Dedomestication

1. Ancestral population structures of 183 rice accessions Dept. of Genetics and Plant Breeding

2. Dept. of Genetics and Plant Breeding

3. De-DomesticationAn Extension of Crop Evolution Dept. of Genetics and Plant Breeding

4. Flow of Seminar • 1 • 2 • 3 • 4 • 5 • 6 Dept. of Genetics and Plant Breeding

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) Dept. of Genetics and Plant Breeding

6. Domestication Domestication Gering et al. (2019) Dept. of Genetics and Plant Breeding

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

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. Oryza sps Oryctolagus cuniculus Scossaet al. (2021) Dept. of Genetics and Plant Breeding

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

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

11. Examples of De-domestication in Crops Dept. of Genetics and Plant Breeding

12. Speculations and Misconceptions Incapable of rapid adaptation Reduced fitness Atavism Gering et al. (2019) Dept. of Genetics and Plant Breeding

13. Sources of Feral Populations Unique Challenges DNA based ancestry reconstructions Sequence Based tests of adaptation Gering et al. (2019) Dept. of Genetics and Plant Breeding

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

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

16. Ecological Niches Wu et al. (2021) Dept. of Genetics and Plant Breeding

17. Ecological Niches Wu et al. (2021) Dept. of Genetics and Plant Breeding

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

19. A • 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 Gering et al. (2019) Dept. of Genetics and Plant Breeding

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

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) Dept. of Genetics and Plant Breeding

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) Dept. of Genetics and Plant Breeding

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) Dept. of Genetics and Plant Breeding

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 Dept. of Genetics and Plant Breeding

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) Dept. of Genetics and Plant Breeding

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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 Dept. of Genetics and Plant Breeding

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

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. • 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). Neighbor-joining tree Dept. of Genetics and Plant Breeding

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. Dept. of Genetics and Plant Breeding

31. Case Study 2: 2018 Dept. of Genetics and Plant Breeding

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). Dept. of Genetics and Plant Breeding

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 Dept. of Genetics and Plant Breeding

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. Dept. of Genetics and Plant Breeding

35. Case Study 3: 2020 Dept. of Genetics and Plant Breeding

36. Materials: • Zang1817 [Tibetan semi-wild Wheat (Triticum aestivum ssp. tibetanumShao)] • 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 Dept. of Genetics and Plant Breeding

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 tauschiiaccessions as an outgroup. a. Neighbor-joining tree b. Principal component Analysis (PCA) Plot Dept. of Genetics and Plant Breeding

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. Dept. of Genetics and Plant Breeding

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

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