This presentation discusses the history and process of plant domestication. It begins with an overview of the origins and timeline of agriculture, noting that domestication of major crops like rice, wheat and maize was completed by 4000 BC. The presentation then covers centers of domestication, key domestication traits, genes controlling traits, and modern techniques like genome sequencing, GWAS, and NGS that are helping to further understand domestication.

1. 1
Welcome

2. 2
Presented by :
Varsha Gayatonde
Supervisor:
Prof. J. P. Shahi
Co-Supervisor
Prof. K. Srivastava

3. 3
Flow of presentation
 History of Agriculture
 Crop domestication
 Centers of domestication
 Domestication genes in crops
 Super-domestication
Polyploidy
Genome sequencing
NGS
GWAS
Finding adoptive genes
Re-wild the plants
Genome editing
Gene sharing
 Conclusion

4. 4
• Story of agriculture dates back to almost 10,000 BC. It was
initiated by people who depended on diets composed of wild
plants and animals.
• By 4000 BC, ancient peoples had completed the
domestication of all major crop species upon which human
survival is dependent, including rice, wheat, and maize.
• Recent research has begun to reveal the genes responsible for
this agricultural revolution boosts “Gene tinkering”.
History of Agriculture

5. 5
Domestication
Human influence  change in genetics of plant population
 leads to “Adaptive syndrome of domestication”
• May be deliberate or not
(“unconscious” or “incidental”)
• Due to change in selective environment and control
over reproduction (e.g., harvesting grains with
sickle, sowing saved seeds)

6. 6
 Domesticated- refers more generally to plants that are
morphologically and genetically distinct from their wild ancestors
as a result of artificial selection, or are no longer known to occur
outside of cultivation.
 Semi-domesticated- as a crop that is under cultivation and
subjected to conscious artificial selection pressures.
 Undomesticated refers to uncultivated plants that continue to be
wild-harvested with no conscious artificial selection pressures
and no discernible morphological and ⁄ or genetic differentiations
that could be used to distinguish them as a domesticate (e.g.
Brazil nut).

7. Nivara
Rufipogon
Glaberrima
7

8. Domesticated Rice
8

9. Wild wheat
9

10. Domesticated Wheat
10

11. Maize
11

12. Domesticated maize
12

13. Barley Domestication
Prognt: H. spontanium
13

14. 14

15. Domesticated Pearl Millet
Pennisetum glaucum
better seed recovery and yield, but less able to survive in natural
conditions compared to wild progenitor.
• more apical dominance (less
branching)
• compact growth habit
• flowering at same time (rather
than spread over long period)
• larger spikes
• non-shattering spikelets
• loss of bristles & glumes around
grains
• larger seeds
• non-dormant seeds
• germinate at same time
15
P.polystachian

16. Oats domestication
Wild- A. sterilis Modern
sativa
16

17. Domestication of Sorghum
S. helepense
S. bicolor
17

18. J.R. Harlan 1976 Sci. American
Divergent
selection for
different
purposes
http://en.wikipedia.org/wiki/Image:Brassica_oleracea0.jpg
http://www.ceh.ac.uk/images/clip_image002_001.jpg
Brassica oleracea cabbage,
broccoli, cauliflower, kale,
romanesco, collards, kohrabi,
brussels sprouts
18

19. Solanum pimpinellifolium
Solanum lycopersicum
19

20. Domestication of carrot
Queen Anne's Lace
Daucus carota
20

21. Domestication of peanut
A. villosulicarpa Hoehne and
A. Stenosperma (Brazil)
AABB
21

22. Domestication of Chilli
22

23. Strawberry
Banana
Musa acuminata , Musa balbisiana
(2n=3x=33) AB genomeFRAGARIA X ANANASSA
Wood berries (F. vesca) and Musky strawberries (F. moschata)
23

