New Project on Molecular Cytogenetics and Genomics of Ensete banana

Stachy enset (Ensete ventricosum) corms held by children in a smallholding in Ethiopia, where enset starch is an important staple and food security crop.

Starchy enset (Ensete ventricosum) corms held by children in a smallholding in Ethiopia, where enset is an important staple and food security crop.

We have a research project starting in 2017 on Ethiopian banana, Ensete ventricosum, for 18 months, in collaboration with Royal Botanic Gardens, Kew (Dr Paul Wilkin) and University of Addis Ababa (Professor Sebsebe Demissew). There is a post-doctoral position working with the project (closed 7 August 2017).

The project “Modelling and genomics resources to enhance exploitation of the sustainable and diverse Ethiopian starch crop Enset” is funded by the Global Challenges Research Fund under a Foundation Award for Global Agricultural and Food Systems Research from the Biotechnology and Biological Sciences Research Council (BBSRC).

Our exciting interdisciplinary project seeks to provide the foundation knowledge to help enable the exploitation of the sustainable and diverse Ethiopian starch crop Enset (Musaceae) to support livelihoods in Africa. To this end, we will integrate genomic sequence, molecular diversity, pathology, tissue culture and cytogenetic data, with field and farmer interview data from Ethiopia.

The researcher on the project will be responsible for carrying out and publishing the genomic and laboratory components of the project. You will lead, conduct, and manage a significant laboratory and informatics project in Leicester, UK, integrating your research with field work, working with the lead Ethiopian partner (Addis Ababa University) and modelling at the Royal Botanic Gardens, Kew, under the guidance of the project team.

The work requires experience in plant molecular biology, markers, cytogenetics and genomics or bioinformatics. Ideally this would involve species (crops) with little background data.

Enquiries about the research are welcome and should be made to Prof Pat Heslop-Harrison on phh4@le.ac.uk or 0794 603 4502.

More information about our Ensete project is given at https://molcyt.org/2017/01/17/banana-ensete-and-boesenbergia-genomics-talk-by-schwarzacher-heslop-harrison-harikrishna/, including a lecture which should have been given to an Ensete audience in Addis Ababa, Ethiopia on YouTube, and slides from a lecture at the Plant and Animal Genome PAG conference, San Diego, January 2017 (slides also on Slideshare). Our lab publication page has other relevant information.

 

MAJOR REVISION to the above information and page 9 August 2017 after the application deadline for the research position.

 

 

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The landscape and structural diversity of LTR Retrotransposons in the Musa genome

Nouroz et al. LTR retrotransposons in Musa. Mol Gen Genomics 2017

334. Nouroz F, Noreen S, Ahmad H, Heslop Harrison JS(P). 2017. The landscape and structural diversity of LTR Retrotransposons in the Musa genome. Molecular Genetics and Genomics 292: 1051-1067. http://dx.doi.org/10.1007/s00438-017-1333-1 Publisher site (££$$€€ needs subscription)

Author version of manuscript: Nouroz_MGG2017_MusaLTRretrotransposons_AuthorVer

Long terminal repeat retrotransposons represent a major component of plant genomes and act as drivers of genome evolution and diversity. Musa is an important fruit crop and also used as a starchy vegetable in many countries. BAC sequence analysis by dot plot was employed to investigate the LTR retrotransposons from Musa genomes. Fifty intact LTR retrotransposons from selected Musa BACs were identified by dot plot analysis and further BLASTN searches retrieved 153 intact copies, 61 truncated and a great number of partial copies/remnants from GenBank database. LARD-like elements were also identified with several copies dispersed among the Musa genotypes. The predominant elements were the LTR retrotransposons Copia and Gypsy, while Caulimoviridae (pararetrovirus) were rare in the Musa genome. PCR amplification of reverse transcriptase (RT) sequences revealed their abundance in almost all tested Musa accessions and their ancient nature before the divergence of Musa species. The phylogenetic analysis based on RT sequences of Musa and other retrotransposons clustered them into Gypsy, Caulimoviridae and Copia lineages. Most of the Musa related elements clustered in their respective groups, while some grouped with other elements indicating homologous sequences. The present work will be helpful to understand the LTR retrotransposons landscape, giving a complete picture of the nature of the elements, their structural features, annotation and evolutionary dynamics in the Musa genome.

