Domestication syndrome in crop plants

Domestication syndrome in crop plants

1. Seminar on Domestication syndrome in crop plants 16-Dec-17 1 PG seminar Anilkumar , C. PALB 5062 PhD scholar

2. In this session---- 16-Dec-17 2 PG seminar

3. Neolithic revolution/Agriculture revolution: 12000 to 10000 years ago Changes: The transition from hunting-gathering to plant agriculture The formation of villages One of the key technological elements of the transition to agriculture was DOMESTICATION . Introduction

4. 16-Dec-17 PG seminar 4 Plant domestication is the genetic modification of a wild species to create a new form of a plant altered to meet human needs ( Doebley et al., 2006) The process by which humans actively interfere with and direct crop evolution. What is domestication..? Continuum of increasing codependence between plants and people

5. 16-Dec-17 PG seminar 5 Incidental- Didn’t happen on purpose. Hunter/gatherers dropped seeds , scared off natural herbivores, disrupted natural environments so that plants could grow. Directed- Humans and plants became dependent on each other, so better plants helped people get healthier, planting more ( and maybe improved) plants, etc . Types of Domestication Agriculture- Human intervention in crop Husbandry, Cultivation and Selection.

6. 16-Dec-17 PG seminar 6 Where did it happen….?? ( Balter , 2007 ) Africa Meso -America Near East China South-America South-East Asia Gepts , P., 2004 6

7. 16-Dec-17 PG seminar 7 How did it happen…??? Is Artificial Selection Analogous to Natural Selection? Unconscious selection: ‘‘that which follows from men naturally preserving the most valued and destroying the less valued individuals, without any thought of altering the breed.’’ (Darwin, 1868) It was no different from natural selection Humans change the conditions in which cultivated species live and reproduce, The phenotypic changes associated with domestication are likely to have arisen via unconscious selection (Harlan, 1992) Natural selection Domestication

8. 16-Dec-17 PG seminar 8 Theories of domestication

9. 16-Dec-17 PG seminar 9 Few examples here..

10. 16-Dec-17 PG seminar 10 What made domesticates to differed from wild….?? There is a common suite of traits that distinguishes most seed and fruit crops from their progenitors (Hammer, 1984) These distinct suite of traits later termed the “ domestication syndrome ” would likely be selected for during the initial stages of domestication (Harlan et al ., 1973 ) Domestication syndrome: It is the subset of traits that collectively form the morphological and physiological differences between crops and their wild progenitors.

11. 16-Dec-17 PG seminar 11 ‘Domestication Syndrome’ traits A variety of physiological changes are also involved . a loss of seed dormancy, a decrease in bitter substances in edible structures changes in photoperiod sensitivity synchronized flowering Compared to their progenitors, food crops typically have larger fruits or grains, more robust plants more determinate growth or increased apical dominance a loss of natural seed dispersal often have fewer (although larger) fruits or grains per plant than their progenitors .

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13. 16-Dec-17 PG seminar 13 Domestication v/s improvement

14. 16-Dec-17 PG seminar 14 Superheroes and masterminds

15. 16-Dec-17 PG seminar 15 Diversification genes .. ‘ Diversification’ genes are the target of selection for phenotypic variation among varieties of a crop , such as different types of starch or flavor Glutinous or sticky phenotype of cooked cereal grains, reflecting the absence (or near absence) of the starch amylose in the endosperm - the glutinous phenotype is favored in select varieties of rice (primarily a subset of japonica varieties of O. sativa ), maize and foxtail millet, and is controlled by unique mutations at the Waxy gene in all these crops. Rice BADH2 gene (2-Acetyi 1-Pyrrlione) - the aromatic phenotype has also been generated via a variety of mutations at the same gene (Gross and Olsen, 2010)

16. 16-Dec-17 PG seminar 16 Methods for identifying domestication genes Biparental QTL mapping Association Mapping Using Unrelated Individuals QTL Mapping Using Advanced Intercross Populations Genomic scans Genome Resequencing and Screening for Selection Signatures

17. 16-Dec-17 PG seminar 17 Classical Examples… Teosinte branched 1 (tb1) QTL of maize controls the difference in apical dominance in maize and teosinte tb1 , it acts as transcriptional regulators , a class of genes involved in the transcriptional regulation of cell cycle Teosinte glume architecture1 (tga1) was identified as a QTL controlling the formation of the casing that surrounds the kernels of the maize ancestor, teosinte tga1 is a member of the squamosa -promoter binding protein (SBP) family of transcriptional regulators Fruitweight2.2 ( fw2.2 ) was identified as a large effect QTL controlling 30% of the difference in fruit mass between wild and cultivated tomato fw2.2 acts as a negative regulator of cell division in the fruit, perhaps via some role in cell-to-cell communication Q is a major gene involved in wheat domestication that affects a suite of traits, including The tendency of the spike (ear) to shatter, The tenacity of the chaff surrounding the grain, and The spike is elongated as in wild wheat or compact like the cultivated forms

