Tag Archives: genetics

Crocus, saffron-omics and the highest value crop

Saffron, Crocus sativus and origin label

Saffron, Crocus sativus and a protected origin label

Saffron, the stigma of Crocus sativus, is the highest priced agricultural product (often €/$25 or £15 per gram) and a good example of a profitable crop with sustainability, cultural and social values, and high labour demand. I have been discussing –omics studies of the crop – the DNA, RNA, metabolites and secondary products – at the annual meeting of a European Science Foundation COST programme Saffronomics.

www.Saffronomics.org logo

www.Saffronomics.org logo

The ‘Action’ aims to coordinate research on Saffron-omics for crop improvement, traceability of the product, determination of authenticity, adulteration and origin to provide new insights that will lead a sound Saffron Bio-Economy. Despite the high price, the spice costs only a few pence/cents per portion, and adds enormously to the flavour and colour of many dishes. Biologically, saffron is the species Crocus sativus, as recognized by Linnaeus, and it is a sterile triploid with 2n=3x=24 chromosomes.

Audience for annual meeting

Audience for annual meeting

The programme of our Annual Meeting opened with the genomics sessions – the DNA, RNA, genetics and epigenetics. I don’t usually start reviews with, nor indeed include, my own talk, but here its content sets the scene for other work discussed at the meeting. I talked about the work of Nauf Alsayid, who shows the lack of any clear DNA differences between any accessions of saffron – whether from Kashmir, Greece, Italy, Spain, Holland or Iran. I cited a paper from 1900, itself reporting work back to 1844, where the French botanist Monsieur Paul Chappellier reported “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 (Chappellier P 1900. Creation of an improved variety of Crocus sativus. J. Royal Horticultural Society XXIV Hybrid Conference Report 275-277 – brilliant download, even available free for Kindle!). Plus ça change, plus c’est la même chose!

Highest quality Saffron from Thiercelin 1809

Highest quality Saffron from Thiercelin 1809

After my talk, Jean Marie Thiercelin, the seventh generation of the major saffron and spice company http://www.thiercelin1809.com told me that his grandfather knew Paul Chappellier, and he commented in the history of saffron production in France: Chappellier knew how to produce 10 to 15kg per ha before the First World War. After the war, saffron production stopped altogether in France, but it has restarted this century, with now some 137 growers on 37 ha but production of only some 5kg per ha.

Continuing with the talks, a DNA-sequence level study of saffron by Gerhardt Menzel with Thomas Schmidt (Dresden) analysed of several Gigabases of genomic survey sequence data, revealing about ten distinct tandemly repeated satellite DNA sequences that could be used to identify chromosomes in saffron by in situ hybridization. The species has a 78% repeat content in the DNA, with about 6% being the rDNA, and many different classes of transposons.

Giovanni Giuliano - High trhougput sequencing of saffron RNA and gene discovery

Giovanni Giuliano – High throughput sequencing of saffron RNA and gene discovery

Giovanni Giliano (with Sarah Frusciante, Italy) demonstrated the carotenoid cleavage dioxygenase from saffron stigmas catlayses the first step in saffron crocin biosynthesis, a clear example of the pathway to the critical secondary product giving saffron its value (http://www.pnas.org/content/111/33/12246.short).


Slivia Fluch - Saffronomics Genomics Working Group Leader

Slivia Fluch – Saffronomics Genomics Working Group Leader

Both Matteo Busconi and Silvia Fluch (Austria) discussed epigenetic differences detected from different saffron collections: important for both understanding the controls on gene expression and for determining the origin of samples. Each producing area seems to have distinct profiles. Caterina Villa (Porto) reported results from use of the plant ‘barcoding’ primers ITS and matK with high resolution DNA melting analysis for saffron authentication, and more detail about the chloroplast genomes was presented from Bahattin Tanyolac and his Turkish colleagues. Although wild species of crocus are of interest from several points of view, only one paper, from Joze Bavcon (Slovenia) discussed these in detail, with a report of the natural hybrid Crocus reticulatus x C. vernus.

