ainhoa foto article

Photo: Sonali Ranade


Scots pine is one of the most commercially used tree species in Sweden. To be able to breed lines with improved growth, survival and properties is of great interest for tree breeders and the forest industry. Unfortunately, the tree breeding cycle of Scots pine lasts between 20 to 30 years and that causes that the evaluation of trees in breeding trials requires several years. In her PhD project Ainhoa Calleja-Rodriguez successfully evaluated new statistical methodologies that can aid to reduce the breeding cycle in the future and to improve the accuracy of the genetic parameters on growth, adaptive traits and wood quality traits of Scots pine. She successfully defended her PhD on Wednesday, 29 may at SLU Umeå.

In her study Ainhoa Calleja Rodríguez evaluated different families of Scots pine in several locations all over Sweden. Geographical variation was important as the environment has big impact on the behavior of the trees and with a new statistical method, called factor analysis, she was able to evaluate more characters simultaneously. Another new method called genomic selection was applied for the first time on Scots pine. Ainhoa showed that it may be possible to evaluate trees already at the seedling stage but also gives more accurate estimations of genetic variation of growth and wood quality traits then traditional methods.

Ainhoa was a student of the UPSC industrial graduate research school of forest genetics, biotechnology and breeding. Therefore, she was doing her PhD project not just as student at the department of forest genetics and plant physiology at SLU but also partly at the Swedish forest research institute Skogforsk, which has one main working focus on tree breeding.

Why did you choose your project?
I felt in love with tree improvement through a previous job experience as research technician and also from my master thesis in Spain, so when a colleague in Spain sent me the announce of this position in Sweden, I just did not doubt a second to send my application.

Did the fact that this PhD program you were in was located both in industry and academia influence the decision of starting on it?
Yes, it did, specially the industry part was essential for me to decide about this position. The fact that 20% of my time could be expend as internship at the host company (Skogforsk in my case), and be in direct contact with the operational breeding program and with the tree breeders, it was what made me decide for this PhD position.

What was most fascinating during your PhD?
The most fascinating was the opportunity of being Industrial PhD Student at the Second Research School of Forest Genetics, Biotechnology and Breeding, because it gave us the opportunity to attend PhD courses with the top professors in quantitative genetics and breeding, as well as to have a “field trip” to visit the most advanced breeding programs in USA and Brazil. Also, performing my internship within Skogforsk was also fascinating, especially because at the end one of the projects became part of the thesis and was key to improve my knowledge of quantitative genetics, linear mixed models and ASReml (the most common software used in plant and animal breeding).

What was the most disappointing experience you had during your PhD?
It was really hard to get good quality marker data for Scots pine. First time we tried, it took more than a year and half to get some data and finally their quality was not enough to use them, so the part of genomic prediction of my thesis was delayed. Fortunately when we tried the second time it did not take that long and we finally could use them.

What are your plans for the future?
Last month I had an interview and got a new job at Skogforsk as researcher, so I am finally going to work with the scientists there in the operational breeding program



About the defence:
The public defence took place on Wednesday, 29th of May in P-O Bäckströms sal at SLU Umeå. The faculty opponent was Heidi Dungey, Senior scientist and Science Leader of Forest Genetics, Scion (New Zealand Forest Research Institution) and her supervisor was Harry Wu.

Title of the thesis: Quantitative Genetics and Genomic Selection of Scots pine
Link to the thesis: https://pub.epsilon.slu.se/16094/

For more information, please contact:
Ainhoa Calleja-Rodriguez
Email: This email address is being protected from spambots. You need JavaScript enabled to view it.
IMG 1605 1920x1080

[2019-05-21] On Saturday, 18th of May, the 5th Fascination of Plants Day was celebrated in Umeå with a public event. Almost 300 visitors came to Kafé Fika at Väven and got involved in many different activities around plants and plant science.

What colours are hidden in the leaves of plants? Why are the interactions between plants and insects so important? What are microalgae and how can they be used? The visitors were invited to hands-on activities around those and other topics. They could isolate DNA from strawberries, prepare seed bombs and learn more about how to grow mushrooms.

The aim of the Fascination of Plants Day is to fascinated people for plants and to generate awareness for the importance of plant science. It was launched under the umbrella of the European Plant Science Organisation (EPSO) and was first organised in 2012 on a European level but is now internationally celebrated. This year more than 800 events across 51 countries were organised.

