Lecture 10: Tools and Approaches for Crop Nutritional Improvement Flashcards
Spontaneous mutations
*Spontaneous phenotype changes
*Genetic drift Random change allelic frequency
*‘Anthropogenic selection’ Selected by farmers/breeders
Darwin called them ‘Sports’ but we don’t know why
Example 1: 1950s:“Dee-geo-woo-gen” in local rice variety Taiwan
Rice (DGWG) (sd1 allele)
* genetic source of semi-dwarfness
* development of high-yielding varieties gibberellin 20-oxidase gene
^ this short variety is less likely to lodge (fall over)
Example 2: increased kernel size and improved colour in maize cultivar
(see notes)
Example 2 – high yield wheat cultivar:
Gibberellin (GA) = diterpenoid phytohormone
* seed germination, stem elongation, leaf expansion
* pollen maturation, flower, fruit & seed development
^ “green revolution” high yielding genes
short stature
stiff straw
fertilizer-responsive
photoperiod-insensitive
^ Wheat (Rht-B1b and Rht-D1b genes) N terminal stop codons TF (DELLA) / gibberellin signaling
Induced mutations: Mutagens
2 types of mutagens: physical and chemical
Physical:
-non-ionising radiation e.g. UV
- ionising radiation:
Particulate radiation
eg. Beta and alpha rays,fast and thermal neutrons
Non particulate radiations
eg. X rays, gamma rays,
ion beams
^ aka Targeting induced local lesions in genomes (TILLING) - the process of seed irradiation
Chemical:
Alkylating agents
eg. EMS, MMS, DMS,nDES, EI, ENU
Base analgues
eg. 5-bromouracil, 5-chlorouracil, 2-amino
purine
Deaminising agents
eg. Mustard gas, azide, caffeine, phenol thiourea
Acradine dyes
eg. Acradine orange, proflavine
Induced mutation process
Seed variety germplasm
Mutagenic treatment
M, generation Variant plants
M2 seeds
M2 generation
Segregation and selection of desired mutant
M 3 generation
Selection of true mutant lines
M4 generation
Homogeneity test mutant lines
Then:
Hybridization
or
Multiplication of seeds
Yield test on multiple locations
-> officially tested new variants
Applications of induced mutagenesis
in improvement of crop quality and nutritional traits in plant breeding:
Oil quality improvement in Soybean, Canola, Peanut, Sunflower, Soybean and Maize
Improvement of protein quality in soybean and maize
High-amylose content cassava preferred by diabetes patients because it lowers the insulin level, which prevents quick spikes in glucose contents.
Oilseed meals low in phytic acid (soybean) desirable in poultry and swine feed
Phytate (anti-nutrient) in barley
High-resistant starch in rice (RS) preferred by diabetes patients
Giant embryos in rice (containing more plant oils); low amylose content; low
protein content (for special dietary needs)
Dark green obovate leaf pod; increased seed size, higher yield, moderately resistant to diseases, increased oil and protein content in groundnuts
Somaclonal variants
Often undesirable BUT Sometimes provide improvement in quality traits
Occur due to chromosomal rearrangements
Causes: Cultivation in sterile media Sterilizing agents Growth regulators Wounding/Light/ROS
(see figures in notes)
Wild species and relatives
Crop wild relatives are the wild cousins of our cultivated crops
They can possess important latent traits - some not present in cultivated crops therefore crossing modern crops with wild relatives can provide traits that make them more productive, nutritious, & resilient.
A vital sources of genetic diversity for developing new crop varieties able to withstand challenges ranging from arable land restriction to climate change.
Threats to wild species and crop relatives
- changes in land use
- the intensification of agriculture
- climate change
- overgrazing, and weeds
Examples of crop breeding with wild (‘ish’) relatives
L. hirsutum, a wild relative of tomato
➢ small green fruits
progeny of cross tomato x L. hirsutum
➢ showed enhanced red colour
➢ others higher carotene content
Viticulture vitis vinifera x vitis rupestris - Grape hybrids with fungal disease resistance & reduced need for pesticides
Transgenes/ biotechnology
Plant breeding of crops through the application of modern tools and techniques
of cell & molecular biology – more accurate and safer than earlier approaches
Conventional breeding: involves mutation, selection and hybridisation
biotech involves: Marker assisted selection, molecular plant breeding, TILLING, next gen sequencing and utilisation of genetic diversity
Biotech approach for crop improvement
1candidate gene selection
( after selection can go directly to gene selection and improved variety )
molecular marker development
2 QTL mapping & Map based cloning
3 Genome wide association study (GWAS)
4 integrated molecular breeding approach
5 marker assisted: backcrossing/ recurrent selection -> genomic selection and development of improved variety
Functional and comparative genomics in marker-assisted breeding & biotechnological methodologies:
see notes for figures:
a) multiple constructs
b) bidirectional promoters
c) 2A peptides
d) Multi-cassette vectors
Genetic basis of traits
3 Types of inheritance governing traits:
- Oligogenic (nuclear)
- Polygenic (nuclear)
- Cytoplasmic (maternal effects)
The number and nature of genes/alleles determine the trait
1.Oligogenic inheritance
Governed by one (or few) major alleles that determine the trait
Each allele has a large and easily detectable phenotype = effect on the expression of quality trait
Differences between high & low trait value is clear e.g. Mendel’s peas
crop examples:
Sorghum - high lysine content
- single gene with incomplete dominance.
