Examensarbeten

Kontaktperson vid HGEN är Anna Maria Johansson.

Kontakta handledaren för mer information om respektive projekt. 

Häst / Horse

The evolution of reproduction and the sex chromosomes

Genomes are vulnerable to selfish genetic elements (SGEs), which enhance their own transmission relative to the rest of an individual's genome but are neutral or harmful to the individual as a whole. As a result, genetic conflict occurs between SGEs and other genetic elements in the genome. Selfish genetic elements that distort Mendelian segregation to favor their own transmission are common in eukaryotic genomes. Segregation distortion can reduce whole organism fitness, resulting in strong counter selection for genes that suppress distorters. Such intragenomic conflicts have the potential to drive bouts of antagonistic co-evolution, i.e. the aggregation of compensatory mutations to restore sex balance. One important consequence of recurrent sex-linked conflict is its potential to drive speciation.

Preliminary data suggests that we have identified several Standardbred stallions with a distorted sex ratio among their offspring. Some sires have significantly more males among their offspring and others have more females. The aim of this project is to dissect the genetic cause behind the distorted sex ratios. The first experiment will consist of developing assays (diagnostic tools) to determine if there are any chromosomal abnormalities in the sex chromosome pair (ECAX and ECAY) among parents and offspring. The development of the assays will be performed as collaboration between Texas A&M University and SLU. In addition to the purpose of this research project, these assays can be used in the future for diagnosis of reproductive problems in horses due to abnormalities in the sex chromosomes. A large proportion of such sex chromosome abnormalities remain undiagnosed in horses due to the lack of an affordable diagnostic tool that allows for avoiding karyotyping tests. If we identify any chromosomal abnormalities in this research project, karyotyping will be performed at Texas A&M under the leadership of Prof Terje Raudsepp. If no sex chromosomal deviations are detected, we aim to map and study selfish genetic elements that may cause the distorted sex ratios.

This will be achieved by

1. identify additional horse half-sib families, in multiple horse breeds, where a distorted sex ratio can be observed over at least two generations (i.e. a stallion and its father both skew the sex ratio among their offspring in the same direction) and
2. whole genome sequencing (long-read) of these horse families. In males, the meiotic drive system usually includes two loci - both a “driver” and a “target”. Drivers are many times linked to an insensitive allele of the target to avoid self-destruction. Therefore, meiotic drive systems tend to reside in regions of the genomes with low recombination (e.g. heterochromatin or sex chromosomes).

Since we previously performed a large-scale copy number variant (CNV) study in European horse breeds, we also aim to investigate if there are any sex-determining genes within these CNV regions.

Pinpointing selfish genetic elements (sex chromosome drivers), as well as compensatory mutations to restore sex balance, could have practical implications in horse breeding. Quite frequently, molecular sexing is performed on horse embryos. In nature, the genetics underlying a meiotic drive system, can lead to lineage splitting and speciation. This is because compensatory mutations may create hybrid incompatibility that could, perhaps, establish reproductive barriers.

Supervisors: Gabriella Lindgren &  Terje Raudsepp (Texas A&M University)

Undersöka effekten av en kandidat mutation för prestation hos travhästar / Testing a candidate mutation for a trotting performance QTL in horses

Vi har nyligen hittat en kandidat mutation som kan påverka prestation hos travhästar. Målet är att undersöka effekten av denna mutation. I projektet ingår molekylärgenetik, bioinformatik och laboratoriearbete, exempelvis PCR och elektrofores. 

 The aim is to investigate the role of this mutation for performance in horses. The project includes molecular genetics, bioinformatics and laboratory work as for example PCR and electrophoresis.

Handledare/supervisor: Gabriella Lindgren, Maria Rosengren

Genetiken bakom ögonsjukdomar hos häst

Handledare: Sofia Mikko

Analys av hårstruktur hos häst / Hair structure analysis in horses

Det är lite som är känt om den genetiska bakgrunden till strukturen av hår samt hur detta påverkas av faktorer som färg, ålder och kön. Projektet är en del av den större studien om mantillväxt med målet är att hitta genetiska faktorer som reglerar hårtillväxt.

Studenten kommer att analysera tagelprover från häst för att bestämma bland annat melanin koncentration och struktur såsom tjocklek och form på hårstråt. Tagelproverna kommer från islandshästar, en ras som har en mycket stor variation av längd och tjocklek av man och svans. Islandshästar har dessutom många olika färger. Här kan du läsa mer om projektet mantillväxt

Knowledge of which genetic factors regulating hair growth and hair structure is limited. This master project is a part of the study about mane growth in horses. The aim is to find mutations that regulate hair growth.