The event in Umeå was organised by scientists from the Umeå Plant Science Centre, the Department of Chemistry, the Department of Ecology and Environmental Sciences, both from Umeå University, the Department of Forest Ecology and Management, Department of Forest Biomaterials and Technology, the Department of Agricultural Research for Northern Sweden, all three from SLU, by Skogforsk, the Forestry Research Institute of Sweden, the Swedish Bonsai society (Bonsaisällskapet) and the Broparken gardening project.

IMG 1418 1920x1080Laxmi Mishra from the Department of Chemistry, Umeå University, demonstrated for the visitors the different looks of thale cress

IMG 1550 1920x1080Johan Westin from Skogforsk presents the fascinating variation of forest trees.

IMG 1545 1920x1080Yohann Daguerre (front left) and Regina Gratz (left back) from UPSC challenged the visitors with their botanical quiz

Photos: Anna Shevtsova

Hong defense 1920x1080Harry Xiaming Wu (left) and Thi Hai Hong Nguyen (right); photo: Sonali Ranade

[2019-05-21] Thi Hai Hong Nguyen analysed how genetic variation influences wood and oil quantity and quality in Norway spruce and Melaleuca, a multi-purpose tree distributed in Australia, Papua New Guinea and South-East Asia. In her Phd thesis, she recommends tree breeding strategies for the two species to optimize their industrial usage. Thi Hai Hong Nguyen successfully defended her PhD thesis on Friday last week, 17th of May 2019.

Do trees that grow faster have lower wood quality and contain less oil or oil of lower quality? Is it better to use only one clone of a species in forestry or can it be of advantage to plant families, that means related trees that do not contain the exact same genetic composition? The answers to those questions are of high interest for the forest industry. Thi Hai Hong Nguyen estimated in her PhD thesis the genetic parameters that influence wood and oil quality and quantity and looked into the effect of genetic variation of Melaleuca and Norway spruce. Based on her results, she gives advices for tree breeding strategies for the two species.

The public defence took place in P-O Bäckströms sal at SLU Umeå on Friday, 17th of May 2019. Faculty opponent was Prof. Steven E. McKeand from the Faculty of Forestry and Environmental Resources, NC State University, USA. The supervisor was Harry Xiaming Wu.

Title of the thesis: Genetics, breeding and deployment of Melaleuca and Norway spruce

Link to the doctoral thesis: https://pub.epsilon.slu.se/16097/

FACS photo 1920x1080Ioanna Antoniadi at the Fluorescence Activated Cell Sorting (FACS) machine; photo: Sara Raggi

Kungliga Skytteanska Samfundet, a scientific academy based in Umeå, hands out every year prizes for outstanding research and cultural commitment. This year, Ioanna Antoniadi, researcher at the Umeå Plant Science Centre, will receive the prize that is assigned to the Faculty of Forest Sciences from SLU.

Ioanna Antoniadi focusses in her research on root development and the role of plant growth factors that are controlling the development. Kungl. Skytteanska Samfundet valued in their motivation for the prize, that Ioanna Antoniadi contributed to an improved understanding of mechanisms that regulate growth and development of plants, a fundamental knowledge with potential application within plant cultivation.

After finishing her PhD at the Imperial College in London, Ioanna Antoniadi moved to Umeå in 2015. She started in the group of Karin Ljung at the Umeå Plant Science Centre, first as a postdoc and now as a researcher. She has published as author or co-author six scientific publications within the last five years and became the expert at UPSC for Fluorescence Activated Cell Sorting (FACS), a very advanced technique that allows detections on the single cell level.

Ioanna Antoniadi independently developed and optimised new methods based on the FACS technique. She could demonstrate that the plant hormone cytokinin forms a gradient in the root tip of the model plant Arabidopsis thaliana, with the highest concentration in the top. These results were published in the prestigious journal Plant Cell and are now well cited. She also contributed to studies about how plants react on the hormone level to different type of stresses, e.g. salt stress and mechanical stress.

Kungl. Skytteanska Samfundet is awarding in total six prizes to young researchers, a cultural prize, the “Margareta och Eric Modigs” prize that is assigned to the Medical Faculty of Umeå University, a prize for a young artist from the Umeå Academy of Fine Arts, a prize for a young musician from the School of Music in Piteå and the “Samfundets stora pris”. All prizes will be officially handed over at the societies “Årshögtiden” on Friday, 24th of May at Sävargården in Umeå.


