Browsing by Subject "tehollinen populaatiokoko"

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  • Siipola, Anne (Helsingin yliopisto, 2019)
    Conservation of the genetic diversity enables population adaption to climate and production system changes and prevents harmful consequences of inbreeding. The aim of this study was to investigate the state of genetic diversity in Finnish Ayrshire and Finncattle breeds (Western, Eastern and Northern Finncattle) based on pedigree information. The data were received from FABA co-op. Average inbreeding coefficient and relationships were estimated for animals born between 1970 and 2017. Effective population sizes were estimated separately for each birth-year group. In addition, genetic contribution of the most important ancestors of the population were investigated. The Software packages RelaX2 and R-program were used to estimate the population parameters. Average inbreeding coefficient had either stayed at the same level or decreased for all breeds except Western Finncattle. Average inbreeding coefficient of Western Finncattle has increased 2.2 %-units during the last 20 years. In addition, average relationships between breeding animals has remained stable in other breeds except Western Finncattle. Estimated effective population sizes were 163 (AY), 78 (PSK) 74 (LSK) and 57 (ISK) for animals born between 2015 and 2017. The most important ancestors to animals born between 2015 and 2017 of each breed were A Lier (AY), Opari (LSK), Asa (ISK) and Fager (PSK). Effective population sizes of different Finncattle breeds were larger than the minimum recommendation of 50 and average relationship coefficients between breeding animals have stabilized during the past few years. Despite this, the diversity of all Finncattle breeds needs to be strictly monitored. The genetic diversity of Finnish Ayrshire is at the sustainable level that is partly due to cooperation of the Nordic breeding organizations. In the future, genomic information will hopefully provide more effective tools to estimate and manage population genetic diversity.
  • Jäntti, Jonna (Helsingfors universitet, 2014)
    Tämän tutkimuksen tavoitteena oli selvittää koirarotujen perinnöllistä monimuotoisuutta ja rotujen välisiä perinnöllisiä eroja. Lisäksi suomalaisia rotuja tarkasteltiin tarkemmin. Tutkimuksessa käytettiin Finnzymes Oy:ltä saatua mikrosatelliittimerkkeihin perustuvaa genotyyppiaineistoa, joka oli alun perin kerätty polveutumismäärityksiä varten. Tämä aineisto oli genotyypitetty 18:lla mikrosatelliittilokuksella. Tutkimuksessa oli mukana 500 yksilöä. Roduittain otokset vaihtelivat välillä 5-49. Rodut edustivat kahdeksaa eri FCI:n roturyhmää. Rotujen sisäisestä monimuotoisuudesta kertova alleelirikkaus vaihteli lokuksittain välillä 1,4-6,4. Keskiarvojen perusteella alleelirikkaus oli suurinta suomenlapinkoiralla ja pienintä bokserilla. Kaikkien rotujen kaikki mikrosatelliittilokukset olivat tilastollisesti merkitsevästi Hardyn-Weinbergin tasapainossa. Havaittu heterotsygotia-aste oli suurin lapinporokoiralla (0,76) ja pienin bokserilla (0,42). Rotujen välistä geneettistä etäisyyttä kuvaavien Fst-arvojen perusteella suurin etäisyys oli bokserin ja cavalier kingcharlesinspanielin välillä (0,39) ja pienin etäisyys oli lapinporokoiran ja chihuahuan välillä (0,07). Nei´n DA –etäisyyksistä suurin (0,58) oli bokserin ja cavalier kingcharlesinspanielin välillä. Pienin etäisyys (0,18) oli puolestaan chihuahuan ja coton de tulearin, chihuahuan ja jackrusselinterrierin, chihuahuan ja suomenlapinkoiran, coton de tulearin ja jackrusselinterrierin sekä jackrusselinterrierin ja suomenlapinkoiran välillä. Suomalaisista roduista karjalankarhukoiralla oli eniten populaation homotsygotiasta kertovia positiivisia Fis –arvoja (12 kpl) ja suurin keskiarvo. Lapinporokoiralla oli eniten populaation heterotsygotiasta kertovia negatiivisia Fis –arvoja (13 kpl) ja pienin keskiarvo. Kytkeytyneitä alleeleita oli eniten lapinporokoiralla (58 kpl) ja vähiten suomenajokoiralla (16 kpl). Suomalaisten rotujen teholliset populaatiokoot vaihtelivat välillä 65-81. Suurin oli suomenlapinkoiralla ja pienin karjalankarhukoiralla. Tutkimuksessa nousivat esille suomenlapinkoira suuren perinnöllisen monimuotoisuutensa vuoksi ja bokseri vähäisen monimuotoisuutensa vuoksi. Yleensä tapahtumat rotujen jalostushistoriassa ja perustajayksilöiden määrä ovat todennäköisesti olleet vaikuttamassa monien rotujen perinnölliseen monimuotoisuuteen.
  • Paakala, Elina (Helsingfors universitet, 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.
