MASTERS THESIS PROPOSAL

Determination of vernalization gene expression patterns using in situ hybridization and qRT-PCR in grass species

Background:

Vernalization, the requirement of a prolonged exposure to low temperatures to accelerate flowering is particularly important for forage grasses to prevent flower development during winter and protect the environmentally sensitive floral organs. Vernalization pathways are significantly different between Arabidopsis and the grasses as the key flowering repressors (FLC in Arabidopsis and VRN2 in cereals) are not conserved. Understanding the control of flowering time in a range of plant species therefore gives us insights into the ancestral control of flowering time and the evolution of alternative mechanisms in different plant lineages.

Aims and Objectives:

To perform gene expression analysis for clone materials of Lolium perenne and Festulolium (F. pratensis x L. perenne) varying in vernalization requirements by using techniques like RNA in situ hybridization (it helps to localize a specific RNA sequence in a portion or section of tissue) and qRT-PCR for quantitative measurements of gene transcription.

Plant materials:

Clones of two genotypes (201, 204) from the Norwegian L. perenne cv Fagerlin and two genotypes (266, 329) from the Festulolium candivar FuRs9806 which differed in vernalization requirement under natural field conditions, i.e. genotype 201 and 266 which flowered without vernalization and genotype 204 and 329 which needed vernalization to flower.

Methods for gene expression studies: RNA in situ hybridization (will be done in collaboration with Prof. Trine Hvoslef-Eide at the Imaging centre, UMB) and also qRT-PCR with selected candidate genes for vernalization (like vrn1, vrn2) and some interesting related genes (which we are expecting from our ongoing RNA seq. exp.)

For more information, Contact:

Postdocs:

Kovi Mallikarjuna Rao: mallikarjuna.rao.kovi@umb.no

Åshild Ergon: ashild.ergon@umb.no,

Professors:

Odd Arne Rognli: odd-arne.rognli@umb.no

Trine Hvoslef-Eide: trine.hvoslef-eide@umb.no

MASTERS THESIS PROPOSAL

Can we detect selection in meadows using next -generation sequencing?

Background:

Next-generation sequencing technologies are making a substantial impact on many areas of biology, including population genetics. However, genome-scale population genetic studies have been accessible only to well-funded model systems. Restriction-site associated DNA sequencing, a method that samples at reduced complexity across target genomes, promises to deliver high resolution population genomic data and thousands of sequenced markers across many individuals. It has found to be an important technology for ecological population genomics.

Aim: To explore associations between allelic/haplotype shifts and location specific (climate) changes in phenotype for utilization in breeding

Plant Materials: Leaf materials of timothy and red clover collected from different locations in Norway over 3 seasons.

Locations:

– Bjørke (south-inland)

– Særheim (south-coastal)

– Kvithamar (Mid-Norway)

– Vågønes (north-coastal)

– Alta (north-inland)

Methods: ddRAD seq. (double digestive restriction-site associated DNA sequencing) strategy to study allele frequency changes and to detect novel markers for breeding.

1) Pooling equal amount of leaf tissue from the leaf samples collected in each location/year and extract DNA.

2) Sequencing the extracted DNA using ddRAD sequencing approach in collaboration with Skog og Landskap.

For more information Contact:

Postdocs:

Kovi Mallikarjuna Rao: mallikarjuna.rao.kovi@umb.no

Åshild Ergon: ashild.ergon@umb.no

Professor: Odd Arne Rognli: odd-arne.rognli@umb.no

MASTER PROJECTS

Supervisor: Professor Jorunn E. Olsen and research scientist YeonKyeong Lee (IPM). Contact: jorunn.olsen@umb.no HOW DOES TEMPERATURE AFFECT THE DAYLENGTH RESPONSES IN TREES? In trees short days are required for formation of winter buds and development of dormancy and frost tolerance. These and other daylength-controlled processes such as flowering are modified by temperature. However, little is known about the underlying mechanisms. Understanding how temperature and daylength interact will help us understand how trees will respond to a changing climate. The project will investigate mechanisms linked to the temperature modification of action of the daylength in trees (aspen and/or Norway spruce), focusing on the roles of stress-resistance-related compounds such as antioxidants and their relationship with the growth controlling hormones. Performance of plants (growth, winter bud formation) will be studied under different light and temperature conditions and chemical analyses of relevant compounds will be done.