About Fluorescence Activated Cell Sorting (FACS):
Cell sorting is a method that allows purification of highly specific cell populations from a mix of cells. It can be for example used to isolate scarce cell types, that are labelled with a fluorescence marker, from a plant tissue. The plant tissue is initially enzymatically digested to remove the cell walls which leads to the formation of protoplasts (plant cells that are surrounded only by the plasma membrane). The protoplast mixture is then loaded into the FACS instrument that acts as an extremely “sharp knife” sorting the cells according to their size, internal complexity and fluorescence. The sorted and isolated cells can then be used for further analyses in downstream applications.



More information about Kungl. Skytteanska Samfundet:
http://skytteanskasamfundet.se

More information about the prize winners 2019:
http://skytteanskasamfundet.se/priser-och-stipendier/2019-2/


For more information about Ioanna Antoniadi’s research, please contact:

Ioanna Antoniadi
Umeå Plant Science Centre
Department of Forest Genetics and Plant Physiology
Swedish University of Agricultural Sciences
Email: This email address is being protected from spambots. You need JavaScript enabled to view it.
Phone: +46 (0)90 786 8628
Twitter: @I_Antoniadi

MarkusSchmid IMG 5981 1920x1080The new Wallenberg Scholar Markus Schmid (photo: Anne Honsel)

[2019-03-25] The Knut and Alice Wallenberg Foundation announced today the names of 22 new Wallenberg Scholars. Markus Schmid, group leader at UPSC and professor at the Department of Plant Physiology, Umeå University, is one of them. He receives a five-year grant that he can invest for his research without any restriction.

Markus Schmid works on the regulation of flowering time. He wants to understand which environmental factors are influencing the plant’s decision to start to flower and how this is regulated in the plant. In the project, that was now approved by Wallenberg, Markus Schmid will focus on the effect of temperature fluctuations not only on flowering but generally on plant growth and development.

“It is a great honour to be appointed Wallenberg Scholar. It gives me and my group security for five years so that we can really focus on our research,” says Markus Schmid. “This project was inspired by observations we made when I was still working in Germany several years ago.”

Then, Markus Schmid and his colleagues had found a mutant of the model plant thale cress (Arabidopsis thaliana) that grows normal at 23 degree Celsius but shows strong developmental defects when grown at 16 degree Celsius. Now they not only want to understand the molecular mechanisms that are underlying this defect but also what controls plant development in response to changing temperatures in general.

“In contrast to most animals, plants have the ability to grow new organs throughout their entire life. Where a new organ is formed is to a large extent genetically determined. However, the growth of the new organ and its final shape is influenced by many environmental signals including temperature”, explains Markus Schmid. “This “phenotypic plasticity” allows plants to adapt fast and flexible to changes in their environment and ensures their survival.”

Markus Schmid will work in this project with the model plant thale cress. He will focus on special tissues, called meristems, that harbour plant stem cells. All new organs derive from those stem cells that are slowly dividing and differentiate to form the specific organ. Markus Schmid and his group want to study how this process is affected by temperature and they want to identify the genes that are involved in this process.

“Markus’ research is very fundamental and will be useful for agriculture and forestry to develop new plant varieties that can cope with a changing climate”, says Ove Nilsson, director of UPSC and since 2013 Wallenberg Scholar. “We are delighted for Markus and that UPSC now has another Wallenberg Scholar. I am myself a Wallenberg Scholar and as a scientist it is the best grant you can have in that it gives you a lot of freedom to pursuit the research where your curiosity leads you”.

The Wallenberg Scholar programme is directed to senior researchers located in Sweden. The funding shall enable them to focus on their research without the pressure of attracting funding. The money can be freely used for the research without any restrictions. After five years, the research of the Wallenberg Scholars will be evaluated and the best ones could get a further extension of the grant for five more years.

Link to the press release from Wallenberg (in English)

Link to the press release from Wallenberg (in Swedish)

Link to the press release from Umeå University (in Swedish only)

For questions, please contact:

Markus Schmid
Umeå Plant Science Centre
Department of Plant Physiology
Umeå University
Email: This email address is being protected from spambots. You need JavaScript enabled to view it.
Phone: +46 (0)90 786 5854
www.upsc.se/markus_schmid

Ministerbesok UPSC 3935 190321 MPN 1920x1080Minister Matilda Ernkrans with Ove Nilsson, director of UPSC, in the Wallenberg Lab 

[2019-03-21] Matilda Ernkrans, Swedish Minister for Higher Education and Research, visited today Umeå University and Umeå Plant Science Centre. She got a tour through the facilities, including the new phenotyping platform and the Swedish Metabolomics Centre, and was discussing actual questions regarding research and society with researcher from UPSC.