Joze Bavcon Crocus of Slovenia Book Cover

Joze Bavcon Crocus of Slovenia Book Cover

The next group of talks discussed the saffron metabolome, the analysis of different constituents of Crocus. Crocus is one of the few species to have its own international standard (ISO3632: http://j.mp/isosaffron ), and both quality and purity are measured (including contamination with stamens and pollen, along with detection of adulteration. Several participants were involved in the formulation of the standard, and Gianluca Paredi reported improvements that need less than the ISO methods needing no less than 23g of stigmas! Natural colours from plants such as Buddliea, Calendula, Curcum, Gardenia, safflower (Carthamus Asteraceae), cochineal (from the insect) and turmeric are widely mixed with saffron.

Chair of the Saffronomics Action Professor Maria Tsimidou

Chair of the Saffronomics Action Professor Maria Tsimidou

The Saffronomics project leader, Maria Tsimidou (Greece), used the three ISO3632 peaks for saffron – colouring strength from crocins absorbing at a peak wavelength of 440nm, aroma from safranal at 330nm, and taste (flavour) from picrocrocin at 257 nm – for examination of quality and authenticity of commercial saffron samples. Of 16 samples, 3 were adulterated, and half of the pure samples were graded in ‘category I’. Another amazing figure quoted was the price of saffron in quantity: of 75 tonnes imported to one county, only 35% is priced at more than $500 per kg. Authentic saffron could not be produced for anywhere approaching $1000/kg (typically $10-$15000/kg), so all this bulk product is fraudulent. Technology sessions in the meeting covered alternative quantification approaches to spectroscopy: Laura Ruth Cagliani in Milan tested  different solvents for extraction for NMR-based metabolomic characterization of authentic saffron distributed within the COST partners as well as the NMR evidence of absence of plant adulteration in those saffron samples.

Moschos Polissiou Saffronomics

Moschos Polissiou Saffronomics

A leading group from Thessaloniki was able to detect adulteration with as little as 15% cochineal. EA Petrakis and Moschos Polissiou demonstrated how FT-IR spectroscopy is promising to quantify small amounts of adulterants in saffron – safflower, Gardenia and tumeric – where diffuse reflectance mode provides rapidity, ease of use and minimal sample preparation. Other important reports discussed aging effects on profile of secondary metabolites (Paraskevi Karastamati Greece) and detection of herbicide residues (Christina Mitsi).

H stable Isotope Map from http://www.earthmagazine.org/article/cold-case-files-forging-forensic-isoscapes

H stable Isotope Map from http://www.earthmagazine.org/article/cold-case-files-forging-forensic-isoscapes

Micha Horacek (Austria) presented new results looking at the ratios of stable isotopes in saffron, a technique increasingly used to determine the origin of all agricultural produce. He showed the impressive map of with the gradient of water (hydrogen and oxygen) isotope ratio from North to South and from East to West in Europe. He also showed the differences in nitrogen stable isotope ratios depending of fertilizer use, and sulphur which depends on the underlying geology. Current work with saffron shows considerable year-to-year variation in the position of accessions from different regions of Europe, but the data is still being collected. Soon Micha will be getting a sample of our own, Leicester-lab-produced, saffron to add to his map!

Our hosts at RIKILT, the Food Safety and Quality Institute, Wageningen University, have much advanced applied science on food quality. An eye-opening talk by John van Duynhoven told us about rehydration of freeze dried blanched carrot with dynamic assessment of water movement in samples with and without blanching, freeze drying at -28 and -150C. Another series of images showed water transport and the impact of pre-cooking of rice, using magnetic resonance imaging MRI as a functional measurement of rice cooking. The final section discussed why crackers don’t crack: vapour transport during shelf life of crackers! Modelling of the nature of water transport links processing & formulation to the structure and on to functional and storage implications.


Fran Azafran - a school book about saffron

Fran Azafran – a school book about saffron

For ESF – COST projects, dissemination and public understanding are important, and participants were treated to a preview of a series of six school books about Fran Azafran and Franny Azafran by Manuel Delgado from Cuenca, Spain. I look forward to seeing these in full, and hopefully to their availability in other languages too.