Keywords: Musa, retrotransposons, Copia, Gypsy, Biodiversity, phylogeny, genomics, evolution.

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Molecular Diversity in some Ghanaian cowpea (Vigna unguiculata) accessions

315. Otwe EP, Agyirifo DS, Galyuon IK, Heslop-Harrison JS. 2017. Molecular Diversity in some Ghanaian Cowpea [Vigna unguiculata L.(Walp)] Accessions. Tropical Plant Biology.:1-11. DOI 10.1007/s12042-017-9184-9
BibT

Cowpea [Vigna unguiculata L. (Walp)] is grown mainly for its protein-rich grains and is consumed in various forms in sub-Saharan Africa. Average grain yield in farmers’ fields is generally low due to a number of biotic and abiotic stresses. One hundred and six cowpea accessions from Ghana, which had previously been evaluated for seedling drought tolerance, were used for this study. This paper attempts to use three multi-locus PCR-based molecular markers; simple sequence repeats (SSR), inter-retrotransposon amplified polymorphism (IRAP) and retrotransposon-microsatellite amplified polymorphisms (REMAP), to analyse genetic diversity in the cowpea accessions. Analysis of the polymorphic bands data indicated that 101 alleles were amplified among 121 cowpea genotypes (83.4%) from 16 SSR primer pairs out of a total of 30 SSR primer pairs. Likewisely, a total of 66 (54.5%) polymorphic bands were obtained from IRAP and a total of 114 (94.2%) highly polymorphic bands obtained from REMAP analysis. The outcome indicated the highly polymorphic nature of the DNA markers, as small groups of these molecular markers were found to be able to identify each of the accessions used. Microsatellite markers (SSRs) and retrotransposon-based markers, like IRAP and REMAP, were found to be highly polymorphic and informative, suggesting that genomic fingerprinting has a major role in characterizing populations

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Speciation in Callitriche (Plantaginaceae): the allopolyploid origin of C. platycarpa

Schwarzacher T, Scrocca V, Johnson K, Gornall RJ. 2016. Speciation in Callitriche (Plantaginaceae): the allopolyploid origin of C. platycarpa. New Journal of Botany. 2016 Sep 1;6(2-3):98-101. DOI: 10.1080/20423489.2016.1271293

Genomic in situ hybridisation (GISH) experiments involving hybridising labelled genomic DNA from the diploid species C. stagnalis, C. obtusangula and C. cophocarpa to chromosome spreads of the tetraploid C. platycarpa (2n = 4× = 20) show that C. stagnalis and C. cophocarpa DNA each hybridise with a different ten chromosomes of the C. platycarpa complement, whereas C. obtusangula DNA does not differentiate between the two genomes. We conclude on the basis of this and other evidence that C. platycarpa is likely to be an allotetraploid derivative of C. cophocarpa and C. stagnalis. This work demonstrates the successful application of GISH to the study of polyploid evolution in the genus Callitriche.

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Chloroplast genomes from apomictic Taraxacum – identity and variation between microspecies

Taraxacum or dandelion chloroplast sequence diversity. Salih et al. PLoS One 2017.

Taraxacum or dandelion chloroplast sequence diversity. Salih et al. PLoS One 2017.

333. Salih RHM, Majeský L, Schwarzacher T, Gornall R, Heslop-Harrison P. 2017.  Complete chloroplast genomes from apomictic Taraxacum (Asteraceae): Identity and variation between three microspecies. PLoS ONE 12(2): e0168008.
doi:10.1371/journal.pone.0168008.

