Worku Mhiret: Biodiversity and its exploitation in Ethiopian Linseed

Worku Mhiret in Linseed trial plots

Worku Mhiret in Linseed trial plots

Worku Mhiret from the University of Gondar, Ethiopia and Pat Heslop-Harrison (University of Leicester, UK) are working on linseed or flax: measuring the diversity of accessions from Ethiopia and comparing this with varieties from Ireland, Canada and elsewhere. We are also making crosses between lines and between cultivars and wild species of Linum;  these are now in the F2 generation. The lines and hybrids are being scored for morphological, disease and quality (oil) characters in the field, and their diversity measured with molecular markers, aiming to find also markers for agronomic and quality characters.

Linum usitatissium, as its Latin name suggests, is truely ‘most useful’. The flax used to make linen, paper and rope, is a bast or phloem-based fibre from the stem of the plant, unlike the cellulose of cotton bolls, and has high-value properties for weaving. The seed oil, linseed oil, has unique food, potential pharmaceutical, and industrial properties – it hardens chemically rather than through drying, so hence its traditional use for cricket bats, paint and putty . Linseed has been grown in Ethiopia for millennia, having food, cultural and economic importance.

The complete project has the title “The molecular and morphological characterization of biodiversity in Ethiopian linseed (Linum usitatissimum) accessions and hybrids”. Currently, some 314,489 molecular marker bands have been assessed across more than 575 lines and hybrid-derivatives.

Farmers and linseed trials in Dhabat, Ethiopia

Farmers and linseed trials in Dhabat, Ethiopia

Linseed Trial Field in Ethiopia

Linseed Trial Field in Ethiopia

Lines which have been evaluated and are of interest for seed production quality are being grown with smallholder farmers as our main project partner and project-owner in Dabat woredas, North Gondar, Ethiopia. Currently, 14 (12 male and 4 female) farmers are involved in the project, and the project results are very promising to get quality seeds with different use values and lines with promising agronomic characters.

Any interested fund donors and researchers can join our project.

Dabat Wored, North Gondar, Ethiopia

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Nauf Alsayaid: PhD student University of Leicester and faculty member Umm Al-Qura University, Kingdom of Saudi Arabia

Nauf Alsayaid

Nauf Alsayaid

My research focuses on understanding the origin and diversity of the genus Crocus (Iridaceae), with particular emphasis on a triploid sterile plant, Crocus sativus (2n=3x=24) that yields Saffron, one of the most expensive spices on earth. The saffron is the stigmas of the flowers, and nearly 200,000 must be collected to give 1kg of spice, valued for its aroma and colour in both sweet and savoury dishes. Saffron is a high value, sustainable crop where improvement is potentially possible through exploitation of diversity within the genus Crocus. It is produced in many countries, with Iran, India (Kashmir), Greece, Italy and Spain being particularly important, each with their own ways of growing and processing the spice. However, the loss of land surface for saffron cultivation, exclusive vegetative multiplication that does not induce genomic variations along the distribution of particular genotypes, may have narrowed down its genetic base, and the process may be still going on. Nevertheless, the actual amount of genetic variability present in Crocus as a genus and in Saffron is largely unknown and it is supposed that Saffron material may be

Paella with rice flavoured and coloured with saffron

Paella with rice flavoured and coloured with saffron

similar around the world.  So an important question is whether the cultivated triploid species has originated only once from its progenitors, or whether there have been several hybridization events.

Saffron does not occur naturally in the wild, and the parental species are yet not defined. Therefore, in my PhD project, I aim to identify the polymorphisms and genomic relationships in species of Crocus section Crocus and some more distant relatives, and particularly the diversity and origin of C. sativus.

Crocus sativus flowers with the stigmas used for saffron

Crocus sativus flowers with the stigmas used for saffron

Since 2009, I have been studying the morphology of the genus Crocus, and exploiting various molecular markers, such as IRAPs, ESTs and SNPs to establish the relationship among the members of the genus and to identify the potential ancestral parents in Crocus sativus. I have also been applying fluorescent in situ hybridization with genomic DNA as probes from various diploid and polyploid candidate ancestors to the chromosomes of C. sativus to identify the species, which may have contributed in the speciation of C. sativus. At present, I am also working to isolate repetitive DNA sequences from various members of the genus Crocus including saffron.

