Cattle are essential for the global food industry through the meat and milk production. It is from an economical point of view in our best interest to make cattle as efficient as possible, whether it is milk or beef production, without negatively influencing their health and welfare. That has led to a steady increase in the interest of genetic analysis of cattle. The sequencing and identification of genomic variation has led to the association of genotypes with phenotypes of interest and the discovery of the underlaying genetic risk factors for many diseases and traits. Diseases or monogenetic traits caused by a single nucleotide polymorphism (SNP), small deletions and insertions or other small mutations are often easy to identify if the correct region is found. The diseases caused by structural variants (SVs), variants larger than 50 base pairs (bp) are still challenging. It is more challenging because they are harder to identify, especially using shortread sequencing technologies. It is therefore still a rather unexplored area for cattle and other domestic species.This thesis looks at SVs found in the Swedish Red and Brown (SRB) cattle to discover breed specific SVs. This was done by creating a pipeline with VCF files as input. The identified SVs were filtered and overlapped with externally identified SVs. The pipeline was tested with two SRB datasets. The structural variant caller, DELLY, performed poorly with low read depth data when comparing single replicate data and combined replicates data. Multiple SVs were identified in all individuals and did overlap with both functional and gene annotation. There was also overlap found with datasets in the European variant archive (EVA). This indicates that the identified SVs are shared among multiple breeds of cattle and that DELLY can be used to develop future pipelines to include long read sequencing technologies and/or data with higher read depth.

The dog brings great joy and is of great benefit to humans, for example as a companion dog, hunting dog, service dog and assistance dog. In some cases, dogs cause problems and society must then intervene. The Act of Supervision of Dogs and Cats aims at preventing damage and significant inconvenience that can be caused by dogs and cats. If a dog causes damage or nuisance according to The Act of Supervision of Dogs and Cats, the law can support a decision to seize a dog by the County Administrative Board or the Police Authority. Often the dog is seized because it has bitten another dog, human or other animal. In case of seizure, an investigation must be carried out by the County Administrative Board to assess the dog's mental and physical status. The Police inspector performs a mental examination of the dog, and a Veterinarian examines the dog's physical status. The County Administrative Board then decides whether the dog should be returned to its owner, rehomed, or euthanized. This study has examined the county administrations' work in Norrbotten, Skåne, Stockholm, Västerbotten, Västmanland and Västra Götaland. A total of 89 dogs were seized in the six counties, between the years 2019–2021, 53 male dogs (approx. 60%) and 36 female dogs (approx. 40%). Euthanasia was the most frequently performed measure, 42 dogs were euthanized. Others were returned or rehomed. In general, all six county administrations carry out careful investigations, but a clear difference between them is how often the county administrations follow the police's proposed measures. The county administrative boards decide on euthanasia more often, 42 out of 89 times (47%), than the police give suggestions on euthanasia, 34 out of 89 times (38%). The new regulation, which entered into force on February 1, 2022, makes it possible for the county administrations to be even more thorough in their investigations of dogs in care. In addition to a mental examination and veterinary examination, the county administrations must also request a statement from the kennel about the dog's behaviour towards people and animals. / Hunden ger stor glädje och gör stor nytta för människan, exempelvis som sällskapshund, jakthund, tjänstehund och assistanshund. I enstaka fall orsakar hundar problem och samhället måste då ingripa. Lagen (2007:1150) om tillsyn över hundar och katter, härefter ”TL” eller ”tillsynslagen” finns för att förebygga skador och avsevärda olägenheter som kan orsakas av hund och katt. Om en hund orsakar skada eller olägenhet enligt TL kan hunden omhändertas av länsstyrelse eller Polismyndigheten. Ofta blir hunden omhändertagen för att den har bitit en annan hund, människa eller annat djur.  Vid ett omhändertagande ska en utredning genomföras av länsstyrelsen för att bedöma hundens psykiska- och fysiska status. Besiktningsman på polisen gör en mentalbesiktning av hunden och veterinär granskar hundens fysiska status. Därefter tar länsstyrelsen beslut om hunden ska återlämnas till sin ägare, omplaceras eller avlivas. I denna studie har länsstyrelserna arbete i Norrbotten, Skåne, Stockholm, Västerbotten, Västmanland och Västra Götaland granskats. Totalt omhändertogs 89 hundar i de sex länen, 2019–2021, 53 hanhundar (ca 60 %) och 36 tikar (ca 40 %). Avlivning var den åtgärd som utfördes oftast, 42 hundar avlivades. Övriga återlämnades eller omplacerades. Länsstyrelserna beslutar oftare om avlivning, 42 av 89 gånger (47 %), än vad polisen ger förslag om avlivning, 34 av 89 gånger (38 %). Generellt gör alla sex länsstyrelserna gedigna utredningar men det som framför allt skiljer dem åt är hur ofta respektive länsstyrelse följer polisens förslag på åtgärd. Den nya föreskriften som trädde i kraft 1 februari 2022 gör det möjligt för länsstyrelserna att bli ännu mer noggranna i sina utredningar av omhändertagna hundar. Utöver mentalbesiktning och veterinärundersökning ska länsstyrelserna även begära utlåtande från uppstallningsplatsen, om hundens beteende mot människor och djur.

