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Saffron Crocus Genetics and Genomics - University of California Davis Seminar

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Saffron Crocus Genetics and Genomics - University of California Davis Seminar

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Saffron is the world's most expensive agricultural crop. Here I discuss challenges with the crop, discovery of its relatives, and possible approaches to crop improvement.

Saffron is the world's most expensive agricultural crop. Here I discuss challenges with the crop, discovery of its relatives, and possible approaches to crop improvement.

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Saffron Crocus Genetics and Genomics - University of California Davis Seminar

  1. 1. Saffron: the most valuable crop in the world – genetics and genomics Pat Heslop-Harrison Twitter: @PatHH1 phh4@le.ac.uk phh@molcyt.com www.molcyt.com www.annbot.com/PGEgroup Trude Schwarzacher, Qing Liu José Antonio Fernández, Marcella Santaella and Crocusbank project Farah Badakshi, Nauf Alsayaid, ZiWei Wang Sharaf Eldin, John Bailey Uploaded on Slideshare PatHH
  2. 2. Saffron: Crocus sativus • The most valuable agricultural crop – $6 per gram • (record high) wheat $0.0003 per gram – 20,000x less • 300 t saffron per year – billion dollar industry • Iran, India, Spain and Greece major producers • From 500,000 stigmas per kg (150,000 flowers) • *Agricultural or horticultural crop that is planted and farmed, sold to consumer as food, intact with little processing (not F1 seed; not wild-collected; not medical; not extracted phytochemical) Used for its organoleptic properties Colour Taste Smell With a small ‘pinch’ per serving – 3 or 4 threads/stigmas
  3. 3. Food fraud Adulterants: Artificial colours: Sunset yellow, tartrazine, Ponceau4R, carmine … Or natural: Gardinia, Safflower (Carthamus tinctorius), turmeric Fibres, hemp, jute
  4. 4. ISO standards normally adopted and tested by national agencies/NGOs/quangos (ASA/FCC/ANSI/UL, BSI) • Safety, quality, performance, quantity, sustainability • Clearly defined, testable, universally applicable • ISO 3632 Spices — Saffron (Crocus sativus L.) • — Part 1: Specification • — Part 2: Test methods Also considering this as a ‘model’ for a spice: a) Rather specialized but simple product; b) Quality is variable; c) Adulteration is major concern; d) Place of origin is important. Our lab’s contribution: NONE! DNA is not useful!
  5. 5. Saffron: organoleptic properties • Colour • Flavour (taste) • Aroma • Crocins 440nm (carotenoid) • Picrocrocin 250nm (monoterpene, carotenoid degradation) • Safranal 330nm (further picrocrocin degradation) Nuclear magnetic resonance (NMR) gives indication of origin among Iranian, Greek and Spanish saffron disputes UV-Vis spectrophotometry - ISO 3632-2 Aqueous saffron extract, a spectrum range 200–700 nm Absorbance values at specific wavelengths of 440, 250, and 330 estimate content of crocins, picrocrocin, and safranal - “colour”, “flavour”, and “aroma” strength
  6. 6. Biology of Crocus sativus Usual questions of domestication: Where did it come from? What are its wild relatives? How much diversity is there? What are yield, quality, and sustainability constraints? How can we improve it?
  7. 7. Key features of the genome of Crocus sativus Genus Crocus, 100 species, Iridaceae, monocot Triploid with 2n = 3x = 24 chromosomes (3 sets of 8) Not naturally occurring, sterile Large genome size – 3,500 Mbp
  8. 8. Key features of the genome of Crocus sativus Fluorescent in situ hybridization with CT/GACA probes Dispersed repetitive DNA
  9. 9. 45S rDNA: 12 sites C. thomasaii genomic probes highlighting repetitive DNA
  10. 10. Groups of three similar but not identical chromosomes
