Postdoctoral PDA RA positions in South China Botanical Gardens Plant Genome Evolution Research Group

South China Botanical Garden, Chinese Academy of Sciences (SCBG, CAS)

Postdocs at the South China Botanical Garden, Chinese Academy of Sciences (SCBG, CAS)

Two post-doctoral positions, one MSc and one PhD position are currently open in the newly established “Plant Genome Evolution Research Group”, Principal Investigator JS (Pat) Heslop-Harrison, at the South China Botanical Garden (SCBG), Chinese Academy of Sciences (CAS), Guangzhou. I’m very happy to be starting this new lab with distinctive research projects.

Musella (or Ensete) lasiocarpa from Yunnan, China: one of the species in the Zingiberales where we will be investigating genome evolution

Musella (or Ensete) lasiocarpa from Yunnan, China: one of the species in the Zingiberales where we will be investigating genome evolution

We have developed an exciting programme at SCBG, with a focus on repetitive DNA and polyploidy in plant genome evolution. While many labs are interested in genes and genomes, repetitive DNA makes up the majority of most genomes and is the most rapidly evolving component. With the ability to generate large amounts of DNA sequence, new technologies for sequencing long continuous stretches of DNA, and better cytogenetic approaches (including use of massive oligonucleotide pools) and new approaches to bioinformatic analysis, we can now tackle important questions about genome evolution. With the broad remit in biodiversity research, the project will use many of the rich genetic resources in major plant groups including the Zingiberales and grasses. Some of the programmes are described in a little more detail on our new SCBG website, http://english.scbg.cas.cn/re/rc/psc/psc11/ . The lab is in a new building on the research site of SCBG, and will be well equipped for efficient work on molecular biology, cytogenetics and bioinformatics. The programme will target publications in high profile journals.

One of the first experiments in the new Plant Genome Evolution Research lab in November 2018.: Dr Qing Liu and researchers.

One of the first experiments in the new Plant Genome Evolution Research lab in November 2018: Dr Qing Liu and researchers.

Pat Heslop-Harrison outside the new research buildings at SCBG. The labs and offices of the Plant Genome Evolution research group are on the ground floor.

Pat Heslop-Harrison outside the new research buildings at SCBG. The labs and offices of the Plant Genome Evolution research group are on the ground floor.

Other background to the PI’s research underpinning the work in SCBG is given at www.molcyt.com, www.molcyt.org, and our publications at Orcid https://orcid.org/0000-0002-3105-2167 or  (not available in China) https://scholar.google.co.uk/citations?user=SAsXvrAAAAAJ&hl=en . I will spend approximately 20% of my time in China with this research group, and 80% in University of Leicester, UK. The Leicester Molecular Cytogenetics Laboratory will continue with a range of separate and distinct projects.

 

The two postdoctoral positions are for a

researcher in molecular cytogenetics and genomics and for a

researcher in bioinformatics and genomics

The job descriptions and requirements are given in the links. The appointment procedures, conditions and employment rules will follow those of SCBG, CAS, and international norms (in Chinese; Google or Bing translate will give the sense of the document). Both posts will be advertised widely on public websites such as http://muchong.com/t-12717186-1 . Applications for the post-doctoral positions will be evaluated soon after receipt, and we are planning to interview short-listed applicants from mid- January 2019. The working language will be English, although it is likely that the successful candidate for at least one of the posts will be fluent in Mandarin/Chinese. We expect the appointments to be highly competitive.

The positions will allow the right candidates the chance to join a small, new, international research team with the opportunity to make significant advances in developing models and elucidating mechanisms of plant genome evolution. Work will be collaborative both within the group and with other researchers, and will have a broader impact in plant breeding, genetics, exploitation of biodiversity and for ecology and conservation.

Applications should be made by e-mail to Pat Heslop-Harrison ( phh@molcyt.com ) and Qing Liu ( LiuQing@SCBG.AC.CN ), including a CV/Curriculum vitae, list of publications and presentations, and a letter describing motivation to join the research group.

