The origin of an old, resource-efficient crop, Broomcorn millet or Panicum miliaceum

Panicum: the origin of tetraploid proso or broomcorn millet

Panicum: the origin of tetraploid proso or broomcorn millet

307. Hunt HV, Badakshi F, Romanova O, Howe CJ, Jones M, Heslop-Harrison JS. 2014. Reticulate evolution in Panicum (Poaceae): the origin of tetraploid broomcorn millet, P. miliaceum. Journal of Experimental Botany. in press March 2014  DOI will be:10.1093/jxb/eru161 soon. Link to proof: Panicum_eru161.

Panicum miliaceum (broomcorn millet) is a tetraploid cereal which was among the first domesticated crops, but is now a minor crop despite its high water use efficiency. The ancestors of the species have not been determined; we aimed to identify likely candidates within the genus, where phylogenies are poorly resolved. Nuclear and chloroplast DNA sequences from P. miliaceum and a range of diploid and tetraploid relatives were used to develop phylogenies of the diploid and tetraploid species. Chromosomal in situ hybridization with genomic DNA as a probe was used to characterize the genomes in the tetraploid P. miliaceum and a tetraploid accession of P. repens. In situ hybridization showed that half the chromosomes of P. miliaceum hybridized more strongly with labelled genomic DNA from P. capillare, and half with labelled DNA from P. repens. Genomic DNA probes differentiated two sets of 18 chromosomes in the tetraploid P. repens. Our phylogenetic data support the allotetraploid origin of P. miliaceum, with the maternal ancestor being P. capillare (or a close relative) and the other genome being shared with P. repens. Our P. repens accession was also an allotetraploid with two dissimilar but closely related genomes, the maternal genome being similar to P. sumatrense. Further collection of Panicum species, particularly from the Old World, is required. It is important to identify why the water-efficient P. miliaceum is now of minimal importance in agriculture, and it may be valuable to exploit the diversity in the species and its ancestors.

Link to proof: Panicum_eru161.

Soon to be available at http://jxb.oxfordjournals.org/content/early/recent and DOI will be:10.1093/jxb/eru161 soon.

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We need to have more scientific mavericks @guardianletters

We need to have more scientific mavericks - @guardianletters

We need to have more scientific mavericks – @guardianletters

306. Braben DW, Allen JF, Amos W, Ball R, Birkhead T, Cameron P, Cogdell R, Colquhoun D, Dowler R, Engle I, Fernández-Armesto F, Fitzgerald D, Heslop-Harrison P, Herschbach D, Kimble HJ, Kroto H, Ladyman J, Lane N, Lawrence P, MacIntyre A,  Mattick J, Pelloni B, Poliakoff M, Randall D, Ray D, Roberts RJ, Seddon K, Self C, Swinney H, Vita-Finzi C. 2014. We need more scientific mavericks. Letter. The Guardian 19 March 2014.

http://www.theguardian.com/science/2014/mar/18/we-need-more-scientific-mavericks

“Science is the belief in the ignorance of experts,” said Richard Feynmanin the 1960s. But times change. Before about 1970, academics had access to modest funding they could use freely. Industry was similarly enlightened. Their results included the transistor, the maser-laser, the electronics and telecommunications revolutions, nuclear power, biotechnology and medical diagnostics galore that enriched the lives of virtually everyone; they also boosted 20th-century economic growth.

After 1970, politicians substantially expanded academic sectors. Peer review’s uses allowed the rise of priorities, impact etc, and is now virtually unavoidable. Applicants’ proposals must convince their peers that they serve national policies and are the best possible uses of resources. Success rates are about 25%, and strict rules govern resubmissions. Rejected proposals are usually lost. Industry too has lost its taste for the unpredictable. The 500 major discoveries, almost all initiated before about 1970, challenged mainstream science and would probably be vetoed today. Nowadays, fields where understanding is poor are usually neglected because researchers must convince experts that working in them will be beneficial.