The student will analyze hair samples from horses to measure melanin content, thickness and shape of the hair strands. The hair samples are from mane and tail of Icelandic horses, a breed with a great variation in length, thickness and color. Click here to read more about mane growth.

Handledare/supervisor: Gabriella Lindgren, Maria Rosengren

Pacing Shetland ponies

The DMRT3 gene is important for gaits and performance in horses and the mutated gene variant is present in high frequency in gaited horse breeds. Homozygozity is normally required for a horse to be able to perform pace. However, while Shetland ponies normally are three-gaited and all tested horses are homozygous for the wild-type allele, we recently identified three Shetland ponies that are able to pace. The aim of this study is to sequence the region around the DMRT3 gene, to investigate if there are any additional mutations in or around the gene that can explain the pacing ability of these ponies.

Supervisor: Gabriella Lindgren, Maria Rosengren

Kartläggning för gener för hårtillväxt

Kunskapen om vilka genetiska faktorer som styr och reglerar hårtillväxt är hittills begränsad. I detta projekt använder vi oss av hästens stora variation i manlängd för att kartlägga faktorer som påverkar hårtillväxt. Målet med studien är att identifiera mutationer för hårtillväxt som förmodligen reglerar hårcykelns längd, dvs från det att ett hårstrå börjar växa tills det att hårstrået faller av och ett nytt hårstrå börjar växa fram. Målet med detta masterprojekt är att sekvensera en av de kandidatgener som har identifierats hos andra raser, hos häst, och undersöka förekomsten av eventuella mutationer hos hästar med olika lång man.

Handledare: Gabriella Lindgren, Maria Rosengren

Genetisk studie av utvecklingsrubbning (krumma föl) hos shetlandsponny

Handledare: Gabriella Lindgren, Sofia Mikko

Associationsanalys av genetiska markörer i islandshästens genom och fenotypiska uttryck såsom exteriör, färgteckning, temperament samt sjukdom 

Handledare: Gabriella Lindgren

Kartläggning av gener för sommareksem hos häst

Läs mer om projektet här

Handledare: Gabriella Lindgren m.fl.

DMRT3-genens ("passgenen") effekt på rörelsemönster hos olika hästraser

Läs mer om projektet här

Handledare: Gabriella Lindgren

Identifiering av nya gener som reglerar rörelsemönster hos häst

Handledare: Gabriella Lindgren 

Färggenetik hos häst - finns det skillnad i hörseldefekter mellan helfärgade respektive vita hästar?

GWAS, CNV, Haplotyper, signatures of selection

Handledare: Sofia Mikko

Genetiken bakom prestations- och hälsoegenskaper hos svenskt varmblod (SWB)

Handledare: Sofia Mikko, Åsa Viklund

Klinisk diagnostik och genetik för att förutse pungbråck hos häst

Handledare: Sofia Mikko

Hund / Dog

How Many Disease-Causing Mutations are Present in an Individual Dog’s Genome?

In this project, the student will first identify the genomic coordinates for all 200 autosomal recessive mutations listed in OMIA and build a data file that includes disease information, gene name and genomic coordinates. In the next step the student will use the data file in a bioinformatics pipeline that will be set up to scan complete canine genomes for those mutations. The results will not only provide valuable information and increase our understanding of how many autosomal recessive mutations are found in an individual dog. It will also be highly relevant for the canine community in guiding and preparing breeders and policy makers in a not too distant future when whole genome sequencing rather than genetic testing for a single mutation may be widely used.

Supervisor: Tomas Bergström, Göran Andersson

Studier av immunmedierade sjukdomar hos hund

Handledare: Göran Andersson

Studier av cardiomyopatienter hos hund

Handledare: Göran Andersson

Ko / Cow

Gris / Pig

Effects of sire breed on litter size in commercial piglet production

Increased litter sizes resulting in increased piglet mortality and reduced vitality in the surviving piglets is a general problem in piglet production globally. In this pilot project we aim to take an applied approach investigating aspects that the farmer can control – the sire breed of the piglets. The student taking on this project will collaborate with applied herd veterinarians and experts within animal health, welfare and geneticists.

Contact person: Katja Nilsson

Hur påverkar fader-ras kullstorleken i kommersiell smågrisproduktion?

Ökad kullstorlek följd av ökad smågrisdödlighet och försämrad vitalitet hos överlevande smågrisar är ett generellt problem i smågrisproduktion i hela världen. I det här pilotprojektet tar vi ett tillämpat grepp och undersöker aspekter som producenten kan kontrollera – valet av fader-ras till smågrisarna. Studenten som väljer detta projekt kommer samarbeta med tillämpade djurhälsoveterinärer, experter på områdena djurhälsa, djurvälfärd och genetik.

