Evolutionary Insights from studying domestication LECTURE 2

Since Darwin there has been great interest in studying domestication to better understand…

1. Relatively recent origins off domesticated crops as distinct species

2. Their importance in terms of practical application (feeding the world)

3. Link to outselves Homo spaiens

4. Potential to integrate recent archeological data in the study of domestication all conspire to make domestication research very insightful

Domesticated species are good to study to understand

1. Early stages of species formation and diversification

2. Tempo or speed of evolution

3. How big of phenotypic change can happen

   • Explore how large morphological or phenotypic changes can occur over relatively short evo time period

Examples that are useful as good models

1. Maize

2. Wheat

3. Rice

4. Apple

Maize→ facts

• Most abundant crop with 800 million tonnes of corn produced annually

• N.America but now world wide

• Ancestor Teosinte

  • looks nothing like maize

  • ‘grain of the gods’

Teosinte

Teosinte: 4 species of genus Zea

• Zea mays→ cloested genetic relationship with cultivated species Zea mays

• These are fully infertile but able to form fertile hybrids

• Found in SW Mexico

• Weed on streams and hillsides

Teosinte vs Maize

Teosinte:

• highly branched

• female inflorescence/ ears are different (cobs)

  • 5-12 kernels

  • wrapped in stony hard casing (to survied in digestive tracts of animals)

  • Mature→ breaks up and dispersed separately

Maize:

• massive ears of corn

  • >500 kernels on each ear

  • Naked (no stony casing)

  • Firmly attached and never dettached

  • remain attached even when the cob falls off the plant

How is teosinte an exception

• most crop plants look discernibly similar to human eye

• but maize and teosinte are noticeable exception

How did this happen?

1. Inter-fertility of Teosinite and Zea mays indicated there was no species barrier between them

2. The use of DNA markers that samples a range of possible ancestors showed that Zea mays ssp. parviglumis was the closest living relative

3. Karyotypes are nearly identical

Wheat→ facts

• 3rd most abundant crop

• 6-700 million tonnes of grain

• Europe, N America

• Types

  • Triticum aestivum→ bread

  • T.turgidum subsp durum→ pasta

• Founder crops first domesticated in Fertile Crescent

  • 10,000 years ago

Story of Wheat domstication

1. Start with wild diploid wheats → Triticum monocoocum

   • cultivated as crop called einkorn wheat

2. Close relative T.Speltoids hybridised with this

3. Gave rise to emmer wheat T. turgidum

   • Tetraploid (long history of cultivation)

4. 8000 emmer wheat hybriside with another diploid wheat

   • T. Tauschii

5. → Modern bread wheat Triticum aestivum

Traits (Domestication syndromes) of domesticated wheat

1. enlargement of grain

2. evo of non-shattering phenotype

   • via toughened rachis that lacks abscission zones

   • Threshing required to remove the grains after harvest

3. High amount os protein gluten

   • gives visco-elatic propertiles→ for bread

Asian Rice→ facts

• Oryza sativa

• second most abundant ceral crop

• 700 million tonnes grown annually

• Asia

History of Asian rice cultivation

1. first in Yangtze river in China 9000 years ago

   • from wild progenitor Oryza rufipogon

2. Gave rise to variety subspecies japonica

Separately

3. Local cultures of Oryza nivara in india

   • but no evidence of domestication

But then

4. Japonica arrive in INdia with the silk trade

5. Led to hybridisation and introgression with local Oryza nivara

6. Introgression→ evoltion of subspecies Indica

7. Indica→ most dominant rice group in the world

Traits (domestication syndrome) of Asian Rice

1. non-shatering

2. loss of red colour in the pericap of the seed

3. emergence of a more erect growth form

Additional domestication in Africa?

Domesticated as Oryza glaberima

BUT

• non-shattering has not evolved in this instance

WHY

• Rice is harvested with baskets, not sickles

Apples→ Facts

• Malus domestica

• Most widely distributed of any perennial crop

• 80 million tons world wide

Apples domestication history→ Starting wild apple

1. Tien shan mountains of central Asia 4000 - 10000 years ago

2. Domesticated from crabapples (wild species)

   • Malus sierversii crabapple in Tien Shan mountains

   • grows in intermediate elevations above the sea level

3. Ten Shan wild apples→ remarkable variety

   • (Criteria for centre of origin!)

