The document discusses genome evolution in plants, with a focus on wheat and its wild relatives. It describes how: - Wheat has a very large and repetitive genome compared to other plants like Arabidopsis. - Repetitive DNA sequences play an important role in genome and chromosome evolution, and can be used to track chromosomes. - Wild relatives like Aegilops ventricosa have been used in chromosome engineering to introduce useful traits like disease resistance to wheat. - Molecular cytogenetics techniques allow studying the inheritance and distribution of repetitive sequences during speciation and hybridization.

1. Pat Heslop-Harrison [email_address] www.molcyt.com pw/user: ‘visitor’ Pathh1 on Twitter and AoBBlog.com

3. Genome evolution: generating biodiversity repetitive DNA – fast & slow evolution engineering – chromosomes & genomes systems understanding new crops

4. Agronomy & Nitrogen Genetics Transgenic Bt insect-resistant maize (& herbicide tolerant)

6. Finding genes, controlling expression: using biodiversity Recombining genes Combining genomes Chromosome engineering Understanding

7. Darwin 1859 The only figure in “ The Origin of Species”

8. Common Ancestor 2n=2x=14 Aegilops ventricosa 2n=4x=28 DDNN Triticum tauschii 2n=2x=14 DD Triticum aestivum 2n=6x=42 AABBDD Triticum durum 2n=4x=28 AABB Triticum monococcum 2n=2x=14 AA Aegilops sp. 2n=2x=14 BB Aegilops uniaristata 2n=2x=14 NN Aegilops 2n=2x=14 Triticum 2n=2x=14

14. Wheat 150 Mbp 17000 Mbp (x113 Arab.) 3300 Mbp (x22 Arabidopsis ) 1 mid-sized human chromosome = Arabidopsis genome 4 average wheat chromosomes = Human genome

15. Wheat Repetitive DNA is a major part of the genome Localised sites – often tandem repeats Dispersed widely – often transposable elements Different families of these repeats have different evolutionary histories and consequences Molecular cytogenetics, comparative genomics and sequence-based studies of species and hybrids show - evolution of these sequences tracks chromosomes through evolution helps genome and chromosome engineering

16. Where each arrow is a single repeat unit - often a multiple of 180 bp but up to 10kb long Head-to-tail organization CGACTAGT CGACTAGT CGACTAGT G GACTAGT CGACTAGT CGACTAGT Crocus spp Probed pCvKB8 Frello, HH 2004.

18. Triticum aestivum 2n=6x=42 DAPI pSc119.2 dpTa1 High copy number – low diversity in each of 3 genomes

20. dpTa1 pSc119.2 Genomic Ae.ventricosa Inheritance of Chromosome 5D Aegilops ventricosa DDNN ABDN AABBDDNN Marne AABBDD CWW1176-4 Rendezvous Piko VPM1 Dwarf A 96ST61 Virtue × × × × Hobbit × {Kraka × (Huntsman × Fruhgold)} Triticum persicum Ac.1510 AABB

21. Correlation between genetic relationships and similarity of dpTa1 hybridization 0 0.1 0.2 0.3 0.4 0.5 0.6 0.7 0.8 0.9 0 0.1 0.2 0.3 0.4 0.5 0.6 0.7 0.8 0.9 1 Coefficient of parentage Proportion of chromosome arms with identical in situ signal

22. Eyespot (fungus Pseudocercosporella ) resistance from Aegilops ventricosa introduced to wheat by chromosome engineering Many diseases where all wheat varieties are highly susceptible

23. Crop standing Lodging in cereals Crop fallen

24. ancestral Low-copy number High-copy number Low-copy number High-copy number Low-copy number High-copy number High copy spp: homogenized, amplification from a limited number of master copies Low copy spp: much variation Schwarzacher, Contento & HH 2009

25. Arabidopsis species – species specific 178bp tandem repeat motif HH et al. Chromosome Research 2003

26. 2n = 26 10 from A. thaliana 2n=2x=10 16 from A. arenosa 2n=2x=16 Kamm, HH et al .