Kontaktperson: Katja Nilsson

Genetisk diversitet hos gris / Genetic diversity of pigs

Knowledge on genetic diversity is important, especially when a breeding resource undergoes large changes. The Swedish Landrace and Swedish Yorkshire pig breeds have experienced such a challenge when merging them into breeding organizations outside Sweden. Breeding goals and husbandry systems in Sweden differ from those in other European countries. Swedish piggeries apply higher animal welfare standards, and it is likely that the genetics of pigs has been selected for such systems. It is possible that the past breeding of the Swedish maternal lines has led to an adaptation of relevant behavioral traits. We have collected samples from Swedish domestic pig breeds and wild pigs to identify underlying population structures. Information will be compared to a world-wide datasets from various domestic and natural pig breeds. The data will provide important information on the structure of the Swedish breeds and establish a background for the possible need of further conservation strategies

Handledare/supervisor: Elisabeth Jonas, Anna M Johansson

Analys av genetisk variation hos Linderödssvin / Analysis of genetic diversity in the Lingered pig breed

Linderödssvin är en gammal svensk lantras. I ett examensarbete kan studenten undersöka hur mycket genetisk variation och inavel som finns inom rasen och hur nära släkt rasen är med andra Europeiska grisraser.

The Linderöd pig is an old Swedish pig breed. In a master thesis the student can investigate how much genetic diversity and inbreeding that is present in the breed and how closely related the breed is to other European pig breeds.

Handledare/supervisor: Anna M Johansson, Elisabeth Jonas

Molekylärgenetiska studier av rörelsemönster och bakbenskvalitet hos suggor

Handledare: Elisabeth Jonas

Får / Sheep

Analys av släktskap mellan svenska fårraser

Handledare: Anna Johansson, Sofia Mikko

Genetisk variation och inavel hos svenska fårraser

Handledare: Anna Johansson, Sofia Mikko, Elisabeth Jonas

Molekylärgenetisk kartläggning av egenskaper hos får

Här kan man välja någon egenskap av: pälsfärg, fertilitet eller horn

Handledare: Anna Johansson

Konserveringsstrategier hos små idisslare i Sverige / Conservation strategies for small ruminants in Sweden

Small ruminants in Sweden, including sheep and goats are characterized by many local breeds and small population sizes. Some of the breeds are part of conservation programs. The project here aims to investigate breed structures and identify conservation strategies using a computer program. The student should also identify relevant breeds and organize data from the breeds. There is a possibly to include molecular genetic data into the analysis.

Handledare/supervisors: Anna M Johansson, Elisabeth Jonas

Get / Goat

Analys av genetisk variation hos svenska getter

Det finns fyra getraser i Sverige: Svensk lantrasget, Lappget, Göingeget och Jämtget. I ett examensarbete kan studenten undersöka hur mycket genetisk variation och inavel som finns inom raserna och hur nära släkt raserna är med varandra. Det finns även möjlighet att istället fokusera på gener för vissa egenskaper, tex gener som påverkar mjölkens egenskaper eller gener som styr pälsfärg.

There are four goat breeds in Sweden: Swedish landrace, Lapp goat, Göringe goat and Jämt goat. In a master thesis the student can investigate how much genetic diversity and inbreeding that is present in the breeds and how closely related the breeds are to each other. There is also a possibility to instead focus on genes associated with some traits in goats, for example genes involved in milk properties or coat colour.

Handledare/supervisors: Anna M Johansson, Elisabeth Jonas

Höns

Molekylär kartläggning av egenskaper hos Lantrashöns

Handledare: Anna Johansson

Älg / Moose

Karaktärisering av prionproteinet hos älg

Handledare: Sofia Mikko

Varför är älgen vit?

Handledare: Sofia Mikko

Katt / Cat

Plattbröst hos bengalkatt

Handledare: Sofia Mikko

Övrigt / Others

CNV validation by qPCR and analysis of biological pathways

Copy Number Variants (CNVs) are a common form of genetic variation influencing phenotypic diversity and disorders across a range of species. In horses’ genome, most of the CNV variation is known to occur in regions that regulate important biological processes such as sensory perception, signal transduction, immunity or metabolism pathways. Recently, we identified several CNVs in a wide range of different horse’s breeds. The aim of this study is, therefore, to validate the identified CNVs by quantitative real-time PCR (qPCR) across different horse populations and investigate they role in biological processes by functional and pathway enrichment analysis.