Barley - high lysine content
- single gene with incomplete dominance.
Safflower - fatty acid composition
- one major gene with three major alleles/isoforms
Tomato - high beta carotene content
- two major genes plus modifiers.
Modifier genes affect phenotypic and/or molecular expression of other genes
- Polygenic inheritance
Cumulative: SEVERAL genes with an ADDITIVE effects on trait that is complex and continuous
There is a range of different degrees of the trait
Features:
Phenotypic trait determined by several genes each with small additive effect
Variation for a trait is continuous from one extreme to another
Complex; phenotypic classification of plants is difficult
Sensitive to environmental changes
Generally low heritability
non-mendelian pattern
– genetic interpretation of quantitative characteristics
- with variance or co-variance
examples:
- cereals and pulses - protein content
-oilseed crop - seed oil content
^governed by polygenes
-carrot - high carotenoid
^complex inheritance pattern
- Cytoplasmic inheritance
Observable physical properties. Non-mendelian and with evolutionary consequences
Phenotype/Trait derived from the maternal phenotype
Irrespective of own genotype
Mother supplying mRNA or proteins to the egg
Environmental factors & maternal effects confuse relationship genotype
& phenotype - reducing the progress under selection breeding
Selection/breeding schemes must make allowances
Examples:
- grain characteristics : seed size & protein content
-Chickpea - protein content
-Maize, soy and rapeseed - fatty acid composition
see table in notes of alt. cytoplasmic inheritance mechanisms in plants
Traits
Characteristics: Agronomic performance and Consumer preference
Plant ‘’domestication syndrome’’ (Hammer, 1984):
Phenotypic changes associated with adaptation under domestication:
1. ‘a specialized mutualism in which a domesticator exerts
control over the reproduction or propagation (fitness) of a
domesticated species to gain resources or services.’
2. ‘Process of adaptation to agro-ecological environments and
human preferences by anthropogenic selection’
see graph in notes of domestication syndrome traits in crops grouped by the primary part of the plant used.
How are crops improved?
Wild plants are poor crops – they did not evolve to serve our needs
Plant domestication – involves enhancing short-term productivity through selection/mods
Conventional breeding – originally phenotype based crosses now through technological developments we are able to conduct gene editing for faster results and greater accuracy
Domestication traits and loci
see notes for figures
^ Examples of domestication traits and associated genes or loci across diverse crop types. A combination of large- and small-effect quantitative trait loci contribute to most domestication-related phenotypes.
Major changes commonly associated with artificial selection:
*Increased yield organs of interest (e.g. seeds or fruits)
*Stronger apical dominance
*Loss of seed dispersal
*Loss of seed dormancy mechanisms
Fast-growing resource-acquisitive strategies:
*decreased herbivore defense
*higher stomatal densities on the upper side of leaves
*increased nitrogen and phosphorus concentration in leaves
Root traits less obvious - pre-adapted for fertile soils thicker roots, less dense
Unintended consequences of plant domestication
undesirable impacts of domestication on several beneficial traits:
Nutritional quality
Plant immunity
Flavour and adaptation
Direct and indirect effects of plant domestication
Direct Effects
- Increased fruit and seed weight
- Increased fruit palatability
- Loss of seed dormancy
- Loss of seed dispersal
- Changed plant architecture
Indirect Effects
- Reduced sugar content
- Reduced seed carotenoids
- Altered seed tocopherol and fatty acid content
- Reduced plant immunity
- Altered root system architecture
- Lower root apical dominance
From Singh (2022) Plant Cell Physiol. 63(11): 1573–1583 An overview of direct and indirect changes resulting from plant domestication. Artificial selection of directly selected traits brought about indirect changes in other plant phenotype
Why is there a requirement for further crop improvement or expansion?
Food / Feed dependency on limited number of crops
Small number of species
Locations differ from origin domestication
~150 plants commonly cultivated today 70% calories from only 15 crops
maize, rice & wheat grains make up 50% of these calories
There are 250.000 extant angiosperms
2500 crops domesticated
yet only 12 provide >90% human staple food!
challenges to feeding the world
- expected 20% increase in population from 7.7 to 9.8 billion by 2050
- limited resources - land, water, nutrients etc.
-climate change impacting food production and crop yield - conventional breeding timelines slow & current genetic gains insufficient
-need innovation to increase food production and sustainability despite these challenges
see GIFS - global institute for food security
Current issue; Hidden hunger
Issue: getting enough calories but not enough nutrients - unbalanced
➢ Productivity varies across globe
➢ Increased competitions for land
➢ Climate change
➢ Environmental deterioration
Agricultural Burden and challenge for global food, resource and energy security
Increase in human population size
Dietary changes
Environmental changes – climate change and pollution
Declining biodiversity
