Diversity and characters in Ethiopian linseed Linum #PAGXXIII Negash Worku

Worku looking at linseed Linum trails in Ethiopia

Worku looking at linseed Linum trails in Ethiopia

Many people have talked about Orphan crops – those where there has been little genetic or other research – and the characterization, evaluation and exploitation of germplasm at the #PAGXXIII Plant and Animal Genome Conference this week. Today, I am talking about work by Negash Worku on the Diversity and Characters in Ethiopian Linseed Accessions. SLIDES BELOW!

Ethiopia is a centre of diversity for linseed, where it is valued for cultural reasons as well as use as food and for export. Limited amounts of the crop are grown widely in Ethiopia, which includes the unique climatic conditions of the tropical highlands (3-15°N, >2000m). A range of some 200 accessions were evaluated for diverse quality, agronomic and morphological traits. They were also genotyped with IRAP (InterRetroelement Amplified Polymorphisms). It is probable that the genetic diversity in this area has not been exploited in breeding programmes. The results show a range of characters which can be exploited, some appropriate for smallholder and commercial farmers in Ethiopia, producing a sustainable, secure, high-value crop meeting agricultural, economic and cultural needs. Analysis of sequence data is likely to allow identification of probes suitable for chromosome identification and potentially tracking chromosomes in breeding programmes.

The slides are on Slideshare, http://www.slideshare.net/PatHeslopHarrison/linseed-linum-or-flax-morphological-molecular-diversity-in-ethiopia-pagxxiii-talk-worku-heslopharrison

Linked here on Molcyt.org there is a preprint of the first paper reporting this work.

Our work with Ethiopian germplasm and the farmer-led trials is overviewed here.

A related post on food security, our interests and needs in water usage and drought is here.


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Transposable Elements in the Musa and Banana Genome: PAGXXIII conference talk

There has been a lot of talk about transposable elements during the Plant and Animal Genome #PAGXXIII meeting this week. As half or more – often 75% – of all the DNA in a plant or animal genome is typically made of class I retrotransposons and class II DNA transposons, this widespread interest is right! My own talk at the Banana genomics session, now live on Slideshare, was one of many of the transposon talks. I focussed on a class of DNA elements, the hAT transposons, where the abundance, diversity and chromosomal localization has not been studied in detail in many species where the hAT elements and their derived MITEs with the major gene deleted. The talk is here: http://www.slideshare.net/PatHeslopHarrison/banana-transposable-elements-the-hat-dna-element-story-pagxxiii

It overviews our work on transposable elements in the Musa or banana genome, using genomic sequence, bioinformatics, diversity panels and in situ hybridization approaches.

References to the work are given at the end of the slideshare.


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2014 in review: Molecular cytogenetics website activity

The WordPress.com stats helper monkeys prepared a 2014 annual report for this blog. Obviously, my New Year’s Resolution must be to put more of the things I do onto the Molcyt.com website, and not have such long gaps. Of course, half-a-dozen posts of more general interest was also put onto AoBBlog.com and I’ll be planning to post more there as well!

Here’s an excerpt:

The concert hall at the Sydney Opera House holds 2,700 people. This blog was viewed about 9,500 times in 2014. If it were a concert at Sydney Opera House, it would take about 4 sold-out performances for that many people to see it.

Click here to see the complete report.

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Diversity in Ethiopian linseed (Linum usitatissimum): morphology and seed oil

Linseed morphological variation. Negash et al. 2015 GRACE Genet Res Crop Evol

Linseed morphological variation. Negash Worku et al. 2015 GRACE Genet Res Crop Evol

Worku N, Heslop-Harrison JS, Wakjira A. 2015. Diversity in 198 Ethiopian linseed (Linum usitatissimum) accessions based on morphological characterization and seed oil characteristics. Genetic Resources and Crop Evolution (GRACE) in press Dec 2014. doi:10.1007/s10722-014-0207-1 (coming soon). And Worku: Linum / Linseed Morphological Diversity in Ethiopia – Author Version.