However, small changes would keep science healthy. Some are outlined in Donald Braben’s book, Promoting the Planck Club: How Defiant Youth, Irreverent Researchers and Liberated Universities Can Foster Prosperity Indefinitely. But policies are deeply ingrained. Agencies claiming to support blue-skies research use peer review, of course, discouraging open-ended inquiries and serious challenges to prevailing orthodoxies. Mavericks once played an essential role in research. Indeed, their work defined the 20th century. We must relearn how to support them, and provide new options for an unforeseeable future, both social and economic. We need influential allies. Perhaps Guardian readers could help?

Donald W Braben University College London
John F Allen Queen Mary, University of London
William Amos University of Cambridge
Richard Ball University of Edinburgh
Tim Birkhead FRS University of Sheffield
Peter Cameron Queen Mary, University of London
Richard Cogdell FRS University of Glasgow
David Colquhoun FRS University College London
Rod Dowler Industry Forum, London
Irene Engle United States Naval Academy, Annapolis
Felipe Fernández-Armesto University of Notre Dame
Desmond Fitzgerald Materia Medica
Pat Heslop-Harrison University of Leicester
Dudley Herschbach Harvard University, Nobel Laureate
H Jeff Kimble Caltech, US National Academy of Sciences
Sir Harry Kroto FRS Florida State University, Tallahassee, Nobel Laureate
James Ladyman University of Bristol
Nick Lane University College London
Peter Lawrence FRS University of Cambridge
Angus MacIntyre FRS Queen Mary, University of London
John Mattick Garvan Institute of Medical Research, Sydney
Beatrice Pelloni University of Reading
Martyn Poliakoff FRS University of Nottingham
Douglas Randall University of Missouri
David Ray Bio Astral Limited
Sir Richard J Roberts FRS New England Biolabs, Nobel Laureate
Ken Seddon Queen’s University of Belfast
Colin Self University of Newcastle
Harry Swinney University of Texas, US National Academy of Sciences
Claudio Vita-Finzi FBA Natural History Museum

http://www.theguardian.com/science/2014/mar/18/we-need-more-scientific-mavericks and http://www.besteducationnews.com/we-need-to-have-more-scientific-mavericks-guardianletters.html

Intranet scan: Guardian_Letter_Mavericks_March2014

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Crocus and the origin of Saffron

Saffron Crocus: molecular work in Leicester

Saffron Crocus: molecular work in Leicester

305. Alsayied N, Schwarzacher T, Heslop-Harrison P. 2014. Crocus: research into the origin of saffron. Botanic Garden Newsletter 5: 3.

Link to scan of Crocus and the origin of saffron article.

The genus Crocus has nearly 100 species, each with unique characters of colour, flowering time or geographical distribution. We are aiming to understand the relationships of the different species, the diversity within species, and in particular the origin and diversity of the most valuable Crocus species, the spice saffron.

Saffron is the dried stigmas of the flower from Crocus sativus, which is grown commercially in many countries, from Iran to Mediterranean Spain and Greece, with significant production also in Kashmir. It is highly prized as a spice and colouring, used in both sweet and savoury dishes, teas, and also with medical applications. About 200 stigmas from 70 flowers go into a gram of the spice. Flowers are picked in the early morning, and the stigmas removed on processing tables in the shade, before the drying process which differs between producers. Despite the high price, though, only a few stigmas are needed to flavour a dish. Saffron does vegetatively, by separation of corms from the parent. Our research is asking the following questions. How many times has saffron originated in nature? What are the ancestors? How different is saffron from different geographical areas? Is it possible to resynthesize the species to breed improved saffron with better disease resistance, easier harvestability, and better use of water in dry areas?

Crocus species show wide diversity in IRAP DNA fingerprint within and between species

Crocus species show wide diversity in IRAP DNA fingerprint within and between species (tracks 1-5 are identical saffron patterns, others are different accessions and different species)

We have analysed the DNA from 21 species, representing the diversity of Crocus, and the ‘barcodes’ from the DNA show substantial differences between the species, shown in an example above where the code is different in each lane (left and right and lane 13 are DNA
reference markers). Analysis of several wild accessions of species also shows considerable variation: lanes 3 to 5 are different collections of the ornamental species Crocus thomasii.