The aim of this study was to investigate how the crime of animal cruelty is constructed and what lies behind these crimes where animals have been suffering.The study's data consisted of 76 animal cruelty judgements, the verdict pronounced between January 2017 and December 2018. Animal cruelty occurred in all of Sweden's counties. Most of the crimes were committed by perpetrators in the age group 50-59 years and men committed more crimes than women. Most of the crimes (92%) also resulted in day fines, which were combined with a suspended sentence in 63% of the cases. In 90% of the cases the day fines were for an amount of SEK 200 or less, and 43% of the perpetrators were given a suspended sentence or day fines of a minimum amount (SEK 50).Neglect concerning the primary lack of care, was the most common crime category (77% of all cases). Dogs were the most frequently affected species within both cases of neglect (39%) as well as in cases of abuse (79%), which is in line with previous studies regarding animal cruelty crimes. Men accounted for 92% of the cases in the crime category of abuse and women accounted for 49% of the cases in the category of neglect. In 40% of the judgments where cats were involved, the animal keeper also kept several other types of animals or had a larger total number of animals (68 animals at most), which may indicate animal hoarding. In almost half of the investigated cases, animals had either died or had to be euthanized because of the crime. It also turned out that some of the perpetrators violated an existing animal ban and nearly 15% of the crimes resulted in new animal bans. Approximately 15% of the judgements indicate animal hoarding and the lack of cooperation between authorities. It also appears that animal bans are not always complied by those who are imposed with the ban and further measures are therefore required for the ban to be complied with. Animal cruelty needs to be studied further and whether the new law on grave animal cruelty turns out to have the intended effect in practice. / Syftet med denna studie var att undersöka hur brottet djurplågeri är konstruerat och vad som ligger bakom dessa brott där djur blivit lidande. Studiens dataunderlag bestod av 76 djurplågeridomar som meddelats mellan januari 2017 och december 2018. Djurplågeri förekom i Sveriges samtliga län. Flest brott begicks av personer i åldersgruppen 50–59 år och män begick fler brott än kvinnor. Merparten av brotten (92 %) ledde till dagsböter, som i 63 % av fallen förenades med en villkorlig dom. I 90 % av fallen låg dagsböterna på 200 kronor eller mindre och 43 % av gärningspersonerna fälldes för brottet med en villkorlig dom eller dagsböter av minimibelopp (50 kr). Vanvård i form av primära skötselbrister var den vanligaste brottstypen (77 % av fallen) och hundar var det djurslag som drabbades oftast i såväl vanvårdsfall (39 %) som misshandelsfall (79 %), vilket är i linje med tidigare studier avseende djurplågeri. Männen stod för 92 % av brottstypen misshandel och kvinnor 49 % inom brottstypen vanvård. I 40 % där djurslaget katt förekom, höll djurhållaren flera olika djurslag men i flera fall även ett stort antal djur (som mest 68 stycken djur), vilket kan tyda på ett tvångsmässigt djursamlande. I närmare hälften av de undersökta domarna hade djur antingen självdött eller behövt avlivas på grund av brottet. Det visade sig även att en del av gärningspersonerna överträtt befintligt djurförbud och närmare 15 % av brotten resulterade i nya djurförbud. Omkring 15% av domarna tyder på djursamlande och ett bristande samarbete mellan myndigheter. Det framkommer även att djurförbud inte alltid efterlevs och att ytterligare åtgärder krävs för att förbudet ska efterlevas. Djurplågeri behöver studeras vidare och om den nya lagen om grovt djurplågeri visar sig få avsedd effekt i praktiken.

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