Chloroplast DNA sequences show substantial variation between higher plant species, and less variation within species, so are typically excellent markers to investigate evolutionary, population and genetic relationships and phylogenies. We sequenced the plastomes of Taraxacum obtusifrons Markl. (O978); T. stridulum Trávniček ined. (S3); and T. amplum Markl. (A978), three apomictic triploid (2n = 3x = 24) dandelions from the T. officinale agg. We aimed to characterize the variation in plastomes, define relationships and correlations with the apomictic microspecies status, and refine placement of the microspecies in the evolutionary or phylogenetic context of the Asteraceae. The chloroplast genomes of accessions O978 and S3 were identical and 151,322 bp long (where the nuclear genes are known to show variation), while A978 was 151,349 bp long. All three genomes contained 135 unique genes, with an additional copy of the trnFGGA gene in the LSC region and 20 duplicated genes in the IR region, along with short repeats, the typical major Inverted Repeats (IR1 and IR2, 24,431bp long), and Large and Small Single Copy regions (LSC 83,889bp and SSC 18,571bp in O978). Between the two Taraxacum plastomes types, we identified 28 SNPs. The distribution of polymorphisms suggests some parts of the Taraxacum plastome are evolving at a slower rate. There was a hemi-nested inversion in the LSC region that is common to Asteraceae, and an SSC inversion from ndhF to rps15 found only in some Asteraceae lineages. A comparative repeat analysis showed variation between Taraxacum and the phylogenetically close genus Lactuca, with many more direct repeats of 40bp or more in Lactuca (1% larger plastome than Taraxacum). When individual genes and non-coding regions were for Asteraceae phylogeny reconstruction, not all showed the same evolutionary scenario suggesting care is needed for interpretation of relationships if a limited number of markers are used. Studying genotypic diversity in plastomes is important to characterize the nature of evolutionary processes in nuclear and cytoplasmic genomes with the different selection pressures, population structures and breeding systems.

http://dx.doi.org/10.1371/journal.pone.0168008

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The agriculture-nutrition-health nexus at the cost of water availability

Terraces conserving water, maize and deserts: the agriculture-nutrition-health nexus. Noorka et al. 2016. ICWRAE 7 proceedings.

Terraces conserving water, maize and deserts: the agriculture-nutrition-health nexus. Noorka et al. 2017. Int J Water Res Arid Env 6: 242-251.

332. Noorka IR, Taufiqullah, Heslop-Harrison JS, Schwarzacher T. 2017. The agriculture-nutrition-health nexus at the cost of water availability in maize diverse genotypes to ensure food security. International Journal of Water Resources and Arid Environments 6(2): 242-251, 2017 ISSN 2079-7079 publisher site: https://psipw.org/attachments/article/401/13e.pdf

Originally published as:  2016. Proceedings of the 7th International Conference on Water Resources and the Arid Environments (ICWRAE 7): 569-578. A presentation by Dr Ijaz Rasool Nooka, University of Sargodha, Pakistan, at the 7th International Conference on Water Resources and the Arid Environments (ICWRAE 7) http://icwrae-psipw.org/ 4-6 December 2016, Riyadh, Saudi Arabia

Link to manuscript: noorka_agriculture_nutrition_health_nexus_water_saudi.

Link to published manuscript: Noorka-Agriculture_Nutrition_Health_Nexus_at_the_Cost_of_Water_AvailabilityIntJWaterRes