Saffron Crocus shows no confirmed diversityy in IRAP DNA 'fingerprint' gels

Saffron, Crocus sativus, shows no confirmed diversity in IRAP DNA ‘fingerprint’ gels

In contrast, when we looked at saffron, each barcode was identical (left), whether the plant was obtained from Spain, Iran, Holland, Greece, the UK or Kashmir. We conclude, therefore, that there is very little, if any, genetic variation in saffron from across the world and the cultivated species only arose once before being distributed widely.

Processing and growth conditions do vary – from sea level to more than a mile high in Kashmir, or from moist to desert conditions, for example – so quality may vary. Adulteration of saffron with dyes and other fibres is also a big problem commercially, and our barcoding work is helping develop tests for authenticity, although not geographical origin. Saffron has three sets of chromosomes (illustrated below), so can be thought of as having three parents (direct ancestors)! Sequencing the three sets of genes shows that two are like the wild species Crocus cartwrightianus, while the other set is more similar to C. pal/asii ssp. pal/asii. These findings have given a strong indication of the answers to questions about saffron’s origin and diversity that have been asked for one and a half millennia!

Many of the plants grown in the botanic gardens are used for research within the University. This work was conducted in the context of the EU project www.crocusbank.org and the ESF network Saffronomics.org .

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In situ hybridization: a course on FISH and ChIp

In situ hybridization of two repetitive sequences to chromosomes of a wild wheat species

In situ hybridization of two repetitive sequences to chromosomes of a wild wheat species

In situ hybridization – a course on FISH and ChIp

In situ hybridization, now largely with fluorescent detection so ‘fluorescent in situ hybridization’ or FISH, is a key method for localizing DNA sequences along chromosomes and occassionally within interphase nuclei. RNA in situ hybridization (not discussed here) is used for locating gene transcripts within nuclei. Chromatin Immunoprecipitation, ChIp, is used to isolate DNA still associated with protein to understand the key interactions between the two types of molecules. A recent commentary of ours discussed some of the uses of this in identifying the packaging of DNA in nucleosomes.

Participants in the UM-ABI FISH and ChIp Workshop (click for high resolution)

Participants in the UM-ABI FISH and ChIp Workshop (click for high resolution)

The course participants made chromosome spreads from medicinal ginger, Bosenbergia rotunda, and banana. Both the course organizer, Prof Jennifer Harikrishna and one of the facilitators, Pat Heslop-Harrison, have been involved with sequencing the banana Musa balbisiana and Musa acuminata genomes in the past year.

Pat Heslop-Harrison presented a public lecture on crops and superdomestication of plants which showed many examples of in situ hybridization as applied to understanding and manipulating plant genomes. The slides from this are on slideshare.  Prof J. S. “Pat” Heslop-Harrison, University of Leicester and Academic Icon, University of Malaya

Chromosomes, Crops and Superdomestication

Crop improvement is reliant on the exploitation of new biodiversity and new combinations of diversity. I will discuss our work on genome structure and evolution, involving processes including polyploidy, introgression, recombination and repetitive DNA changes. Identification and measurement of diversity and relationships assists in use of new gene combinations or new crops, through synthesizing new hybrid species, by chromosome engineering or by transgenic strategies. We are studying crops including wheat, Brassica and banana, using genome sequencing, repetitive sequence comparison, and cytogenetics. Plants, pathogens and farmers have been involved in a three-way fight since the start of agriculture, and the concept of superdomestication involves systematic identification of needs from crops, only then followed by finding appropriate characters and bringing them together in new varieties. Crops will continue to deliver the products needed for food, fibre, fuel and fibre in an increasingly sustainable and safe manner.

