1,779명 동북아시아인의 전장 유전체 데이터를 기반으로 한 참조 패널 생성과 유전학적 인구 특성 구조 및 약리 유전체학 프로파일의 연구

학위논문 (박사) -- 서울대학교 대학원 : 의과대학 의과학과, 2020. 8. 김종일.서론: 전장 게놈 해독 (WGS)의 비용 감소와 생산량 증가로 인간 게놈 연구의 대상자 수가 점차 늘어나고 있다. 특정 인구에 대한 대규모의 WGS는 인간 대상 유전체학 연구에서 매우 중요하며, 더 나아가 정밀의학 실현을 위한 인구집단에 대한 집단 유전체학적 이해와 약리 유전체학적 프로파일의 정확한 구축을 위해 대규모 WGS 데이터의 필요성은 지속해서 대두되고 있다. 하지만 대부분의 그 연구의 대상이 유럽인 중심으로 편중 되어있는 것이 현실이다. 방법: 우리는 한국인과 몽골인, 일본인, 중국인, 홍콩인 1,779명으로부터 생산한 전장 유전체 서열 분석 데이터를 활용하여 NARD (Northeast Asian Reference Database)를 구축하였다. NARD는 1000 게놈 프로젝트 3단계 (1KGP3)에 포함되지 않았던 한국계와 몽골계 인구의 새로운 유전적 다양성을 제공한다. 우리는 NARD와 1KGP3의 유전자형 데이터를 병합하고 re-phasing 방법으로 높은 성능의 통합 데이터 세트를 생성하였다. 앞서 한국과 몽골 인구에 대해 NARD 정도의 규모와 정밀성을 갖춘 데이터가 발표된 적은 없었다. NARD는 앞으로 동북아시아의 유전체학 분야에 더 정확하고 새로운 통찰을 제공할 것이다. 우리는 이 데이터를 토대로 한 PCA, FST 분석과 계통수 분석을 통해 인구 유전체학적 연구를 진행하였다. 우리는 또한 동북아시아의 약리학적 특성을 밝히는 시도를 하였다. 약물 반응과 관련된 단일 염기 다형성 (SNP) 및 BCL2L11 (BIM) 인트론 영역의 결손을 포함하는 구조적 변이, 면역 체크 포인트 차단 (ICB)에 대한 효험과 관련이 있는 HLA 영역을 포함한 동북아시아 특이적 변이를 조사하였다. 결과: re-phasing 방법으로 병합된 NARD와 1KGP3의 패널을 이용한 동아시아인 대상 imputation은 기존 패널들의 성능과 비교하여 가장 높은 정확도를 보였으며 특히 희귀 변이와 저 빈도 변이에 대해 그 향상이 두드러졌다. 우리는 인구 구조 분석을 통해 기존에 알려진 것과 달리 한국인, 몽골인, 일본인과 중국인 및 동남아시아인 사이에 뚜렷한 차이가 존재한다는 것을 확인할 수 있었다. NARD에서 일정 이상 빈도로 존재하는 변이는 환자를 대상으로 한 검사나 연구에서 단백질을 변성시키는 변이의 허위 후보를 제거하는데 활용될 수 있다. NARD에서는 총 1,480만여 개의 기존에 보고되지 않았던 신규 변이가 발견되었다. 그리고 약리 유전체학적 분석에서 타이로신 키나아제와 면역 체크 포인트 억제제의 효과 감소가 다른 지역에 비해 동북아시아에서 더 빈번하게 나타남을 보였다. NARD 참조 패널은 https://nard.macrogen.com/ 에서 임퓨테이션 파이프라인과 함께 제공된다. 결론: 우리는 동북아시아인 대상으로 가장 정확한 참조 패널을 구성하였다. 이 참조 패널은 연구목적으로 누구나 쉽게 사용할 수 있게 웹을 통해 제공된다. 또한 동북아시아의 인구 구조 및 약물 유전체학적으로 더욱 정밀한 통찰을 제공했다. 우리의 연구는 앞으로 동북아시아 정밀 의학 시대를 열기 위한 추가적인 연구의 초석이 될 것이다.Introduction: Whole-genome sequencing (WGS), an important technique in genome research, is becoming bigger the number of subjects thanks to both the increase of sequencing capacity and the decrease of sequencing cost. Large scale WGS for specific human populations with deep depth coverage is necessary to study population genomics. Moreover, the need for large-scale deep WGS datasets is emerging to precisely understand the pharmacogenomics profile for precision medicine in Northeast Asia in line with the global trend. However, most of the WGS studies are currently biased to Europe. Methods: We constructed the Northeast Asian Reference Database (NARD) using whole-genome sequencing data of 1,779 individuals from Korea, Mongolia, Japan, China, and Hong Kong. The NARD provides the genetic diversity of Korean and Mongolian ancestries that were not present in the 1000 Genomes Project Phase 3 (1KGP3). We re-phased the genotypes merged from the NARD and the 1KGP3 to construct a more robust union set of haplotypes. Mongol and Korean samples have never