At the podium

At the podium

Like the best of the projects, I feel that saffron science has moved in the last decade, (including research in the consortia www.crocusbank.org and www.saffronomics.org) with notable fundamental, technical and applied outcomes of our research. We know about its relatives and genome structure, key genes, metabolic processes and the key secondary products, and even understand epigenetic control, corm growth and dormancy. After 4000 years of being sold fake saffron, the fraudsters know now that we can test for saffron purity and quality!

Marta Rodlan (Vice Chair of the Action), Jose Antonio Fernández Perez and Jean Marie Thiercelin: key people in saffronomics

Marta Rodlan (Vice Chair of the Action), Jose Antonio Fernández Perez and Jean Marie Thiercelin: key people in saffronomics

Saffronomics Meeting Book Cover

Saffronomics Meeting Book Cover

A new day dawning: Hemerocallis as a model organism

Hemerocallis Genetic model organisms have revolutionized science, and today, with the rapid advances in technology, there is significant potential to launch many more plant species towards model status. However, these new model organisms have to be carefully selected.

Hemerocallis (the daylily) satisfies multiple criteria for selection and deserves serious consideration as a subject of intensive biological investigation. Several attributes of the genus are of great biological interest. These include the strict control of flower opening and, within a short period, the precisely regulated floral death by a programmed cell death system. The self-incompatibility system in Hemerocallis is also noteworthy and deserves more attention. Importantly, the genus is widely cultivated for food, medicinal value and ornamental interest. Hemerocallis has considerable potential as a ‘nutraceutical’ food plant and the source of new compounds with biomedical activity. The genus has also been embraced by ornamental plant breeders and the extraordinary morphological diversity of hybrid cultivars, produced within a relatively short time by amateur enthusiasts, is an exceptional resource for botanical and genetic studies.

This paper in AoB PLANTS explores these points in detail, explaining the reasons why this genus has considerable value – both academic and socio-economic – and deserves new resources devoted to its exploration as a model. Its impact as a future model will be enhanced by its amenability to cultivation in laboratory and field conditions. In addition, established methods for various tissue and cell culture systems as well as transformation will permit maximum exploitation of this genus by science.

Rodriguez-Enriquez, M.J., and Grant-Downton, R.T. (2012) A new day dawning: Hemerocallis (daylily) as a future model organism. AoB Plants 5: pls055 doi: 10.1093/aobpla/pls055

Proteaceae, Banksia, Macadamia nuts and the Annals of Botany Cover

Leucospermum flowers in the family Proteaceae on the cover of Annals of Botany

Leucospermum flowers in the family Proteaceae on the cover of Annals of Botany

Our videoblog discusses plants in the family Proteaceae, a well-known Southern hemisphere family with many beautiful and well-known representatives in Africa and Australia. The striking red flowers of the genus Leucospermum, from South Africa feature on the cover of the Annals of Botany for this year. Banksia is a well-known Australian genus, the bottle brush flowers, with attractive flowers and remarkable cone-like fruits. Protea, the type genus for the family, is from South Africa; the name of both genus and family is apposite, being named after the Greek God Proteus who was very variable in his form. Interestingly, there are no important food crops originating from Australia, despite its large area and range of climatic zones, and the now world-wide importance of Eucalyptus as a tree for construction timbers and paper-making fibre. In the family Proteaceae, Macadamia is the most internationally-significant food plant of any Australian native species; it’s very fat-rich nuts (75%) are widely available and much appreciated.

 

 

The videoblog is on YouTube:

Feeling sleepy

Medicago truncatula Like most animals, plants also sleep at night. At least, many do, but not, unfortunately, Arabidopsis, and our scientific over-reliance on this one species has hampered understanding of nyctinasty, sleeping movements of leaves. A new commentrary in PNAS discusses the genetic basis for sleepy plants, and is well worth a read:

Genetic basis of the “sleeping leaves” revealed. PNAS USA 6 July 2012, doi: 10.1073/pnas.1209532109

See also:

Conserved genetic determinant of motor organ identity in Medicago truncatula and related legumes. PNAS USA, 11 June 2012, doi: 10.1073/pnas.1204566109

Not so green as they’re cabbage looking

Not so mellow yellow There have been some very interesting papers published recently on how plants withstand diseases. Plants seeingly lack the sophisticated immune system of mamals, so discoveries of how they use the genes they have is noteworthy.

