Trends in plant breeding

1. Current Trends in Plant Breeding: Training in
PGR use in pre-breeding and varietal
development practices
(November 12-13, 2019)
Abdul GHAFOOR
ghafoor59pk@yahoo.com

2. What is plant breeding?
 Induced evolution for nutritious food security, “Accelerated and
targeted evolution”.
 Genetic improvement of plants with desired traits and selecting
progeny with improved performance.
 Application of genetics principles to crop improvement.
 Systematic procedures to improve crop plants by conventional
as well as novel techniques.
 Manipulation at DNA sequence level, and introduction of new
genes through modern plant breeding tools.
 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 PROGRAM

3. Background information

4. 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

5. 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

6. 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

7. 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.

8. Breeding technologies

9.  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)

10. 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
So why use proteomics at all?
 It is proteins, not genes or mRNA, that are the functional
agents of the genome
 Transcriptome information is only loosely related to protein
levels
 Abundant transcripts might be poorly translated, or quickly
degraded
 Three steps
Preparation, Separation, Characterization

11. 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

12. Isolation of mRNA at two stages of
developments, each mRNA sample
represents all genes expressed at that
stage
Convert mRNA to cDNAs by RT using
fluorescently labeled deoxyribonucleotide
triphosphates
Add the cDNAs to a microarray, fluorescent
cDNAs anneal to complementary
sequences on the microarray
Each fluorescent spot represents a gene
expressed in the cells. Isolation of mRNA
from cells at two stages of developments,
each mRNA sample represents all genes
expressed in the cells at that stage
 Experiments
performed under
different conditions
 Determines effect of
conditions on
expression
 Produces huge
amount of data
 Lots of repeats
required -
expensive
Transcriptomic protocol

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

14. 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 decades]
 Genome editing [Future hope]?
 Bioinformatics [OMICS data mining & management]
 OMICS coincides with dramatic improvements in molecular
biology, computers, internet

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

16. 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

17. Why use GM methods sometimes and
molecular breeding others?
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 ?

18. Bioinformatics: Data Mining

19. 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

20. 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/

21. “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

22. Knowledge is
power, but
complete and
accurate

23. 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

24. Future breeding technology?
 New technologies to enhance traditional and novel breeding
techniques without diverting resources
 GM varieties
 Speed breeding and pre-breeding
 Gene editing and trans-genes to the future of 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

25. 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.

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