been released on the scale and the depth of the NARD level. It is expecting to shed light on novel and accurate insights to population genomics. To investigate the population structure, we performed PCA analysis, the fixation index (FST) analysis, phylogenetic tree construction, and ADMIXTURE analysis. We also tried to reveal the pharmacogenetic characteristics of Northeast Asians. We looked at various types of variants specific to Northeast Asians, the single nucleotide polymorphisms (SNPs) related to drug responses including rs116855232 in NUDT15, the SVs including BCL2L11 (BIM) intronic deletion, and the HLA haplotypes related to the responsiveness of immune checkpoint blockade (ICB) therapy. Results: The re-phasing approach we used to enhance the panel merged of the NARD and the 1KGP3 established a robust imputation reference panel for Northeast Asians, which yields the greatest accuracy in the genotype imputation especially for rare and low-frequency variants of Northeast Asians compared to the existing panels. Population genomics analyses demonstrated the significant differentiation among Koreans, Mongolians, Japanese, and mainland East Asians (Chinese and Southeast Asians), in contrast to previous studies that highlighted the close genetic relationships in Northeast Asian populations. The NARD variants catalog covered 14.8 million novel SNPs, which is improving the disease-related variants discovery by reducing the potential pathogenic candidates with common frequency redefined from rare frequency. Pharmacogenomics profiling suggested that the inefficiency of tyrosine kinase and the inhibition of immune checkpoint prevailed in Northeast Asians. The workbench of the imputation pipeline with the NARD panel is available at https://nard.macrogen.com/. Conclusions: We constructed the most accurate genotype imputation panel for Northeast Asian with public availability. We also unveiled the detailed Northeast Asian population structure and pharmacogenomic observations. Our work will contribute to further studies into the era of precision medicine for not only Northeast Asian but also the global population.Introduction 1 Whole-genome sequencing for human genomics 2 Genotype imputation with a population-specific reference panel 6 Population genomics based on whole-genome sequencing 9 Pharmacogenomics and precision medicine 12 Material and Methods 14 Results 29 Discovery of genetic variants including SNPs, indels, and structural variations 30 Population genomics analyses to reveal genetic architecture 33 Imputation accuracy improved with the NARD reference panel 37 Pharmacogenomics for precision medicine in Northeast Asians 44 Discussion 84 References 89 Abstract in Korean 103Docto