(Draft text 8/12/2018 to be confirmed.)

Main entrance to the SCBG, occupying 1155 ha (2800 acres) in the North of Guangzhou

Main entrance to the SCBG, occupying 1155 ha (2800 acres) in the North of Guangzhou

The main conservatory/greenhouse complex of the South China Botanical Garden, including tropical, aquatic, and, in a cooled area, alpine species.

The main conservatory/greenhouse complex of the South China Botanical Garden, including tropical, aquatic, and, in a cooled area, alpine species.

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IAEA-FAO Manual on mutation breeding and introduction to plant breeding and selection

IAEA/FAO Manual on Mutation Breeding Book Cover 2018. Download from http://www.fao.org/3/I9285EN/i9285en.pdf

IAEA/FAO Manual on Mutation Breeding Book Cover 2018. Download  free from http://www.fao.org/3/I9285EN/i9285en.pdf

346. Nielen S., Forster BP, Heslop-Harrison JS. 2018. Mutagen effects in the first generation after seed treatment: biological effects of mutation treatments. Chapter 4 In: FAO/IAEA. Manual on Mutation Breeding – Third edition. Spencer-Lopes MM, Forster BP, Jankuloski L (eds), Food and Agriculture Organization of the United Nations. Rome, Italy. 301 pp. Free download of whole book:

http://www.fao.org/3/I9285EN/i9285en.pdf

The third edition of the Manual on Mutation Breeding, prepared by the IAEA/FAO (International Atomic Energy Agency/Food and Agriculture Organization of the United Nations) Joint Division in genetics and plant breeding describes advances in plant mutation breeding, in irradiation techniques as well as in the use of chemical mutagenesis, in seed-propagated and vegetatively propagated crops, and in the types of traits that we believe warrant urgent attention to achieve the set target of global and nutritious food security for all. It also provides a comprehensive overview and guidelines for new high-throughput screening methods – both phenotypic and genotypic – that are currently available to enable the detection of rare and valuable mutant traits and reviews techniques for increasing the efficiency of crop mutation breeding. Over 3275 mutant varieties in more than 220 plant species have to-date been officially released worldwide (see http://mvd.iaea.org/). Their value is measured in billions of dollars of additional revenue, in millions of cultivated hectares and – most importantly – in innumerable people leading happy and healthy lives.

Chapter 4 discussed the first mutation population (M1) suffers from physiological disorders as a result of the mutagen treatment. This is a major reason why phenotypic selection for mutation cannot be done in the M1 generation. In addition, most induced mutations are recessive and therefore the mutant phenotype cannot be observed until the mutation is homozygous. Moreover, the mutation induced is originally a one-cell event and is not present in every cell of the plant. Thus, M1 plants must be regarded as chimeric plants. For practical purposes the most important effects are growth retardation, sterility and death of the M1 plants. Physiological disorders may be linked to chromosomal and/or extrachromosomal damage, but a separation of the two causes is usually not possible.
Regardless of these effects, the general weakened state of M1 plants usually means that the M1 population should be grown in benign (stress-free) environments to maximise growth, fertility and the production of the next (M2) generation.

346. Nielen S., Forster BP, Heslop-Harrison JS. 2018. Mutagen effects in the first generation after seed treatment: biological effects of mutation treatments. Chapter 4 In: FAO/IAEA. Manual on Mutation Breeding – Third edition. Spencer-Lopes MM, Forster BP, Jankuloski L (eds), Food and Agriculture Organization of the United Nations. Rome, Italy. 301 pp. Free download of whole book:

http://www.fao.org/3/I9285EN/i9285en.pdf

 

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A global strategy for the conservation and use of coconut genetic resources 2018-2028

345. Baudouin L, Heslop-Harrison P, Pereira MG. 2018. 3.9.2 Preparing the era of marker-assisted breeding – Chapter 3. Where we need to be to secure diversity and promote use. In Bourdeix R & Prades A (Eds.), A Global Strategy for the Conservation and Use of Coconut Genetic Resources 2018-2028. pp 169-171. Montpellier, France. Bioversity International. ISBN 13:978-92-9043-984-4 Download from Bioversity Website.