 

A second lecture, Genome evolution – tales of scales, discussed DNA to crops, genes to repetitive DNA, days to aeons http://www.slideshare.net/PatHeslopHarrison/genome-evolution-tales-of-scales-dna-to-cropsmonths-to-billions-of-years-chromosomes-to-ecosystems

Some DNA sequences are recognizable in all organisms and originated with the start of life. Others are unique to a single species. Some sequences are present in single copies in genomes, while others are present as millions of copies. The total amount of DNA in cells of an advanced eukaryotic species can vary over three orders of magnitude, and chromosome number can vary similarly. How can such huge variations be accommodated within the constraints of organism growth, development and reproduction? What are the evolutionary implications of these huge variations? How can we use the information to understand plant evolution, cytogenetics, genetics and epigenetics? What are the implications for future evolution, biodiversity and responses of plants during plant breeding or climate change?

OTHER INFORMATION AND PICTURES FROM THE COURSE WILL BE PASTED BELOW

List of items required for the course

List of equipment required for in situ hybridization

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Spectroscopy and DNA concentration measurement

Spectroscopy

Spectroscopy (from GE Life Sciences)

DNA concentration measurement is fundamental to most molecular biology methods. What is the basis of DNA concentration measurement? I’m always happy to find an article which has detail at the level you need to know! In a free magazine, VWR BioMarkers, there is a very useful article from GE Life Sciences.

http://media.vwr.com/interactive/publications/VWR_bioMarke_2013/Magazine/files/assets/basic-html/index.html#7

A local copy of the spectroscopy handbook is here  GE_Spectroscopy_Handbook_DNA_Protein_litdoc:. From page 6 has the DNA-RNA specific information. (The original was at http://www.gelifesciences.com/gehcls_images/GELS/ Related%20Content/Files/1354014938539/litdoc29033182_20130728225752.pdf in 11/2013 without the break after related but seems to be broken.)

There are detailed explanations of the significance of A260/A280 ratio, A260/A320 ratio and A320 background correction, and clear comments on what is ‘good’ DNA “For DNA the result of dividing the 260 nm absorption by the 280 nm needs to be greatrr or equal to 1.8 to indicate a good level of purity in the sample. For RNA samples this reading should be 2.0 or above” and “An A260/A230 ratio of 2 or above is indicative of a pure sample.”

Even with an increasingly ubiquitous Nanodrop, molecular biologists should have a basic knowledge of what is being measured by absorbance readings, as is given in this GE reference.

Meanwhile, how do you avoid order-of-magnitude errors? How else can you measure DNA concentration? As a molecule which can be several meters long, DNA in solution markedly changes the viscosity of water or buffer. A solution of genomic DNA in water can be checked by dipping the end of a yellow (200ul) tip, held in the hand, into the solution. As it is pulled out,  a solution of 1ug/ul (that is, 0.1%) DNA will stick to the end of the tip, forming a meniscus, and break when the tip is about 1mm from the surface of the solution. Even a solution of 200ng/ul will be noticeably more ‘sticky’ to the tip than buffer or water alone. At 3ug/ul, you probably noticed you had difficulty in dissolving the DNA, and a distinct thread will be produced when pulling the tip out. Since most genomic DNA solutions you work with in molecular biology are between 250 and 2500ng/ul, you can impress your colleagues by measuring the DNA with a pipette tip, and never be embarrassed by making a 2-fold error in concentration with some experience!

Whenever DNA is run on a gel, you will be using a size marker or ladder next to the lanes with your DNA. The documentation with the ladder will tell you how many ng of DNA are included in each band of the ladder. By comparing brightness of the your bands with the standard, you can determine the amount of DNA in your preparations run on a gel. Again, whenever you are looking at a gel, visually quantify the amount of DNA in a band – then you will be prepared for the amount you expect for the next experiment!

DNA in solution is easily broken even when handled gently. If you vortex DNA, or suck it vigorously through a syringe needle of pipette tip, it will shear to a few hundred base pairs. Then the estimate of concentration from viscosity observation will differ from the concentration measurement by spectroscopy.