Morphological and molecular characterization of germplasm is important for the sustainable exploitation of crops. Linseed or flax (Linum usitatissimum L.) is a multipurpose crop grown in many environments for food, feed, fibre and industry. In Ethiopia, a centre of diversity for linseed, it is valued for food and export. Here, we aimed to develop and use a set of morphological descriptors to determine levels and patterns of diversity in Ethiopian germplasm from the tropical highlands (3-15°N, >2000 m a.s.l.) in 198 Ethiopian traditional varieties. The Ethiopian traditional varieties included plants with both fibre and oil-seed stem-branching morphotypes, although most were relatively small-seeded. Traditional variety oil quality was assessed; oil content was as low as 30% compared to 47% reported elsewhere. Days-to-flowering and days-to-maturity varied widely and were highly heritable. Ethiopian linseed had dominant and recessive yellow seed genotypes; some had a recessive twinned or conjoined-seed character. The descriptors developed here will be useful for genetic mapping and selection of breeding lines. The results show the range of characters which can be exploited in breeding lines appropriate for smallholder and commercial farmers in Ethiopia, producing a sustainable, secure, high-value crop meeting agricultural, economic and cultural needs.

And Worku: Linum / Linseed Morphological Diversity in Ethiopia – Author Version.

See also related post: http://molcyt.org/2013/05/07/worku-mhiret-biodiversity-and-its-exploitation-in-ethiopian-linseed/ about the trials.

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The diversification and activity of hAT transposons in Musa genomes

Musa hAT element organization, abundance and phylogeny. Menzel et al. Chromosome Research 2015

Musa hAT element organization, abundance and phylogeny. Menzel et al. Chromosome Research 2014

Menzel G, Heitkam T, Seibt KM, Nouroz F, Müller-Stoerme M, Heslop-Harrison JS, Schmidt T. 2014. The diversification and activity of hAT transposons in Musa genomes. Chromosome Research 22: 559–571. DOI 10.1007/s10577-014-9445-5 and Pubmed link ID: 25377178 And author print hATs in Musa _2014_CR_MenzelEtAlAuthorVersion2014.

Sequencing of plant genomes often identified the hAT superfamily as largest group of DNA transposons. Nevertheless, detailed information on the diversity, abundance and chromosomal localization of plant hAT families are rare. By in silico analyses of the reference genome assembly and BAC sequences, respectively, we performed the classification and molecular characterization of hAT transposon families in Musa acuminata. Musa hAT transposons are organized in three families MuhAT I, MuhAT II and MuhAT III. In total, 70 complete autonomous elements of the MuhAT I and MuhAT II families were detected, while no autonomous MuhAT III transposons were found. Based on the terminal inverted repeat (TIR)-specific sequence information of the autonomous transposons, 1722 MuhAT I- and MuhAT II-specific miniature inverted repeat transposable elements (MuhMITEs) were identified. Autonomous MuhAT I and MuhAT II elements are moderately abundant in the sections of the genus Musa, while the corresponding MITEs exhibit an amplification in Musa genomes. By fluorescent in situ hybridization, autonomous MuhAT transposons as well as MuhMITEs were localized in subtelomeric, most likely gene-rich regions of M. acuminata chromosomes. A comparison of homoeologous regions of M. acuminata and Musa balbisiana BACs revealed the species-specific mobility of MuhMITEs. In particular, the activity of MuhMITEs II showing transduplications of genomic sequences might indicate the presence of active MuhAT transposons, thus suggesting a potential role of MuhMITEs as modulators of genome evolution of Musa.

