Evolution as a guide for future crop breeding and design LECTURE 3

Four components to the concept of Food security

1. Food availability

   • enough nutritous food of sufficent quality needs to be available to people for consumptin

2. Food access

   • individuals and households must be able to acquire sufficient food to be able to eat

   • healthy, nutritous diet or have access to sufficient resources needed to grow their own food

3. Food utilisation

   • people must have access to sufficient quantity and diversity of food to meet nutritional needs

   • but must also be able to eat and properly metabolise such food

4. Stability

   • food may be available and accessible and in order for people not to feel insecure

   • state of affairs needs to be enduring rather than temporary or subject to fluctuations

I.e ascpetrs of food secuity

1. Is there food

2. Can it be accessed

3. Is it good/digestible

4. Is it sustainable

Threat to food security

→ by 2030

• 33% pop rise

• 30% demand on water

• food and energy up 50%

Why is this threat happening?

1. pop size increase

2. increase wealth

3. reduction in imporvement in crop yield

4. impact of climate change on land availability

5. conflicts demanding land aside for

   • biofuels or

   • maintain biodiversity and store carbon

Why does more wealth increase demand for food?

• increase flexibility of income

• use of meat as primary foodstuff increases

• creates additional difficulty for global food supply

Why does meat production increase food supply difficulty

• conversion of plant calories to animal→ 10% efficiency

• meat demand = x10 fold increase demand on crop production

e.g 1/3 of world total cereal production= animal feed

• therefore, as meat demands increase, more demand on cereals

Crops amounting to 2/3 os calories consumed by global population

1. maize

2. rice

3. wheat

4. soybean

To ensure they feed enough people

• yield increases 2 in last 50 years

How?

• agronomic improvements

• technological improvements

• intensive breeding

→ optimise yield within genetic limits of each species

Why are yield increases slowing down?

1. natural variation within key crop species

   • largely been exploited

2. Availability of land

→ this is not good for the predicted increases in demand

• calorie demand from crops with x2 in the next 30-35 years

1. Example of this→ rice yield yield increase slow down

• increase 42% in 1980s

but only by

• 6% between 2000 and 2010

2. Land availability

Limited by:

• soil type

• elevation

• climate

• But also other factors!:

  • acidification/ desertification of land (due to intense agriculture)

  • increased urbanisation

  • biofuels e.g in USA

  • increased pressure tokeep global diversity/carbon stores

• Climate change→ IMPACTS all of these

Many of the solutions of these relies on

• Plant science

Genetic bottle neck

• rapid reduction in effective size of a population

• may occur through a variety of causes

What do bottle necks do to gene pool

• reduce the variation

  → less genetic diversity is present to pass onto future generations

What does this loss of genetic diversity lead to

• overall reduced robustness in the population:

  • impairing its ability to survive new challenges with adaptation

    • e.g cannot adapt well to climate change

How can genetic diversity increase again?

1. gene flow from another population

2. genetic diversity slowly accumulate again as random evolve in the surviving population

   • until mutation-selection balance is reached

When do bottle necks occur

• small group is reproductively isolated from a main population

  • e.g Founder effect→ paritularly relevent for domestication process

  • where founder evenets can occur at a number of different stages

Domestication Bottleneck

1. limited part of species diversity is selected for

2. cultivated crop likely has limited diversity compared with wild species from which it originates

After this initial bottle neck

Diversity may increase

How?

1. unconscious or conscious selection in different local ecological situations

2. introgression from wild populations

What can happen next?

Second potential bottleneck

• ‘dispersal’ bottleneck:

Why?

1. When crops introduced outside their centre of domestication

2. where smaller diversity of domesticated crop is used as the genetic basis for the new location

Ultimate effect of prolonged selection (over 1000s of years)

• Reduced allelic diversity

• limited genetic pool

→ hard to work with to get new pest and disease resistance traits

How can low gene pool be helped?

• Using crop wild relatives/ ancestral progenitors

Importance of ancestral progenitors and other crop wild relatives

• the traits of the modern crop species can only really be understood by comparison with the progenitor species

• the inter-fertility of the ancestral progenistor species and drevived crop species can enable tools to resolve the genetic basis of domestication

BUT ALSO USEFUL FOR:

• identifying the evo ancestors of crop species

  → relating to the issue of genetic bottlenecks and allelic diversity

Definition of crop wild relatives

• wild plant taxon that has an indirect use derived from its relatively close genetic relationship to a crop

As they have not been domesticated

• Represent a vast reservoir of ‘lost’ genetic diversity:

  • genes for resistance to high temps, drought, pests, disease

  • taste, nutrition and yield

Therefore…

• Use in introgression with crop species is common

E.g s of introgression

1. Oryza nivara wild rice cross with Oryza sativa subcp

• → strong and extensive resistance to a pathogen grassy stunt virus

2. Tomato cultivars cross with the wild

   → disease resistances

What is critical before doing introgression?