Supervisor: Gabriella Lindgren, Marina Solé

Sällskapsdjurens roll för en hållbar utveckling (sociala, miljömässiga och ekonomiska aspekter)

Det talas mycket om kor som klimatbovar, om antibiotikaanvändning i lantbruket, om betande djurs betydelse för biologisk mångfald. Men sällskapsdjurens betydelse för en hållbar utveckling diskuteras nästa aldrig. Ett exjobb i detta ämne kan genomföras på många olika sätt men jag föreställer mig att data samlas in från litteraturen och genom intervjuer av experter. Sedan gäller det att beskriva positiva och negativa konsekvenser av nyttjandet av sällskapsdjur och att få ihop en syntes. Att identifiera och beskriva målkonflikter är en viktig del av arbetet. Exjobbet kan göras mycket brett (många djurslag och alla tänkbara hållbarhetsaspekter) eller smalt, enligt studentens intresse. Ett exempel på en hypotes för ett smalare exjobb är: ”Det är mer hållbart med små hundar än stora hundar”. I jämförelsen mellan små och stora hundar skulle ingå foderåtgång och fodertillverkningens klimat- och miljöeffekter, antibiotikaförbrukning, hundens betydelse för hundägarens hälsa, privatekonomi etc. Beroende på vilken inriktning studenten väljer letar jag upp lämpliga medhandledare.

Handledare: Lotta Rydhmer

Genomics of domestication

There have been many genomic studies that detect regions and genes that have been selected during animal domestication (e.g. in pigs, chickens, cattle, dogs, sheep). These projects would use that knowledge in combination with other genetic databases, to test hypotheses about domestication.

• Neural crest cell genes in domestication. The most popular hypothesis to explain the genetics of domestication is the neural crest cell hypothesis, which hypothesises that many shared features of domestic animals are due to changes in the development of the neural crest – an embryonal structure that contributes to many vertebrate-specific features. This project could estimate whether there is an enrichment of neural crest cell genes among genes selected in domestication. In order to do that, one would gather neural crest cell genes from the developmental genetic literature and identify the orthologues in domestic animals, and genes selected during domestication from many selection mapping studies of domestic animals.
• Gene coexpression networks in domestication. There is suggestive evidence that genes selected in domestication tend to be hub genes in gene networks, that potentially regulate many other genes. This project could use data from gene expression atlases of domestic animals to create gene coexpression networks, and estimate the network topology around genes selected during domestication from many selection mapping studies of domestic animals.

Supervisor: Martin Johnsson

Computational models to understand the response to genomic selection

These projects are suitable for students who are interested in genomics and have some programming experience.

• The effect of recombination rate on genomic selection. Recombination rate is known to influence the distribution of genetic variation in the genome, but is mostly ignored in breeding simulations. This project could use maps of recombination rate in livestock species to create breeding simulations with more realistic genomes, and investigate the effect on genetic variation and change in allele frequency.
• The effects of machine learning methods for genomic selection. Several machine learning methods have been proposed for genomic predictions, that may give higher accuracy for predicting genetic values when there is dominance and gene—gene interaction. This project could use simulation to evaluate the effect on genetic gain, change in genetic variance and allele frequency of some of these new methods, compared to conventional genomic prediction methods.

Supervisor: Martin Johnsson

Computational models for reproducible methods in genetics

These projects are suitable for students who are interested in genetic data analyses and have some programming experience. Projects under this theme could relate to using a mixture of simulation and publicly available data to investigate:

• The power of methods for detecting lethal recessive haplotypes from genotype data. Recessive lethal alleles have been detected in several different domestic species (e.g. cattle, pigs and horses) at surprisingly high frequencies by looking for “missing homozygote haplotypes”. One open question is how powerful and precise these methods are. The project could look into the effects of balancing selection and popular sires (which can lead to higher allele frequencies), the properties different tests, and the genetic parameters of the lethal allele (partial dominance, partial penetrance) etc.
• Estimating transgenerational effects in the presence of genetic variation. There is a whole literature on estimating transgenerational epigenetic effects in animals who are exposed to some stimulus in a laboratory, then mated to produce offspring that are assayed for transgenerational changes (for one or two generations). However, such analyses risk confounding with genetic differences, if there is residual genetic variation – which there often is, even in supposed inbred strains. The project could use simulation to create experimental pedigrees with different amounts of residual genetic variation and true transgenerational effects, and investigate whether the analyses used in such studies can disentangle them.
• Genomic intervals for genome-wide association. In a genome-wide association study of a livestock species, how far from the most significant marker is the locus likely to be? This project could use simulation to generate genome-wide association study data with known true locations, and test methods that researchers in the livestock genomics field use to create intervals around association hits.