  11. 11. Meiosis in triploid Crocus cultivars Saffron and the garden Crocus Golden Yellow are both sterile triploids. In situ hybridization to Golden Yellow) mitotic metaphases shows four pairs of chromosomes of C. flavus origin (2n=8) labelled red with genomic DNA from C. flavus, and six chromosomes of C. angustifolius origin (2n=12) labelled green with genomic DNA from C. angustifolius Golden Yellow, also named Dutch or Mammoth Yellow; see Orgaard, HH et al. 1997
  12. 12. ‘Golden Yellow’ triploid 2n=3x=14 C. flavus 2n=2x=8 (8 yellow) C. angustifolius 2n=2x=12 (6 green) Orgaard, Jacobsen & HH ‘Stellaris’ hybrid diploid 2n=2x=10 C. flavus 2n=2x=8 (4 green) C. angustifolius 2n=2x=12 (6 blue)
  13. 13. Metaphase I in triploid Golden Yellow Four bivalents C. flavus (2n=2x=8) origin Six univalents from C. angustifolius (2n=2x=12)
  14. 14. Origins of Crocus sativus From C. cartwrightianus by autotriploidy C. cartwrightianus crossed with a related species involving unreduced gamete F1 hybrid between 2 species crossed with 3rd species with an unreduced gamete 1 2 3 1 2 3 1 2 3 5 III + 3 II + 3 I 8 III ? John Bailey
  15. 15. Crocus sativus Pachytene DAPI Synaptonemal complex (SC) spreading Silver staining
  16. 16. Meiotic prophase in triploid Saffron (C. sativus) ASY-1 antibodies (Franklin and Armstrong) show the progression of lateral element formation and pairing
  17. 17. C. sativus meiotic pachytene
  18. 18. Mid Zygotene Pachytene Diplotene Early Zygotene Dynamic of centromeres during meiosis Sepsi A, Higgins JD, Heslop-Harrison JS and Schwarzacher T, 2017. CENH3 morphogenesis reveals dynamic centromere associations during synaptonemal complex formation and the progression through male meiosis in hexaploid wheat Plant Journal 89: 235-249 doi: 10.1111/tpj.13379 CENH3 centromere ASY1 associated with the lateral elements ZYP1 central element of the synaptonemal complex
  19. 19. (b) Centromere depolarisation and SC formation during Zygotene Interphase Leptotene Zygotene Late Zygotene Telomere bouquet Homologue chromosome pairs Centromeres ZYP1 Early Zygotene 1 2 3 Subtelomeric synapsis Interstitial alignment Interstitial elongation (a) Centromere, telomere and chromosome arm dynamics in meiotic prophase I. Sepsi et al. Plant Journal 2017
  20. 20. SH genomic in u hybridization es not ferentiate nomes Crocus sativus
  21. 21. Variable IRAP patterns in 11 Crocus species, including intra-specific variation (19-21 and 22-24) In this gel, 8 is most similar to saffron (5) C. sativus C. hadri C. cart C. pallasii
  22. 22. Identical patterns in IRAP gel with diverse Saffron accessions (not 18, of garden-origin)
  23. 23. ATPsynthase diversity RED are Saffron Crocus sativus sequences Three clades, all representing multiple species
  24. 24. g ATP synthase subunit delta families Ziwei Wang, Qing Lui, Mathieu Rouard et al. T2T Ensete glaucum genome assembly BioRXiv/Gigascience
  25. 25. Crocus cartwrightianus close diploid Taxonomically in Series Crocus Genus Crocus, Iridaceae, Monocotyledons Wild Crocus accessions show high levels of diversity with several DNA marker systems Current data points to C. cartwrightianus (2 genomes) and one of the C. pallasii subspecies as the ancestors of C. sativus but no very close collection found yet
  26. 26. Retroelement Markers Retrotransposon LTR LTR Retrotransposon LTR LTR Retrotransposon LTR LTR Retrotransposon LTR LTR Insertion IRAP – InterRetroelement PCR Retrotransposon LTR LTR Retrotransposon LTR LTR
  27. 27. How does chromosome number change? How does the genome get so large? Qing Liu Avena genome evolution from grass common ancestor
  28. 28. How does chromosome number change? How does the genome get so large? Qing Liu - Avena genome evolution from grass ancestor • Remarkable and uniform expansion of genome
  29. 29. Identical patterns in IRAP gel with diverse Saffron accessions (not 18, of garden-origin)
