De-domestication

1. 16-05-2022 Dept. of Genetics and Plant Breeding 2
Ancestral population structures of 183 rice accessions

2. 16-05-2022 Dept. of Genetics and Plant Breeding 3

3. De-Domestication
An Extension of Crop Evolution
16-05-2022 Dept. of Genetics and Plant Breeding 4

4. Flow of Seminar
INTRODUCTION
MECHANISMS OF FERALIZATION
ADAPTATION IN FERAL ORGANISMS
AN EXTENSION OF CROP EVOLUTION COMPLEXITY
CASE STUDIES
CONCLUSION
16-05-2022 Dept. of Genetics and Plant Breeding 5
1
2
3
4
5
6

5. Domestication
Crop domestication is the process of artificially selecting plants to increase
their suitability to human requirements: taste, yield, storage, and cultivation
practices.
Henriksen et al. (2018)
16-05-2022 Dept. of Genetics and Plant Breeding 6

6. Domestication
Anthropology
Plant and
Animal Science
Behavioural
and
Developmental
Biology
Domestication
Gering et al. (2019)
16-05-2022 Dept. of Genetics and Plant Breeding 7

7. The flow of domesticated organisms and their genes into noncaptive settings has important
conservation implications.
Gering et al. (2019)
16-05-2022 Dept. of Genetics and Plant Breeding 8

8. Feralization/De-domestication
• Escape of domesticated plant and animal races from regime of
artificial selection.
• It can be intentional, or unintentional.
• On the surface, feralization appears linear.
• In reality, it is a convoluted demographic process.
Oryctolagus cuniculus Oryza sps
Scossa et al. (2021)
16-05-2022 Dept. of Genetics and Plant Breeding 9

9. • Loosening of artificial selection pressure would have facilitated de-
domestication of crops.
Rice Transplanting Direct Sowing
Feralization
Barnyard grass in Paddy field
Weedy rice in Paddy field
Wu et al. (2021)
16-05-2022 Dept. of Genetics and Plant Breeding 10

10. Evolution of weedy rice
Li et al. (2017)
16-05-2022 Dept. of Genetics and Plant Breeding 11
BHA- Black Hull Awned type
SH- Straw-coloured Hull type

11. Examples of De-domestication in Crops
16-05-2022 Dept. of Genetics and Plant Breeding 12

12. Speculations and Misconceptions
Gering et al. (2019)
16-05-2022 Dept. of Genetics and Plant Breeding 13

13. Sources of Feral Populations
Unique Challenges
1. DNA based ancestry
reconstructions
2. Sequence Based tests of
adaptation
Gering et al. (2019)
16-05-2022 Dept. of Genetics and Plant Breeding 14

14. MECHANISMS OF FERALIZATION
Endoferal Exoferal
Exo-Endoferal
Examples:
Weedy Rice
Tibetan semiwild Wheat
Examples:
Tibetan weedy Barley
Feral Callery Pear
Examples:
California wild radish
Weedy Sunflower
Wu et al. (2021)
16-05-2022 Dept. of Genetics and Plant Breeding 15

15. Evolutionary forces that shape
Feral Gene Pools
and Traits
Gering et al. (2019)
16-05-2022 Dept. of Genetics and Plant Breeding 16

16. Ecological Niches
• Natural environments.
• Human disturbed lands
with no farming.
Non-
agroecosystems
•Farming Lands.
Agroecosystems
Wu et al. (2021)
16-05-2022 Dept. of Genetics and Plant Breeding 17

17. Ecological Niches
Wu et al. (2021)
16-05-2022 Dept. of Genetics and Plant Breeding 18

18. • Based on the current understanding ,
WHY??
Notably, de-domestication has
not been reported in maize and
soyabean , possibly because of
their specific genome
compositions.
Wu et al. (2021)
16-05-2022 Dept. of Genetics and Plant Breeding 19

19. • Viewing feralization ‘in light of admixture’ helps to
clarify how future gene flow can impact outcomes
and consequences of the process.
• These interpopulation differences result in both
genetic and phenotypic variation which would likely
be affected by further introgression.
• Admixture from domestic sources can also convert
wild populations into exoferal ones and accelerate
their responses to new selection pressures.
• The geographical distribution and phenotypic
consequences of this crop–wild admixture vary
widely by case.
B
C
Figures : A. Wolf × Dog Hybrid B. Farmed × Wild Salmonid
Hybrid
C. Chicken × Red jungle Hybrid
A
Gering et al. (2019)
16-05-2022 Dept. of Genetics and Plant Breeding 20

20. Adaptation in Feral Organisms
• Fitness Consequences of Admixture
i. Direct measurements of growth, survival, reproduction, and health
in hybrids.
ii. Functional analyses.
iii. Experimental tests in laboratory systems.
Gering et al. (2019)
16-05-2022 Dept. of Genetics and Plant Breeding 21

21. Shattering for Seed Dispersal
• The non-shattering trait is under intensive
artificial selection in the domestication of most
crops.
• Whereas high shattering is a key trait for wild
species and weeds to ensure successful and
efficient offspring dispersal.
Qiu et al. (2020)
16-05-2022 Dept. of Genetics and Plant Breeding 22

22. An Extension of Crop Evolution Complexity
The conventional view of crop evolution
includes domestication to landrace
from wild plants and improvement of
modern cultivars from the landrace.
Wu et al. (2021)
16-05-2022 Dept. of Genetics and Plant Breeding 23

23. An Extension of Crop Evolution Complexity
In the new view, feral plants (de-
domesticates) form the fourth node
and, therefore, extend crop
evolutionary complexity.
Wu et al. (2021)
16-05-2022 Dept. of Genetics and Plant Breeding 24