A study is made of the use and conservation of important crop plant biodiversity under limited water supply to combat water stress conditions prevailing now throughout the world, creating food shortages and reducing agricultural sustainability. The main objective here is to find suitable plant material which can be grown in arid environments by using crosses and checking the combining abilities, to bear water stress in their life cycles. The most versatile plant, maize, is used by line × tester mating fashion to estimate general and specific combing ability in self and cross combinations of diverse maize genotypes under different water stress environments in Pakistan. Twelve parental genotypes, comprising eight lines and four testers, were crossed to produce 32 F1 hybrids. In next crop season the parents along with their hybrids were evaluated with three water treatments in two seasons. Results showed the nature and magnitude of general and specific combining ability for grain yield and yield related traits like plant height, leaf area, number of kernels per row, ear length, ear diameter, grain yield per plant and harvest index. The significant estimates of GCA and SCA suggested the importance of both additive and non-additive gene actions for the expression of the traits which can help for the selection of parents to be used for the development of useful synthetics and hybrids resilient to contrasting water regimes.

 

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Banana, Ensete and Boesenbergia Genomics talk by Schwarzacher, Heslop-Harrison, Harikrishna

Comparative genomic analysis in Zingiberales: what can we learn from banana to enable Ensete and Boesenbergia to reach their potential?
Talk for Plant and Animal Genomics #PAGXXV

Molecular cytogenetics can address challenges in crops with relatively little background knowledge. This talk shows some work around Ensete ventricosum, known as enset, ensete, False banana, Abyssynian or Ethiopian banana, and also with fingerroot ginger, Boesenbergia rotunda.

Slides are on Slideshare at http://www.slideshare.net/PatHeslopHarrison/banana-ensete-and-boesenbergia-genomics-schwarzacher-heslopharrison-harikrishna

A ten minute talk on Ensete prepared for an audience knowledgeable about Ensete but with less background in genomics is also embedded below from YouTube.

Abstract and text from slides pasted below YouTube video. (https://youtu.be/RZJCDQVedVU – the embed does not work in the conference centre).

Comparative genomic analysis in Zingiberales: what can we learn from banana to enable Ensete and Boesenbergia to reach their potential?
Talk for Plant and Animal Genomics XXV 25 – San Diego January 2017
Trude Schwarzacher, Jennifer A. Harikrishna and Pat Heslop-Harrison, University of Leicester and University of Malaya
phh(a)molcyt.com
Within the Zingiberales there are many orphan crops that are grown in Africa and Asia where recently started genomic efforts will have an impact for the future understanding and breeding of these crops. Advanced genomics and genome knowledge of the taxonomically closely related genus Musa will help identify genes and their function. We will discuss relevant recent work with Musa and results from DNA sequencing, examinations of diversity and studies of genome structure, gene expression and epigenetic control in Boesenbergia and ensete. Ensete is an important starch staple food in Ethiopia. It is harvested just as the monocarpic plant starts to flower, a few years after planting, and the stored starch extracted from the pseudo-stem and corm. A genome sequence has been published, but there is little genomics. Characterization of the diversity in the species and understanding of the differences to Musa will enable selection and breeding for crop improvement to meet the requirements of increasing populations, climate change and environmental sustainability. Boesenbergia rotunda is widely used in traditional medicine in Asia and has been shown to produce secondary metabolites with antiviral activity. For high throughput propagation and metabolite production in vitro culture is employed; embryogenic calli of B. rotunda in vitro are able to regenerate into plants but lose this ability after prolonged periods in cell suspension media. Epigenetic factors, including histone modifications and DNA methylation are likely to play crucial roles in the regulation of genes involved in totipotency and plant regeneration. These findings are also relevant to other crops within the Zingiberales. Further details will be given at http://www.molcyt.com

Banana, Ensete and Boesenbergia Genomics – Schwarzacher, Heslop-Harrison, Harikrishna