Population dynamics and genetic connectivity in recent chimpanzee history

Knowledge on the population history of endangered species is critical for conservation, but whole-genome data on chimpanzees (Pan troglodytes) is geographically sparse. Here, we produced the first non-invasive geolocalized catalog of genomic diversity by capturing chromosome 21 from 828 non-invasive samples collected at 48 sampling sites across Africa. The four recognized subspecies show clear genetic differentiation correlating with known barriers, while previously undescribed genetic exchange suggests that these have been permeable on a local scale. We obtained a detailed reconstruction of population stratification and fine-scale patterns of isolation, migration, and connectivity, including a comprehensive picture of admixture with bonobos (Pan paniscus). Unlike humans, chimpanzees did not experience extended episodes of long-distance migrations, which might have limited cultural transmission. Finally, based on local rare variation, we implement a fine-grained geolocalization approach demonstrating improved precision in determining the origin of confiscated chimpanzees

Uurali rahvaste geneetiline ajalugu läbi isaliini N ja autosoomse varieeruvuse prisma

Väitekirja elektrooniline versioon ei sisalda publikatsiooneEuroopast Lääne-Siberini levinud uurali keelkond postuleeriti enam kui saja aasta eest. Mitme põlvkonna eri teadusvaldkondade teadlaste töö tulemusena on kogutud aukartustäratav andmestik selle keelkonna rahvaste kohta, kuid erilise huvi objektiks on jäänud küsimus nende ühisest päritolust, võimalikust algkodust ja rändeteedest, mille kohta on välja pakutud arvukalt huvitavaid hüpoteese. Eelkõige geograafiast sõltuvas isalt pojale päranduvate Y-kromosoomi variantide ehk isaliinide jaotusmustris eristub selgelt haplogrupp N, mis seob nii Euroopa kui Aasia põhjaaladel elavaid rahvaid ning iseloomustab ka suurt osa uurali keeli kõnelevatest meestest. Käesoleva doktoritöö eesmärgiks oli esiteks rakendada kaasaegseid DNA järjestustehnoloogiaid hindamaks haplogrupi N fülogeneetilise puu sisestruktuuri ja alamklaadide ekspansiooniaegu ning levikut Põhja-Euraasias. Teiseks testida uusimate statistiliste meetoditega võimaliku geneetilise ühisosa olemasolu uurali keelesugulaste vahel, tuginedes ülegenoomsetele genotüpiseerimisandmetele. Selgus, et haplogrupp N on tõenäoliselt algselt pärit Põhja-Hiinast või mandrilisest Kagu-Aasiast ning haplogrupi sisemine struktuur koosneb mitmest piiritletud geograafilise levikuga alamklaadist. Ühel neist, haplogrupi N3 alamklaad N3a3’6, mille levikuaja algus jääb umbes 5000 aasta tagusesse aega, on tähelepanuväärselt lai geograafiline levik, mis ulatub Läänemere idakaldalt kuni Mongoolia ja Vene Beringiani ning hõlmab märkimisväärse osa kõikidesse suurematesse Põhja-Euraasia keelkondadesse kuuluvatest meestest. Ülegenoomsete andmete põhjal on enamusel uurali keeli kõnelejatest piiratud, kuid tuvastatav hiljutine tõenäoliselt Siberi päritolu geneetiline ühisosa, mis vihjab keelte levikuga kaasas käinud inimeste rändele. Samas on see ühine geneetiline komponent seotud ulatuslikumate ida poolt lähtunud mõjutustega Kirde-Euroopa kaasaegsete rahvaste geenifondile, mis tõenäoliselt ei piirdunud ainult uurali keeli rääkinud inimeste sisserändega.The Uralic linguistic family has been postulated for more than a hundred years with a current distribution area spanning from Europe to West Siberia. The prehistory of Uralic languages and their speakers has been under scrutiny of several generations of scientists from a variety of scientific fields. Numerous hypotheses have been proposed regarding their common origin, dispersal routes and possible homeland, but these questions continue to remain scientifically disputable. A clear disruptor in the pattern of geography-dependent distribution of Y-chromosomal paternal lineages is haplogroup N that unites populations across entire north Eurasia and describes a fair share of Uralic-speaking males in both northeastern Europe and west Siberia. First aim of this thesis was to apply novel DNA re-sequencing approach to resolve the inner phylogenetic structure of haplogroup N and estimate coalescent ages along with geographic distribution of its inner subclades. Second aim was to test for a common autosomal genetic substrate between Uralic speakers using novel statistical methods. The results suggest hg N to initially originate from North China or Mainland Southeast Asia and contain several novel subclades with distinct phylogeographic spread. One such subclade, N3a3’6 within subhaplogroup N3, displays an expansion time of 5000 years, but has a remarkably wide geographic distribution ranging from the eastern shores of the Baltic Sea to Mongolia and Pacific Russian Beringia, encompassing a considerate fraction of men from all major linguistic families in north Eurasia. Whole genome data shows a small, yet significant autosomal genetic component of possible Siberian ancestry shared between most of the Uralic-speaking populations, suggesting a migratory contribution to the dispersal of the languages. This component is part of a broader eastern influence on the genepool of modern northern Europe and was probably not limited to the spread of extant Uralic languages.https://www.ester.ee/record=b526783