AN EPIGENETIC MEMORY INVOLVED IN CLIMATIC ADAPTATION OF TREES Compared to higher temperature, low temperature during embryo (seed) development in Norway spruce improves winter survival of the plants resulting from these seeds. This is probably due to an epigenetic memory effect which affects gene expression in the plants. Understanding the epigenetic memory effect will help us understand how plants will respond to a changing climate.

The project aims at understanding the epigenetic memory effect by studying how temperature during embryo development affects gene activities in the embryo and offspring plants grown under different light and temperature conditions. (Cooperation with the Forest and Landscape Res. Inst.).

ENVIRONMENTAL CONTROL OF PLANT MORPHOLOGY AND GROWTH The ability to control elongation growth in synchrony with environmental changes is an important adaptive trait, enabling plants to compete and survive under unfavourable conditions. Due to climate change, the difference between day and night temperatures is diminishing. Since plants respond differently to temperature in light and darkness such changes might affect their adaptability. However, currently there is limited detailed knowledge about such temperature-light climate interactions. Besides helping us to understand how plants will respond to a changing climate, such knowledge will also improve our possibilities to exploit plant responses in an environmentally sustainable greenhouse industry. Chemical growth retardants are used to control plant morphology to make them easy to handle and in accordance with the customer`s preferences. It is highly desirable to reduce their use due to significant health and environmental concerns. The project aims to investigate how temperature interacts with light quality and day length in modulation of elongation growth in plants. The involvement of plant hormones in this respect will be studied.

UV-B AS A MORPHOGENETIC SIGNAL In recent years it has been realized that UV-B is not only a damaging agent, but also a morphogenetic signal acting together with other climatic signals such as visible light and temperature. However, effects of interaction between UV-B and other climatic factors such as temperature are not clear. UV-radiation is also known to induce formation of protective flavonoids. However, the relationship between induction of UV-protection and the modulation of morphology is not clear. In addition to an ecological relevance of understanding UV-B-temperature interactions, particularly with respect to climatic change, responses to UV-B may be exploited as a morphogenetic signal in the greenhouse industry to replace the use of chemical growth retardants.

The project aims at understanding effects of UV-B-temperature interaction and the involvement of plant hormones in response to UV-B as a morphogenetic signal and induction of UV-B-protecting substances. Growth experiments under different UV-B-temperature conditions will be performed and experiments with application of plant hormones and use plant hormone mutants will be performed. Chemical analyses of relevant substances are also possible.

Master themes from

Professor Trine Hvoslef-Eide, IPM (Head of the Imaging Centre Campus Ås)

Topics in: Developmental plant biology, plant breeding, bioinformatics.

The topics are suitable for Biology-, Plant Science and Biotechnology students

My research group has focused on studying abscission (knopp- og blomsterfall) since 2001, we have elucidated on this topic from three different angles:

1) Looking for abscission specific genes in poinsettia 2) Describing the changes in the cell walls during abscission 3) Exploring the induction of abscission, with particular interest in the plant hormones involved

Therefore, we have many different angles to specify some of these aspects. By being involved in these themes, you will have the chance to publish your Master thesis as an article (or part of one) in an international journal, if you provide conscientious work with good results.

I recently spent one year research time at the University of Minnesota, USA and have fresh ideas and good collaborative partners there.

Many of the topics can be reduced to accommodate a 15 stp Bachelor thesis, if this is what you are looking for.

Abscission in our model system, poinsettia

Themes involving the model plant poinsettia to study abscission

Hormones involved in floral abscission in poinsettia (julestjerne)

Auxin (IAA):

Electronmicroscopy studies of auxin (IAA) transport in poinsettia – 30 stp: The effect of the auxin transport inhibitor NPA combined with studies in a transmission electron microscope (TEM) using antibodies against IAA. Collaboration with the University of Minnesota, USA.