Keywords Musa acuminata, Musa balbisiana, genome assembly, BAC, hAT transposons, FISH

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The damaging bureaucracy of academic peer preview

  • 309. 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, Hall J, Heslop-Harrison P. Herschbach D, Kimble HJ, Kroto H, Ladyman J, Lawrence P, MacIntyre A, Mattick J, Pelloni B, Randall D, Ray D, Roberts RJ, Seddon K, Self C, Swinney H, Vita-Finzi C. 2014. Peer preview tyranny: The damaging bureaucracy of academic peer preview. Letters. The Daily Telegraph 3 June 2014; p 21. http://www.telegraph.co.uk/comment/letters/10870609/The-damaging-bureaucracy-of-academic-peer-preview.html; commentary at http://www.telegraph.co.uk/science/science-news/10870995/Nobel-winners-say-scientific-discovery-virtually-impossible-due-to-funding-bureaucracy.html
  • SIR – Under current policies, academic researchers must submit their proposals to a small group of their closest competitors – their peers – for consideration before they might be funded. Peers selected by funding agencies are usually allowed to deliver their verdicts anonymously. They assess the proposal’s suitability for funding, whether it would be the best possible use of the resources requested, and determine, if it were successful, the probability that it might contribute to the national economy in some way. If the answers are satisfactory the proposal has roughly a 25 per cent chance of being funded. Peer preview is now virtually unavoidable and its bureaucratic, protracted procedures are repeated for every change in direction or new phase of experimentation or for whatever an applicant might subsequently propose. Consequently, support for research that might lead to major new scientific discoveries is virtually forbidden nowadays, and science is in serious danger of stagnating. Many scientists privately deplore these policies but their professional standing often depends on their acquiescence – a catch-22 that effectively diminishes public opposition to the policies. We call upon funding agencies to support sustained, open-ended research in unfashionable fields.
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Needs for understanding water and food security

Tube wells using water from deep aquifers for irrigation. How can the water be used most efficiently? Are the aquifers being depleted?

Tube wells using water from deep aquifers for irrigation. How can the water be used most efficiently? Are the aquifers being depleted?

“The earth’s land surface receives about 110,000 km3 of rainfall annually. More than half of this water is evapotranspired (transmitted from soils and through plants to the air); about 20,000 km3 falls on land that is cultivated in some form; and about 40,000 km3 becomes available in dams, lakes, rivers, streams and aquifers for human and environmental uses”

I make three critical recommendations for Water and Food Security: a robust, global measurement framework for water; a major genetic research effort related to crop water usage; and education at all levels that is critical to future agricultural sustainability

The water figures above come from the Food and Agricultural Organization of the United Nations Committee on World Food Security – High Level Panel of Experts on Food Security and Nutrition who were commissioned to prepare a report on Water and Food Security. [Guess the organizations who like acronymys: FAO UN WFS (and WFS with a different W) HLPE FSN all appear on the web!] The draft report makes some science-based contribution to the facts and defining needs for water usage and its availability with respect to food security, but in many areas is off-topic and does not cover the ground in relation to the request of the UN Committee on Food Security. People have been invited to comment on the report, and here I am giving my comments and response. I have significant reservations about the impact of the report in the present format.

At a little over 100 pages, it is far from concise, and is poorly structured, so data, recommendations and the key messages are lost. Unfortunately, I think the draft report also misses key aspects where robust scientific advice is needed to inform political, policy and treaty decisions or recommendations. Although indicated in the Terms of Reference, the target audience and route to implementation of recommendations should be made explicit and the report needs focus. I think that many areas of the third chapter, ‘Governing water for FSN’, stray into political issues, when the purpose of this report (and the Terms of Reference) is to provide scientific underpinning for robust policy advice.

In particular, I think there are three critical recommendations required in terms of Water and Food Security.
First, a robust, global measurement framework to collect data a world-wide map with high spatial and temporal (seasonal) resolution is required for water availability, usage and quality, throughout the world. This will inform policy decisions and give a base-line for interventions.
Second, a major genetic research effort is required to understand the genetic variation available within current and candidate agricultural plants, and to an extent animals (including fish and insects), as related to the efficiency of water usage; and to study how this variation can be exploited in current and prospective socioeconomic and farming conditions.

