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.

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. 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. Food fraud
Adulterants:
Artificial colours: Sunset yellow, tartrazine, Ponceau4R, carmine
…
Or natural: Gardinia, Safflower (Carthamus tinctorius), turmeric
Fibres, hemp, jute

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. 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. 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?

8. 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

9. Key features of the genome of
Crocus sativus
Fluorescent in situ
hybridization with
CT/GACA probes
Dispersed repetitive
DNA

10. 45S rDNA: 12 sites
C. thomasaii genomic probes
highlighting repetitive DNA

11. Groups of
three similar
but not
identical
chromosomes

12. 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

13. ‘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)

14. Metaphase I in triploid Golden Yellow
Four bivalents C. flavus (2n=2x=8) origin
Six univalents from C. angustifolius (2n=2x=12)

15. 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

16. Crocus sativus Pachytene
DAPI
Synaptonemal
complex (SC)
spreading
Silver staining

17. Meiotic prophase in triploid Saffron (C. sativus)
ASY-1 antibodies (Franklin and Armstrong) show the progression of lateral element formation and
pairing

18. C. sativus meiotic pachytene

19. 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

20. (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

21. SH genomic in
u hybridization
es not
ferentiate
nomes
Crocus sativus

22. 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

23. Identical patterns in IRAP gel with
diverse Saffron accessions (not 18, of garden-origin)

24. ATPsynthase diversity
RED are Saffron Crocus sativus sequences
Three clades, all representing multiple
species

25. g
ATP synthase subunit delta families
Ziwei Wang, Qing Lui, Mathieu Rouard et al.
T2T Ensete glaucum genome assembly
BioRXiv/Gigascience

26. 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

27. Retroelement Markers
Retrotransposon LTR
LTR
Retrotransposon LTR
LTR
Retrotransposon
LTR LTR
Retrotransposon LTR
LTR
Insertion
IRAP – InterRetroelement PCR
Retrotransposon LTR
LTR
Retrotransposon
LTR LTR

28. How does chromosome number change?
How does the genome get so large?
Qing Liu
Avena
genome
evolution
from grass
common
ancestor

29. 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

30. Identical patterns in IRAP gel with
diverse Saffron accessions (not 18, of garden-origin)

31. 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

32. 200 saffron accessions
from 15 countries
150 Crocus spp. 250 accessions
12 countries
Curator: Marcelino de los Mozos

40. 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?

41. Epigenetics in Oil Palm
Phenotype appears 5 years after tissue culture

42. •

43. 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) 

44. 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

48. 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”

51. 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 …

52. Would like speakers to give perspectives on
Diversity, Equity and Inclusion and associated
activities

55. Outputs
•CROPS
• Fixed chemical
energy
Inputs
–Light
–Heat
–Water
–Gasses
–Nutrients

56. 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

57. 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