Modeling the demographic history of Drosophila melanogaster using Approximate Bayesian Computation and Next Generation Sequencing Data

The main goal of this thesis was to develop demographic models of the fruit fly Drosophila melanogaster using Approximate Bayesian Computation and Next Generation Sequencing Data. These models were used to reconstruct the history of African, European, and North American populations. Chapter 1 deals with the demographic history of North American D. melanogaster. This project was motivated by the release of full-genome sequences of a North American population, which showed greater diversity than European D. melanogaster although the introduction of the fruit fly to North America dates back to only �200 years ago. Here, we tested di�erent demographic models involving populations of Zimbabwe, The Netherlands, and North Carolina (North America). Among the tested models we included variants with and without migration, as well as a model involving admixture between the population of Africa and Europe that generated the population of North America. We found that the admixture model �ts best the observed data and we estimated the proportion of European and African admixture in the North American population. This population has 85% European and 15% African ancestry. We also estimated other population parameters including population sizes (current and ancestral) and divergence times. Con�cerning previous studies we also estimated the divergence between African and European populations to be around 19,000 years ago. Chapter 2 deals with gene flow of D. melanogaster between African and European populations. Gene flow in D. melanogaster is well acknowledged but has not been quanti�ed using DNA sequence data. Previous studies from the late 80's based on allozymes found that the number of migrants per generation (Nm) was around 2 between several populations distributed worldwide. Here we used ABC methods and full-genome sequences to estimate the rate of migration between a population from Rwanda in Africa and a population from France. We found that Nm is around 10, which may imply there was a signi�cant increase of gene flow in the last few decades. Our estimates show that the migration rate between these two populations is not necessarily symmetrical, with migration from Europe to Africa being higher than the opposite, although the di�erence does not seem to be significant. The study of gene flow is relevant because it constitutes an important force in population genetics. Theoretical studies have shown that, under neutrality, it is enough to have one migrant per generation to stop two populations from diverging and speciating, and if migration is strong enough it can also overcome the e�ect of selection. Chapter 3 focuses on the sequencing of 130 full genomes of D. melanogaster from Africa and 9 from France. This project made use of haploid embryos, a new technique introduced in 2011 that allows the development of haploid D. melanogaster, which is then used for sequencing. The main goal of this project was to characterize these populations in terms of their diversity, admixture, and di�erentiation. We found that the most diverse population comes from Zambia, which is now thought to be much closer to D. melanogaster 's center of origin. We also found a signi�cant amount of non-cosmopolitan admixture in several African populations, meaning that there exists a signi�cant amount of back migration from Europe to Africa (corroborating the fi�ndings of chapter 2). In order to identify admixture tracts a new method was developed for this purpose, which uses a hidden Markov model to locate admixed regions along the genome. Admixed regions, as well as regions showing high levels of identity by descent were masked for downstream population genetics analyses. These full genomes constitute the second e�ort of the Drosophila Population Genomics Project (DPGP 2) and are now available for the scienti�c community

The French Canadian founder population : lessons and insights for genetic epidemiological research