 

The fact that single immune receptors conferring multiple resistances to taxonomically unrelated pathogens may not be exceptional gives plant breeders a strong incentive to identify and to use common virulence targets as leads to discover broad-specificity resistance genes:
Dual disease resistance mediated by the immune receptor Cf-2 in tomato requires a common virulence target of a fungus and a nematode. PNAS USA 06 June 2012 doi: 10.1073/pnas.1202867109 Plants lack the seemingly unlimited receptor diversity of a somatic adaptive immune system as found in vertebrates and rely on only a relatively small set of innate immune receptors to resist a myriad of pathogens. Here, we show that disease-resistant tomato plants use an efficient mechanism to leverage the limited nonself recognition capacity of their innate immune system. We found that the extracellular plant immune receptor protein Cf-2 of the red currant tomato (Solanum pimpinellifolium) has acquired dual resistance specificity by sensing perturbations in a common virulence target of two independently evolved effectors of a fungus and a nematode. The Cf-2 protein, originally identified as a monospecific immune receptor for the leaf mold fungus Cladosporium fulvum, also mediates disease resistance to the root parasitic nematode Globodera rostochiensis pathotype Ro1-Mierenbos. The Cf-2–mediated dual resistance is triggered by effector-induced perturbations of the apoplastic Rcr3pim protein of S. pimpinellifolium. Binding of the venom allergen-like effector protein Gr-VAP1 of G. rostochiensis to Rcr3pim perturbs the active site of this papain-like cysteine protease. In the absence of the Cf-2 receptor, Rcr3pim increases the susceptibility of tomato plants to G. rostochiensis, thus showing its role as a virulence target of these nematodes. Furthermore, both nematode infection and transient expression of Gr-VAP1 in tomato plants harboring Cf-2 and Rcr3pim trigger a defense-related programmed cell death in plant cells. Our data demonstrate that monitoring host proteins targeted by multiple pathogens broadens the spectrum of disease resistances mediated by single plant immune receptors.

And there is also the recent work showing that plants can pass acquired defenses against pests and pathogens on to their offspring: Memory Tools for Plants – how plants pass defenses to offspring through a complex molecular network

 

Plants are clearly a lot smarter than many people give them credit for. The question is, are we smart enough to use these new discoveries to help feed ourselves in the future?

Free paper — Genome size in Anthurium evaluated in the context of karyotypes and phenotypes

Little is known about the genome of Anthurium other than chromosome observations, which frequently indicate supernumerary (“B”) chromosomes. New genome size estimates for 34 species and nine cultivars presented here  provide insights into genome organization and evolution in this very large genus.

AoB PLANTS Handling Editor involved in an exciting commercial paw paw breeding programme

A recent report places AoB PLANTS Handling Editor Kermit Ritland at the center of a commercial breeding programme of paw paw. “This guy Si Brown is so interesting” Kermit comments; “[He] made a cold call to me one day, that is the way venture capitalists work. Si got a degree in Plant Ecology from McGill University but ended up in business, and does all these high-end business deals […] Botany and business can work together.”

Free paper — Identification of Stylosanthes guianensis varieties using molecular genetic analysis

Molecular genetic diversity and population structure analysis were used to clarify the controversial botanical classification of Stylosanthes guianensis.  In this paper, the accessions were clustered in nine groups, each of which was mainly composed of only one of the four botanical varieties.

Phenomics – technologies to relieve the phenotyping bottleneck

It's wheat Jim, but not as we know it Global agriculture is facing major challenges to ensure global food security, such as the need to breed high-yielding crops adapted to future climates and the identification of dedicated feedstock crops for biofuel production (biofuel feedstocks). Plant phenomics offers a suite of new technologies to accelerate progress in understanding gene function and environmental responses. This will enable breeders to develop new agricultural germplasm to support future agricultural production. This review presents plant physiology in an ‘omics’ perspective, covers some of the new high-throughput and high-resolution phenotyping tools and discuss their application to plant biology, functional genomics and crop breeding.

Phenomics – technologies to relieve the phenotyping bottleneck. Trends Plant Sci. Nov 8 2011