Browsing by Subject "inbreeding"
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(2020)The traditional method of estimating inbreeding is based on pedigree information, which only considers the known common ancestors of the animals. In recent years, the animal breeding sector has introduced new genomic tools in breeding schemes. The aim of this study was to estimate and compare the level of inbreeding in Finnish Yorkshire and Finnish Landrace pigs using pedigree and genomic methods. Data consisted of pedigree and genotype information from both breeds. In pedigree data there were 503 315 Landrace and 549 296 Yorkshire animals after pruning for pedigree completeness and errors in the data. In the genotype data, there were 522 individuals of Landrace and 934 individuals of Yorkshire animals after pruning. Inbreeding coefficients (FPED) were estimated from pedigree data using RelaX2 program and for genomic data using PLINK by detecting runs of homozygosity (FROH). Percentage of homozygosity (FPH) was also studied from genomic data. Yearly rate of inbreeding based on pedigree raised steadily. Average inbreeding coefficients from year 2014 were 0.10 for Landrace and 0.15 for Yorkshire. The average inbreeding coefficient based on ROHs for animals born in year 2014 were 0.21 for Landrace and 0.25 for Yorkshire animals. Correlation between pedigree-based estimate and genomic-based FROH was found to be quite low for both breeds; 0.51 for Landrace and 0.58 for Yorkshire. The correlation between the two genomic based methods FROH and FPH was high, 0.86 for Landrace and 0.89 for Yorkshire. The level of inbreeding was found to be quite high in both breeds. The genomic-based estimates were higher overall than pedigree-based estimates, which indicates that pedigree data are missing some common ancestors. Based on the results, the level of inbreeding in Finnish pig breeds should be monitored to maintain sufficient genetic diversity in the populations.
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(2020)Sukusiitosaste antaa tietoa populaation monimuotoisuuden tilasta ja voi vaikuttaa eläinten tuotantokykyyn. Perinteisesti sukusiitosasteet on laskettu sukupuutietojen avulla, mutta tämä menetelmä ottaa huomioon vain tunnetut yhteiset esivanhemmat. Viime vuosina on alettu käyttää enenevissä määrin genomiseen aineistoon pohjautuvia sukusiitosasteen arvioita. Tutkielman tavoitteena oli laskea sukusiitosasteet kahdelle eri suomalaiselle sikarodulle käyttäen sukupuu- ja genomista-aineistoa, sekä tarkastella niiden eroavaisuuksia. Sukupuuaineiston rajauksen jälkeen maatiaisrodun eläimiä oli 503 315 ja yorkshirejä 549 296 yksilöä. Genomisessa aineistossa oli käytettävissä karsinnan jälkeen 522 maatiaista ja 934 yorkshireä. Sukusiitosasteet (FPED) arvioitiin sukupuuaineistosta käyttäen RelaX2 ohjelmaa. Genomiset sukusiitosasteet laskettiin samankaltaisuuden jaksoista (runs of homozygosity) käyttäen PLINK ohjelmistoa. Lisäksi genomisesta aineistosta laskettiin yleinen homotsygotia-aste (FPH). Sukupuuaineistoihin perustuva sukusiitosasteiden vuosittainen nousu oli tasaista. Sukusiitosasteiden keskiarvot sukupuuaineistosta laskettuna vuonna 2014 syntyneille eläimille oli 0.10 maatiaiselle ja 0.15 yorkshirelle. ROH pohjaiset sukusiitosasteiden keskiarvot olivat vuonna 2014 syntyneille eläimille 0.21 maatiaiselle ja 0.25 yorkshirelle. Korrelaatio sukupuupohjaisen ja genomiseen ROH menetelmään perustuvan sukusiitosasteen välillä oli kohtalainen molemmilla roduilla: 0.51 maatiaisella ja 0.58 yorkshirellä. Genomisten FROH ja FPH menetelmien välinen korrelaatio oli suuri, 0.86 maatiaisella ja 0.89 yorkshirellä. Sukusiitosaste oli tämän tutkimuksen mukaan korkea molemmissa tutkituissa roduissa. Yleisesti ottaen genomiset menetelmät tuottivat korkeammat sukusiitosasteen arviot. Tutkielman tulosten perusteella suomalaisten sikarotujen sukusiitosastetta tulisi seurata, jotta riittävä geneettinen monimuotoisuus voidaan tulevaisuudessa säilyttää.
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(2011)The aim of this master’s thesis was to study genetic diversity within and between ten dog breeds. The original data was produced by Finnzymes Oy and it contained raw data files that were used to genotype microsatellite markers. The final data contained information from 395 dogs belonging to ten fairly different dog breeds. The amount of dogs per breed was from 31 to 53. The data was genotyped with 18 microsatellite markers. A llelic richness varied between 2,0 – 9,9. The most variable microsatellite locus was AHT137 and the least variable AHTk211. Over all loci allelic richness was highest in Jack Russell Terrier and lowest in Cavalier King Charles Spaniel. S c hipperke had the largest amount of microsatellite loci that were not in Hardy- Weinberg equilibrium. In Coton de Tulear, German Shepherd Dog and Finnish Lapphund all microsatellite loci were in Hardy-Weinberg equilibrium. The lowest overall heterozygosity was in Cavalier King Charles Spaniel (0,50) and highest in Finnish Lapphund (0,73). The only statistically significant FIS-values were in Schipperke in locus INU030 (0,39) and over all loci (0,11). The most distant breeds according to FST-value were Cavalier King Charles Spaniel and Rough Collie (0,34) and the closest breeds were Chihuahua and Coton de Tulear (0,07). Overall between breeds diversity was 17,7 %. On the grounds of these results the ten breeds are distinct populations. Coton de Tulear had clearly the highest amount of allele pairs in linkage disequilibrium (94) and Tibetan Spaniel the lowest amount (15). Effective population size was lowest in Rough Collie (35) and highest in Chihuahua (86). Based on many population genetic measures Cavalier King Charles Spaniel, Rough Collie and Schipperke seem to have the lowest genetic diversity and Chihuahua, Jack Russel Terrier and Finnish Lapphound the highest. Reasons for different levels of genetic diversity can be found on histories of these dog breeds.
Now showing items 1-3 of 3