27. S.vav42!248 Afacer1 T.mono106/42!133pt1 T.mono106/42!155pt1 Ae.umb106/208!1911 Ae.umb106/208!1810 Ae.umb106/208!2012 S.vav147!259pt1 Pet w 25/208!088 Pet w 25/208!077 S.vav106/208!215pt1 S.vav106/208!204pt2 S.vav106/208!215pt2 S.vav25/208!182 S.mon42!136 Pet 22594 25/42!3324 Pet 22594 25/42!3425 CS/325/208!1820 S.vav25/208!193 T.tau25/147!2524pt2 CS/325/147!2322pt2 L.moll25/42!156 Pet w25/147!123 CS/325/208!1719 CS/325/147!2120 Pet w25/147!3231 Ae.umb25/147!124 Ae.umb25/208!168 L.moll25/42!167 119Repeat2 Pet w 25/208!099 S.mon147!1811 S.vav106/208!204pt1 119Repeat3 S.vav147!2711pt1 S.mon25/147!081 T.mono25/208!1212 S.vav42!237pt1 S.vav42!237pt2 T.tau25/147!2625 T.tau25/147!2726 Ae.umb25/208!157 T.tau25/208!1517 T.tau106/42!177 Ae.umb25/42!091 L.moll25/42!189 CS/325/208!1618 T.tau25/147!2524pt1 CS/325/147!2322pt1 Pet 22594 25/208!2325 Pet 22594 25/147!1918 Pet 22594 25/208!2426 T.tau25/208!1315 T.tau25/208!1416 Ae.umb25/147!135 Ae.umb25/147!146 Ae.umb25/208!179 915 120bp repeat unit family in Triticum , Aegilops and Secale species 119Repeat1 Homology between sequences 70-100% in Triticum/Aegilops and Secale species Contento, HH, Schwarzacher 2009 Pet 2259425!315 Colour blocks represent species High copy, High diversity T.tauschii (D genome) S. cereale (R genome)

28. 119 repeats: showing homogenization and amplification High copy species Low copy species Drosophila: Kuhn, HH et al. 2009/2011 Medicago: watch this space: Mondin et al.

29. Mutation Rearrangement Duplication Deletion Homogenization Sequences Genes / motifs Repetitive DNA Chromosomes Chromosome sets (‘Genomes’) Genotypes/CVs Species Genera and above Crops / wild species Selection Speciation

30. Arachis hypogaea – 2n=4x=40 In situ hybridization of two BACs including repeats Contrasting distribution of their major repeat families Ana Claudia Guerra Araujo et al in prep 2011, EMBRAPA, Brazil

32. Cell fusion hybrid of two 4x tetraploid tobacco species Patel, Badakshi, HH, Davey et al 2011 Annals of Botany

34. Hybrids involving 2 genomes A and B, diploid and triploid but all sterile Red AAA Palayam codan AAB (two bunch yellow, one green) Peyan ABB (green cooking banana), Njalipoovan AB (yellow) Robusta AAA (green ripe) Nendran AAB Poovan AAB (one yellow bunch) Red AAA Peyan Varkala, Kerala, India,

37. www.crocusbank.org Saffron Diversity and Origins

38. From C. cartwrightianus by autotriploidy C. cartwrightianus crossed with a related species involving unreduced gamete F1 hybrid between 2 species crossed with 3 rd species with an unreduced gamete 1 2 3 1 2 3 1 2 3 John Bailey 5 III + 3 II + 3 I 8 III ?

39. Crocus sativus Pachytene DAPI

40. Late Pachytene Crocus sativus Anti-ASY-1 associates with the lateral element (antibody from Arabidopsis, Chris Franklin lab, Birmingham)

41. Current commercial varieties Wild collections Landraces Germplasm banks Different populations Individuals New diversity Hybridization Cell fusion Induced mutations Tissue culture How is diversity reflected in the genome?