Supervisor: Martin Johnsson

Häst / Horse

The evolution of reproduction and the sex chromosomes

Genomes are vulnerable to selfish genetic elements (SGEs), which enhance their own transmission relative to the rest of an individual's genome but are neutral or harmful to the individual as a whole. As a result, genetic conflict occurs between SGEs and other genetic elements in the genome. Selfish genetic elements that distort Mendelian segregation to favor their own transmission are common in eukaryotic genomes. Segregation distortion can reduce whole organism fitness, resulting in strong counter selection for genes that suppress distorters. Such intragenomic conflicts have the potential to drive bouts of antagonistic co-evolution, i.e. the aggregation of compensatory mutations to restore sex balance. One important consequence of recurrent sex-linked conflict is its potential to drive speciation.

Preliminary data suggests that we have identified several Standardbred stallions with a distorted sex ratio among their offspring. Some sires have significantly more males among their offspring and others have more females. The aim of this project is to dissect the genetic cause behind the distorted sex ratios. The first experiment will consist of developing assays (diagnostic tools) to determine if there are any chromosomal abnormalities in the sex chromosome pair (ECAX and ECAY) among parents and offspring. The development of the assays will be performed as collaboration between Texas A&M University and SLU. In addition to the purpose of this research project, these assays can be used in the future for diagnosis of reproductive problems in horses due to abnormalities in the sex chromosomes. A large proportion of such sex chromosome abnormalities remain undiagnosed in horses due to the lack of an affordable diagnostic tool that allows for avoiding karyotyping tests. If we identify any chromosomal abnormalities in this research project, karyotyping will be performed at Texas A&M under the leadership of Prof Terje Raudsepp. If no sex chromosomal deviations are detected, we aim to map and study selfish genetic elements that may cause the distorted sex ratios.

This will be achieved by

1. identify additional horse half-sib families, in multiple horse breeds, where a distorted sex ratio can be observed over at least two generations (i.e. a stallion and its father both skew the sex ratio among their offspring in the same direction) and
2. whole genome sequencing (long-read) of these horse families. In males, the meiotic drive system usually includes two loci - both a “driver” and a “target”. Drivers are many times linked to an insensitive allele of the target to avoid self-destruction. Therefore, meiotic drive systems tend to reside in regions of the genomes with low recombination (e.g. heterochromatin or sex chromosomes).

Since we previously performed a large-scale copy number variant (CNV) study in European horse breeds, we also aim to investigate if there are any sex-determining genes within these CNV regions.

Pinpointing selfish genetic elements (sex chromosome drivers), as well as compensatory mutations to restore sex balance, could have practical implications in horse breeding. Quite frequently, molecular sexing is performed on horse embryos. In nature, the genetics underlying a meiotic drive system, can lead to lineage splitting and speciation. This is because compensatory mutations may create hybrid incompatibility that could, perhaps, establish reproductive barriers.

Supervisors: Gabriella Lindgren &  Terje Raudsepp (Texas A&M University)

Selection strategies in SWB

An overview of response to selection strategies and recommendations for the future

Supervisor/handledare: Åsa Viklund

Undersöka effekten av en kandidat mutation för prestation hos travhästar / Testing a candidate mutation for a trotting performance QTL in horses

Vi har nyligen hittat en kandidat mutation som kan påverka prestation hos travhästar. Målet är att undersöka effekten av denna mutation. I projektet ingår molekylärgenetik, bioinformatik och laboratoriearbete, exempelvis PCR and elektrofores.

We have found a candidate mutation that may regulate harness racing performance in horses. The aim is to investigate the role of this mutation for performance in horses. The project includes molecular genetics, bioinformatics and laboratory work as for example PCR and electrophoresis.

Handledare: Gabriella Lindgren, Maria Rosengren

Analys av hårstruktur hos häst / Hair structure analysis in horses

Det är lite som är känt om den genetiska bakgrunden till strukturen av hår samt hur detta påverkas av faktorer som färg, ålder och kön. Projektet är en del av den större studien om mantillväxt med målet är att hitta genetiska faktorer som reglerar hårtillväxt.

Studenten kommer att analysera tagelprover från häst för att bestämma bland annat melanin koncentration och struktur såsom tjocklek och form på hårstråt. Tagelproverna kommer från islandshästar, en ras som har en mycket stor variation av längd och tjocklek av man och svans. Islandshästar har dessutom många olika färger. Läs mer om projektet mantillväxt här.  

The student will analyze hair samples from horses to measure melanin content, thickness and shape of the hair strands. The hair samples are from mane and tail of Icelandic horses, a breed with a great variation in length, thickness and color. Click here to read more homepage about mane growth.