Wild Crocus vernus in Italy

Wild Crocus vernus in Italy

The final analysis of my results shall give a broad picture of the phylogeny of Crocus species and the genomes present in the domesticated species of Saffron. We will be able to conclude whether all saffron is genetically nearly identical, or whether there is variation. Finally, when parental species are identified, we aim to attempt and make new hybrids to resynthesize saffron and compare the different forms.

The research is in the framework of two international projects, the EU FP7 proejct Crocusbank and the COST European programme in Science and Technology Saffronomics studying the biology of saffron and other crocuses, and looking at the quality of the spice.

Nauf Alsayaid (PhD student University of Leicester/faculty member Umm Al-Qura University, Kingdom of Saudi Arabia)

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The origin of saffron: Crocus sativus

The saffron crocus, C. sativus

The saffron crocus, C. sativus

Our research projects are studying the origins and diversity in several polyploid crops: banana, wheats, Brassica, Panicum millets, Nicotiana and the saffron crocus, Crocus sativus. The spice saffron is the stigmas of the flowers, and widely appreciated in Indian and Mediterranean cooking. Saffron crocus is a sterile triploid, with 2n=3x=24 chromosomes – that is, 3 sets of eight. Unlike another cultivated triploid crocus ‘Golden Yellow’ that is widespread in gardens in the spring, the ancestors of saffron are not clear. Within a framework from the Crocusbank EU project and now the ESF Saffronomics project, Nauf Alsayaid and Farah Badakshi have been looking at the relationships, sequences and chromosomes of saffron and wild Crocus species, using a range of molecular and cytogenetic methods. Emanuele Ranieri from the University of Perugia, Italy, joined the project as an Erasmus student and has been working on some of the sequences; he is now completing his thesis.

Happily, Emanuele’s thesis solves the mystery of the origin of saffron: Krokus (Κρόκος) was a beautiful Arkadian young boy in love with the nymph Smilax but Hera, out of jealousy, turned him into a flower and Smilax was turned by the god into bindweed. While the molecular DNA sequence data is not conclusive, I think that it rules out the alternative explanation that Krokus was a companion of Hermes and was accidentally killed by the god during game of discus. Hermes was so remorseful by his death that he transformed Krokus’ body into a flower.

I wonder if our final papers from project will agree with the explanation based on Hera’s transformation?

 

Correction: Whoops – proofing error has C. versus not C. sativus.

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Dr Ijaz Rasool Noorka – Collaborator from University of Sargodha, Pakistan and Visiting Research Fellow

Dr Ijaz Rasool Noorka, University of Sargodha, Pakistan

Dr Ijaz Rasool Noorka, University of Sargodha, Pakistan

Dr Ijaz Rasool Noorka has broad interests in the development of productive and sustainable agriculture for Pakistan and developing countries. His interests complement those of the Molecular Cytogenetics Group, and have enabled us to extend our consideration of the outcomes and impact of our work on exploitation of biodiversity by chromosome engineering.

Ijaz has been a Visiting Research Fellow in the University of Leicester for a year ending in May 2013, holding a highly competitive and prestigious fellowship from the Higher Education Commission, Islamabad, Pakistan. While in Leicester, his practical work included a range of molecular and cytogenetics approaches with wheat, maize and linseed: measuring diversity using IRAP and other markers in Pakistani and control accessions, crossing wheat lines, and in situ hybridization. He was involved in many discussions and the development of concepts and projects related to sustainable agriculture, bringing a wide range of insight into the challenges facing agriculture and food production worldwide. What are the genetic requirements of crops now and in the future to meet the need for more food without trashing the planet? How do we address the challenges of increasing food production in the face of reducing water availability for agriculture and climate change or instability? He was tremendously productive during his Fellowship in completing and publishing many manuscripts based on previous research and on new thoughts and research carried out, and making two visits to the Kingdom of Saudi Arabia with including a high-profile presentation for World Water Day in March, along with other useful visits and conferences.