  1. 1. Comparative genomic analysis in Zingiberales: learning from banana to enable Ensete and Boesenbergia to reach their potential Banana Genomics – Tue 17 Jan 2017 10.30 PACIFIC SALON 6-7 Mathieu Rouard & Angelique D’Hont Trude Schwarzacher and Pat Heslop-Harrison phh@molcyt.com http://www.molcyt.org
  2. 2. Ensete ventricosum 2nd genus in Musaceae enset, ensete, false banana
  3. 3. • Germplasm: Bizuayehu Tesfaye, Hawassa, Ethiopia
  4. 4. 6
  5. 5. The Global Musa Genomics Consortium • To assure the sustainability of banana as a staple food crop by developing an integrated genetic and genomic understanding, allowing targeted breeding, transformation and more efficient use of Musa biodiversity
  6. 6. • Vision: Musa genetic diversity is secured, valued and used to support livelihoods through sustainable production and improved food and nutrition security. • Actions aim to i) assess Musa genetic diversity, ii) conserve the entire Musa gene pool, iii) maximize use of genetic diversity, iv) apply genomics tools to banana to better support breeding and v) document and make information accessible.
  7. 7. Genomics changes study of taxonomy, phylogeny, diversity Revolutionizes crop genetics and breeding Exploits Musa as a reference
  8. 8. Diploid chromosomes in Musaceae (blue DAPI stain) with centromeric element labelled
  9. 9. Ty1-Copia element Rather few in Ensete RepeatExplorer: Graph-based clustering of related sequences, program/approach by Novák P, Neumann P, Pech J, Steinhaisl J, Macas J. RepeatExplorer: a Galaxy-based web server for genome-wide characterization of eukaryotic repetitive elements from next-generation sequence reads. Bioinformatics. 2013 Mar 15;29(6):792-3. Ensete has a published genome sequence: Harrison J, Moore KA, Paszkiewicz K, Jones T, Grant MR, Ambacheew D, Muzemil S, Studholme DJ. A draft genome sequence for Ensete ventricosum, the drought-tolerant “tree against hunger”. Agronomy. 2014 Jan 17;4(1):13-33. Some abundant tandem repeats in Ensete genome
  10. 10. Analysis with RepeatExplorer A978 Petunia Ensete repetitive DNA distribution Not huge abundance of repetitive sequences in Ensete – 25% of genome Taraxacum
  11. 11. 1000 bp 800 bp Azhar M, Heslop-Harrison JS. Genomes, diversity and resistance gene analogues in Musa species. Cytogenetic and genome research. 2008 May 7;121(1):59-66.
  12. 12. • Abiotic stresses – water, wind, nitrogen, plant nutrition • Biotic stresses – disease – competition, nematodes, fungi, bacteria, viruses, rodents • Environmental challenges – Soil, water, climate change, sustainability • Social challenges – Urbanization, population growth, mobility of people, under-/un-employment – Farming is hard, long work – increased standard of living
  13. 13. • Lee Wan Sin, Gudimella Ranganath, Norzulaani Khalid & Jennifer Ann Harikrishna • Centre for Research In Biotechnology for Agriculture (CEBAR) University of Malaya, Malaysia • Abiotic stress causes >50% of crop losses & is expected to worsen: • Urbanisation & population growth lead to reduction in arable land and fresh water for irrigation • Climate change models predict more extremes of drought and floods (including for Malaysia and other SE Asian countries) • Drought  irrigation  increased salinity  flooding in coastal regions
  14. 14. Transcriptome alignment to banana *genome Use assembled transcriptome to indicate transcript identity and abundance Distribution of transcriptome (31,390 non-redundant unigenes) >99.5% unigenes mapped Coverage >40X 2,000 to 3,200 (6 to 10% of the unigenes) map to each chromorosme Bar lengths reflect numbers of non redundant reads ~5% up-reg ~4% down in NaCl
  15. 15. Transcriptome: Differential expression Gene Ontology (GO) assignments of transcripts (unigenes) non-differentially-expressed / differentially-expressed Binding Transporter activity Cellular & metabolic processes Catalytic activity Response to stimulus 2,993 (9.5%) of the de novo assembled unigenes observed to be differently expressed in salt-stressed banana root (~5% up-reg ~4% down-regulated)