• determining the closest relatives

However there is a problem with using wild crop relatives!

• they may have gone extinct!

→ 40-50% of all CWR are threatnend with extinction

Key threats to the crop wild relatives

• land-use change

• climate change

  → likely 31/50 in S.Amereica of Archis likely to go extinct

• nitrogen deposition

• invasive species

How are they managed?

• identify their distribution in wild

• identify potential risk of extinction

  → inform seed banking strategies

ex-situe conservation

Why is it an issue to be polyploid?

e.g Cavendish banana= triploid

→ but low genetic diversity for pest etc

Introgession?

• progenitor speceis is diploid

  → introgression= sterile triploids

How to get around this issue?

Resynthesise polyploids e.g with wheat

1. go back in evo time

2. re-create the polyploid with the original progenitors

3. Makes a sterile triploid progeny but then

4. treat with chemicals (cochicine)→

5. Artificially induce chromosomal doubling

   → synthetic polyploids (hexaploids)

OVERALL: now have a hexaploid of kinda ancestral??

Now have re-synthesised hexaploidy, what to do with is?

1. cross with modern varieties

2. get the benefits of introgression

Limitations of this method?

• need a good understanding of evo history of the polyploid event

Issue with having only 4 crops accounting for 2/3 of calories

1. lack of resilience in systems

   • (increased risk in catastrophic interruption of food supply)

2. Vast majority of modern breeding and domestication efforsta re likewise focussed on relatively few species

   → excluded domestication of other crops

What are orphan crops?

• diverse set of minor crops

• locally or regionally important

BUT

• not commercially traded

Importance of orphan crops where they are grown

• very important

• provide income for the poorest farmers

• serve staples in local diet

Due to orphan crops having less domestication they are…

• less productive

• untenable at larger agricultural scales

• benefit less from basic research

Could orphan crops help food security?

• potential speedy domestication?

• rapidly speed up crop improvement

• decrease food security challenges

What is needed to help speed up domestication process

1. evo understanding of domestication syndrome

   • which traits are important and in whcih order?

2. evo insights into underlying similarity and differences in genetic changes that underpin convergent domestication traits

   • e.g the shared transciptional changes etc

   • e.g shattering and stickiness→ same genes underlie them but different crops= homolgous gene

Therefore, if you want to try take an evo informed approach to inducing domestication

• good to start finding the gene for a trait in one crop and finding same (homoglous) gene in the other crop

  → may have different function but still useful

→ Candidate gene approach

How to rapidly domesticate orphan crops, suggested things?

1. classical breeding sped up with genomic technologies

• BUT→ still lengthly and tedius due to random recombination and undirected mutagenesis

2. Introgression of beneficial alleles?

   • BUT→ can get unwanted genetic material linked to genes

   • have to do lots of backcrossing to get rid

3. CRISPR/Cas→ does work!! gene editing

How does CRISPR/Cas help rapid orphan domestication

1. Apply candidate gene approach

2. Find useful homologous target gene in new or orphan crop→ with no domestication

3. target creation of mutations e.g sall deletions

OVERALL→ can take progenitor crops→ and convert to domesticated crop species

• in a few years

Example of CRISPR/Cas crop sped domestication→ Tomato

1. Took wild progenitor of tomato

2. Disrupted size genes known from studies that were known to→ domestication

3. Compared to wild type

Results:

→ increased bushiness of plant

→ 3x fruit size

→ 10 x fold number of single experiment

→ x5 nutrition

Nitrogen fixation in our 4 ceral crops

• does not happen

• need to make this happen!

• So less reliant on fertilisers

Origin of nitrogen fixation?

• molecularly from one origin

  → suggests that engineering nitrogen fixation is diffisult

BUT

• origin of nodulation dates back later→ so may not need nodules for nitrogen fixation

→ May be able to artificially do this in plant then?

→ Nodule formation has happened as many as 9 times!

• must be convergent mechanisms→ available for de novo genetic engineering!!

Nodulation vs Arbuscualr mycorrhizal symbiosis signalling

• Share similar signalling pathways

  • cytokinins and auxin etc

This means:

• provide encouraginment for engineering nitrogen-fixing monocots as orthoglous components of the machinery, should already be present in functioning cereal crops

  → Therefore should be easy!

Overall things that will help decrease food insecurity

1. Increase genetic diversity→ introgression with wild

   • Polyploidy re-synthesising

2. Domesticate orphan crops

3. Engineering nitrogen fixation in cereal crops

Summary of stuff

• Food security→aspects

• Problem→ low gene diversity in 4 crops

• Solution:

  • Introgression with wild crops

    • Issues: polyploidy, wild crops endangered, genes that we dont want

  • Rapid domestication of orphan crops

    • Issues: finding genes to dom, genes dont want→ CRISPR/cas9

  • Nitrogen fixation artifically engineer