   • Garden of Eden

Apples story of domestication

1. Apples spread arounf by migrating humans along Silk Roads

2. Apples crossed with local crab apples

   • e.g Malus baccata in SIberia nad M. Sylvestris in Europe

3. Evidence for westard movement

   → patches of wild but large sweet apples in mountains in Afganistan, Turkey and Iran

Why is it hard to grow apples with your desired traits

• Malus domestica is not self-fertilising

• Has weak pollen incompatibility mechanisms

  → Accept pollen from a range of different species

  OVERAL: doesn’t breed true from seed

I.e: If plant the seed, unlikely the apple will taste the same

How to get over this barrier→ Grafting

Role of hybridisation and polyploidy

1. Polyploidy x hybridisation→ intant speciation event

   • if a tetraploid species is formed, it is difficult to then back cross to diploid→ NEW SPECIES

   • advantageous and not diluted by backcrossing to the wild-species

2. Hybridisation→ rapid addition of novel allele and novel genetic combination→ Raw material for further adaptation

   • Powerful as a crop is migrated into new environments and habitats

   • Introgression→ is fab to gain some genes from species adapted to that habitat

   • As seen in rice and apples (as they cross with local crabs)

3. Heterosis or Hyrbid vigour

   • where hybrid outperforms its parents

   • (function of heterozygosity)

Few genes of Large effect or many gnes of small effect

• it is important to understand the genetic basis of these domsticaiton syndromes

• To understand how they have evolved

• Looking at maize vs tsosinte is common because they look so different!

Use QTL to find if multiple genes for a trait or not

A valuable tool in understanidnt he genetic basis of phenotypic differences

Teosinte and MAize can cross to produce fertile hyrbids

A good tool is the

• ability to interbreed and produce fertile F1

• e.g F2 is a good tool

  → Allows for Quantitative Trait Locus Analysis (QTL)

How to do a QTL analysis

1. Tkae two organims which different by a trait

2. Have set of genetic molecular markers that can distinguish betweent he parental lines

   • e.g RFLPS

3. Crossed to produce F1 generation

4. F1 are crossed to give further set of recominants

5. F2 phenotypes are scored

6. Genetic markers are scored and a correlation between Phenotype is found (a GTL)

7. Finds genetic parts that associated with phenotpes

   • unlinked markers will not be associated

Early QTL analysis in Maize/Teosinte showed

• much of the phenotypic divergence for key domestication traits (branching)

• attributeed to 5 regions of the genome

Suggests:

→ only a few genes underpinned the divergence

Identifying particular genes

1. Branching→ teosinte branched1 (tb1) Locus

   • branched allele in Teosinte

   • unbranched in maize

2. teosinte glume architecture 1

   • teosinte→ covered grains

   • maize→ uncovered grains

3. Ears per branch→ grassy tillers 1 (gt1)

   • teosinte allele → multiple eats per branch

   • maize→ single ear per branch

How does Teosinte branched1 work?

• Encodes a TCP transcription factor

  → Changes expression pattern:

  • TB1 is a repressor of axillary meristems:

Maize→ expression of tb1 is elevated compared to Teosinte

• THEREFORE: expression results in repression of the side branches

  • No branches in maize

So is it small no. genes large effect or large number of genes with small effects?

Single gene loci controlling major quantitative traits

• many examples

BUT

• There are still 100s 1000s genes across a genome show evidence of selection through domestication

→ Kinda complex

What does identification of underlying genes for domestication syndromes help to answer?

• Possible to ask whether evolutionary genetic mechanisms underlying common domestication traits are similar across crops and crop origins

• e.g What genetic mechanisms lead to this convergent evolution?

  • Using QTL can compare genetic basis of convergent traits across unrelated crop species

    → numerous similar genes underlying similar processes are emerging

Examples of shared genetic mechanisms for convergence

1. Branching→ teosinte branched 1 in Maize

   • also in: millet and barley

2. Seed shattering→ YABBY transcription factor called shattering1

   • mutated → suppression of abscission zone

   • or translocation and fusion with another gene→ inactivation

   • In Maize and minor contributer in rice

3. Glutinous Grains (large amounts of amylopectin)→ Waxy gene

   • Mutation→ glutinous

   • In Rice and in millet and Barley

     • Independent mutation in the waxy gene

4. Colour→ loss of colour is common because seed coat colour can delay germination

   • MYB transcription factor e.g in grapes

     • mutation= red→white (stops anthocyanin genes)

   • MYB also in Amaranthus

     • distant relative

       → also mutations in MYB that controls anthocyanin production

Overall this shows…

1. As selection pressures are the same in domestication, domestication follows similar genetic pathways (in distant crops)

2. This suggests that if evolution of these happened again, it would be through the same genetic mechanisms

3. Important in understanding the genetic architecture of any kind of trait

4. Can be useful model for looking at evo in natural situations