42. Wsm-1: only highly effective source of resistance to WSMV

43. Mace wheat Graybosch et al. 2009 In situ: Niaz Ali & Schwarzacher

45. C Figure 5: Root tip metaphase (A, B and D) and meiotic prophase (C) chromosomes after FISH and immunostaining with antibody against 5-methyl cytosine (5meC). The diploid D-genome ( Ae. tauschii ) chromosomes show heavy methylation (green) along all arms (A) including some, but not all, Afa/dpTA1 sites (red). In hexaploid wheat lines N02Y2016, N02Y5075 and ‘Millennium’ (B, C and D) more uneven methylation is observed with many centromeres showing less DNA methylation. At pachytene (C), DNA methylation levels (green) of the alien Th. intermedium arm (line N02Y5075, arrow, red) are similar to the average wheat chromatin, but notably the translocated Th. intermedium arms show low methylation in mitotic metaphase (arrows in B). The line ‘Millennium’ (D) has no alien chromatin, and most of its D-genome chromosomes (red) show DNA methylation levels (green) similar to the other wheat chromosomes. Afa/dpTa1 Anti 5 meC Ae. tauschii DNA Anti 5 meC Th. intermedium Anti 5 meC Th. intermedium DNA Anti 5 meC Niaz Ali, Trude Schwarzacher 2012

46. Retrotransposons Class I transposable elements RNA intermediate DNA transposons Class II transposable elements Cut-and-paste

47. … Dotplot comparisons at scale of 10,000s bp Two Musa chromosomes are >95% homologous with gaps Faisal Nouroz 2012

48. Brassica rapa (AA) Brassica nigra (BB) Brassica juncea (AABB) Brassica napus (AACC) Brassica carinata (BBCC) Brassica oleracea (CC) 2n=20 2n=36 2n=34 2n=16 2n=38 2n=18 The Brassica genus is monophyletic, from single common ancestor. What has changed in the DNA sequences?

49. B. napus (AACC, 2n=4x=38) – hybridized with C-genome CACTA element red B. oleracea (CC, 2n=2x=18) B. rapa (AA, 2n=2x=20) Alix et al. The CACTA transposon Bot1 played a major role in Brassica genome divergence and gene proliferation. Plant Journal

50. Alix, HH et al Plant J 2008

51. 01/10/11 Dotter plot of Brassica oleracea var. alboglabra clone BoB028L01 x Brassica rapa subsp. pekinensis clone KBrB073F16 with transposable elements. Brassica oleracea (C genome) sequence Brassica rapa (A genome) sequence Dot-plots of genomic sequence from homoeologous pairs of BACs An inversion Region of low homology Region of high homology between A and C sequence Transposed (moved) sequence 500bp Insertion-gap pair: present in A 4kb Insertion-gap pair: present in C genome gi 195970379 vs. gi 199580153 Microsatellite kb Sequence level at scale of 100s to 1000s of bp – analysis by dotplot