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From vegan to meat: human diet and trophic levels

TrophicLevelsHumanPNAS2013

Trophic levels of human population from vegetarian (white) to carnivorous (purple). From Bonhommeau et al. PNAS 2013

Where are humans in the food chain? Bonhommeau et al. address this question in PNAS, apparently for the first time, in detail across all countries and over the period from 1961 that FAO statistics on food consumption and production are available (FAOstat.FAO.org).

If we ate only the primary producers – plants – we would have a trophic level of 2. Much of China and indeed the rest of Asia, the lightest colours on the map above, is not far from this vegan trophic level of food consumption. If we ate only products of vegetarian animals (cow milk, or rabbit meat for example), our trophic level would be 3. Apex predators such as polar bears or whales that eat other carnivorous animals have a tropic level of 5.5. For the human population of different countries, the highest is Iceland, but many of the other countries in the dark colour of the picture above are similar with a trophic level of 2.5, meaning a diet of half plants and half (vegetarian) animal origin. In fact, the human diet includes few non-vegetarian animals – veal calf and some fish (farmed which are fed on fishmeal and wild such as mackerel) are obvious exceptions.

The PNAS paper also considers temporal changes. The increase in animal consumption in China and India is evident: the trophic level  increasing from 2.05 to 2.20 in the last half-century. Iceland, in contrast, has declined from the exceptionally high 2.76 to 2.57.

Sylvain Bonhommeau, Laurent Dubroca, Olivier Le Pape, Julien Barde, David M. Kaplan, Emmanuel Chassot, and Anne-Elise Nieblas 2013. Eating up the world’s food web and the human trophic level PNAS 2013 : 1305827110v1-201305827.

Link to abstract/Paper ($$££)  dx.doi.org/10.1073/pnas.1305827110

ABSTRACT:

Trophic levels are critical for synthesizing species’ diets, depicting energy pathways, understanding food web dynamics and ecosystem functioning, and monitoring ecosystem health. Specifically, trophic levels describe the position of species in a food web, from primary producers to apex predators (range, 1–5). Small differences in trophic level can reflect large differences in diet. Although trophic levels are among the most basic information collected for animals in ecosystems, a human trophic level (HTL) has never been defined. Here, we find a global HTL of 2.21, i.e., the trophic level of anchoveta. This value has increased with time, consistent with the global trend toward diets higher in meat. National HTLs ranging between 2.04 and 2.57 reflect a broad diversity of diet, although cluster analysis of countries with similar dietary trends reveals only five major groups. We find significant links between socio-economic and environmental indicators and global dietary trends. We demonstrate that the HTL is a synthetic index to monitor human diets and provides a baseline to compare diets between countries.

Significance
Here we combine ecological theory, demography, and socioeconomics to calculate the human trophic level (HTL) and position humans in the context of the food web. Trophic levels are a measure of diet composition and are a basic metric in ecology, but have never been calculated for humans. In the global food web, we discover that humans are similar to anchovy or pigs and cannot be considered apex predators. In addition, we show that, although countries have diverse diets, there are just five major groups of countries with similar dietary trends. We find significant links between HTL and important World Bank development indicators, giving insights into the relationship between socio-economic, environmental, and health conditions and changing dietary patterns.

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Aquaculture, farming and development: an FAO consultation

Pearl River Fish Farms, Guangzhou, China

Pearl River Fish Farms, Guangzhou, China

Aquaculture has major prospects for providing high quality, palatable protein for people. Compared to other animals, the conversion of plants into animal protein in fish, shellfish and crustaceans is very efficient: the ratio of input food to output is less than 2:1 (typically 1.6 to 1.8:1), compared to 2.5 to 3:1 for pigs and poultry, and 5 to 10 or more for cattle. This is most likely because fish and shellfish are cold-blooded and hence do not need to expend energy on keeping warm. Fish and shellfish farming has a long history – fish ponds are ubiquitous in mediaeval buildings, and gardeners in older houses in the UK continuously dig through ancient shells – but has declined since. Now, fish farming or heavily managed fisheries are having a upsurge worldwide. The picture shows expanding fish farms in China along the Pearl River in Guangzhou, while the video below shows managed fishing of tilapia in Lake Hawassa, Ethiopia.