Trude Schwarzacher and HK Chaudhary discuss field selections and trials with students

Trude Schwarzacher and HK Chaudhary discuss field selections and trials with students

Thirdly, education is critical to future agricultural sustainability, ecological management, capacity building and equality. This recommendation should cut across other issues, and is important at all levels from primary school through to post-graduate and farmers.
While I am critical of the excessive length of the report, with discourses on management of somewhat peripheral water-related issues, I believe it does not give enough emphasis to the significant successful (or unsuccessful, and including reactive interventions to water problems) examples where science-based policy changes and management, implemented by farmers and regional governments, have occurred with respect to water and food security (including sustainable usage) usage in many countries over the last century.
– The significant Australian successes are not well covered – they go far beyond the water reform legislation in 2007- 2008; water management has become central in every family farm in that country (many of thousands of hectares) in the last two decades.
– Going further back, the remediation of arguably the greatest human-caused environmental catastrophe, in the 1930s, of the dust-bowls of the Western US, was an example of successful agricultural and water management reacting to a major problem.
– Within this century, two significant new policies are already having major effects on agricultural water usage as well as current and future, The Kingdom of Saudi Arabia has implemented major structural and regulatory changes, away from the plan for high production of cereals (self-sufficiency, as initiated in the 1980s) because it became clear in the 2000s that it is too resource-intensive in terms of water: trade with countries with more water is more efficient and sustainable for cereals. In the Indian Punjab, region-wide changes in agriculture now mean double cropping of much land, but depletion of aquifers was becoming a major possibility; restrictions on irrigation dates are now implemented.

It is good that the report considers the entirety of the position of water in food security and socioeconomic context. However, it is grossly imbalanced: the term ‘sanitation’ is mentioned no less than 133 times, more than twice ‘drink’… or ‘indust’…, or four times ‘salin’…! This is but one example where peripheral issues have high prominence, and I think that major rebalancing is required to focus on key issues. As another example where key issues are buried, the global population change is mentioned multiple times (2050 and two billion more people and increase in meat and oil consumption), the global figure means little compared to the impact in individual countries. For example, on page 16, the graph should show population growth for Ethiopia as well as other lines: the progress from famine of 1984 to a reasonably fed population now, with growth from 40 million to 96 million in the same period, is remarkable.

With respect to my three aims set out above,
I believe it is important that all countries have a rigorous measurement framework for the status of water with a national, high resolution grid, and finer resolution in the vicinity of open water or aquifers (coasts, lakes or major rivers). The appropriate grid scale and parameters must be defined in conjunction with timescales and resource implications, but my suggestion would be 10km over most areas and 1km in water-impacted regions. There should, though, be robust, evidence-based reasons regarding grid size and where a larger grid is appropriate, as it will be in landscapes with even geology, vegetation and unchanging features. The measurements should include water input, flows/extraction, evapotranspiration, groundwater, water tables, salinity, and BOD among other routine parameters. Page 9 notes “In water, data is very often a challenge for action. Data definition, quality and transparency, precision at lower geographical scales, disaggregation by users, and gaps are the biggest issues.” but there is little mention later of the need for international data. Section 8 also has some relevant material.
How will this be implemented? The single mention of “remote sensing” on p79 is extremely weak: it is a key technology for assessment and monitoring of water amounts, distribution, quality and flow; policy definition, development and research on new water usage approaches, even for plant breeding selection approaches. Is it satellite, aircraft, ROV, in situ transponders/sondes? The one mention of remote sensing in the draft report is even in the context of “citizen science” – I would suggest data collection on water is a major duty of every government (as, indeed, it has been up to now) and remote sensing is undoubtably the way to improve the quality and granularity of water data for use by national governments, geographical regions, and international organizations.

As pointed out, water availability is highly variable across time and space and characterised by the complex interactions. Other key methods are isotope analysis with environmental isotopes to assess water resources, recharge of aquifers, nutrient flow an

Irrigated cereal plots in the Persian Gulf

Irrigated cereal plots in the Persian Gulf using groundwater from surrounding mountains

d other aspects of monitoring of water and aquifers: training and standardization of these methods is required. There are problems with current published statistics including quality, granularity, comparison/standardization of types.