La population canadienne-française a une histoire démographique unique faisant d’elle une population d’intérêt pour l’épidémiologie et la génétique. Cette thèse vise à mettre en valeur les caractéristiques de la population québécoise qui peuvent être utilisées afin d’améliorer la conception et l’analyse d’études d’épidémiologie génétique. Dans un premier temps, nous profitons de la présence d’information généalogique détaillée concernant les Canadiens français pour estimer leur degré d’apparentement et le comparer au degré d’apparentement génétique. L’apparentement génétique calculé à partir du partage génétique identique par ascendance est corrélé à l’apparentement généalogique, ce qui démontre l'utilité de la détection des segments identiques par ascendance pour capturer l’apparentement complexe, impliquant entre autres de la consanguinité. Les conclusions de cette première étude pourront guider l'interprétation des résultats dans d’autres populations ne disposant pas d’information généalogique. Dans un deuxième temps, afin de tirer profit pleinement du potentiel des généalogies canadienne-françaises profondes, bien conservées et quasi complètes, nous présentons le package R GENLIB, développé pour étudier de grands ensembles de données généalogiques. Nous étudions également le partage identique par ascendance à l’aide de simulations et nous mettons en évidence le fait que la structure des populations régionales peut faciliter l'identification de fondateurs importants, qui auraient pu introduire des mutations pathologiques, ce qui ouvre la porte à la prévention et au dépistage de maladies héréditaires liées à certains fondateurs. Finalement, puisque nous savons que les Canadiens français ont accumulé des segments homozygotes, à cause de la présence de consanguinité lointaine, nous estimons la consanguinité chez les individus canadiens-français et nous étudions son impact sur plusieurs traits de santé. Nous montrons comment la dépression endogamique influence des traits complexes tels que la grandeur et des traits hématologiques. Nos résultats ne sont que quelques exemples de ce que nous pouvons apprendre de la population canadienne-française. Ils nous aideront à mieux comprendre les caractéristiques des autres populations de même qu’ils pourront aider la recherche en épidémiologie génétique au sein de la population canadienne-française.The French Canadian founder population has a demographic history that makes it an important population for epidemiology and genetics. This work aims to explain what features can be used to improve the design and analysis of genetic epidemiological studies in the Quebec population. First we take advantage of the presence of extended genealogical records among French Canadians to estimate relatedness from those records and compare it to the genetic kinship. The kinship based on identical-by-descent sharing correlates well with the genealogical kinship, further demonstrating the usefulness of genomic identical-by-descent detection to capture complex relatedness involving inbreeding and our findings can guide the interpretation of results in other population without genealogical data. Second to optimally exploit the full potential of these well preserved, exhaustive and detailed French Canadian genealogical data we present the GENLIB R package developed to study large genealogies. We also investigate identical-by-descent sharing with simulations and highlight the fact that regional population structure can facilitate the identification of notable founders that could have introduced disease mutations, opening the door to prevention and screening of founder-related diseases. Third, knowing that French Canadians have accumulated segments of homozygous genotypes, as a result of inbreeding due to distant ancestors, we estimate the inbreeding in French Canadian individuals and investigate its impact on multiple health traits. We show how inbreeding depression influences complex traits such as height and blood-related traits. Those results are a few examples of what we can learn from the French Canadian population and will help to gain insight on other populations’ characteristics as well as help the genetic epidemiological research within the French Canadian population

Beyond broad strokes: sociocultural insights from the study of ancient genomes

The amount of sequence data obtained from ancient samples has dramatically expanded in the last decade, and so have the type of questions that can now be addressed using ancient DNA. In the field of human history, while ancient DNA has provided answers to long-standing debates about major movements of people, it has also recently begun to inform on other important facets of the human experience. The field is now moving from mostly fixating on large-scale supra-regional studies to also taking a more local perspective, shedding light on socioeconomic processes, inheritance rules, marriage practices and technological diffusion. In this review, we summarize recent studies showcasing these types of insights, focusing on methods used to infer sociocultural aspects of human behaviour. This often involves working across disciplines that have, until recently, evolved in separation. We argue that multidisciplinary dialogue is crucial for a more integrated and richer reconstruction of human history, as it can yield extraordinary insights about past societies, reproductive behaviors and even lifestyle habits that would not have been possible to obtain otherwise

Molekularna disekcija inbriding depresije za svojstva kvalitete sperme kod goveda