18. 16-Dec-17 PG seminar 18 shattering4 ( sh4 ) is a major QTL controlling whether the seed fall off the plant (shatter) as in wild rice or adhere to the plant as in cultivated rice sh4 encodes a gene with homology to Myb3 transcription factors . A single amino acid change in the predicted DNA binding domain converts plants from shattering to non-shattering Rc is a domestication-related gene required for red pericarp in rice Two independent genetic stocks of   Rc  revealed that the dominant red allele differed from the recessive white allele by a 14-bp deletion within exon 6 - originated in japonica cultivar and spread into indica cultivars.

19. 16-Dec-17 PG seminar 19 Super-domestication The processes that lead to a domesticate with dramatically increased yield that could not be selected in natural environments without new technologies. The array of genome manipulations enable barriers to gene exchange to be overcome and have lead to super-domesticates with dramatically increased yields, resistances to biotic and abiotic stresses, and with new characters for the marketplace. Hybrid rice can be considered a super-domesticate Conversion of a crop from C3 to C4 photosynthesis would certainly be a super-domesticate. (Vaughan et al. 2007) PLANT BREEDERS GENOMIC SCIENTISTS SUPER DOMESTICATION leads to

20. 16-Dec-17 PG seminar 20 Effect of selection during domestication Selection is expected to reduce diversity at domestication related genes and tightly linked loci One common feature of the domesticated genomes is the reduction of genetic diversity in crops relative to the wild progenitors This reduction has two causes: Genetic bottleneck Selective sweep (Tang et al ., 2010)

21. 16-Dec-17 PG seminar 21 It depends on The bottleneck population size The duration of bottleneck The loss in diversity was not experienced equally by all genes in the genome Genetic bottleneck (Tang et al ., 2010 )

22. 16-Dec-17 PG seminar 22 Effect of Artificial Selection on Genetic Diversity of Maize Genes. Bottleneck effect (Yamasaki et al., 2005)

23. 16-Dec-17 PG seminar 23 A selective sweep is the reduction or elimination of variation among the nucleotides in neighboring DNA of a mutation as the result of recent and strong positive  natural selection A strong selective sweep results in a region of the genome where the positively selected  haplotype  (the mutated allele and its neighbours ) is essentially the only one that exists in the population, resulting in a large reduction of the total genetic variation in that chromosome region. Selective sweep Size of selective sweep Time of selection Strength of selection Recombination rates ( Tang et al ., 2010 )

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25. 16-Dec-17 PG seminar 25 Case study:1 Aim of the study: Attempt identify gene responsible for prostrate growth and erect growth habit Mapping the gene on to chromosome

26. 16-Dec-17 PG seminar 26 O . rufipogon O. sativa

27. 16-Dec-17 PG seminar 27 Teqing ( indica cultivar) × YJCWR ( O . rufipogon ) F 1 × IL Named it as YIL18

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29. 16-Dec-17 PG seminar 29 Linkage analysis : F 2 derived from cross between YIL 18 and Teqing showed that prostrate growth was completely controlled by a single semi-dominant gene, PROG1 (PROSTATE GROWTH 1 ), located between SSR markers RM298 and RM481 on short arm of chromosome 7 Output of the study Positional cloning study: demonstrate that in the O. rufipogon genome was a key gene ( PROG1 ) controlling prostrate growth. Tissue specificity study: they followed GUS reporter gene method detected GUS expression in the tiller base, leaf-sheath pulvinus and lamina joint, but not in the root, leaf blade and culm

30. 16-Dec-17 PG seminar 30 Case study:2 Preamble: Why did a crop domestication gene hinder breeding with a modern breeding gene responsible for the beneficial ‘‘ jointless ’’ trait in tomato, and how can this genetic interaction be overcome and exploited ?

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32. 16-Dec-17 PG seminar 32 fresh-market hybrid breeding

33. 16-Dec-17 PG seminar 33 Understanding crop domestication - Implications Up- and down-regulation of transcription factors Application of selection screens to identify genes contributing to the success of best varieties QTL cloning for key agronomic genes Screening wild relatives and unimproved varieties to recover superior alleles (allele mining) that failed to pass through the domestication and improvement bottlenecks

34. conclusion 16-Dec-17 34 PG seminar

35. 16-Dec-17 35 PG seminar