53. 9-bp TSD (TATCCTATT) 6-bp TIR and 66-bp imperfect sub-TIR 551-bp BART1 TE TSD TIR TIR TSD 01/10/11 TATCCTATT G C G C AA TT GTC AATA ATAGCAC TTTTT GAAG TTT ATG TCTCAAAATAGCACT AGAAGGAG AAAGTCACAAAAAT GATA TTCATTAAAG GGTA AAATAT CTCTTATATCCTTGGTTT AAAA TTAAATAAACAAAC AAAAA TAAAT AAAAA TAAAT AAAAAAAA TG AAAAAAAA GAAAT TTTTTTT ATAGTTTCAGATTATATGTTTTCAGATTCG ATTTTTTTTTT ATTTTTTT ATTTTTTT CGAA ATTTTTTTTT T ATTTTTTTT CAA ATTTTCTTTTT ATAATTT AAAAA TACTTTTTGAAACTG TTTTTTT A ATTTTT ATTTTTT ATTTTAGTATTT ATTTTTT AT AAAA TTTTAA ACCC TAATTCCTAA ACCCC C ACCCC TTAACTCTAA ACCC TAAGGTTTGGATTAATTA ACCC AATGGATATAA GTGT ATATTT ACCT CTTTAATGAA ACCT ATTTTTGTGACTTT GAATCTTG AGTGCTA C TTTG G GA ACA AAA A CTTGGTTTG GTGCTAT CCTA GTC TT TT T C T C TATCCTATT TACCACCCTTCTTTGTTC AATACTTTTTACAGTTTTTGGAAAGGACATGTTTCTTCTATCATCACTTAATGGTTATATATGTATGAGAAGTTTGAAAGAGATTACACTGTTTTGGAATATTAAAAAAAAAAGATATTACAAGATCTGATTTTGTTTGTATTTTAAAATT CTACCAAATCTCTCCTCAAAATCTTG GTCAAAGTCCAAAAATCCAAATATCTCAGTTAAATTCCACCAAATATGAAATCCTAAAACTTTTCCAAAATAGTTCAATAAGCCCT TAGTG TTTGGTG AAGTGAATGGATGCTCGCATTAGTTACTAT GAGCCGATTCTCGCTCTTGCG AAAGCTAAAGAGGAAAAGGCCTTCG CATTGCAGAAGAGCTGGCTGCC AGCGAGCAAGAGGTTTTCAATATT GGCTTGTGGAAAATTTGTTGC CACTTTTGCTTTACTAAGGAATGAAATAATACTTGTTTTTTTTTTTCATGGTTAATATTAGAAGATATAATTTCCTTTGAAGTTAGATTACGTTTCTTTAT GTCGACGAAGTGAAGAAATATTG TCTTGTTTAT GGTTCCTTCTAGTCCCAACC TTTTTTCAAGAAGGTACAGTACGTGTCAGGATTTATATGGATATACACA Brassica rapa with inserted 542bp sequence not present in B. oleracea. 9bp TSD (red letters and arrow) and TIR (blue). Flanking primers used in PCR (next slide) as blue arrows on sequence Faisal Nouroz 2011

54. Brassica rapa (AA) Brassica nigra (BB) Brassica juncea (AABB) Brassica napus (AACC) Brassica carinata (BBCC) Brassica oleracea (CC) Young Old

55. 700 bp hAT Microsatellite 715 bp hAT 1016 bp in LINE 258 MITE 402 bp hAT 237 bp Mariner Like Inversion 914 bp LINE 2781 bp MuDR Like 505 bp Unknown 1655 bp in B.rapa 380 in B.rapa 670 bp hAT 819 bp Unknown 524 bp SINE 216 bp SINE 1189 bp Mariner Like 3869 bp TE 1080 bp LINE 242, 644 & 274 bp SINEs Brassica oleracea (C genome; EU642504.1) Brassica rapa (A genome; AC189298.1) TEs in B. oleracea 1284 bp Unknown

56. DAPI O. violaceus genomic DNA DAPI Xianhong Ge, Farah Badakshi, Heslop-Harrison and Schwarzacher 2012

57. Zyp1 Asy-1 O.violaceus Run 16 slide 5/7 Alien chromosome is partly unpaired and partly paired with Brassica chromosomes

58. Finding genes, controlling expression: using biodiversity Recombining genes Combining genomes Chromosome engineering Understanding

59. How many genes are there? 1990s: perhaps 100,000 in human 2000: 25,000 How does this give the range of functions and control? Najl Valeyev

60. Susanne Barth, Ulrike Anhalt, Celine Tomaszewski

61. Anhalt, Barth, HH 2009 Formidable genetic and environmental interactions

62. Anhalt UCM, Heslop-Harrison JS, Piepho HP, Byrne S, Barth S. 2009. Quantitative trait loci mapping for biomass yield traits in a Lolium inbred line derived F2 population . Euphytica 170: 99-107.