24. Domesticates are not the terminal point in crop evolution, although it is often
assumed that they are not capable of rapid adaptation due to low genetic
diversity as a result of drastic genetic bottlenecks
Genetic bottlenecks imposed on crop plants during domestication and through
modern plant-breeding practices.
Tanksley and McCouch, 1997
16-05-2022 Dept. of Genetics and Plant Breeding 25

25. Importance of Feral Population
• Feral populations can be used to improve domesticated populations.
• Offer opportunities to understand important concepts applicable to many
different fields of study.
• Powerful models for understanding complex population changes not fully
resolved by studying domesticated, wild, or ancient genomes alone.
• Adaptive introgression.
Example: Cherry Tomato
Mabry et al. (2021)
16-05-2022 Dept. of Genetics and Plant Breeding 26

26. 16-05-2022 Dept. of Genetics and Plant Breeding 27

27. • Aim: Examine the origin and adaptation of the two major strains of weedy
rice (Black hull awned weedy rice & Straw hull weedy rice)found in the
United States.
Materials:
18 Straw hull (SH) Weedy rice
20 Black hull awned (BHA) Weedy rice.
145 previously published Oryza genome sequences.
(89 cultivated rice accessions (44 indica, 16 aus, 10 tropical japonica, 14 temperate japonica
and 5 aromatic), 53 wild progenitor accessions (43 O. rufipogon & 10 O. nivara); and 3 weedy
rice from central China).
Methods:
Whole genome sequencing (Illumina Hiseq 2000).
Phylogenetic Analyses (MEGA7).
2017
16-05-2022 Dept. of Genetics and Plant Breeding 28

28. Number of raw SNPs and their distributions in the wild, cultivated and weedy rice genome.
2,94,08,917
16.7
%
9.7%
16-05-2022 Dept. of Genetics and Plant Breeding 29

29. • To assess the evolutionary relationships of the
US weed strains to the other Oryza samples,
they performed phylogenetic analyses based
on 1,381,040 homozygous SNPs in MEGA7.
Neighbor-joining tree
• Wild rice accessions (dark green) are divided
into different groups. The japonica (orange)
and aromatic (light green) rice varieties form
a clade. The BHA (red), SH (purple), and
Chinese (black) weedy rice strains cluster
with indica (light blue) and aus (pink).
16-05-2022 Dept. of Genetics and Plant Breeding 30

30. Divergence time between cultivated (indica and aus)and weedy (BHA, SH and Chinese) rice
To further explore the timings of weed origin, they used BEAST32 to estimate the relative
divergence times between each weed type and its closest crop relative.
16-05-2022 Dept. of Genetics and Plant Breeding 31

31. Case Study 2:
2018
16-05-2022 Dept. of Genetics and Plant Breeding 32

32. • Materials:
• Tibetan barley,
• Qingke landraces and cultivars from Tibetan inhabited areas,
• Tibetan weedy barleys (including two brittle rachis samples),
• Eastern and western barley landraces and cultivars.
• Methods:
• Whole genome sequence (Illumina Hiseq 2000).
• Population structure analyses(PHYLIP 3.68).
16-05-2022 Dept. of Genetics and Plant Breeding 33

33. Resequencing of 177 barley genomes generated a total of 8.5 terabase (Tb) of high-quality cleaned
sequences and revealed 56.3 million (M) SNPs and 3.9 M small insertions and deletions (INDELs).
a. Neighbor-joining tree
b. Principal component Analysis (PCA) Plot
16-05-2022 Dept. of Genetics and Plant Breeding 34

34. Molecular and spatial variants in Vrs1
Gene structures (exon: red bar; intron: yellow bar; UTR: blue bar) of Vrs1 with
the relative positions of the SNPs (triangle) and INDELs (rhombus), respectively.
16-05-2022 Dept. of Genetics and Plant Breeding 35

35. Case Study 3:
2020
16-05-2022 Dept. of Genetics and Plant Breeding 36

36. Materials:
Zang1817 [Tibetan semi-wild Wheat (Triticum aestivum ssp. tibetanum Shao)]
245 Wheat accessions (including world-wide wheat landraces, cultivars as well as
Tibetan landraces)
Methods:
Draft genome sequence (Hiseq2500 v2).
Population structure analyses(ADMIXTURE).
Hiseq2500 v2
16-05-2022 Dept. of Genetics and Plant Breeding 37

37. • Tibetan semi-wild wheat is a unique form of hexaploid wheat.
• To provide insights into their evolutionary origin, they performed a comprehensive
population structure analyses of available accessions based on 364,856 high confidence
homologous SNPs on sub-genome D using Aegilops tauschii accessions as an outgroup.
a. Neighbor-joining tree b. Principal component Analysis
(PCA) Plot
16-05-2022 Dept. of Genetics and Plant Breeding 38

38. • Furthermore, genome-wide nucleotide diversity was lower in the Tibetan semi-wild wheat
population (π = 5.38 × 10−4) than in landrace-counterparts (π = 5.67 × 10−4), indicating a
limited genetic background of Tibetan semi-wild wheat available during the adaptation
process in the Tibetan Plateau.
Eight demographic models considered in the demographic analysis on the origin of the
Tibetan semi-wild wheat.
16-05-2022 Dept. of Genetics and Plant Breeding 39

39. Best fitting parameters for the eight models of demographic analysis on the origin of Tibetan semi-wild
wheats.
16-05-2022 Dept. of Genetics and Plant Breeding 40

40. 16-05-2022 Dept. of Genetics and Plant Breeding 41

41. 16-05-2022 Dept. of Genetics and Plant Breeding 42