At the University of Sargodha, Pakistan, Assistant Professor Ijaz Noorka is growing trials of various species, in particular wheats, and working with water management projects integrated with genetic resources. He combines his research and teaching with being Editor of the International Journal of Agriculture and Applied Sciences (IJAAS), Secretary General, Pakistan Agricultural Scientist Society (PASS), and President of the World Forum on Climate Change, Agriculture and Food Security (WFCCAFS). Previously, he served at the On-Farm Water Management Wing, Department of Agriculture, Government of the Punjab, Pakistan for World Bank, Asian Development Bank Funded Projects. He has delivered International lectures and presented research papers at International conferences at Egypt, China, Morocco, South Africa, Iran, Abu Dhabi, Japan, Sudan, Kuwait, India, Malaysia, France, Italy, Singapore, UK, Dubai, Turkey and Kingdom of Saudi Arabia. As well as more than 60 academic publications in Journals, Ijaz has published over 100 articles in Agricultural magazines, newspapers, and through agricultural awareness campaigns at Radio and TV shows.

At the farewell party in Leicester, Dr Noorka noted that he wants to divert his attention towards the improvement and upgrading of Pakistani agriculture and the rural people’s life: to extract all of his experience from field, laser levelling and water course improvement to wide hybridization, new germplasm, molecular markers and fluorescent in situ hybridization, translating to increase the poor people farm income. He also noted Pat Heslop-Harrison’s kindness and international exposure, Dr Trude Schwarzacher’s guidance, and discussions with other groups including Professor David Twell with gene transformation techniques and Prof Sir Alec Jeffery with expert discussions and seminars, as well as the University facilities, extra-curricular activities and Leicester life in a beautiful atmosphere. Pat Heslop-Harrison discussed the commitment of his laboratory to the Millennium Development Goals (MDG), and particularly how the use of biodiversity has both short and long term impacts on 1, eradicating extreme poverty and hunger; 7, ensuring environmental sustainability; and 8, building a global partnership for development (and our work can impact on the remaining goals by improving livelihoods and health).

We look forward to ongoing and productive collaborations.

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Micronutrients in wheat grain

Mitotic and meiotic chromosomes Wheat-Aegilops lines from Neelam et al.

Mitotic and meiotic chromosomes in Wheat-Aegilops lines from Neelam et al.

Following the earlier post on the fate of nutrients and micronutrients applied to crops as fertilizers, today’s paper is about micronutrients in grains, showing enhanced grain micronutrients in wheat-Aegilops longissima lines. Dr HS Dhaliwal from Himachal Pradesh, India, and colleagues including Chetan Patokar, now a research student in the Molecular Cytogenetics group here, study advanced introgression lines, and show approximate doubling of grain iron, zinc, copper, manganese and calcium.  Genes related to grain micronutrient accumulation are located on Ae longissima chromosome arms 2S and 7S, although currently the lines have poor fertility and harvest index so further recombination with chromosomes in elite wheat will be required. The authors suggest these genetic stocks can start to address the ‘hidden hunger’ of the two billion people eating cereals who suffer from iron and zinc deficiency.

Link to paper: Development and molecular characterization of wheat- Aegilops longissima derivatives with high grain micronutrients
Kumari Neelam, Nidhi Rawat, Vijay K. Tiwari, Nikita Ghandhi, Patokar Chetan Arun, Sundip Kumar, Sangharsh K. Tripathi, Gursharn S. Randhawa, Ramasre Prasad and Harcharan S. Dhaliwal

Australian Journal of Crop Science 7(4):508-514 (2013)

