only C. reticulatum is
crossable with cultivated chickpea
 Other species requires novel techniques [growth hormones,
embryo rescue, ovule culture, and tissue culture techniques]
 Cold tolerance and resistance to wilt, foot rot, root rot,
and Botrytis gray mold [C. reticulatum and C. echinospermum]
 Novel techniques, interspecific hybrids between C.
arietinum × C. judaicum , C. arietinum × C. pinnatifidum, C.
arietinum × C. cuneatum, and C. arietinum × C. bijugum
 These interspecific hybrids have contributed significantly toward
the development of genomic resources for chickpea
improvement
 Examples in other field crops
Pre-breeding for biotic and abiotic stresses

27. Abstract
Pre-breeding for improvement of
agronomic, quality and nutrition-related
traits along with tolerance to biotic and
abiotic stresses
Pre-Breeding for Future Climate Smart
Crops

28. Pre-Breeding: Past, Present Status and
Future Scope
 Natural phenomenon continued evolution
 Limited genetic variability in cultivated germplasm,
hence pre-breeding in most crop improvement
programs has a potential
 Phenotyping and genotyping to identify lines with
enhanced genetic base and minimum undesired
linkage
 Initiatives and Hope for Enriching Cultivated Gene
Pool Through Genomics-Assisted Pre-Breeding

29. Concluding remarks
Sufficient diversity in landraces and wild relatives
Multiple choices for genes and breeding programs
Pre-breeding activities be initiated to generate new
PGR
Useful variability to develop new high-yielding
cultivars, resistant to stresses and broad genetic base
Novel techniques for pre-breeding [5–10 years]
Genomic-assisted pre-breeding to overcome the
linkage drag and to facilitate focused transfer of useful
genes from CWR & LR for genetic enhancement of
crop plants

30. Current Trends in Plant
Breeding

31. What is plant breeding?
Induced evolution for nutritious food security,
“Accelerated and targeted evolution”.
Genetic improvement of plants with desired traits
through application of genetics.
Systematic procedures to improve crop plants by
conventional as well as novel techniques.
Crop improvement is a cyclic process of identifying
new variation, crossing, selection, and fixing favorable
traits.
Fundamentally breeding is evolution by artificial
selection.
SELECTION IS THE BASIS OF ANY BREEDING

32. Background information

33. The 21st
century took
us from gas
lamps to
Google and
steamships to
space shuttles
And the world population
quadrupled in just over 100
years
The Recent Past –
Scientific Plant Breeding

34. Norman Borlaug, “father of the green
revolution”
Nobel Laureate
Norman Borlaug 1914-2009
One of the most
significant
accomplishments
of 20th century
science was the
development of
lodging-resistant,
high-yielding
semi-dwarf grain
varieties

35. Plants were domesticated in parallel in
several regions
Reprinted by permission from Macmillan Publishers Ltd.:
[Nature] Diamond, J. (2002). Evolution, consequences and future
of plant and animal domestication. Nature 418: 700-707,
copyright 2002.
Wheat, barley, pea, lentil
~ 13,000 years ago
Rice, soybean
~ 9000 years ago
Rice, bean
~ 8500 years ago
Corn, squash, bean,
potato
~ 10,000 years ago

36. The Challenge ….
In the next 50 years, we have to
produce more food than we have
in the last 10,000 years. We need
to find ways to employ
technology and science to
increase production to feed the
only living a hungry planet
Food security and sustainability will depend on
advances in plant-based agriculture. We need to
develop higher-yielding plants that are more
nutritious, use water and nutrients more
efficiently, and can tolerate more variation in the
environment.

37. Breeding technologies

38.  Field-based Phenomics Research
 Greenhouse System
 Biotic and a-biotic
 Quality and nutrition
 Controlled Growth House for precise
lighting and temperature control
 Feature extraction and machine
learning
 Biometry and computational biology
 Computer software for analyses
 Multidisciplinary team for
interpretation
Controlled Environment Phenomics Facility
(CEPF)

39. Proteomics
Organisms have one genome, but multiple proteomes
Proteomics is the study of the full complement of
proteins at a given time
Microarrays are easier, and more established
It is proteins, not genes or mRNA, that are the
functional agents of the genome
Three steps
Preparation, Separation, Characterization

40. Transcriptomes
Hereditary information encoded in the DNA (or RNA)
Set of all mRNAs ("transcripts”) produced from a
genome
Complete set of transcripts for a given organism
Specific subset of transcripts present in a
particular cell type or under specific growth
conditions
Transcriptome varies because it reflects genes that
are actively expressed at any given time

41. Modern plant breeders use
molecular methods including DNA
sequencing and proteomics as
well as field studies

42. Historical way to plant breeding
Phenomics [since civilization]
Plant biology and genetics [a century old]
Molecular biology [5 decades]
Analysis of genomes [1990’s]
Metabolomics [analysis of metabolites]
Transcriptomics/Proteomics [2 decades]
GMO [2-3 decades]
Genome editing [Future hope]?
Bioinformatics [OMICS data mining & management]
OMICS coincides with dramatic improvements in
molecular biology, computers, internet

43. Genome sequence data are available for many
important plants
Maize

44. Genetic Modification (GM)
Elite tomato Disease resistant
plant (need not be
same species)
Elite, disease resistant tomato
Recombinant DNA (or GM)
allows a single gene to be
introduced into a genome.
This method can be faster
than conventional breeding

45. GM methods and molecular breeding
Molecular breeding
Desired trait must be
present in population
Genetic resources must
be available
Plant should be
propagated sexually
GM
Gene can come from any
source
Biosafety issues, plant
can be propagated
vegetatively
Genetic resources ?