Handledare/Supervisor: Gabriella Lindgren, Maria Rosengren

CNV validation by qPCR and analysis of biological pathways

Copy Number Variants (CNVs) are a common form of genetic variation influencing phenotypic diversity and disorders across a range of species. In horses’ genome, most of the CNV variation is known to occur in regions that regulate important biological processes such as sensory perception, signal transduction, immunity or metabolism pathways. Recently, we identified several CNVs in a wide range of different horse’s breeds. The aim of this study is, therefore, to validate the identified CNVs by quantitative real-time PCR (qPCR) across different horse populations and investigate they role in biological processes by functional and pathway enrichment analysis.

Handledare: Gabriella Lindgren, Marina Solé

Molekylärgenetiska studier av gener som reglerar atletisk prestation hos travare

Handledare: Gabriella Lindgren

Molekylärgenetiska studier av gener som reglerar rörelsemönster hos häst

Handledare: Gabriella Lindgren

Kartläggning av gener för hårtillväxt

Handledare: Gabriella Lindgren, Maria Rosengren

Molekylärgenetisk kartläggning och karaktärisering av genen för bukskäck hos häst

Studenten bör ha labberfarenhet och ha gått genomanalyskursen.

Handledare: Sofia Mikko

Genetisk bakgrund till prestationsegenskaper hos häst

Molekylärgenetisk studie

Handledare: Sofia Mikko

Ko / Cow

Genetiska faktorer och miljöfaktorer som påverkar upptag av råmjölksantikroppar i mjölkkalvar / Genetic and environmental factors influencing uptake of colostrum antibodies in dairy calves

The antibody quality of the colostrum is essential for the newborn calf, as it depends on the passive transfer of colostral antibodies during the first 24 hours of life to stay healthy and survive until weaning. A high proportion of the cows have insufficient antibodies in the colostrum. There are also calves that do not obtain as much antibodies as expected; this is called failure of passive transfer (FPT). We suspect that there is a genetic component involved in this variation. The objective of this project is to analyze different factors that influence the uptake of antibodies in newborn calves.

The student will measure IgG antibodies in colostrum and milk samples using an Indirect ELISA. Next, he/she will compare these results with corresponding calf serum IgG values previously measured. And finally, using statistical analysis (R software), he/she will estimate genetic parameters such as heritability for colostrum IgG, calf IgG and other traits.

Supervisors: Juan Cordero, DJ de Koning

Examensarbeten vid Interbull

The Interbull Centre acts as the operational unit for Interbull and Interbeef, a permanent subcommittee and a working group of the International Committee for Animal Recording (ICAR), respectively.

The Interbull Centre facilitates the exchange of cattle genetics worldwide by performing international genomic and genetic evaluations of dairy and beef cattle from altogether 35 countries.

As such, Interbull Centre supports the dairy and beef industry with accurate genetic information on bulls for use by importers and exporters, thereby facilitating selection of best genetics worldwide.

The MSc candidate interested in performing a project on international genetic/genomic evaluations of cattle, should contact Interbull Centre to assess the feasibility of a tailor-made project with mutual benefit to the candidate and Interbull Center.

Supervisor: Interbull Centre (tbc)

Gris / Pig

Effects of sire breed on litter size in commercial piglet production

Increased litter sizes resulting in increased piglet mortality and reduced vitality in the surviving piglets is a general problem in piglet production globally. In this pilot project we aim to take an applied approach investigating aspects that the farmer can control – the sire breed of the piglets. The student taking on this project will collaborate with applied herd veterinarians and experts within animal health, welfare and geneticists.

Contact person: Katja Nilsson

Hur påverkar fader-ras kullstorleken i kommersiell smågrisproduktion?

Ökad kullstorlek följd av ökad smågrisdödlighet och försämrad vitalitet hos överlevande smågrisar är ett generellt problem i smågrisproduktion i hela världen. I det här pilotprojektet tar vi ett tillämpat grepp och undersöker aspekter som producenten kan kontrollera – valet av fader-ras till smågrisarna. Studenten som väljer detta projekt kommer samarbeta med tillämpade djurhälsoveterinärer, experter på områdena djurhälsa, djurvälfärd och genetik.