Developing food crops with enhanced mineral concentrations is one of the most sustainable and cost effective approaches for alleviation of micronutrient. This article aims at development and molecular characterization of wheat- Aegilops longissima derivatives with high grain micronutrients (iron, zinc, copper, manganese, calcium, magnesium and potassium). Aegilops longissima (2n=14, SlSl) accession 3506 with high grain micronutrients was used for transferring these traits to elite wheat (Triticum aestivum) cultivars through wide hybridization. The fertile HD2687/L3506//WL711 BC1F3 derivatives were developed through selfing and selection for chromosome constitution, meiotic stability and micronutrient concentrations was done at each generation. Sixteen derivatives were finally selected and characterized. The selected backcross derivatives showed enhanced grain iron, zinc, copper, manganese, calcium, magnesium and, potassium concentrations over the parental wheat cultivars by up to 183.6%, 243.6%, 135.18%, 160.42%, 223.29%, 43.90% and 35.05%, respectively. Introgression of chromosomes 2, 7 and 1 from Ae. longissima, confirmed by plant waxiness,GISH, anchored wheat SSR markers and HMW glutenin subunit profiling and was found to be associated with enhanced micronutrients in the derivatives.

Local intranet link: Micronutrients_Chetan_Ae._longissima__AJCS[1]

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New views on fixed nitrogen and other nutrients in crops and the environment

The five key threats of too much or too little nutrients

The five key threats of too much or too little nutrients. Figure ES1 from Sutton et al. “Our Nutrient World”

Two works have been published which substantially update long-standing views about nitrogen and crops. The first, Bender et al. (2013), points out that the whole nutrient balance of maize, and applications of NPK (nitrogen, phosphate and potassium) and micronutrients may well not have kept pace with their removal from fields – because of yield and harvest index – with modern varieties. While nitrogen (and NPK responses) are probably trialled regularly, other elements may not be. Their data show that a hectare of maize crop has no less than 286 kg of N, 202 kg of K2O, down to 80g of boron, and typically 60% of this is removed in the grain yielded by the crop. In the UK, a typical cereal crop would have c. 150 kg N /ha (http://www.ukagriculture.com/farming_today/fertiliser_data.cfm), pretty much what is reported as being removed in this paper.

Bender, R. R., Haegele, J. W., Ruffo, M. L., & Below, F. E. (2013). Nutrient uptake, partitioning, and remobilization in modern, transgenic Insect-Protected maize hybrids. Agronomy Journal105 (1), 161+. URL http://dx.doi.org/10.2134/agronj2012.0352 (abstract below)

The second work gives a global overview of nutrient management and was published on 18 February 2013 as a report, Sutton et al.,  on behalf of the “Global Partnership on Nutrient Management and the International Nitrogen Initiative”. It concludes that “The world’s N and P cycles are now out of balance, causing major environmental, health and economic problems”, and, in agreement with Bender et al., “Insufficient access to nutrients still limits food production and contributes to land degradation in some parts of the world”. The report has a call to action as well: “A new global effort is needed to address ‘The Nutrient Nexus’, where reduced nutrient losses and improved nutrient use efficiency across all sectors simultaneously provide the foundation for a Greener Economy to produce more food and energy while reducing environmental pollution.” A clear cartoon of the nitrogen cycle is also given in the report, and is reproduced at http://blog.ecoagriculture.org/2013/03/20/our-nutrient-world_unep /   : there has been some, although limited, discussion of the report in the blogosphere.

I’m been very suspicious for years of figures like “over 80% of Nitrogen is in fact lost to the environment through runoff, erosion, and greenhouse gas emissions”. Obviously, in a steady state, 100% of the nitrogen is eventually returned to the atmosphere, and unlike carbon, there are no gigantic long-term stores like limestone (calcium carbonate, CaCo3) or fossil fuels (coal, gas and oil). But the Bender et al. paper shows 60% is actually removed for food use!

Mark Sutton, the lead author, writes about aspects of the report at http://cehsciencenews.blogspot.co.uk/2013/02/nitrogen-narratives-in-nairobi.html: ”We need nitrogen, but we need to manage it better. And really: every citizen needs to know nitrogen. Because until they do, the politicians will not be empowered to make decisions, and start taking the local, national and intergovernmental conversation to the next stage.”