24. Wild Soybean
Glycin soja,2n=40
Cultivated soybean
Glycin max 2n=40
24

25. Increased in domesticate
seed germination
determinate growth
longer pods
bigger (heavier) seeds
earliness
harvest index (seed yield/biomass)
Decreased in domesticate
seed dispersal
seed dormancy
twining
number of nodes
length of internode
number of pods
photoperiod sensitivity
Common Bean Phaseolus vulgaris
http://www.plantsciences.ucdavis.edu/gepts/pb143/pb143.htm
© Paul Gepts
25

26. Wild pigeon pea
Cajanus cajanifolius
Cultivated pigeon pea
26

27. 27

28. 28
WHY OTHERS ARE NOT DOMESTICATED?
• 350,000 plants
• 4,629 mammals
• 9,200 birds
• 10,000,000 insects
• 500,000 fungi
• But only 200 plants,
• 15 mammals, 5 birds and
• 2 insects are
domesticated!
• Spread of these few species
• Little change since early
agriculture
• Repeated domestication of these
species (sometimes)
• Lack of new species even with
attempts with species known to be
valuable .Some groups are good
candidates with no domestication
eg. ferns, sub-Saharan mammals ...

29. 29
WHY OTHERS HAVE TO BE DOMESTICATED
 New uses and demands – biofuels, animal feed,
medicinal/neutraceutical, water/climate, food changes
 Knowledge why species aren’t suitable for domestication or
were not useful
 Better understanding of genetics and selection
 Sustainability of production
 Reliability of production
 To meet the food demand in an alternative way
WHY OTHERS HAVE TO BE DOMESTICATED?

30. 30
Reallocate biomass for human use
 More efficient metabolism and photosynthesis: increase
leaf surface, decrease root system, increase leaf
longevity
 Grains: more fertile florets, larger inflorescence OR
number of ears  different ways to get more seed
 Larger seeds (automatic vs. deliberate selection)
 Oil plants: increased oil content or more seed
 Fiber plants: long, strong fibers
Domestication syndrome

31. 31
Centers of Domestication
Fuller, 2011

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Centers of Domestication in India
Fuller, 2011

33. 33
Indian centers of domestication
 South India (Deccan centre): Vigna radiate, Vigna mungo,
Macrotyloma uniflorum (Horse gram), Sataria verticillata, S. plumila,
wheat (macaroni) and two rowed barley.brachiaria ramosa.
 Orissa: (Mahanadi river): Pegion pea, Horsegram, mung, small millets
like Echinichloa, Paspalum and Sataria.
 The Middle Ganges: (Harappan civilization) Oryza nivara, O rufipogon
and wild sativa. Sateria pumia, Cannabis sativa even the diffusion of
japonica rice.
 Saurashtra: (Harappan civilization): Eleucine coracana, Sateria italica,
Paicum spp, Brachypodia, pearl millet and sorghum Dollicos lablab.
 The Himalayan foothills of the Punjab region: Was a centre of
diversity for Japonica type rice and many temperate fruits and
vegetables.

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DOMESTICATION RELATED TRAITS CONTROLLED BY
ONLY FEW GENES
Trait Crops
Plant architecture/growth habit Rice,maize,millets,bean,tomato
Flowering time/photoperiod sensitivity Rice,maize,sorghum,bean,tomato
Fruit size Tomato , egg plant
Grain size Rice,maize,sorghum,bean
Seed dispersal Brassica , rice
Inflorescence modification Brassica
Dormancy Bean

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Genes Crop Moleular and phenotypic function Causative change
Genes identified as controlling domestication traits
tb1 Maize Transcriptional regulator (TCP); plant and
inflorescence structure
regulatory change
tga1 Maize Transcriptional regulator (SBP); seed casing amino acid change
qSH1 Rice Transcriptional regulator (homeodomain);
abscission layer formation, shattering
regulatory change
Rc Rice Transcriptional regulator (bHLH); seed color disrupted coding
sequence
sh4 Rice Transcriptional regulator (Myb3); abscission
layer formation, shattering
regulatory/amino
acid change
fw2.2 Tomato Cell signaling; fruit weight regulatory change
Q Wheat Transcriptional regulator (AP2); inflorescence
structure
regulatory/amino
acid change
Vrs1 Barley Inflorescence structure Premature stop Amino acid change
Genes of interest in crop domestication and
improvement