Kontaktperson: Katja Nilsson

Molekylärgenetiska studier av rörelsemönster och bakbenskvalitet hos suggor / Molecular genetic studies of movement patterns and leg quality in sows

Leg quality is an important selection criteria for pigs. Certain leg characteristics have been linked to problems with movement and thus a reduced life length in sows. However, the classification of leg characteristics can be influenced by the technician evaluating the fundament. We have identified an interesting region on the genome associated with a poor quality of the hind legs in pigs. The project here aims to further investigate the genetic background of the leg characteristics. The student should organize the phenotypic data and use molecular genetic data to further investigate the genetic background of the traits. Different options are given for projects: The student can perform a genome-wide association analysis to identify regions associated with the leg character traits. There is the option to analyze data from whole-genome sequencing from pigs with diverse hind leg scores. Alternatively, there is the possibility to identify candidate genes and further analyze these in the laboratory using PCR, Sanger sequencing and possibly some genotyping methods.

Handledare/supervisor: Elisabeth Jonas

Genetisk diversitet hos gris / Genetic diversity of pigs

Knowledge on genetic diversity is important, especially when a breeding resource undergoes large changes. The Swedish Landrace and Swedish Yorkshire pig breeds have experienced such a challenge when merging them into breeding organizations outside Sweden. Breeding goals and husbandry systems in Sweden differ from those in other European countries. Swedish piggeries apply higher animal welfare standards, and it is likely that the genetics of pigs has been selected for such systems. It is possible that the past breeding of the Swedish maternal lines has led to an adaptation of relevant behavioral traits. We have collected samples from Swedish domestic pig breeds and wild pigs to identify underlying population structures. Information will be compared to a world-wide datasets from various domestic and natural pig breeds. The data will provide important information on the structure of the Swedish breeds and establish a background for the possible need of further conservation strategies

Handledare/supervisor: Elisabeth Jonas, Anna M Johansson

Analys av genetisk variation hos Linderödssvin / Analysis of genetic diversity in the Lingered pig breed

Linderödssvin är en gammal svensk lantras. I ett examensarbete kan studenten undersöka hur mycket genetisk variation och inavel som finns inom rasen och hur nära släkt rasen är med andra Europeiska grisraser.

The Linderöd pig is an old Swedish pig breed. In a master thesis the student can investigate how much genetic diversity and inbreeding that is present in the breed and how closely related the breed is to other European pig breeds.

Handledare/supervisor: Anna M Johansson, Elisabeth Jonas

Get / Goat

Analys av genetisk variation hos svenska getter

Det finns fyra getraser i Sverige: Svensk lantrasget, Lappget, Göingeget och Jämtget. I ett examensarbete kan studenten undersöka hur mycket genetisk variation och inavel som finns inom raserna och hur nära släkt raserna är med varandra. Det finns även möjlighet att istället fokusera på gener för vissa egenskaper, tex gener som påverkar mjölkens egenskaper eller gener som styr pälsfärg.

There are four goat breeds in Sweden: Swedish landrace, Lapp goat, Göringe goat and Jämt goat. In a master thesis the student can investigate how much genetic diversity and inbreeding that is present in the breeds and how closely related the breeds are to each other. There is also a possibility to instead focus on genes associated with some traits in goats, for example genes involved in milk properties or coat colour.

Handledare/supervisors: Anna M Johansson, Elisabeth Jonas

Konserveringsstrategier hos små idisslare i Sverige / Conservation strategies for small ruminants in Sweden

Small ruminants in Sweden, including sheep and goats are characterized by many local breeds and small population sizes. Some of the breeds are part of conservation programs. The project here aims to investigate breed structures and identify conservation strategies using a computer program. The student should also identify relevant breeds and organize data from the breeds. There is a possibly to include molecular genetic data into the analysis.

Handledare/supervisors: Anna M Johansson, Elisabeth Jonas

Får/Sheep

Gener och miljöfaktorer som påverkar skinnkvalitet hos får/Genes and environmental factors involved in leather quality in sheep

I det här projektet kan redan tillgänglig genotypdata och sekvensdata användas för att titta på skillnader mellan raser med större respektive mindre risk för skinnskador. Även data från en enkät till fårägare kan användas. Om studenten vill göra labarbete så finns möjlighet för sekvensering av kandidatgener i ytterligare prover. Examensarbetet kan göras i ämnena husdjursvetenskap eller biologi.

I det här projektet kan redan tillgänglig genotypdata och sekvensdata användas för att titta på skillnader mellan raser med större respektive mindre risk för skinnskador. Även data från en enkät till fårägare kan användas. Om studenten vill göra labarbete så finns möjlighet för sekvensering av kandidatgener i ytterligare prover. Examensarbetet kan göras i ämnena husdjursvetenskap eller biologi.