  30. 30. Every grower/trader says “My saffron is the best in the world” Relatively unusual in use in savory & sweet dishes, hot & cold, water, milk & alcoholic drinks • My comment “Use saffron for your local dish” • India: gravy (‘curry’) and rice • Spain: paella • Greece: tea/alcohol, sweets • Iran: rice
  31. 31. 200 saffron accessions from 15 countries 150 Crocus spp. 250 accessions 12 countries Curator: Marcelino de los Mozos
  32. 32. Biology of Crocus sativus Usual questions of domestication: Where did it come from? What are its wild relatives? How much diversity is there? What are yield, quality, and sustainability constraints? How can we improve it?
  33. 33. Epigenetics in Oil Palm Phenotype appears 5 years after tissue culture
  34. 34.
  35. 35. 4/6/2022 Modulation of Methylation • McrBC digest probed with retrotransposon probe: sharp bands, presumably activated and episomal expression Preliminary results with anti-methyl-cytosine indicate differences between ortet right, more methylated) and mantled regenerants (left, less methylated) 
  36. 36. Flowering (ab)normalities Phenotype Multiple abnormalities Genetic mantling Fully mantled, no reversion Partially mantle reversion Differentiation (♀,♂) Cause Chromosomal loss, deletion, rearrangement Gene mutation (base change) Telomere shortening Repetitive DNA variation (Retro)transposon insertion Retrotransposon activation Methylation Heterochromatinization Chromatin remodelling Histone modification Developmental regulation programmed abortion
  37. 37. By Monsieur Paul Chappellier 1899 reporting work from 1844 onwards (known to father of partner in Crocusbank, Jean Marie Thiercelin, seventh generation of saffron and spice company, http://www.thiercelin1809.com/, “for the Saffron, there is only known a single and unique species; for ages it has not produced a single variety”, writing that he was importing bulbs Naples, Athens, Austria, Spain, Cashmere and China. Advertised for seeds with money prize from 1850 to 1853. “Peculiarities of structure of the monstrous flowers” He reports a hybrid with “mania for stigmatisation … teratological phenomeon has … practical and agricultural side … I try to transform the floral organs into stigmas” … “so far, these hybrids have had but a botanical and theoretical value, but … it is reasonable to expect a slight effort to be made in order to arrive at an improved type … render veritable service to Saffron cultivators”
  38. 38. Biology of Crocus sativus Where did it come from? What are its wild relatives? How much diversity is there? What are constraints? How can we improve it? Challenges that are central to our research programme The PanGenome, genome evolution (structural, copy number), repetitive DNA, polyploidy, biodiversity …
  39. 39. Would like speakers to give perspectives on Diversity, Equity and Inclusion and associated activities
  40. 40. Outputs •CROPS • Fixed chemical energy Inputs –Light –Heat –Water –Gasses –Nutrients
  41. 41. E,D & I and Citation of work • Huge tendency to cite only work from North America, Europe and advanced countries of Asia and Australasia • Brilliant work from the rest of the world might be hard to find, or researched and written slightly differently to our conventions. It needs to be found and cited (for fundamental not ‘just’ regional reasons) • Find and cite more global papers • Changing my marking criteria for Undergraduates to include use of global literature to achieve the highest grades
  42. 42. Saffron: the most valuable crop in the world – genetics and genomics Pat Heslop-Harrison Twitter: @PatHH1 phh4@le.ac.uk phh@molcyt.com www.molcyt.com www.annbot.com/PGEgroup Trude Schwarzacher, Qing Liu José Antonio Fernández, Marcella Santaella and Crocusbank project Farah Badakshi, Nauf Alsayaid, ZiWei Wang Sharaf Eldin, John Bailey Uploaded on Slideshare PatHH

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