Studies of auxin (IAA) transport using the auxin transport inhibitor NPA combined with quantification using Gass Chromatography-Mass Spectroscopy (GC-MS) in poinsettia

Gibberellins(GA)

– 30 stp. Collaboration with the University of Minnesota (UMN), USA. The quantification of IAA will be done at UMN.

Gibberellins (GAX) and floral abscission in poinsettia – 30-60 stp. Quantification using Gass Chromatography-Mass Spectroscopy (GC-MS) in poinsettia – 30 stp. Collaboration with the University of Minnesota (UMN), USA. The quantification of GAs will be done at UMN.

Electron microscopy studies of gibberellins (GA) in poinsettia

Abscisic acid (ABA)

– 30 stp: Use of paclobutrazol (an inhibitor of GA biosynthesis) combined with studies in a transmission electron microscope (TEM) using antibodies against GA. Collaboration with the University of Minnesota, USA.

Electron microscopy studies of abscisic acid (ABA) and its interactions with auxin and gibberellins in poinsettia

– 30-60 stp: Use of paclobutrazol (an inhibitor of GA biosynthesis) and NPA (an auxin transport inhibitor) on poinsettia buds combined with studies in a transmission electron microscope (TEM) using antibodies against ABA to study interactions between these hormones in the buds. Collaboration with the University of Minnesota, USA.

Gene expression studies in poinsettia

RNA in situ hybridization in poinsettia

RNA in situ hybridization using genes differentially displayed during abscission in poinsettia

– 30-60 stp. We have many gene sequences from previous studies on differentially displayed genes that can be further examined using RNA in situ to study their expression in time and space in poinsettia buds.

Quantitative Real-Time PCR studies of hormone genes in poinsettia(30-60 stp)

q-RT-PCR quantification studies in poinsettia using genes associated with auxin (IAA), gibberellins (GA) or abscisic acid (ABA)

There are many genes involving these hormones that we can use to make probes for the quantification of their expression during time intervals of floral abscission in poinsettia. A student will start with one of the hormones and continue with others, depending on size of the thesis and the results obtained.

Gene mining comparing Cassava, Jatropha and poinsettia- bioinformatics

Alignment of Differential Display gene sequences from poinsettia with the sequences from the published Cassava genome – 30-60 stp. The Cassava genome was published in 2009, Jatropha in 2011. Since poinsettia, Jatropha and Cassava all belong to the same family, Euphorbiaceae, these

genome comparisons can be very helpful to e.g. mine for longer sequences of the gene sequences we have previously found in poinsettia. The interested student must have at least one bioinformatics course. Depending on the size (30 or 60), the work can also be extended to doing some laboratory work on the selected sequences to obtain full length genes through RACE.

Themes in plant breeding and fingerprinting

Growers in Norway have approached UMB to continue their breeding work from the 1990’s in begonia. The topics in this section are therefore in close collaboration with these producers and will enable the students to get networks in the Norwegian greenhouse industry.

Begonia breeding

Growers are interested in new cultivars of Christmas begonia and novel colours in Begonia x pendula. The obtained new cultivars will be part of their offer to foreign breeders, in exchange for access to their cultivars.

Crosssings and induced mutation breeding in Christmas begonia (Begonia x cheimantha) and subsequent selection for desired traits– 30-60 stp.

Crosssings and induced mutation breeding in tuberous begonias (Begonia pendula) and subsequent selection for desired traits

– 30-60 stp.

Begonia fingerprinting

In order to protect novel varieties in a global market, having them fingerprinted is one way of obtaining this. The student(s) will use different restriction enzymes in combination to obtain unique fingerprints describing each variety. These topics will be in collaboration with Prof. Odd Arne Rognli (IPM).

Fingerprinting in Christmas begonia (Begonia x cheimantha) -30 and 60 stp.

Fingerprinting in tuberous begonia (Begonia pendula

) -30 and 60 stp.