In the volume: Bourdeix R, Prades A. and members of COGENT (compilers) 2018. A global strategy for the conservation and use of coconut genetic resources 2018-2028. COGENT 239 pp. Published by Bioversity International, Rome.

See also the Summary Brochure: Global strategy for the conservation and use of coconut genetic resources 2018 -2028 for a more concise synthesis of the full Global Strategy for
the Conservation and Use of Coconut Genetic Resources which has been developed by experts both in coconut genetics and breeding, as well as other from along the coconut value chain. COGENT considers that the Global Strategy will provide an informed and realistic foundation for prioritizing coconut research and development. The goal is to use this Strategy to invigorate the commercial coconut sector in a sustained manner, while protecting food security, by encouraging partnerships that increase the impact of research and adoption of technological innovations. COGENT encourages international, regional and national public research organizations, development agencies, NGOs, the private sector and other stakeholders to use the priorities set out herein to guide their activities
and investment decisions.

CoconutGenomics.jpg

Link to book “A global strategy for the conservation and use of coconut genetic resources 2018-2028”

Grown on more than 12 million hectares, the coconut palm (Cocos nucifera L.) is a culturally and economically important livelihood crop for millions across Southeast Asia, the Asia-Pacific, Africa and Latin America. Fully developed and strategically used, coconuts could help increase food production, improve nutrition, create employment opportunities, enhance equity and help conserve the environment. The future of global coconut production and livelihoods critically depends on the availability of genetic diversity and the sustainable use of this broad genetic base to breed improved varieties. Harnessing and conserving agrobiodiversity are critical to sustainably boosting productivity and livelihoods, and addressing important challenges including those posed by climate change or pest and disease epidemics. More than 95% of coconut farmers are resource-poor smallholders lacking the voice needed to influence government policy or private sector practices.

Phenotypic differences are found between coconut plants, and particularly between four sets of populations: Indo-Atlantic Talls, Pacific Talls, Pacific Dwarfs and introgressed Talls. We plan GBS experiments where each of these genetic groups will be represented by two cultivars with 25 individuals per population, so about one and half hectares of coconut plantation will be required. This set will have to be planted by the breeders interested in developing a genomics-based approach and who are ready to plant the field plots needed for this approach. Germplasm exchanges will have to be carefully monitored, preferably going through a quarantine centre having disease indexing facilities.

Phenotypic characterization will include:
• Phenology and biomass assessment (leaves, stem, roots and reproductive apparatus) which provides the net balance of the ontogenic development and the entire integration of the metabolism efficiency at plant scale.

Nuclear DNA will be sequenced using two complementary techniques, Illumina HiSeq2500 (~150 bp) with a ≈ 80 x coverage, Roche 454/454+ (coverage ≈15x). A new BAC library will be constructed for dwarf genotype and BAC clones will be sequenced to get the coverage of 4 x. Targeted re sequencing of the coconut genome for the specific loci will be done using solexa. A saturated map will be produced by anchoring a core set of SNP markers and available SSR markers to the existing map.

Genotyping by sequencing will be followed for a minimum of 100 individuals each from a population created in Côte d’Ivoire (for saturated linkage map itself), and from a population created in the Philippines (for subsequent QTL mapping). These progenies and their parent palms will represent the global diversity of coconut. A progeny from China,
derived from the cross between the Hainan Tall and the Malayan Yellow Dwarf, will also be integrated within a few years.

Functional annotation consists of attaching biological information to genomic elements to annotate their biochemical, biological, regulatory or interactive functions.