Ministerbesok UPSC 3987 190321 MPN 1920x1080At the new phenotyping platform 
Ministerbesok UPSC 4005 190321 MPN 1920x1080At the Swedish Metabolomics Centre 
Ministerbesok UPSC 4055 190321 MPN 1920x1080Discussion in the UPSC lunchroom
Photos: Mattias Petersson
Jansson Stefan 5135 042409 MPN 1920x1080Jansson Stefan (Photo: Mattias Pettersson)

[2019-03-19] Stefan Jansson, Professor at the Department of Plant Physiology, talked on the radio show Morgonpasset on Radio Sweden P3. He explained how trees know that it is autumn, genetic relationships between trees, if they have feelings and why trees can be green in winter.

Please find the full interview here: https://sverigesradio.se/avsnitt/1271073

BKT 2017 1920x1080 MalinGronborgBarbara Terebieniec (Photo: Malin Grönborg)

[2019-03-14] Barbara Terebieniec, PhD student at the Department of Plant Physiology, wanted to identify the factors that determine the shape of a leaf. Using different systems biology approaches, she and her colleagues identified genes that are controlling leaf shape in European aspen. Barbara Terebieniec successfully defended her PhD thesis today at Umeå University.

Why did you choose your project?

I was interested in working with populations and phenotypic traits and leaf shape is one of the most obvious characteristics of the plant phenotype.

What was most fascinating during your PhD?

I was collecting buds throughout the summer and cross-sectioned them to prepare them for the microscope. Like this, I could follow the full development of a leaf from the start until the bud flash under the microscope. That was very fascinating to see.

What was most disappointing during your PhD?

In collaboration with SciLifeLab, we developed and optimized the Spatial Transcriptomics (ST) method for our poplar bud samples. After we successfully optimized the ST method for our bud samples, we realized that the current resolution of this technique for plant samples is too low for the tiny buds. So, we could not answer all our questions even though we achieved what we planned in this project.

What do you like about UPSC?

UPSC with all the people from different countries creates this nice multicultural bubble. I met many nice people and made lots of new friendships.

What are your plans for the future?

Two years ago, I started working on my own start-up. I was very frustrated about keeping track of my lab samples in commonly used -80°C freezers. Our idea was to develop FreezFiler, a digital, non-intrusive system using computer vision. It can be placed on the -80°C freezer to read barcode tagged samples and simplifies the inventory of the freezers. We are now on the way to register a company and launch our first product. It means a lot of work, but also a lot of excitement and I am looking forward for these new challenges.

About the PhD thesis

Barbara Terebieniec and her colleagues exploited several different bioinformatics approaches to identify genes that are controlling leaf shape. Their results show that leaf shape is controlled by a complex network of many different genes and that each of those genes contributes minorly to the final leaf shape.

They compared the genetic setup of a collection of aspen trees with different leaf shape and identified genes that are associated with leaf shape. In a next step, they showed that a number those genes also play a role during leaf development. For this, they compared the genetic setup of leaves of different age, developing on one individual tree.

In an additional approach, Barbara Terebieniec optimized successfully the method spatial transcriptomics for aspen buds together with researchers from SciLifeLab. With this technique they hoped to identify those genes that are specifically expressed in the developing leaf within the bud. Even though they successfully established the method, they could not resolve spatially which genes were active during leaf development in the very young leaf because the size of the tissue was too small for the technique.

About the defence:

Barbara Terebieniec defended her thesis entitled “Using systems genetics to explore the complexity of leaf shape variation in Populus tremula” on Thursday, 14th of March. The public defence took place at 10:00am in Lilla hörsalen (KB.E3.01) in the KBC building, Umeå University. Faculty opponent was Chung-Jui Tsai from the Department of Genetics, University of Georgia, USA. Supervisor of the PhD thesis was Nathaniel Street.