Poinsettia breeding

This has been a long-term interest, here we can compare different transformation techniques to see the effect on gene copy numbers, the distribution of chimeras etc. These topics will be in collaboration with Crop & Food Research, New Zealand and a breeding company in Japan.

Studies of transformation techniques using genes involved in the anthocyanin biosyntehsis to obtain novel colours and study the distribution of chimeras (more than one gene composition

)- 60 stp

Themes in cell- and tissue cultures – mass propagation

I can offer themes in mass propagation of various plants, come and see me to discuss if we can work on the plant you are particularly interested in!

Master thesis titles.

Impact of elemental sulphur on strawberry powdery mildew with its application time of the day and duration.

Elemental sulphur is an oldest fungicide, first recommended for disease control at 1802. Elemental sulphur is still widely used against fungal pathogens, including powdery mildews the world's most familiar (yet poorly known) plant pathogens. While the rapid development of fungicide resistance isolates of powdery mildew for all commercially available fungicide classes, there is no reports of fungicide resistance development against elemental sulphur keep its potential in disease control. In Norwegian greenhouse industry vaporized sulphur is used as fungicides. Restrictive legal attitude toward chemical use and consumer preferences of non chemical products demands the optimization of elemental sulphur application. There is lack of information on whether elemental sulphur has any role in altering host plant resistance, in addition to its known direct effect on fungi. Further, little is known about application time and application duration of sulphur during daily cycles for efficient powdery mildew disease management. These questions will be answered by series of greenhouse and growth chamber experiments.

Growth chamber experiments will be conducted with strawberry/tomato/ cucumber

plants. Sulphur vapour will be applied for following duration 0 h daily (control) 2 h daily 4 h daily 6 h daily

Greenhouse and growth chamber experiments will be conducted in parallel. Three greenhouse compartments (also in growth chambers), two of which having sulphur burner turned on for duration which is determined as optimum from the experiment above (e.g. 2 h) with time of application of Control (no sulphur) 20:00-22:00 02:00-04:00

Inoculated and non inoculated plants those exposed and non exposed to vaporized sulphur will be analysed for changes in host plant resistance Chemical analysis Microscopy

Mechanism of UV-B on powdery mildew disease suppression and its efficiency under different doses of blue light.

We have recently reported the efficiency of short term UV-B applied daily during nighttime on powdery mildews of roses, strawberries and cucumber. We also confirmed the that the efficiency of UV-B depends on background light quality during UV-B application. Blue/UV-A light reduced the efficiency of UV-B against powdery mildew, while red light increased its efficiency. However there is lack of knowledge on whether the effect of UV-B is directly upon pathogen or indirectly via altering host plant resistance. In addition, whether the effect of blue light on UV-B efficiency is dose dependent or not.

DNA damage detection Diseased plants will be exposed to the treatments of 16 h light and 16 h light with

UV-B of 1 Wm-2 for 10 min. Fungal DNA will be extracted as described in (Brurberg et al., 2011) with slight

modification. DNA damage will be assessed by ELISA method described in (Takeuchi et al.,

2007) Or

Fungal spore will be collected by spore sampler and stained with fluorescence antibody specific for DNA damage.

Fluorescence intensity will be measured under microscopy

Experiments will be conducted with UV-B in combination with different blue light doses. Severity of powdery mildew will be assessed DNA damage under each treatment will be assessed

Optical properties of healthy and powdery mildew diseased cucumber leaves and its impact on leaf photosynthesis under low and high irradiance growth light.

Powdery mildew is devastating fungal disease in greenhouse cucumber. At severe stage, it can cause economic losses via photosynthetic reduction, photo assimilate translocation towards pathogen. One of the reason of reduced photosynthesis may due to changes in optical properties of diseased leaves. Our preliminary experiments showed 10 % more light reflection of diseased cucumber leaves compared to healthy leaves. Here in this experiment we want to test whether this 10 % loss of light will reduce leaf photosynthesis at low (100 µmol m-2s-1) and high (600 µmol m-2s-1) growth irradiances.