Runs Of Homozygosity (ROH) are a newly introduced approach for identifying inbreeding in diploid individuals. This approach is more reliable and available than pedigree data, but the lack of universal standards about ROH definition and identification introduces serious bias in ROH studies. In this thesis, ROH were analyzed in five cattle breeds (Brown Swiss, Fleckvieh, Norwegian Red, Pinzgauer and Tyrol Grey). The effects of SNP chip density and genotyping errors were tested on Brown Swiss, Pinzgauer and Tyrol Grey in order to establish the most optimal settings for precise estimation of levels of autozygosity. Data from the 50 k chip led to an overestimation of the number of ROH shorter than 4 Mb, since the analysis could not identify heterozygous SNPs present on the denser chip. Conversely, data from the denser chip underestimated the number of ROH longer than 8 Mb, unless the presence of a small number of heterozygous SNP genotypes was allowed within a ROH. Using this options ROH were identified in Brown Swiss, Fleckvieh, Norwegian Red and Tyrol Grey. Levels of autozygosity were calculated and compared with pedigree inbreeding coefficients. For all four breeds, population inbreeding levels estimated by the genomic inbreeding coefficients FROH > 8 Mb and FROH > 16 Mb were similar to the levels estimated from pedigrees. In contrast, inbreeding estimates based on FROH > 1 Mb and FROH > 2 Mb were considerably higher than pedigree-derived estimates. Pearson correlations between FROH and FPED ranged from 0.50 to 0.72, as dependent on pedigree depth. In the analysis of inbreeding depression a significant influence of FPED, FROH2 - 4 Mb and FROH > 2 Mb on total number of spermatozoa in 554 Fleckvieh bulls was found. Exact autozygous regions that influence this trait were detected on chromosomes 7, 10, 17, 20, 22 and 27 containing 41 genes. Five obvious candidate genes were found which are known to be directly associated with spermatogenesis, energy levels in spermatozoa and osmotic balance of the sperm. In conclusion, genotyping errors and SNP chip density do affect estimates of autozygosity from ROH, ROH distributions (number and size) enables precise estimation of autozygosity at individual and population levels in cattle and genomic autozygosity does have influence on bull semen quality.“Runs Of Homozygosity” (ROH) nov su pristup utvrđivanja inbridinga kod diploidnih organizama i smatraju se pouzdanijim i više dostupnim od rodovnika, no nedostaju jedinstveni standardi za njihovu uporabu. U ovoj disertaciji ROH su analizirani kod pet pasmina goveda (Brown Swiss, Fleckvieh, Norwegian Red, Pinzgauer i Tyrol Grey). Utjecaj gustoće genomske informacije (SNP chipa) i utjecaj genotipskih pogrešaka na detekciju ROH-ova istražen je na pasminama Brown Swiss, Pinzgauer i Tyrol Grey. SNP chip manje gustoće sustavno je precjenjivao broj ROH-ova <4 Mb, što je uzrokovalo i precjenjivanje inbridinga. Gušći SNP chip podcjenjivao je velike segmente osim u slučaju kada se dozvoljavao određen broj heterozigotnih genotipova. Koristeći ova saznanja procijenjen je ROH inbriding (FROH) za populacije Brown Swiss, Fleckvieh, Norwegian Red i Tyrol Grey, te je uspoređen s koeficijentima inbridinga iz rodovnika (FPED). Za sve četiri populacije vrijednosti FROH > 8 Mb i FROH > 16 Mb bile su slične vrijednosti FPED dok su FROH > 1 Mb i FROH > 2 Mb vrijednosti inbridinga bile mnogo veće od FPED. Pearsonovi korelacijski koeficijenti između FROH i FPED bili su rasponu od 0.50 do 0.72, a vrijednost je ovisila o dubini rodovnika. Kod analize inbriding depresije uočen je značajan utjecaj FPED, FROH2 - 4 Mb i FROH > 2 Mb na ukupan broj spermatozoida kod bikova Fleckvieh pasmine. Detekcija autozigotnih regija koje utječu na ovo svojstvo otkrila je regije na kromosomima 7, 10, 17, 20, 22 i 27 u kojima je pronađen 41 gen od kojih je pet izglednih kandidata, jer su povezani sa spermatogenezom, razinom energije spermatozoida i osmotskom ravnotežom spermatozoida i sjemene tekućine. Sve navedeno dovodi sljedećih zaključaka; greške genotipizacije i gustoća SNP chipa imaju utjecaj na identifikaciju ROH-ova; ROH metodom procijenjena autozigotnost predstavlja dobar pokazatelj stupnja inbridinga; autozigotnost genoma je povezana s plodnošću bikova

Molekularna disekcija inbriding depresije za svojstva kvalitete sperme kod goveda