  16. 16. Fingerroot ginger – Bosenbergia rotunda – Zingiberales
  17. 17. • Project on Boesenbergia lead by Norzulaani Khalid & Jennifer Ann Harikrishna Genome sequence Secondary products Tissue culture changes Epigenetics – DNA and chromatin modification
  18. 18. Boesenbergia rotunda PRO-METAPHASE histone H3 dimethylated lysine K4 (49-1004) euchromatin mark at the end of the chromosomes centromeric heterochromatin not stained DAPI H3K4me2 Harikrishna, Khalid, Bailey, Schwarzacher B1-1-O2
  19. 19. Boesenbergia rotunda INTERPHASE histone H3 mono- methylated lysine K9 (49- 1006) hetero- chromatin mark DAPI H3K9me1 Harikrishna, Khalid, Bailey, Schwarzacher overlaps most of the strongly DAPI stained chromocentres (the large DAPI strong area in the middle of the nucleus is due to being the thickest part of the squashed nucleus) B1-3-A
  20. 20. Boesenbergia rotunda METAPHASE histone H3 di- methylated lysine K9 (49- 1007) hetero- chromatin mark DAPI H3K9me2 Harikrishna, Khalid, Bailey, Schwarzacher Mainly stains centre of chromosomses where we assume the location of centromeric heterochromatin to be B1-5-O12
  21. 21. Outputs –CROPS – Fixed energy Inputs –Light –Heat –Water –Gasses –NutrientsLand
  22. 22. Outputs –CROPS – Fixed energy 25 Inputs –Light –Heat –Water –Gasses –Nutrients – Light – Heat – Water – Gasses – Nutrients
  23. 23. Agricultural production • Agronomy • Genetics • Genetics for production systems – technological solutions for sustainable agriculture
  24. 24. Dr Adugna Wakjira, DDG, Ethiopian Institute of Agricultural Research (and co- author/colleague) “Our government recognizes biotechnology as one of the transformative tools to accelerate agricultural development … exemplified by Parliament’s amendment to a more progressive and permissive legislation of biotechnology” But needed quickly: training of new scientists to deliver local solutions. Certainty needed
  25. 25. • United Nation’s Sustainable Development Goal (SDG) targets for 2030, namely Target 15 (Protect, restore and promote sustainable use of terrestrial ecosystems, sustainably manage forests, combat desertification, and halt and reverse land degradation and halt biodiversity loss), with implications for Target 2 (End hunger, achieve food security and improved nutrition and promote sustainable agriculture)
  26. 26. Comparative genomic analysis in Zingiberales: learning from banana to enable Ensete and Boesenbergia to reach their potential Trude Schwarzacher and Pat Heslop-Harrison phh@molcyt.com http://www.molcyt.org
  27. 27. The genome and genomics of Enset Workshop on Enset (Ensete ventricosum) for Sustainable Development: Current research trends, gaps and future direction for a coordinated multidisciplinary approach in Ethiopia Organizer Sebsebe Demissew – October 2016 Pat Heslop-Harrison phh@molcyt.com http://www.molcyt.org
  28. 28. Molecular Cytogenetics Group http://www.molcyt.com Pat Heslop-Harrison Trude Schwarzacher and colleagues Impacts outside academia Legislation: European Parliament & Commission Breeding new, sustainable crop varieties Sequencing of whole genomes Discussing risk assessment and scientific advice with EU Health Commissioner Dr Vytenis Adriukaitis We study genomes and evolution mechanisms to find, measure and exploit genetic variation in crops, farm animals, and their wild relatives Developing superdomestication strategies to exploit biodiversity for sustainable agriculture Work on hybrids and alien introgression with novel quality / disease resistance characters Wheat with virus resistance identified in the group in breeding trials Diversity, wild genes and recombination in species and landraces DNA sequences we find confer stress resistance in crops New methods for biotechnology Food fraud and safety detection Reviewing research programmes Editing Journals

 

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