Cucumber plants will be inoculated with powdery mildew at inoculum levels of 0 spores per ml 100 spores per ml 10000 spores per ml 1000000 spores per ml

Inoculated plants will be exposed to either low or high irradiance levels Leaf photosynthesis and photo-system II efficiency will be assessed in series Diseased leaf area will be assessed in series by digital image analysis Optical properties of leaves from all treatments will be measured and light

harvesting efficiency will be calculated

Day extension spectral quality and its’ ratio on canopy photosynthesis of cucumber under stable optimum and dynamic temperature conditions.

Plants are continuously exposed to changing environments especially air temperature, relative air humidity and quality and quantity of the light spectrum. Under greenhouse production system, these environmental variations can be reduced with additional cost of environmental regulation. The purpose of this study is to examine the canopy photosynthesis of cucumber plants with day extension spectral qualities and its’ ratio under dynamic temperature condition 10 to 35 °C).

Cucumber plants at 4 leaves stage will be grown in gas exchange chamber under dynamic temperature conditions with solar radiation. Supplemental light will be supplied when natural light goes below threshold. Daily lighting period will be 12 h.

Experiment 1 Day extension lighting of 4 h daily will be supplied by different spectral quality

sources (Red, Blue Red & Blue, Full spectrum) under stable air temperature conditions (20-30 °C during day, min 18 °C during night).

Optimum spectral qualities will be selected and used in experiment 2

Experiment 2 Stable day (25-30 °C) and stable night (min 18 °C) air temperature + 4 h of day

extension light quality Fluctuating day (10-30 °C) and fluctuating night (min 10 °C) air temperature + 4

h of day extension light quality Stable day (25-30 °C) and fluctuating night (min 10 °C) air temperature + 4 h of

day extension light quality Fluctuating day (10-30 °C) and stable night (min 18 °C) air temperature + 4 h of

day extension light quality

Experiment 3 Combinations selected from experiment 2 will be tested under normal and

enriched CO2 environments

Why do some grasses succeed in the cold north?

A systems biology perspective

Background

The Pooideae subfamily of the grasses contains economically important cereals like wheat (Triticum aestivum), barley (Hordeum vulgare) and oat (Avena sativa), and forage grasses like ryegrass (Lolium perenne) and meadow fescue (Festuca pratensis). Common for all species of this sub-family is adaptation to cold climate and they constitute more than 90% of all grasses in northern parts of Europe, Asia and America. However, we still do not know the adaptive features responsible for the success of Pooideae in cool areas and how these features evolved within the subfamily.

Classical comparative genomics views differentiation of species as a process driven by diverging protein coding sequences (genes). Over ten years of genomics, however, is starting to paint a different picture where species differentiation is driven by diverging regulatory sequences affecting gene regulation and gene interactions; related species are not primarily consisting of slightly different genes, but of the same genes used (regulated) slightly differently. Once referred to as junk DNA, the non-coding regions of genomes is today known as the regulatory genome. Recently, systems biology has provided us with computational tools to reverse-engineer regulatory networks from regulatory genome information and gene expression data. In this project, we propose to study cold adaptation in grasses, not by comparing orthologous genes (comparative genomics), but by comparing regulatory networks across species (comparative regulomics). This will allow us to identify novel network properties, ranging from individual genes to network motifs, that have diverged in model species and that we can investigate further in non-model Pooideae species.

The master thesis:

Work with identifying gene networks is ongoing and the master student will test the expression of the genes identified in the network(s) in the model species Brachypodium distachyon and the non-model species Nardus stricta. We will use controlled climate experiments to induce responses to different cold treatments in Brachypodium distachyon and Nardus stricta. Leaf samples will be collected during the cold treatments to test expression of the genes identified in the regulatory network analysis using qRT-PCR. Wheat, rice and barley will be included as controls to see if the results from the network study are transferable to a targeted gene expression approach.

The master student will work in a team with both plant scientists and bioinformaticians. The master student will design and conduct experiments to test some of the most interesting hypotheses regarding the evolution of cold adaptation not discovered by previous comparative genomics studies.