The recommended of the citation is a snappy: Sutton M.A., Bleeker A., Howard C.M., Bekunda M., Grizzetti B., de Vries W., van Grinsven H.J.M., Abrol Y.P., Adhya T.K., Billen G.,. Davidson E.A, Datta A., Diaz R., Erisman J.W., Liu X.J., Oenema O., Palm C., Raghuram N., Reis S., Scholz R.W., Sims T., Westhoek H. & Zhang F.S., with contributions from Ayyappan S., Bouwman A.F., Bustamante M., Fowler D., Galloway J.N., Gavito M.E., Garnier J., Greenwood S., Hellums D.T., Holland M., Hoysall C., Jaramillo V.J., Klimont Z., Ometto J.P., Pathak H., Plocq Fichelet V., Powlson D., Ramakrishna K., Roy A., Sanders K., Sharma C., Singh B., Singh U., Yan X.Y. & Zhang Y. (2013) Our Nutrient World: The challenge to produce more food and energy with less pollution. Global Overview of Nutrient Management. Centre for Ecology and Hydrology, Edinburgh on behalf of the Global Partnership on Nutrient Management and the International Nitrogen Initiative. Download from http://initrogen.org/index.php/publications/our-nutrient-world/ or 

Direct link for local users: http://molcyt.files.wordpress.com/2013/03/our-nutrient-world_ceh_nitrogencycle.pdf 

Literature citations:

Bender, R. R., Haegele, J. W., Ruffo, M. L., & Below, F. E. (2013). Nutrient uptake, partitioning, and remobilization in modern, transgenic Insect-Protected maize hybrids. Agronomy Journal105 (1), 161+.  URL http://dx.doi.org/10.2134/agronj2012.0352

Modern maize (Zea mays L.) hybrids coupled with improved agronomic practices may have influenced the accumulation and partitioning of nutrient uptake since the last comprehensive studies were published. The objective of this study was to investigate nutrient uptake and partitioning among elite commercial germplasm with transgenic insect protection grown under modern management practices. Plants were sampled at six growth stages and divided into four fractions for nutrient determination. Total nutrients required per hectare to produce 23.0 Mg ha–1 of total biomass with 12.0 Mg ha–1 of grain included 286 kg N, 114 kg P2O5, 202 kg K2O, 59 kg Mg, 26 kg S, 1.4 kg Fe, 0.5 kg Mn, 0.5 kg Zn, 0.1 kg Cu, and 0.08 kg B. A 10-d period (V10–V14) denoted the maximum rates of accumulation on a per day basis for dry weight (439 kg), N (8.9 kg), P2O5 (2.4 kg), K2O (5.8 kg), Mg (2.2 kg), S (0.7 kg), Zn (14.2 g), Mn (18.0 g), B (3.3 g), Fe (95.3 g), and Cu (3.0 g). Th e majority of total uptake occurred post-flowering for P, S, Zn, and Cu. Harvest index values of P (79%), S (57%), Zn (62%), and N (58%) were identified in the grain. These results provide much needed data on the nutrient uptake and partitioning of current hybrids, and provide an opportunity to further refi ne fertilizer method and timing recommendations for maize biomass and grain production.

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Zubeda Chaudhry: Collaborator from Hazara University, Pakistan and Visiting Research Fellow

Dr Zubeda Chaudhry

Collaborator Dr Zubeda Chaudhry, Hazara University, Pakistan

Dr Zubeda Chaudhry has been a Visiting Research Fellow in the Molecular Cytogenetics Lab, University of Leicester, for a year ending in April 2013. She has been working on the characterization of WRKY transcription factors in the banana (Musa) genome during her Fellowship here, supported by a highly competitive and prestigious fellowship from the Higher Education Commission of Pakistan.

Zubeda has been a staff member at Hazara University since 2009, acting as Chairperson of the Department of Botany, conducting the Board of Study, and holding two successful Green Days Celebrations for Botany students. She has been invited by many institutes for lectures, and  also organised many events for invited lectures from dignitaries in sciences. She ran a substantial project at the Botanical Garden at Hazara University funded by the Pakistan Science Foundation, as well as submitting a project proposal for setting a Bioinformatics department for women at Hazara University to deliver an associated Degree to the women’s colleges. She remains as general secretary for MEXT alumni of Pakistan, participating in many national and international conferences and presenting her research on molecular biology and gene cloning.