Handledare/Supervisor: Anna M Johansson

Gener som styr ullens färg hos svenska får eller getter/Genes involved in coat colour in Swedish sheeps or goats

I det här projektet kan redan tillgänglig genotypdata och sekvensdata användas för att undersöka gener associerade med färg hos får. Hos getter kan kandidatgener sekvenseras. Examensarbetet kan göras i ämnena husdjursvetenskap eller biologi.​

This project will use already existing genotype and sequencing data from sheep or generate sequence data from goats. The master thesis project can be done in the subjects Animal science or Biology.

Handledare/Supervisor: Anna M Johansson

Höns

Kartläggning av egenskaper hos lantrashöns

Handledare: Anna Johansson

Hund

Ärftligt betingad variation på jaktegenskaper registrerade vid drevprov för tax

Ändamålet med drevprov är att bibehålla och förbättra hundens jaktegenskaper som långsamt drivande jakthund. Detta görs på hare, kanin, räv, rådjur och hjort. Bedömningspoäng ges på bland annat hundens sök, drevsätt, skall, samarbete och lydnad.

Några förslag på analyser:

• Fenotypiska och genetiska korrelationer mellan registrerade egenskaper
• Arvbarhetsskattningar på registrerade egenskaper och eventuellt på framräknade aggregerade egenskaper från principalkomponentanalys
• Andra variationsorsaker som exempelvis månad, djurslag, dommareffekter, temperatur
• Skattning av kullleffekter

Handledare: Erling Strandberg (samt Erik Wilsson, extern)

Övrigt / Others

Genomics of domestication

There have been many genomic studies that detect regions and genes that have been selected during animal domestication (e.g. in pigs, chickens, cattle, dogs, sheep). These projects would use that knowledge in combination with other genetic databases, to test hypotheses about domestication.

• Neural crest cell genes in domestication. The most popular hypothesis to explain the genetics of domestication is the neural crest cell hypothesis, which hypothesises that many shared features of domestic animals are due to changes in the development of the neural crest – an embryonal structure that contributes to many vertebrate-specific features. This project could estimate whether there is an enrichment of neural crest cell genes among genes selected in domestication. In order to do that, one would gather neural crest cell genes from the developmental genetic literature and identify the orthologues in domestic animals, and genes selected during domestication from many selection mapping studies of domestic animals.
• Gene coexpression networks in domestication. There is suggestive evidence that genes selected in domestication tend to be hub genes in gene networks, that potentially regulate many other genes. This project could use data from gene expression atlases of domestic animals to create gene coexpression networks, and estimate the network topology around genes selected during domestication from many selection mapping studies of domestic animals.

Supervisor: Martin Johnsson

Computational models to understand the response to genomic selection

These projects are suitable for students who are interested in genomics and have some programming experience.

• The effect of recombination rate on genomic selection. Recombination rate is known to influence the distribution of genetic variation in the genome, but is mostly ignored in breeding simulations. This project could use maps of recombination rate in livestock species to create breeding simulations with more realistic genomes, and investigate the effect on genetic variation and change in allele frequency.
• The effects of machine learning methods for genomic selection. Several machine learning methods have been proposed for genomic predictions, that may give higher accuracy for predicting genetic values when there is dominance and gene—gene interaction. This project could use simulation to evaluate the effect on genetic gain, change in genetic variance and allele frequency of some of these new methods, compared to conventional genomic prediction methods.

Supervisor: Martin Johnsson

Computational models for reproducible methods in genetics

These projects are suitable for students who are interested in genetic data analyses and have some programming experience. Projects under this theme could relate to using a mixture of simulation and publicly available data to investigate:

• The power of methods for detecting lethal recessive haplotypes from genotype data. Recessive lethal alleles have been detected in several different domestic species (e.g. cattle, pigs and horses) at surprisingly high frequencies by looking for “missing homozygote haplotypes”. One open question is how powerful and precise these methods are. The project could look into the effects of balancing selection and popular sires (which can lead to higher allele frequencies), the properties different tests, and the genetic parameters of the lethal allele (partial dominance, partial penetrance) etc.
• Estimating transgenerational effects in the presence of genetic variation. There is a whole literature on estimating transgenerational epigenetic effects in animals who are exposed to some stimulus in a laboratory, then mated to produce offspring that are assayed for transgenerational changes (for one or two generations). However, such analyses risk confounding with genetic differences, if there is residual genetic variation – which there often is, even in supposed inbred strains. The project could use simulation to create experimental pedigrees with different amounts of residual genetic variation and true transgenerational effects, and investigate whether the analyses used in such studies can disentangle them.
• Genomic intervals for genome-wide association. In a genome-wide association study of a livestock species, how far from the most significant marker is the locus likely to be? This project could use simulation to generate genome-wide association study data with known true locations, and test methods that researchers in the livestock genomics field use to create intervals around association hits.

Supervisor: Martin Johnsson