Contact: Siri Fjellheim (siri.fjellheim@umb.no)

Evolution of photoperiodic response in Pooideae as an adaptation to life in the North

Background

Timing of flowering is one of the most crucial factors for reproductive success of flowering plants. In cool areas where the growth season is short the plants mainly make use of temperature and day length as queues to flowering at right time. This is controlled by two molecular pathways – the vernalization and photoperiodic pathways. Photoperiod is an environmental cue that many organisms use to regulate seasonal changes in behaviour, migration and reproduction. At temperate and subarctic latitudes, photoperiod, light quality and temperature are major environmental signals that plants sense in order to synchronize their flowering time with the changing seasons. Variation in flowering time of plants contributes to local adaptation to different growth conditions and hence clinal variation in flowering time is commonly believed to be a sign of adaptive evolution.

The Pooideae subfamily of the grasses contains economically important cereals like wheat (Triticum aestivum), barley (Hordeum vulgare), oat (Avena sativa) and forage grasses like ryegrass (Lolium perenne) and meadow fescue (Festuca pratensis). Common for all species of this sub-family is adaptation to cold climate, predominantly at Northern latitudes. In northern parts of Europe, Asia and America more than 90% of the grasses belong to this subfamily. However, which adaptive features lies behind the key to the success of Pooideae species in cool, Northern areas and how these characters evolved within Pooideae remains to be investigated. The economically important Pooideae grasses all belong to what is defined as the core Pooideae (Poeae, Aveneae, Bromeae, and Triticeae). Brachypodium distachyon is a model species for the grasses in the Pooideae subfamily. It is a temperate species placed as a sister group to the core Pooideae species. The closest relative to Pooideae is rice and this is a plant that flowers in short days. However, all species of the core Pooideae and Brachypodium flower in long days. Little is known about requirement for flowering of more basal Pooideae species and if they flower in long or short days. It can be assumed that the switch from flowering in short days to flowering in long days is an adaptation to life in the North.

To gain insight and knowledge of evolution of photoperiodic response in subfamily Pooideae the basal Pooideae species should be studied. Nardus stricta, Melica nutans and Stipa ssp. will be used as representatives of the basal Pooideae species.

The master thesis:

Test different ecotypes of Nardus stricta, Melica nutans and Stipa ssp. for response to different photoperiodic treatments. Ecotypes of N. stricta, M. nutans and Stipa ssp. have been collected in a geographically wide range throughout Europe. The different ecotypes will be tested under controlled conditions to four different photoperiodic treatments (8, 12, 16 and 20 hours photoperiod). Response to different photoperiodic treatments will be measured as days to flowering. Leaf samples will be sampled throughout the experiment and expression profiles for different candidate genes for flowering will be characterized using qRT-PCR.

Contact: Siri Fjellheim (siri.fjellheim@umb.no)

Landscape genetics and phylogeography of two temperate grass species

Background

The main forces shaping the genetic structure of populations are genetic drift, gene flow and selection. The present day genetic structure and diversity distribution of populations bear signatures from both historical and contemporary evolutionary processes. Historical processes are e.g. geological or climatic events that happened a long time ago, that have ceased to work now, but that still significantly influences genetic diversity patterns. A well documented example is the range shifts of Holocene glaciations in Eurasia that have significantly influenced the present day genetic structure of numerous plants and animals through their expansion from/retraction to glacial refugia in the Iberian Peninsula, Italy, Balkans or even further east and north. Contemporary processes include more recent and ongoing processes acting within populations. These are mainly gene flow, genetic drift and selection where gene flow will act to minimize differences between populations and genetic drift and local adaptation will make populations differentiate. On a large geographic scale, there will be spatial variation in both gene flow and selection and variation in morphological and phenological traits may well vary independently of variation in neutral genetic markers. To elucidate both historical and contemporary population genetic processes several different marker types must be utilized. Traditionally, chloroplast DNA (cpDNA) markers have, because of their low mutation rate, been used to reveal historical genetic patterns such as post-glacial expansions from refugial areas, whereas neutral genetic markers with higher mutation rates such, as SSRs and AFLP, are used to study contemporary processes.