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Genes Crop Moleular and phenotypic function Causative change
c1
r1
Maize Transcriptional regulator (MYB); kernel color and
Transcriptional regulator (bHLH); kernel color
regulatory change
sh2 Maize pyrophosphorylase; supersweet sweet corn transposon
insertion
su1 Maize isoamylase; sweet corn gene amino acid change
brix9-2-5 Tomato Invertase; fruit soluble solid content amino acid change
ovate Tomato Unknown; fruit shap early stop codon
R Pea Starch branching enzyme; seed sugar content transposon
insertion
ehd1 Rice B-type response regulator; flowering time amino acid change
hd1 Rice Transcriptional regulator (zinc finger); flowering
time
disrupted coding
sequence
waxy Rice Starch synthase; sticky grains intron splicing
defect
rht Wheat Transcriptional regulator (SH2); plant height early stop codon
vrn1 Wheat Transcriptional regulator (MADS); vernalization regulatory change
vrn2 Wheat Transcriptional regulator (ZCCT); vernalization amino acid change
Genes Identified as Controlling Varietal Differences

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Process of domestication over the years…
Rachel S. Meyer, 2012

38. 38
Genetic bottleneck
 Cultivated crops undergone with narrowing of diversity problem
 But this is not the case in weeds
 Weeds are the major threats from the beginning of domestication till
today
 Problem arose due to
1. Crop mimicry
2. Genetic assimilation
3. Genetic evolution

39. 39
Super- Domestication
 Vaughn et al (2007) first used the term super-domestication
 The processes that lead to a domesticate with dramatically
increased yield that could not be selected in natural environments
from naturally occurring variation without recourse to new
technologies.
 Super-domesticates can be constructed with knowledge led
approaches based on current needs using the range of new
technologies now available.
 Plants exploited for continuous selection introduction hybridization
etc. which boosted the process of domestication but now the plant
genetic engineering approach is exploiting plants towards synthetic
biology.

40. 40
How to use diversity
• Cross two varieties
• Genome manipulations
Cell fusion hybrids
• Chromosome manipulation: Backcross a new species
• Generate recombinants: Chromosome recombinations
• Use a new species, wild/ germplasm
Transgenic approach, Modern mutagenesis, synthetic gene
construction by utilizing green florescent protein, genome editing,
NGS, GWAS, sequencing etc……………

41. 41
Reduce genetic bottlenecks through
polyplodization
 More vigour
 SC
 Buffering capacity
 Heterotic advantage
 Enhaced vegetative
charachers
 Enhanced oil
 Meiotic stability

42. 42
Approach 1: Use one tetraploid and one diploid as parents (4X – 2X) followed by the
chromosome doubling of triploid hybrids (Chrom doubling)
a) Cross between B. juncea (AjAjBjBj ) and B. oleracea (CoCo) to produce hexaploids
(AjAjBjBjCoCo).
(b) Cross between B. napus (AnAnCnCn) and B. nigra (BniBni) to produce hexaploids
(AnAnBniBniCnCn).
(c) Cross between B. carinata (BcaBcaCcaCca) and B. rapa (ArAr) to produce hexaploids
(ArArBcaBcaCcaCca).
Approach 2: Use three tetraploids as parents
(a) Cross between B. napus (AnAnCnCn) and B. carinata (BcaBcaCcaCca) to produce unbalanced
allotetraploids (AnBcaCnCca – unreduced gametes: gametes with the somatic chromosome
number, and cross with B. juncea (AjAjBjBj) to obtain allohexaploids (AnAjBcaBjCnCca
(b) Cross between B. napus (AnAnCnCn) and B. juncea (AjAjBjBj) to produce unbalanced
allotetraploids (AnAjBjCn – unreduced gametes) and cross with B. carinata (BcaBcaCcaCca) to
obtain allohexaploids (AnAjBcaBjCnCca).
(c) Cross between B. carinata (BcaBcaCcaCca) and B. juncea (AjAjBjBj) to produce unbalanced
allotetraploids (AjBcaBjCca - – unreduced gametes) and cross with B. napus (AnAnCnCn) to obtain
allohexaploids (AnAjBcaBjCnCca).
Approach 3: Use three diploids as parents (2X – 2X – 2X) Cross between B. rapa (ArAr), B.
nigra (BniBni) and B. oleracea (CoCo) sequentially to obtain hexaploid hybrids (ArArBniBniCoCo).

