Plant domestication and diversification

Question 1

Human food evolution overview

Answer 1

**Hunter gatherers **foraged wild cereals, fruits and nuts -> time demanding + not reliable resource

Cultivation/ domestication began to replace foraging 3,000 - 10,000 years ago -> shift in investment to few plants (change in behavioral ecology)
-> 24 regions were cultivation arose
-> key region= fertile crescent of wheat (middle east)

Diversification occured as the domsticated planst spread, became locally adapted and culturally desirable traits were selected for (LANDRACES)

Question 2

The genetics behind domestication and diversification

Answer 2

Domestication and diversificaiton was controlled by few genes of large affect (although whole genome effected due to selective sweeps and continued selection today)

1) Initial DOMESTICATION
* 8/9 Domestication genes encode transcriptional regulators (profound changes)

2) Subsequent DIVERSIFICATION
* > ½ Diversification genes encode enzymes (subtle changes)

Question 3

Key domestication traits

Answer 3

1) Increase germination success

Loss of seed dormancy

Used to lie dormant until suitable conditions but now need all to germinate + be harvested at same time

Example: loss of dormancy in the common bean
- 5-bp insertion within gene expanding pectin acetylestrase-8 that may result in the loss of seed dormancy

Increase in seed size

Increasing seed size increases the emergence depth (important when growing in soil tillage) and fruit size

Example: Seed size in domesticated einkorn wheat

2) Increase ease of harvesting

Loss of shattering

Loss of shattering means crops are dependent on humans for propogation and survival

Example: Rice domestication
- Wild Kasalath (smooth abscission region) does not retain seeds while Nipponbare (rough absission region) does retain seeds
- Mutation 12,000 bp upstream in qSH1 (also known as OS-rpl) regulatory region leads to expression of qSH1 transcription regulator and a rough abscission layer
- TRANSCRIPTION REGULATOR

3) other

Changes in physiology

Changes in architecture

Example: Branching in maize
- TE (hopscoch) insertion 60,000 bp upstrem of TEOSINE BRANCHED 1 gene lead to expression
- TB1 supresses lateral growth rate
- TRANSCTIPTION REGULATOR

Example: increase in size of tomato (origonally size of a pea)

**Loss of photoperiod sensitivity **

Example: wheat
-> selected for reduced photoperiod sensitivity, allowing them to flower and set seed across a wider range of latitudes and growing conditions.
-> wheat in middle east = long photoperiods + warm.
-> Wheat in N Europe = cooler, more rain, more variable photoperiod year round

Question 4

Key diversification traits

Answer 4

Selection for preferable cooking / processing qualities, desirable visual / gustatory features

naked grain

Maize (species-wide)
->V reduced podcase
->Less labour-intensive to process after harvest = easily milled
-> Partly controlled by TGA1 gene
-> TRANSCTIPTION REGULATION

Wheat (variety-specific)
->Evolved twice separately
->Hulled variety kept as hull = improved storability + more reliable germination

**Food preferences **

Popcorn
->Toughened pericarp – popcorn maize varieties
Fragrant rice
-> Loss of betaine aldehyde dehydrogenase lead to increased 2-acetly-1-pyrroline = fragranced

Sticky rice
-> Sticky due to reduction in amylose levels in grain starch due to loss of starch biosynthesis enzyme
-> Mutation in intron 1 splice-donor (in waxy gene) -> splicing prevented = no functional mRNA
-> ENZYME CHANGE

Question 5

Domestication vs natural selection

Answer 5

Mutation in the same position upstream of rpl gene is responsible for the loss of seed shattering during rice domestication and the difference in seed shattering between Arabidopsis and Brassica

Nipponbare = rough absission region stopping shedding
Kasalath = smooth absission region allowing shedding

Arabidopsis = replum allowing shedding
Brassica = no replum stopping shedding

In both cases there is the same mutation upstream of the RPL gene (c-t or g-t) in the promoter region leading to expression of Transcription regulator. This leads to replum loss or a rough abscission region.

• experiments could induce expression of replum in barassica by converting C -> T or loss of replies in arabidopsis

Question 6

Overall

Answer 6

Hunter gathering

Domestication -> TF
- Loss of seed dormancy
- Increase in seed size
- Loss of shattering
- Changes in physiology
- Changes in architecture
- Loss of photoperiod sensitivity

Diversification -> Enzymes
- Loss of hard case
- Specific food preferenes

Similarity between natural seleciton and domestication

Question 7

Tomato example

Answer 7

Domesticated in coastal peru (small fruited weeds in maize crops) and then transported to Europe by the conquistadors in the sixteenth century
- severe bottleneck during tomato spread
- Breeding should consider introgression lines (especially to get resistant genes)
- Example: yellow leaf curl virus resistance gene from SCL was introgressed into modern variety

A study found 186 domestication sweeps and 133 improvement sweeps but 21% of the domestication sweeps overlapped with the improvement sweeps

Key domestication traits:

Increase in fruit size
- Mutation in the promotor region of the Fw2.2 QTL which encodes negative regulator of cell division. Reduced its total transcription leading to an increase in fruit weight by 30%
- Reduction in fasciated transcription which encodes TF leads to more locules (compartment)

Increase seed size

4 key phases of later breeding focusin on:

Yield
- Jointless mutant reduces crop loss due to premature fruit drop
- Jointless mutant lacks abscission zone stopping the fruit from dropping off (ethylene stimulates enzymes that degrade middle lamella between cells and abscission zone)

Shelf life (slowing ripening process)
- decrease in ethylene responsiveness leads to delay ripening + decreased fruit spoilage during transport
- Selection for the non-ripening (nor-> Encodes mutant ethylene receptor ) and ripening inhibitor (mutant rin-> encodes MADS-box transcription factor regulating ethylene production) mutations
Taste

Nutritional quality

GM used in tomatoes

• GMO: FLAV-SAVR -> improved shelf life and fungal resistance
• GE: Japan engineered tomatoes to produce high levels of GABA (produced in the brain) -> stress reduction and treatment for high blood pressure and insomnia

Risk of negative epistasis with GE:
-> For example, a founder mutation enlarged the leaf-like organ in fruits, while a more recent mutation eliminated the flower abscission zone. –> In combination, these mutations resulted in undesirable branching and sterility due to epistasis