The master thesis:

As part of a larger project on evolution of temperate grasses, the master student will study genetic diversity in Nardus stricta and Melica nutans, and Stipa ssp. Both chloroplast DNA markers and AFLP markers will be utilized to reveal population genetic processes acting in populations on different timescales to shape population structure, levels of genetic diversity and distribution of genetic diversity.

Contact: Siri Fjellheim (siri.fjellheim@umb.no)

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Potential MSc thesis topics in wheat genetics and breeding:

Association mapping of agronomically important traits in wheat

Plant breeding can be greatly enhanced by the identification of genes controlling important traits, which is now possible in wheat and other crop species with the availability of whole genome high-density marker arrays with thousands of Single Nucleotide Polymorphism (SNP). A representative set of 214 wheat cultivars and breeding lines with relevance for Norwegian wheat breeding is these days being genotyped with 81500 SNP markers. The same material has also been phenotyped for many different traits in field trials over the last years. On the basis of this, we have several interesting research tasks that are suitable for master thesis projects:

1. What is the genetic diversity of Norwegian wheat compared to wheat cultivars from other parts of the world and what are the key genes for adaptation to the Nordic climate?

Data on the 81500 SNP markers will be used to assess the overall genetic diversity of the Norwegian wheat breeding material and compare that to cultivars and breeding lines from other parts of the world that are also genotyped with the same markers. SNP marker data from recombinant inbred line (RIL) populations will be used to construct genetic linkage maps. These linkage maps will make it possible to select “neutral” markers along the chromosomes that can be used to determine the overall population structure of the Norwegian breeding material. The student will used advanced statistical tools to identify key chromosomal areas and tightly linked molecular markers to genes involved in determination of plant height, heading date and maturity date based on data from field trials. The work can be supplemented with greenhouse experiments under controlled conditions to provide data for mapping of day length sensitivity and vernalization response. Several genes for these traits have been cloned and the sequence diversity at these loci can be studied as part of this master thesis project.

SupervisorsMorten Lillemo, IPM

:

Åsmund Bjørnstad, IPM

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2. What are the main genes for Fusarium resistance in Norwegian wheat?

Fusarium head blight (FHB) is a major disease problem in the Norwegian wheat production. Several pathogens of the genus Fusarium can attack the heads of cereals and produce mycotoxins that make the grains unsuitable for human or animal consumption. Breeding of cultivars with improved resistance to FHB has top priority both in Norway and internationally. While big efforts are made to introgress new sources of resistance into adapted germplasm, the main objective of this master thesis project is to identify the main genetic loci involved in FHB resistance in the Norwegian breeding material by utilizing the marker data from the 81500 SNP markers. The student will do association mapping based on

existing data from field experiments and perform further evaluation of FHB resistance in the Norwegian breeding material in artificially inoculated and mist irrigated field trials.

SupervisorsMorten Lillemo, IPM

:

Åsmund Bjørnstad, IPM

3. What are the main genes for leaf blotch resistance in Norwegian wheat?

Leaf blotch caused by Stagonospora nodorum is a severe disease on wheat in Norway and other areas with a temperate and rainy climate. Insufficient resistance causes severe grain shriveling and reduced yield in years with favorable conditions for the disease and is a main cause of fungicide application.

S. nodorum and other leaf blotch pathogens interact with their hosts in an inverse gene-for-gene manner based on necrotrophic effectors (NEs, also known as host-selective toxins) that are recognized by corresponding sensitivity loci in the host. These sensitivity loci are thought to be resistance (R) genes to biotrophs that are “hijacked” by the necrotrophic pathogen to trigger programmed cell death. To date, six NEs and corresponding host sensitivity loci have been described for the wheat - S. nodorum pathosystem. This has opened up new possibilities in resistance breeding by identification and elimination of host receptors.