43. 43
Continue….
Guijun Yan, 2012

44. 44
Applications of Genomic
tools in Super-Domestication

45. 45
Genome Sequencing
Potential methods of sequencing:
1. Clone by clone approach
2. Whole genome shotgun approach
3. Combination of the two methods
Till today no. of cultivated plants completely sequenced -85
2016- Arachis duranensis
2015- Solanum cumersonii (Wild potato)
(Ref- NCBI)

46. 46
GWAS
It is a study design in which many markers spread across a genome,
are genotyped and test a statistical association with a phenotype are
performed locally along the genome.
It is also an examination of many common genetic variants in different
individuals to see if any variant is associated with a trait.
Used in successfully studying maize, sorghum and barley
Method is efficient for large scale, low cost genotyping (even with the
minimum number of SNPs)
Cannot be utilized generally because it needs large population size.
GWAS identify rare alleles more precisely.
If small population we can opt NAM.

47. 47
GWAS and whole genome prediction
Xuehui Huang and Bin Han, 2014

48. 48
Five high throuput genotyping methods
Xuehui Huang and Bin Han, 2014

49. 49
Role of NGS in domestication
 Capture of novel genes from wild species will be made easier by
understanding the molecular events associated with crop domestication.
 Re-sequencing of domesticated species can identify low diversity regions
resulting from selection during domestication.
 To identify gene-specific sequences to aid the cloning of homologues of key
domestication genes from wild relatives.
 Candidate genes from wild and domesticated plant populations can define
diversity of target genes in wild populations and lead to the discovery of key
genes for important traits by association analysis.
 NGS of amplicons of large numbers of candidate genes from wild and
domesticated plant populations can define diversity of target genes in
wild populations and lead to the discovery of key genes for important
traits by association analysis.

50. 50
NGS
 supports the rapid domestication of new plant species and the efficient
identification and capture of novel genetic variation from related species.
 Allows whole-genome analysis to determine the genetic basis of
phenotypic differences.
 NGS allows rapid expansion of genomic analysis to investigation of non-
model species
 Made rice study easy by related grass
 cost-effective method for plant identification
 useful strategy to analysis the chloroplast genome sequence from whole-
genome shot-gun sequencing
 facilitates managing this diversity and any changes in crop performance
over time due to genetic drift.
 Patterns of gene expression have been evaluated in hybrids using NGS.

51. 51
Two Approaches to Finding Adaptive Genes
Ross-Ibarra et al.2007

52. 52
Techniques to re-wild the plants
(transgene free)
1.
Introgression
breeding
2.
Specific
insertion of
lost genes
3.
Precision
mutagenesis
Palmgren et al.,2014

53. 53
Process of rewilding
Palmgren et al.,2014

54. 54
Synthetic biology projects
(i) Modifying cereals, including wheat, to fix atmospheric nitrogen
(ii) Redesigning metabolic pathways to increase the yield of
secondary metabolites or to generate compounds with enhanced
properties
(iii) Transferring the C4 photosynthesis pathway to rice.
(iv) Modifying the glycosylation pathway in plants to accommodate
production of therapeutic proteins.
(v) Introducing synthetic signal transduction systems that respond to
external cues