63. Kim, HH, Cho et al. 2011 Science Signaling Circadian Clock regulation after Leloup & Goldbeter cf Andrew Millar in Arabidopsis X X Y Y Z Z

64. Synchronization without external regulators

65. Live version: YouTube – pathh1 channel phaseportrait.avi

67. Heslop-Harrison 2012. www.tinyurl.com/domest Crop Genome size 2n Ploidy Food Rice 400 Mb 24 2 3x endosperm Wheat 17,000 Mbp 42 6 3x endosperm Maize 950 Mbp 10 4 (palaeo-tetraploid) 3x endosperm Potato 900 Mbp 48 4 Modifed leaf Sugar beet 758 Mbp 18 2 Modified root Cassava 770 Mbp 36 2 Tuber Soybean 1,100 Mbp 40 4 Seed cotyledon Oil palm 3,400 Mbp 32 Fruit mesocarp Banana 500 Mbp 33 3 Fruit mesocarp

68. United Nations Millennium Development Goals - MDGs Goal 1 – Eradicate extreme poverty and hunger Goal 2 – Achieve universal primary education Goal 3 – Promote gender equity and empower women Goal 4 – Reduce child mortality Goal 5 – Improve maternal health Goal 6- Combat HIV/AIDS, malaria and other diseases Goal 7 - Ensure environmental sustainability Goal 8 - Develop a global partnership for development

70. Pat Heslop-Harrison [email_address] www.molcyt.com pw/user: ‘visitor’ and AoBBlog.com

71. Mutation Rearrangement Duplication Deletion Homogenization Sequences Genes / motifs Repetitive DNA Chromosomes Chromosome sets (‘Genomes’) Genotypes/CVs Species Genera and above Crops / wild species Selection Speciation

72. Many of the repetitive sequences are retrotransposons and DNA transposons Some are microsatellite motifs Some are satellites – including the most rapidly evolving sequences Repetitive DNA rapid evolution in copy number, location and sequence, with diverse turnover mechanisms often marks the major differences between closely related species it is hard to analyse by next generation or whole-genome sequencing methods

73. Pat Heslop-Harrison phh4@le.ac.uk Twitter: pathh1 www.molcyt.com pw/user: ‘visitor’

74. Gypsy elements are present in 25% of all BAC clones Barley gypsy: Vershinin, Druka, Kleinhofs, HH: Planf Mol Biol 2002; cf Brassica Alix & HH Plant Mol Biol 2005

75. Schematic representation of insertion in Brassica rapa and other Brassica genomes. Green, red, blue and black boxes showing DNA motifs. ……………… ..………………. 1 246 TSD TIR 542-bp TE TIR TSD 790 1000 Rapa185F Rapa177R Rapa8002 Rapa141F B. rapa (47186-48200) B. oleracea (66,350-66750) B. rapa (AA) B. juncea (AABB) ……………… ..………………. B. napus (AACC) ……………… ..………………. ……………… ..………………. ……………… ..………………. = A = T = C =G B. nigra (BB) B. oleracea (CC) B. carinata (BBCC) B. oleracea (GK97361) Hexaploid Brassica (carinata x rapa)

76. Stochastic fluctuations preserve stable oscillations ensure robustness of the oscillations to cell-to-cell variations Robustness analysis requires stochastic simulation JongRae Kim et al. Stochastic noise and synchronisation during Dictyostelium aggregation make cAMP oscillations robust. PLoS Computational Biology 2007

77. Jeong-Rae Kim, HH & Kwang-Hyun Cho. J Cell Sci 2010

79. Higher yielding Disease-resistance Well-adapted Better nutrition use BIOTIC & ABIOTIC STRESS Mutant cultivars no mutation negative mutation Crop improvement by mutation techniques Pierre Lagoda

81. Tandem Repeats Simple Sequence Repeats Dispersed Repeats Functional Repeats Retroelements Genes Typical Fraction 10% 5% 10% 15% 50% 10%