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The master student will utilize the marker data from the 81500 SNP markers and field data from disease trials to identify the main genetic factors for leaf blotch resistance or susceptibility in the Norwegian breeding material. The student will also take part in further evaluation of leaf blotch resistance in field trials and conduct seedling assays in the greenhouse with differential isolates of S. nodorum in order to identify specific NE-sensitivity loci in the Norwegian wheat material.

SupervisorsMorten Lillemo, IPM

:

Andrea Ficke, Bioforsk

4. What are the main genes for pre-harvest sprouting resistance in Norwegian wheat?

Rainy autumns provide challenging conditions for wheat production in Norway and the bread-making quality can be completely destroyed by pre-harvest sprouting while the seeds still remain in the spikes in the field. In the 2011 growing season, more than 80 percent of the Norwegian wheat harvest did not meet the requirement for food quality due to this problem. Nevertheless, genetic variation exists for this trait, and there is a need to develop wheat varieties with higher levels of resistance to pre-harvest sprouting. Molecular markers can greatly enhance the breeding efforts to improve this trait, but requires identification of the main genetic factors controlling seed dormancy and susceptibility to pre-harvest sprouting in the Norwegian wheat material. This is the main objective of this master thesis project.

Data on the 81500 SNP markers will be analysed together with existing phenotypic data from field experiments in order to identify key genetic loci controlling seed dormancy and pre-harvest sprouting in the Norwegian wheat material. The student will also perform new field evaluation of pre-harvest sprouting-related traits and evaluate seed dormancy of the Norwegian wheat material under controlled environmental conditions in the greenhouse.

SupervisorsMorten Lillemo, IPM

:

Anne Kjersti Uhlen, IPM

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5. Development of high-throughput KASP markers for wheat breeding. While plant breeding can be greatly enhanced by the application of molecular markers, these markers need to be evaluated for their effect on the phenotype and be amenable to high-throughput genotyping in a cost-effective manner. Our research group has over the years worked closely together with Graminor to identify and validate molecular markers for the wheat breeding program. Most of the markers that are used today are expensive and labour-consuming SSR markers.

With the current availability of high-density SNP marker in wheat we aim at replacing the current SSR markers with more cost-effective and high-throughput SNP markers. For this we will utilize the KASP (KBiosciences Allele-Specific PCR) system. The student will be involved in the identification of potential SNP markers for use in the breeding program on the basis of existing phenotypic data and high-density linkage maps based on the 81500 SNP markers.

KASP primers will be designed based on the most promising SNP markers and tested on breeding populations in the Graminor wheat breeding program to evaluate their potential in wheat breeding. We are currently involved in the development and testing of KASP markers for many important traits including resistance to powdery mildew, Fusarium head blight and leaf blotch as well as pre-harvest sprouting, baking quality and agronomic characters like plant height and earliness. This master thesis project can be tailored according to both the student’s interests and current priorities in the breeding program.

SupervisorsMorten Lillemo, IPM

:

Muath Alsheikh, Graminor

For further information about these master thesis topics, please contact: Morten Lillemo e-mail: morten.lillemo@umb.no Phone 6496 5561

Seasonal regulation of growth and resource allocation in grasses

Background

The annual cycle in growth and development in perennial grasses is intimately regulated by environmental factors which indicate the time of year. Hence, there is an annual cycle in the pattern of resource allocation between leaf growth, root growth, storage, tiller formation or flowering and seed production. Factors like photoperiod, red light: far red light-ratio and night temperature affects this allocation through modulation of gene expression and hormone levels, and possibly by other means. Climate change involves changes in the length of the growing season, and thereby plants will be exposed to new combinations of temperature and light conditions. How will such changes affect seasonal patterns in growth and development of grass plants?

Work to be done

• Growth experiments under controlled conditions. Test the effects of light and temperature variables (including interactions) on growth, development and resource allocation

• Measure expression of relevant genes (optional)

• Study species variations / genetic variation in plant responses (optional)

Contact

Post doc Åshild Ergon, ashild.ergon@umb.no, tel. 64965552 Professor Jorunn E. Olsen, Jorunn.olsen@umb.no, tel 64965635