The year in Leicester is the second substantial period abroad for Zubeda: she studied at Tohoku University, Japan, as a Monbugakshu Recipient and obtained PhD degree in 1998. After completing her PhD she returned to the National Agricultural Research Centre, Chuck Shahzad Islamabad and served there till 2008. Afterwards I joined International Islamic University Islamabad (IIUI) as Associate professor on TTS in Biotechnology Department, before moving to Hazara.

Zubeda writes, “My Post-doctorate research work was a fantastic experience It was great opportunity to refresh my scientific skills and my writing skills and great chance to get familiar with the advanced research tools and protocols, particularly focusing on the transcription factors in the class WRKY, a characteristic motif in their proteins. There were three complementary parts to my work, first the identification of these motifs within the Musa/banana DNA sequence (bioinformatics); secondly design of primers to amplify WRKY-related sequences from genomic DNA of diverse Musa accessions, followed by sequencing and sequence analysis/comparison (molecular biology); and thirdly DNA in situ hybridization to identify the locations of the WRKY genes along the chromosomes of various diploid and triploid cultivars of banana (molecular cytogenetics). This work involved a wide range of techniques including use of various informatics programs and databases and the manipulation of DNA sequences, isolation of DNA, PCR primer design, DNA amplification  and preparation for sequencing, probe preparation for In situ hybridization, the preparation of chromosome spreads and procedures of in situ hybridization, fluorescence light microscopy, and then the analysis of images and DNA sequence information. These are a range of critical techniques that are required for modern molecular genetics,

The real appreciating matter was the working environment which was quit suitable. I had wonderful time there. To work under the supervision of Prof-Pat Heslop-Harrison was a great opportunity for learning the transposable element, retrotransposon and other similar components of chromosomes.  Wet lab experience in combination with Bioinformatics was a stepping stone for me to explore new ideas. The advance techniques including genius system for contig alignment in order to search homology of the contigs and exploring the genome to identify Polymorphism has been a wonderful new knowledge for me. Dr Trude Schwarzacher guided me the FISH Protocol and invited me to participation in her valuable lectures, she has great visionary impact to my understanding of the concept of Molecular Cytogenetic Studies.

As a result my core expertise beside Plant tissue culture are Plant Molecular cytogenetic, Bioinformatics, system Biology including Gene sequencing ,FISH, Probe preparation, PCR. During my Post Doctorate research work I have participated in an international conference organized by OWDC in Kuwait, and presented a poster. Proposed research papers from my work are now in progress.

My Post Doctorate work expertise will be beneficiary for my country in the future as demands are increasing for sustainable food production. This work will serve for the livelihood improvement for the peoples of Pakistan.

Banana fruits growing

Banana fruits growing

Pakistan is an agriculture based country and future demand for food is burning issue not only in Pakistan but also all over the world, my ambition is to set a Musa Resource Centre. By establishing a diversified Musa Resource Centre in Islamabad with emphasis to Pesticide Reduction Plan which will be helpful to attain the targets of sustainable food production, we will be able develop a joint research scheme by writing a project proposal and will submit to donor agencies across the world. This will help not only for delivering the advance techniques among the students but also enhance a healthy edible banana production. This also shall create job opportunities for new graduates in our country. Further this advance knowledge will equip the students with techniques serve them being useful resources anywhere.

I am confident that this project can deliver my expertise for the improved food production for future and will import great impact on potential local consumers as well as for foreign exporters. I wish to see complete supply chain of Healthy Banana Production in Pakistan, starting from collection of all types of Banana Germplasm and establishment of Molecular Breeding Lab for future disease resistant, pesticide free, improved banana production in and to develop it in collaboration with the world Musa Genome Resource Centre. This work will strengthen international partnership along value chain to our food resources.”

It has been great having here in the lab in Leicester, and we look forward to more collaborations.

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