55. 55
Synthetic biology projects
Nicholas J. Baltes et al., 2015

56. 56
Refactoring the N fixation gene cluster
from Klebsiella
Karsten Temme et al., 2012

57. 57
Continue….
Karsten Temme et al., 2012

58. 58
Genome editing
Sequence specific nucleases
1. Meganucleases
2. ZFMs –Zink finger motifs
3. TALENs- Transcription activator like effector nuclease
4. CRISPR/ CAS-9 – Clustered interspaced short palindromic
repeats
q.mp4

59. 59Khaoula Belhaj et al., 2015

60. 60
Genome modifications achieved in plants using sequence
specific nucleases
Type of DNA
modification
Nuclease Delivery
methods
Plants Targets
Trait stacking Megnucleases Bombardment Cotton Intergenic sequence
ZFN Bombardment Maize Transgene
Rewriting host
DNA
Megnucleases Stable integration Maize Intergenic sequence
ZFN Stable integration Soybean Transgene
TALEN Stable integration Barley PAPhy_a
TALEN Agrobacterium
T-DNA (transient)
Oryza sativa SWEET14
TALEN No; Protoplasts Arabidopsis,
Tobacco
AtTT4, AtADH, NbSurB
TALEN Bombardment Wheat MLO
TALEN Protoplasts;
Stable integration
Maize PDS, IPK1A, IPK, MRP4
CRISPR/Cas Protoplasts;
Agrobacterium
T-DNA (transient)
Tobacco;
Arabidopsis
Sorghum, Oryza
OsSWEET14, transgene

61. 61
Type of DNA
modification
Nuclease Delivery
methods
Plants Targets
Rewriting host
DNA: large
deletion
Zinc-finger
nuclease
Stable
integration
Tobacco Transgene
CRISPR/Cas Protoplasts;
Stable
integration
Rice Labdane-related
diterpenoid gene
clusters
on Chr 2, 4 and 6
Zinc-finger
nuclease
Agrobacterium
T-DNA
(transient)
Tobacco CHN50, transgene
Zinc-finger
nuclease
Whiskers Maize IPK1
CRISPR/Cas Protoplasts Rice PDS
Controlling gene
expression
TALE repressor
(SRDX)
Stable
integration
Arabidopsis RD29A, transgene
Zinc-finger
activator (VP16)
Stable
integration
Brassica
napus
KasII
Continue..

62. 62
Application of genome editing
1. Introduction of precise and predictable modifications directly in an elite
background.
2. multiple traits can be modified simultaneously .
3. NHEJ enables gene knockout and targeted modifications.
4. Introduction of transgenes at defined loci that promote high-level
transcription and do not interfere with the activity of endogenous genes .
5. Site-specific nucleases also allow targeted molecular trait stacking -low
risk of segregation .
6. CRISPR/ Cas is a transgene free approach – No regulatory burdens
7. frequency of off-target mutations is well below that caused by chemical
and physical mutagenesis techniques.
8. In future can be utilized for metabolic engineering and molecular farming.

63. 63
Six-way Venn diagram showing the distribution of shared gene
families (sequence clusters) among M. acuminata, P. dactylifera,
Arabidopsis thaliana, Oryza sativa, Sorghum bicolor and Brachypodium
distachyon genomes.
A D’Hont et al. Nature 2012 doi:10.1038/nature11241

64. 64
Achieving super-Domestication
:INTROGRESS-RECREATE-CREATE-
DOMESTICATE?REDOMESTICATE
• Mobilizing left out genetic
variation still available in
land races and wild and
weedy species.
• Replaying the evolutionary
tape( resynthesis in
polyploids)
• Domesticate/redomesticate

65. 65
We can admire and emulate how indigenous people still domesticate
plants, create biodiversity and manage it to sustain their future. "There
is no equivalently dynamic or flexible crop breeding in modern
agriculture to promote biodiversity; we still have much to learn from
traditional knowledge Jan Salick, 2012