FAO has now asked for comments on a consultation document from a “High Level Panel of Experts” on Fisheries and Aquaculture. The draft version 0 is at: HLPE-Fisheries_and_Aquaculture_Draft-V0_18-Nov-2013 locally, or from FAO at this link.

Tilapia - The fish and global harvest (Wikipedia)

Tilapia – The fish and global harvest (Wikipedia)

The huge increase in farming of just one species, Tilapia, is illustrated in the report (right).

Of course, aquaculture is not the only source of enhanced protein: many ways to process proteins (and particularly soybean) are possible. There has been some discussion on the web about insects as food. Insects have a long history as both domesticated and co-domesticated species, in both cases dating back to the start of agriculture 10,000 years ago. The genomes of honeybees and silkworms show selective sweeps have occurred during domestication, and the cultivated species are substantially different from their wild relatives. Hundreds of insect pest species of animals, plants and human habitations have undergone strong selection too.

My comments for the report consultation are as follows:

I am making some brief comments on the zero draft consultation “The Role of Sustainable Fisheries and Aquaculture for Food Security and Nutrition, dated 18 November 2013.http://www.fao.org/fsnforum/cfs-hlpe/fisheries-and-aquaculture-V0

I am a geneticist with interests including improvement of agricultural species, food security and environmental sustainability. There are many important issues addressed in this document; as is stated, despite aquaculture having a 2,500 year history, modern research has been surprisingly limited.

As an overall comment, I felt that many of key statements in the report were unreferenced or referenced to weak and discursive reports rather than rigorous factual studies. This suggests a need for study, and at a number of points in the report, there should be a recommendation of research that is required.

I thought that the references and discussion of the importance of fish genetics was considerably under-represented in the report. Genetics could well have its own complete section, not just a subsection of 3.4. With respect to recommendation 12 of p. 81 line 39, can there be some precise consideration of the genetic features being looked for in species used for aquaculture? Disease again is mentioned, but the epidemiology of fish diseases, as well as their nature and control options, should be looked at in more detail, particularly in relationship to prophylatic controls (antibiotics etc) and having in place control measures and associated legistation.

There is an excellent consideration of the feeds used for fish from page 47. However, there is surprisingly limited consideration of the future feeds, where it is essential to change to more plant-based products. What is required? Why are current plant meals not universal? Will land-based crops or algal foods be more important? What should plant breeders be looking for in producing fish feed?

I felt a few points were underdiscssed at other points: food safety issues may be greater with fish, despite the number of preservation of approaches – drying, salting, cold-chain, processed … Can reduce post-consumer waste – bones and offal used more efficiently (‘co-products) and not discarded? Where is the profit and added value here? There is an excellent consideration of feed conversion figures – but I expect the pork figure has improved considerably since 1999. The report states “Fish oil, which cannot be readily replaced, is expected to continue to slowly increase”: to me, this sounds rather like comments on whale oil 30 years ago. Both plant breeding and plant-oil processing can easily replace in a decadal timescale.

I think the report should include chapters on footprinting of various aquaculture systems: it is important to have both a carbon footprint and a water footprint for aquaculture, carried out in a rigorous and defendable way (unlike, say, the rediculous water ‘use’ figures for beef production which are widely cited). There could be a SWAT analysis of several areas: genetics, preservation, genetic resources, nutrition inputs and outputs.

While the statements about little work on fish are in general true, it is by no means only the case: there are huge parallels with plant domestication, and already there are large genomics projects (stickleback; danio). The genomics revolution can quickly influence fish breeding, and the Canadian Salmon genomic DNA sequence is soon to be published, while that of tilapia is also nearly available. Genetics will be much quicker using these resources, and it should be noted somewhere that already, transgenic fish are already available for purchase, the only animal and vertebrate in this category (albeit for the tropical fish hobbyist).

The report is very valuable in emphasizing the importance and growth in aquaculture, and its contribution to both food security and human nutrition, and I hope will lead to increased amounts of appropriate research and the applications of that research.

 

 

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