46. Bioinformatics: Data Mining

47. Role of Bioinformatics
Software packages
Genetics & image analysis and interpretation
Simple to complex
Relationships between breeding populations
and breeding methodologies
Downstream analysis of experiments
OMICS more complex interpretations
Data standards and data bases

48. Bioinformatics and databases
 Latest biological data gathered, organised and
disseminated through large databases
 EBI, NCBI, Pfam, SMART, SWISS-PROT, TAIR
 Information in bioinformatics databases
 Sequences, structures, homology searches
 Fast search engines allow access to databases
 Improved tools for analysis of sequences
www.ebi.ac.uk/, www.ncbi.nlm.nih.gov/Genbank/,
www.ncbi.nlm.nih.gov/,
http://www.rcsb.org/pdb/home/home.do, www.sanger.ac.uk/,
smart.embl-heidelberg.de, www.arabidopsis.org/

49. “Omics” Overview
 Analyses of plants; agronomy, physiology, genetics
 Genomics; DNA markers, QTLs, Association
mapping, Sequencing, structural
 Transcriptomics; set of all mRNAs ("transcripts”)
produced from a genome, functional
 Proteomics; set of all proteins produced under a
given set of conditions
 Both can vary because they reflect genes that
are actively expressed at any given time
 Transcriptomics and proteomics are both powerful,
but are used differently, transcriptomics is cheaper
and more user friendly than proteomics

50. Knowledge is
power, but
complete and
accurate

51. Breeding crops for a second green
revolution
 Gene revolution
 Second green revolution
 Develop plants and
minimize environmental
degradation
 Enhancing human health
 Advances in genetics
 Advancement of OMICS
 Skills improvement
 Robotics
 Smart breeding

52. Future breeding technology?
 New technologies to enhance traditional and novel
breeding techniques without diverting resources
 GM varieties, Non-GM varieties
 Speed breeding and pre-breeding
 Gene editing and trans-genes for future crop
improvement
 Genetic principles and structural genetic information
(MAS, MAB, QTLs, Association mapping, exploitation
of untapped ex-situ diversity)
 Genome sequences and functional information
 Knowledge of metabolic pathways
 Advancing field, greenhouse and laboratory
manipulation

53. 2030 Agenda for Sustainable Development
The 2030 Agenda for Sustainable Development, 17
SDG, 1 January 2016.
Crop breeding are the priority areas of FAO under
SDG 1, 2, 3, 5, 12, 13, 15 & 17 directly or indirectly.

54. 1. https://www.frontiersin.org/articles/10.3389/fpls.2019.00434/full
2. https://journals.plos.org/plosone/article?id=10.1371/journal.pone.0167855
3. https://www.frontiersin.org/articles/10.3389/fpls.2013.00309/full
4. Increasing homogeneity in global food supplies and the implications for food security.
5. Proc. Natl. Acad. Sci. U.S.A. 2014; 111: 4001-4006
6. Plant genetic resources conservation and utilization: the accomplishment and future of a societal insurance
policy. Crop Sci. 2006; 46: 2278-2292
7. Barley landraces from the Fertile Crescent: a lesson for plant breeders. in: Brush S.B. Genes in the Field: On-
Farm Conservation of Crop Diversity. International Development Research Center, 2000: 51-76
8. Recent progress in the ancient lentil.J. Agric. Sci. 2006; 144: 19-29
9. Genotype by environment interactions in barley (Hordeum vulgare L): different responses of landraces,
recombinant inbred lines and varieties to Mediterranean environment. Euphytica. 2008; 163: 231-247
10. Specific adaptation of barley varieties in different locations in Ethiopia. Euphytica. 2009; 167: 181-195
11. Agricultural biodiversity is essential for a sustainable improvement in food and nutrition security.
Sustainability. 2011; 3: 238-253
12. Protecting crop genetic diversity for food security: political, ethical and technical challenges.
Nature. 2010; 6: 946-953
13. World Conservation Monitoring Centre Groombridge B. Global Biodiversity: Status of the Earth's Living
Resources. Chapman & Hall, 1992
14. Estimating genetic erosion in landraces – two case studies. Genet. Resour. Crop. Evol. 1996; 43: 329-336
15. A new plant disease: uniformity. CERES. 1994; 26: 41-47
16. Landraces: importance and use in breeding and environmentally friendly agronomic systems. in: Maxted
N. Agrobiodiversity Conservation: Securing the Diversity of Crop Wild Relatives and Landraces. CAB
International, 2012: 103-117
17. Agricultural biodiversity is essential for a sustainable improvement in food and nutrition security.
Sustainability. 2011; 3: 238-253
Further reading

55. “Selection is the basic option for
utilization of induced evolution for
healthy and nutritive food security to
ensure peace on the only living
globe"