• Measure of water use efficiency (WUE) and gas exchanges, possibly complemented
by the carbon isotopic signature (13C/12C ratio) is liable to uncover variations
between genetic groups and between individuals in the transpiration and
photosynthetic processes.
• Assessment of leaf functional traits (leaf life-span, leaf area, specific leaf area, etc)
are likely to shed light on the differences between Tall and Dwarfs.
• Finally, metabolomic analyses of biological samples (leaflets, inflorescence stalk,
sap, fruits) will reveal variations of the amount of components, such as minerals, in
relation with total non structural carbohydrates as well as metabolite profiling
across cultivars.
In complement to this approach, collecting soil samples from the sites of these
experiments for future metagenomics analysis will indicate if performance/
characteristics are related to soil microflora rather than genotype or epigenetics.
It is also essential to develop a genomic approach to identify and link molecular
marker associations with disease resistance genes. This will allow marker-assisted
selection (MAS) in segregating populations from various resistant or tolerant
germplasm sources.

 

345. Baudouin L, Heslop-Harrison P, Pereira MG. 2018. 3.9.2 Preparing the era of marker-assisted breeding – Chapter 3. Where we need to be to secure diversity and promote use. In Bourdeix R & Prades A (Eds.), A Global Strategy for the Conservation and Use of Coconut Genetic Resources 2018-2028. pp 169-171. Montpellier, France. Bioversity International. ISBN 13:978-92-9043-984-4 Download from Bioversity Website.

Local copy is linked here: Coconut Strategy for Conservation and Genetics Resources Bioversity Cogent Bourdeix_2018

In the volume: Bourdeix R, Prades A. and members of COGENT (compilers) 2018. A global strategy for the conservation and use of coconut genetic resources 2018-2028. COGENT 239 pp. Published by Bioversity International, Rome.

32 page Coconut Strategy Summary of the whole volume is locally linked here: Summary of Coconut Global Strategy for Conservation, Genetics and Genetic Resources Bioversity 2018

 

 

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Obituary for Dr Mark Goodwin

The late Dr Mark Goodwin talking to Ethiopian farmers and children

The late Dr Mark Goodwin (1960-2018) talking to Ethiopian farmers and children

I am so saddened to write about the sudden death of my good friend, colleague and co-project leader, Mark Goodwin. We had very extensive common interests in the application and delivery of research for developing countries, research ethics, and in the role and importance of tertiary education and pedagogy. His inputs to my thinking about these areas have been critical to my research and how it impacts other people throughout the world, and I will so much miss the opportunities for discussions and working together in the future. His loss is an enormous shock: we spent much of his last day together discussing research and dissemination, and finalizing plans for his summit in Ethiopia the following week.

I first got to know Mark well 10 years ago in the context of the link with University of Gondar. He had real vision behind developing the PhD studentships to support staff members at the Ethiopian University. During previous visits to Ethiopia with Mark, we saw many scientific and cultural highlights together, all of which I am sure were applied in our research and teaching in the future (videos where we were together are on Youtube: Fishing tilapia in Lake Hawassa  or investigating conservation plantings to stop hillside erosion in Aksum). He brought extensive and insightful personal input to every one of us involved in the project, and was a true driver. I also saw a lot of Mark’s incredible help to individual students: in a time when so many want students to be considered as numbers and something to do form-filling correctness, he knew every single one he worked with, and would go out of his way to support them in any way he could, always working so the special talents of individuals came out. He challenged administration if needed or sorted out difficult issues. Examples include arranging for his project students to spend time with me in structured interviews, or finding ways to arrange suitable accommodation and subsistence payments, or working to obtain grants or funding to support visits.

Mark Goodwin (right) with Tesfeye Bizuayeu and Pat Heslop-Harrison in an Enset germplasm collection field

Mark Goodwin (right) with Tesfeye Bizuayeu and Pat Heslop-Harrison in an Enset germplasm collection field

In our current joint project on Abyssinian banana, enset or Ensete ventricosum, Mark, as co-Investigator, has been ensuring we go far beyond scientific goals towards building a group of collaborative stakeholders – including HEIs and established agricultural research organisations. The website http://enset-project.org/ is one of the outputs, with huge input to the contents and structure from Mark. Through Mark’s expertise, we could ensure our research aims were kept close to the agriculture, environmental, social and economic development issues, we kept engagement with the research, showed the necessary commitment to implementing the outcomes through collaborations, networking and negotiation.