  • Sjöblom, Kateriina (Helsingfors universitet, 2017)
    Länsisuomenkarja on pienilukuinen populaatio, joka on altistunut sukulaistumiselle ja suku-siitosasteen nousulle. Tutkimuksen tavoitteena oli selvittää länsisuomenkarjan populaation nykytilanne laskemalla tehollinen populaatiokoko, sukusiitosasteen kehitys vuosina 1950‒2014 sekä sukusiitosasteen muutos sukupolvea kohden eri ajanjaksoina. Lisäksi tavoitteena oli tarkastella vanhojen 1960‒80-luvulla syntyneiden sonnien käytön vaikutusta populaati-on perinnölliseen tasoon sekä sukulaistumisen ja sukusiitoksen rajoittamiseen. Populaatioparametrien laskennassa käytettiin sovelluksia RelaX2 ja EVA. Länsisuo-menkarjan teholliseksi populaatiokooksi saatiin 103, mikä on suositusten (50‒100) rajoissa. Niin ikään sukusiitosasteen muutos sukupolvea kohden vuosina 1950‒2014 oli 0,58 %, mikä on suositusten rajoissa (0,5‒1 %). Kuitenkin sukusiitosasteen muutos sukupolvea kohden viime vuosikymmeninä on ollut hieman yli suositusten (1,2 %). Länsisuomenkarjan populaation keskimääräinen sukusiitosaste on noussut tasaisesti vuodesta 1970 alkaen. Sonneista, joilla vielä on annoksia varastossa, alhaisimmat sukulaisuudet nuoriin naarai-siin olivat seuraavilla sonneilla: Ryhti 0,22 %, Viinamäen Akvaviitti 0,33 % ja Lehmon-niemen Aromi 0,49 %. Suurimmat geneettiset kontribuutiot nykyiseen sukupolveen olivat seuraavilla sonneilla: Opari 15,0 %, Tahto 12,6 % ja Pennalan Vekkuli 9,8 %. Simuloitu vanhojen sonnien käyttö parituksissa sai aikaan keskimääräisen sukulaisuuden laskun sekä sukusiitosasteen nousun hidastumisen. Vanhojen sonnien käytöllä oli kuitenkin odotettu negatiivien vaikutus perinnölliseen edistymiseen (kokonaisjalostusarvoon). Lyhyellä aikajänteellä tarkasteltuna länsisuomenkarjan populaatio vaikuttaisi olevan suhteellisen hyvässä tilassa. Kuitenkin sukusiitosasteen nousu saattaa uhata populaation monimuotoisuutta pitkällä tähtäimellä. Vanhojen sonnien harkittu käyttö kahden tai kol-men uuden nuorsonnin tuottamiseksi sukupolvea kohti saattaisi olla järkevä ratkaisu.
  • Ettala, Anna (Helsingfors universitet, 2015)
    The aim of this study was to analyze the development and population structure of the Finnhorse's parentage. The coefficient of inbreeding, the time between generations and the effective population size was studied in the whole population. The effective number of founders and ancestors in the population was determined. The number of horses in the whole population was 77 925 animals. The time between generations was 12.6 years on average. On average, the time between generations was two years longer for stallions than for mares. The effective population size of the Finnhorse was 181, which is sufficient to preserve the genetic diversity of the gene pool. It also examined the degree of kinship and inbreeding with the development of advanced, runner, riding, working - and small horse the direction of the corresponding parameters between the years 1960-2012 and compared with the results obtained in this term. There were 9 585 horses registered in different breeding sections: 6 385 horses in the trotter section, 1 734 horses in the working section, 1 027 horses in the riding second and 439 small Finnhorses. The average coefficient of relatedness in the whole population in 1960–2012 was 2,7-10,7%. The average inbreeding coefficient of inbreeding in the whole population was 1-4,4%. Inbreeding has evolved over the last few decades in the same way as in the past. Stock recorded a runner horses degree of relatedness is, however, significantly increased in recent years. The relatedness between the trotter section and the rest of the population was in the same range than in the whole population. The results of this research concerning different variables were similar to those gathered from studies on other horse breeds. The coefficient of inbreeding and relatedness of the Finnhorse is low enough to ensure that the genetic diversity of the breed will not diminish in the future.
  • Partanen, Reeta-Maria (Helsingin yliopisto, 2018)
    Effective population size is one of the most important concepts in population genetics. Large enough effective population size is important in maintaining genetic variation in populations. The aim of the study was to estimate effective population size in Landrace and Yorkshire populations and to find out if there is variation in the effective population size between chromosomes and chromosome segments. Effective population sizes were estimated using changes in allele frequencies across generations. Estimation was done from a SNP-genotype data consisting of 1020 Landrace and 1824 Yorkshire boars born in 1996-2013. Average effective population size in Landrace was approximately 40 individuals when estimated at chromosome level and approximately 47 individuals when estimated from chromosome segments. In Yorkshire, the respective estimates were around 37 and 46 individuals. It was noticed that there is variation in the estimated effective population size in both Landrace and Yorkshire populations. In Landrace, the largest chromosome-wise estimates of the effective population size were four times larger than the smallest estimates. The largest chromosome segment based estimates were 21 times larger than the smallest estimates. In Yorkshire, the largest estimates of chromosome-wise effective population size were three times larger and the largest estimates of chromosome segment based effective population size as much as 35 times larger than the smallest ones. The estimates of average effective population size in this study were clearly smaller in both breeds than the estimates of effective population sizes in previous studies that were based on pedigrees or linkage disequilibrium between SNPs. Chromosome-wise or chromosome segment based estimates of effective population size can be utilized in maintaining genetic variation in populations and in optimizing breeding programs.