Runs Of Homozygosity (ROH) are a newly introduced approach for identifying inbreeding in diploid individuals. This approach is more reliable and available than pedigree data, but the lack of universal standards about ROH definition and identification introduces serious bias in ROH studies. In this thesis, ROH were analyzed in five cattle breeds (Brown Swiss, Fleckvieh, Norwegian Red, Pinzgauer and Tyrol Grey). The effects of SNP chip density and genotyping errors were tested on Brown Swiss, Pinzgauer and Tyrol Grey in order to establish the most optimal settings for precise estimation of levels of autozygosity. Data from the 50 k chip led to an overestimation of the number of ROH shorter than 4 Mb, since the analysis could not identify heterozygous SNPs present on the denser chip. Conversely, data from the denser chip underestimated the number of ROH longer than 8 Mb, unless the presence of a small number of heterozygous SNP genotypes was allowed within a ROH. Using this options ROH were identified in Brown Swiss, Fleckvieh, Norwegian Red and Tyrol Grey. Levels of autozygosity were calculated and compared with pedigree inbreeding coefficients. For all four breeds, population inbreeding levels estimated by the genomic inbreeding coefficients FROH > 8 Mb and FROH > 16 Mb were similar to the levels estimated from pedigrees. In contrast, inbreeding estimates based on FROH > 1 Mb and FROH > 2 Mb were considerably higher than pedigree-derived estimates. Pearson correlations between FROH and FPED ranged from 0.50 to 0.72, as dependent on pedigree depth. In the analysis of inbreeding depression a significant influence of FPED, FROH2 - 4 Mb and FROH > 2 Mb on total number of spermatozoa in 554 Fleckvieh bulls was found. Exact autozygous regions that influence this trait were detected on chromosomes 7, 10, 17, 20, 22 and 27 containing 41 genes. Five obvious candidate genes were found which are known to be directly associated with spermatogenesis, energy levels in spermatozoa and osmotic balance of the sperm. In conclusion, genotyping errors and SNP chip density do affect estimates of autozygosity from ROH, ROH distributions (number and size) enables precise estimation of autozygosity at individual and population levels in cattle and genomic autozygosity does have influence on bull semen quality.“Runs Of Homozygosity” (ROH) nov su pristup utvrđivanja inbridinga kod diploidnih organizama i smatraju se pouzdanijim i više dostupnim od rodovnika, no nedostaju jedinstveni standardi za njihovu uporabu. U ovoj disertaciji ROH su analizirani kod pet pasmina goveda (Brown Swiss, Fleckvieh, Norwegian Red, Pinzgauer i Tyrol Grey). Utjecaj gustoće genomske informacije (SNP chipa) i utjecaj genotipskih pogrešaka na detekciju ROH-ova istražen je na pasminama Brown Swiss, Pinzgauer i Tyrol Grey. SNP chip manje gustoće sustavno je precjenjivao broj ROH-ova <4 Mb, što je uzrokovalo i precjenjivanje inbridinga. Gušći SNP chip podcjenjivao je velike segmente osim u slučaju kada se dozvoljavao određen broj heterozigotnih genotipova. Koristeći ova saznanja procijenjen je ROH inbriding (FROH) za populacije Brown Swiss, Fleckvieh, Norwegian Red i Tyrol Grey, te je uspoređen s koeficijentima inbridinga iz rodovnika (FPED). Za sve četiri populacije vrijednosti FROH > 8 Mb i FROH > 16 Mb bile su slične vrijednosti FPED dok su FROH > 1 Mb i FROH > 2 Mb vrijednosti inbridinga bile mnogo veće od FPED. Pearsonovi korelacijski koeficijenti između FROH i FPED bili su rasponu od 0.50 do 0.72, a vrijednost je ovisila o dubini rodovnika. Kod analize inbriding depresije uočen je značajan utjecaj FPED, FROH2 - 4 Mb i FROH > 2 Mb na ukupan broj spermatozoida kod bikova Fleckvieh pasmine. Detekcija autozigotnih regija koje utječu na ovo svojstvo otkrila je regije na kromosomima 7, 10, 17, 20, 22 i 27 u kojima je pronađen 41 gen od kojih je pet izglednih kandidata, jer su povezani sa spermatogenezom, razinom energije spermatozoida i osmotskom ravnotežom spermatozoida i sjemene tekućine. Sve navedeno dovodi sljedećih zaključaka; greške genotipizacije i gustoća SNP chipa imaju utjecaj na identifikaciju ROH-ova; ROH metodom procijenjena autozigotnost predstavlja dobar pokazatelj stupnja inbridinga; autozigotnost genoma je povezana s plodnošću bikova