Link to the thesis: urn:nbn:se:umu:diva-156464


For more information, please contact:

Barbara Terebieniec
Umeå Plant Science Centre
Department of Plant Physiology
Umeå University
Email: This email address is being protected from spambots. You need JavaScript enabled to view it.
https://www.kleinlabs.eu/

SPPS prizes 2019 1920x1080The three SPPS awardees from UPSC (from left to right): Åsa Strand, Torgny Näsholm and Karin Ljung (Photo: Anne Honsel)

The council of the Scandinavian Plant Physiology Society (SPPS) has selected the winners of the SPPS Prizes 2019. Three of the seven awardees are affiliated with the Umeå Plant Science Centre. Karin Ljung receives the SPPS Prize, Åsa Strand the Physiologia Plantarum Prize and Torgny Näsholm receives the SPPS Innovation Prize together with Barbara Halkier from the DynaMo Center at the University of Copenhagen.

SPPS is awarding biannually six prizes to acknowledge scientists, located in one of the Nordic countries, for outstanding achievements in plant sciences. Karin Ljung, group leader at UPSC and professor at the Swedish University of Agricultural Sciences (SLU), is receiving the SPPS Prize for her extensive and significant contributions to plant science. She started her own group at UPSC in 2005 and is now for five years in a row acknowledged as one of the Highly Cited Researchers by Clarivate Analytics. Her research focusses on root growth and development and the role of plant growth substances in these processes.

The Physiologia Plantarum Prize goes to Åsa Strand for her recently published ground-breaking work. Åsa Strand, also UPSC group leader and professor at Umeå University, wants to understand how the chloroplasts and mitochondria communicate with the nucleus. Her group identified in one of her recent publications in the journal Nature Communications a new molecular link that synchronizes gene expression in the chloroplast and the nucleus during seedling development in response to light. The Physiologia Plantarum Prize is the only SPPS prize that is open to all researchers world-wide and not only to SPPS-members.

The SPPS Innovation Prize honours scientists who manage to transfer their basic plant research into practical applications. Torgny Näsholm, associated group leader at UPSC and professor at SLU, and Barbara Halkier, professor at the University of Copenhagen and head of the DynaMo Center, are sharing the prize this year. Torgny Näsholm demonstrated that trees use amino acid molecules as nitrogen source. His findings led to the development of new fertilizers. Barbara Halkier and her group are working on plant-specific substances that are serving for example as defence compounds. Based on their results, they have together with Bayer Crop Science developed a new, more resistant oilseed crop.

The other three awards go to Jens Sundström and Charles Melnyk, both from the Swedish University of Agricultural Sciences (SLU) in Uppsala, and to Moona Rahikainen from the University of Turku. She receives the SPPS Best PhD thesis prize. Jens Sundström receives the SPPS Popularisation Prize, a prize that awards public engagement for plant research. Charles Melnyk gets the SPPS Early Career Prize to honour the significant progress he made in setting up his independent research group. The awards are officially handed over in the biannual SPPS Congress that will be held this August in Umeå.

More information about the prizes on the SPPS homepage: http://spps.se/spps-prizes/

More information about the prize winners:
Karin Ljung: www.upsc.se/karin_ljung
Åsa Strand: www.upsc.se/asa_strand
Torgny Näsholm: www.upsc.se/torgny_nasholm and https://www.slu.se/en/cv/torgny-nasholm/
Barbara Halkier: https://dynamo.ku.dk/people/halkier/
Jens Sundström: https://www.slu.se/en/departments/plant-biology-forest-genetics/research/groups/jens-sundstrom/
Charles Melnyk: https://melnyklab.wordpress.com/
Moona Rahikainen: https://www.utu.fi/en/people/moona-rahikainen
Link to her PhD thesis: https://www.utupub.fi/bitstream/handle/10024/145000/AnnalesAI582Rahikainen.pdf?sequence=1&isAllowed=y

Sommarin marianne 0801 110923 EBE 1920x1080Marianne Sommarin, Professor at the Department of Plant Physiology, Umeå University (Photo: Elin Berge)

The University board of Umeå University has decided to award Marianne Sommarin with Umeå University’s Medal for Merit. The Medal is given to people that made particularly significant contribution to the University.

Marianne Sommarin started to work as guest professor at the Umeå Plant Science Centre in 2003 and became Professor at Umeå University in 2018. She was Deputy Vice-Chancellor of Umeå University in the years 2008-2016, advisor for the Vice-Chancellor and had assignments for a number of national research infrastructures. She is currently chair of the national board of the MAX IV Laboratory, the Swedish synchroton facility.

Find more information in the Swedish Press Release from Umeå University