I feel so fortunate to have spent a lot of time with Mark on his last day. We had lunch together in the University cafeteria, and had a typical wide-ranging discussions about delivery of impact for research projects and research assessment, the challenges he had just faced so successfully in leading the recruitment of Undergraduate students to the University, how we can ensure a high profile for the need for higher education for international development within governments and the UK, project supervision ideas and challenges, the latest news on our publications and so much more. We moved on to the topic of a meeting we had planned later in the afternoon: Mark was leading the organization of a summit and other meetings in Hawassa and Addis Ababa, Ethiopia, the following week. Mark was found in his office later that evening. He was looking forward to making inputs to the delivery of the development goals, and steering the scientific outputs to seeing how they could be used in education and dissemination, in policy and in application, in sustainable agriculture, economic or rural development, and environmental improvement.

Mark Goodwin with Worku Mhiret in the field in Ethiopia

Mark Goodwin with Worku Mhiret in the field in Ethiopia

I will certainly miss too discussions with Mark about wider issues of ethics, music and arts, global culture and history. He was truly a great friend, and one I could always rely upon. I know he will be missed by his many students and collaborators throughout the world.

Mark was taken from us far too early, but his contributions will live on through his huge impact to both research application and implementation, the development of higher education structures internationally, research evaluation and pedagogy, teaching in the UK and abroad, and the delivery of the projects for development.

Pat Heslop-Harrison

A notice about the sad loss of Mark is also published on the University of Leicester website, giving more details of his huge contributions to the Department of Genetics and Genome Biology and the School of Biological Sciences.

 

 

 

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Biodiversity in Ethiopian linseed: molecular characterization of landraces

342. Mhiret WN, Heslop-Harrison JS. 2018. Biodiversity in Ethiopian linseed (Linum usitatissimum L.): molecular characterization of landraces and some wild species. Genetic Resources and Crop Evolution 65: 1603–1614. https://doi.org/10.1007/s10722-018-0636-3 or author version: Linseed Linum Ethiopia Molecular Diversity Worku Mhiret GRACE 2018 Author Version

Linseed molecular biodiversity and variation. Negash and Heslop-Harrison 2018 GRACE Genet Res Crop Evol 65: 1603

Molecular characterization of germplasm is important for sustainable exploitation of crops. DNA diversity was measured using inter-retrotransposon-amplified-polymorphism and inter-simple-sequence-repeat markers in 203 Ethiopian landraces and reference varieties of linseed (flax, Linum usitatissimum) and wild Linum species. Molecular diversity was high (PIC, 0.16; GD, 0.19) compared to other reports from the species. Genotyping separated reference from landrace accessions, and clustered landrace accessions from different altitudes and geographical regions. Collections showed evidence for recent introduction of varieties in some regions. The phylogeny supported L. bienne Mill. as the progenitor of domesticated L. usitatissimum. Markers developed here will be useful for genetic mapping and selection of breeding lines. The results show the range of characters that 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.

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ImmunoFISH – Simultaneous visualisation of proteins and DNA sequences gives insight into meiotic processes in nuclei of grasses

Sepsi A, Fábián A, Jäger K, Heslop-Harrison JS, Schwarzacher T. ImmunoFISH: simultaneous visualisation of proteins and DNA sequences gives insight into meiotic processes in nuclei of grasses. Frontiers in Plant Science. 9: 1193. https://doi.org/10.3389/fpls.2018.01193

Combined Immunolabelling and In Situ Hybridization FISH. Sepsi et al. 2018. Frontiers Plant Sci 9: article 1193

Combined immunolabelling and in situ hybridization FISH. Sepsi et al. 2018. Frontiers Plant Sci 9: article 1193