It is remarkable that no mention of different crops and plant breeding opportunities except as “Seed multiplication/drought resistant seeds” and “Crop genetic improvement programme/Animal genetic resources/ Genetic improvements can lead to crops that required less water or are more drought resistant” as a vague reference in a table at the very end (p. 101). Such research is critical to the sustainable intensification of agriculture, and the increase of appropriate, rain-fed or ground-water based, agricultural production systems to feed people without overuse of water resources. Plant breeders and research scientists recognize not only that there are huge differences between difference crop species in water use and water quality requirements, but there is also extensive genetic variation within existing crop species and their wild relatives. With more research, the genetics can be discovered and applied to ensuring productive agriculture while using less water.

Ensete trails - Ethiopian banana - trials with PHH and  Bizuayoue Tesdaye. An important crop for food security in drought years

Ensete – Ethiopian banana – trials with PHH and Bizuayoue Tesdaye. An important crop for food security in drought years

There is also need to consider nutritional aims in the breeding context – of both the plants (beyond water requirements), with respect to nitrogen and other nutrients; and importantly with respect to the nutritional value of the crops, the major impactor on human health.
The genetic needs should be in the context of existing programmes but not exclude potential significant contributors: CGIAR Centres, the Joint IAEA/FAO Genetics and Plant Breeding programme, national agricultural research centers (NARs), Universities and the private sector.

A key to ‘Water and Food Security’ is education. There is minimal mention in the report of this aspect beyond a phrase “how to provide small farmers in particular with the necessary information to improve productivity, access to markets etc. In this process, the use of open source software should be the basis of all developments in this field”. Why the limitation to small farmers? Why open source? The private sector has an excellent track record in delivery of products to farmers and teaching them how to use them. Indeed, heavily protected technology such as mobile phones, internal combustion engines, personal computers, or even (unnecessary) soft and alcoholic drinks, have the widest market penetration even when ‘open-source’ equivalents exist. (In the context of open-ness, much more of a problem is that Governments keep publicly-funded data of water use and quality secret.)
The use of water for efficient agriculture starts with the farmer, and it is critical that farmers are given access to up-to-date research and demonstrations of best-practices in water-efficient agriculture. They are the people – female and male – who will make the difference to agricultural water usage and ensure food sustainability. Broader education occurs through early-adopters with demonstration technology, University and NAR outreach centres staffed with people trained to undergraduate or Masters-level. In much of South India for example, the benefits of large numbers of such people are clear in the disease-control and agronomy practices which are now universal. Involvement of communities at all levels, from use of questionnaires through to community partnerships or cooperatives, can deliver sustainable water usage.

Beyond the farmer-level, University research with appropriately trained biologists, agronomists, and geographers is critical to understand the role of water in the environment and food security. Political interference has no part in this science-based training, and there have been problems in implementing and establishing fundamental aspects of agricultural developments. The implementation requires high level governmental support with appropriate funding; international collaborations as the way to develop the new technologies required now and in the next 100 years.

Unfortunately, I feel that the current Draft report is too vague and does not address key issues in a way that has an implementation pathway. No doubt that major interventions are required to increase the sustainability of use of the world’s water, with efficient usage and increased production from agriculture. This can be achieved by measuring water usage, improving the genetics of crops, and teaching people. The policy questions need to be well defined, and lead to high quality and robust scientific advice feeding into those policy questions.

Professor J.S. (Pat) Heslop-Harrison November 2014
Department of Biology
University of Leicester
Leicester LE1 7RH UK
E-mail: phh4@le.ac.uk Skype: Pat.HH Twitter: PatHH1
Websites: http://www.molcyt.com http://www.sblab.org
Phone: +44/0 116 252 5079 / 3381 FAX: +44/0 116 252 2791


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