ImmunoFISH is a method combining immunolabelling (IL) with fluorescent in situ hybridisation (FISH) to simultaneously detect the nuclear distribution of proteins and specific DNA sequences within chromosomes. This approach is particularly important when analysing meiotic cell division where morphogenesis of individual proteins follows stage-specific changes and is accompanied by a noticeable chromatin dynamism. The method presented here is simple and provides reliable results of high quality signal, low background staining and can be completed within 2 days following preparation. Conventional widefield epifluorescent or laser scanning microscopy can be used for high resolution and three-dimensional analysis. Fixation and preparation techniques were optimised to best preserve nuclear morphology and protein epitopes without the need for any antigen retrieval. Preparation of plant material involved short cross-linking fixation of meiotic tissues with paraformaldehyde (PFA) followed by enzyme digestion and slide-mounting. In order to avoid rapid sample degradation typical of shortly fixed plant materials, and to be able to perform IL later, slides were snap-frozen and stored at -80C. Ultra-freezing produced a remarkable degree of structural preservation for up to 12 months, whereby sample quality was similar to that of fresh material. Harsh chemicals and sample dehydration were avoided throughout the procedure and permeability was ensured by a 0.1–0.3% detergent treatment. The ImmunoFISH method was developed specifically for studying meiosis in Triticeae, but should also be applicable to other grass and plant species.

 

Sepsi A, Fábián A, Jäger K, Heslop-Harrison JS, Schwarzacher T. ImmunoFISH: simultaneous visualisation of proteins and DNA sequences gives insight into meiotic processes in nuclei of grasses. Frontiers in Plant Science. 9: 1193. https://doi.org/10.3389/fpls.2018.01193

 

 

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An Immortalized Genetic Mapping Population for Perennial Ryegrass: A Resource for Phenotyping and Complex Trait Mapping

Velmurugan J, Milbourne D, Connolly V, Heslop-Harrison JS, Anhalt UC, Lynch MB, Barth S. 2018. An immortalized genetic mapping population for perennial ryegrass: a resource for phenotyping and complex trait mapping. Frontiers in Plant Science 9: article 717https://doi.org/10.3389/fpls.2018.00717

Lolium Genetic Map and RI lines showing population structure. Velmurugan et al. 2018. Frontiers in Plant Science 9: article 717

Lolium Genetic Map and RI lines showing population structure. Velmurugan et al. 2018. Frontiers in Plant Science 9: article 717

To address the lack of a truly portable, universal reference mapping population
for perennial ryegrass, we have been developing a recombinant inbred line (RIL)
mapping population of perennial ryegrass derived via single seed descent from a
well-characterized F2 mapping population based on genetically distinct inbred parents
in which the natural self-incompatibility (SI) system of perennial ryegrass has been
overcome. We examined whether it is possible to create a genotyping by sequencing
(GBS) based genetic linkage map in a small population of the F6 generation of this
population. We used 41 F6 genotypes for GBS with PstI/MspI-based libraries. We
successfully developed a genetic linkage map comprising 6074 SNP markers, placing a
further 22080 presence and absence variation (PAV) markers on the map. We examined
the resulting genetic map for general and RIL specific features. Overall segregation
distortion levels were similar to those experienced in the F2 generation, but segregation
distortion was reduced on linkage group 6 and increased on linkage group 7. Residual
heterozygosity in the F6 generation was observed at a level of 5.4%. There was a high
proportion of chromosomes (30%) exhibiting the intact haplotype of the original inbred
parents of the F1 genotype from which the population is derived, pointing to a tendency
for chromosomes to assort without recombining. This could affect the applicability
of these lines and might make them more suitable for situations where repressed
recombination is an advantage. Inter- and intra-chromosomal linkage disequilibrium
(LD) analysis suggested that the map order was robust. We conclude that this RIL
population, and subsequent F7 and F8 generations will be useful for genetic analysis
and phenotyping of agronomic and biological important traits in perennial ryegrass.

https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5991167/pdf/fpls-09-00717.pdf

https://doi.org/10.3389/fpls.2018.00717

Keywords: perennial ryegrass, Lolium perenne, recombinant inbred lines (RIL), genotyping by sequencing, mapping population, phenotyping

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