Haplotype Diversity of Partial Cytochrome b Gene in Kebumen Ongole Grade Cattle

Cytochrome b gene is commonly used to figure out the genetic variation in animals. This research was designed to explore specific markers of Kebumen Ongole grade cattle and to understand the relationship between Kebumen and Brahman cattle using mtDNA cyt b sequences. The sequence of mtDNA cytochrome b gene of 14 individuals Kebumen Ongole grade cattle and 15 individuals  Brahman cattle was determined by using polymerase chain reaction and sequencing with a pair of primer. The haploview software was utilized to linkage disequilibrium (LD) analysis. As a result, 36 SNPs (single nucleotide polymorphisms) with 8 haplotypes were identified in Kebumen Ongole grade cattle. In contrast, a small number of SNPs (7) and haplotypes (6) were observed in Brahman cattle. The homozigosity in Brahman cattle was  higher than that in Kebumen Ongole grade cattle cattle. Moreover, based on mtDNA sequences, 50% of Kebumen Ongole grade cattle had 85% similarity with Brahman cattle. The SNP number and LD values of Kebumen Ongole grade cattle were greater than those of Brahman cattle. It was presumed that Brahman cattle might be introduced into Kebumen territory. In conclusion, some of Kebumen Ongole grade cattle have genetic relation with Brahman cattle. In addition, the information of SNP and haplotype results from this research can be used as markers to differentiate breeds of animals

Maternal lineages and diversity of the growth hormone gene of South African goat populations

The maternal lineages and origins of the South African goat populations are unknown and hence pose challenges for breed characterization and conservation. This study investigated the maternal lineages of South African goats using complete mtDNA and ascertained the genetic diversity in the growth hormone gene within and between populations. Illumina MiSeq next generation sequencing was used to generate the full length of the mtDNA (16.64 kb) and growth hormone (2.54kb) genes in 50 goats of the commercial South African Boer (n =9), captive feral Tankwa (n =9), and SA village goat populations (n =32). The non-descript village populations were sampled from villages of the four major goat-producing provinces; (i) Hobeni village, Elliotdale municipality and Pechelsdam village, Inxubayethemba municipality in Eastern Cape (n=8), (ii) Coniliva and Ngubo villages in Msinga municipality Kwa-Zulu Natal (n=8), (iii) Mukovhabale village, Mutale municipality and Muila-muumone, Makhado municipality in Limpopo (n=8) and (iv) Pella village (n=6), Moses Kotane municipality North West (n=8) provinces of South Africa. A total of 184 SNPs and 55 AA changes were observed across the complete mtDNA genome. High within-population variation was observed in all the groups, ranging from 98.60 to 99.52%. A low FST (FST = 0.003-0.049) indicated close relatedness and possible gene flow between SA goat populations. Haplotypes and clades observed in the D-loop, COX1 and whole mtDNA network trees demonstrated relationships between South African goat populations. The South African goats clustered with Chinese goats from lineages A and B, suggesting common maternal lineages between the Chinese and South African goat populations. The results also suggested that the bezoar (Capra aegagrus) is a possible ancestor of South African domestic goats. A range of 27 to 58 SNPs per population were observed on the growth hormone gene. Amino acid changes from glycine to serine, tyrosine to cysteine and arginine to glycine were observed at exon 2 and exon 5. Gene diversity ranged from 0.8268 ± 0.0410 to 0.9298 ± 0.0050. Higher within breed diversity (97.37%) was observed within the population category consisting of SA village ecotypes and the Tankwa goats. Highest pairwise FST values ranging from 0.148 to 0.356 were observed between the SA Boer and both the SA village and Tankwa feral goat populations. The maximum likelihood phylogenetic analysis indicated nine genetic clades, which reflected close relationships between the South African populations and the other international breeds. Results imply greater potential for within population selection programs particularly with SA village goats.Life and Consumer SciencesM.Sc. (Statistical Genomics

소와 돼지의 구조 변이의 특성 및 집단 간 차이 연구

학위논문(박사) -- 서울대학교대학원 : 자연과학대학 협동과정 생물정보학전공, 2023. 8. 김희발.Structural variation (SV) is a class of genomic alteration that involves segments of DNA longer than 1 kb. SVs can affect gene expression, function, and evolution, and are associated with various phenotypes and diseases. In this study, I investigated the population differentiation and characteristics of SVs in cattle and swine, two important domesticated animals with complex evolutionary histories. I used various genomic approaches to analyze SV in three research chapters that focused on copy number variation (CNV), a type of SV that involves deletion or duplication of DNA segments. Literature review about SV and approaches for identifying SV are summarized in the first chapter. The second chapter examined the population differentiated CNV of Bos taurus, Bos indicus, and their African hybrids, revealing the impact of hybridization and selection on CNV diversity. The third chapter compared the CNV between Eurasian wild boar and domesticated pig populations, uncovering the signatures of domestication and adaptation on CNV patterns. The fourth chapter presented the chromosome-level genome assembly of Hanwoo, a Korean native cattle breed, and the pangenome graph of 14 B. taurus assemblies. The study identified Hanwoo-specific regions and structural variants that may be related to phenotypic traits and adaptation. These chapters collectively demonstrated the power and utility of population genetics of SVs for studying the evolution and disease of cattle and swine and provided valuable resources and insights for future research.구조 변이(structural variation, SV)는 1 kb보다 긴 DNA 영역의 변화를 포함하는 유전체 변이의 한 종류이다. 구조 변이는 유전자 발현, 기능에 영향을 미치며 다양한 형질과 질병과 관련되어 있으며, 진화의 역사 추정을 위한 단서이다. 본 연구에서는 복잡한 진화 역사를 가진 두 가지 중요한 가축인 소와 돼지의 구조 변이의 집단 유전학을 연구하였다. 유전차 상의 다양한 구조 변이 중에서, 특히 구간의 결실 또는 중복을 포함하는 구조 변이의 한 형태인 복제 수 변이(copy number variation, CNV)에 초점을 맞춘 3개의 주제들을 연구하기 위해 다양한 유전체학적, 생물정보학적 방법을 활용하였다. 제1장에서는 구조변이와 구조변이의 집단 유전학적 특성 및 분석 방법 등 본 논문에 포함된 기본 지식과 연구 동향을 정리하였다. 제2장에서는 Bos taurus, Bos indicus 및 그들의 교잡으로 형성된 아프리카 소들 간의 차별화된 복제 수 변이를 조사하여 교잡과 선택이 CNV 다양성에 미치는 영향을 밝혔다. 제3장에서는 유라시아 멧돼지와 가축화된 돼지 집단 간의 복제 수 변이를 비교하여 가축화와 적응에 따른 CNV 패턴의 특징을 발견하였다. 제4장에서는 한우의 염색체 수준의 고품질 genome assembly와 14개 Bos taurus 유전체들의 pangenome graph를 제시하였다. 이 연구에서 형질과 적응과 관련될 수 있는 한우 특이적 영역과 구조 변이를 확인하였다. 본 논문은 소와 돼지의 진화와 질병을 연구하기 위한 구조 변이의 집단 간 차이와 특성을 연구하여, 진화적 관점의 해석을 제공하였으며, 이는 향후 연구를 위한 귀중한 자료와 통찰력을 제공하였다.ABSTRACT I CONTENTS III LIST OF TABLES V LIST OF FIGURES V CHAPTER 1. LITERATURE REVIEW 1 1.1. Structural variation and population genetics 2 1.2. Methods used to study structural variation of different populations in a same species. 2 CHAPTER 2. POPULATION DIFFERENTIATED COPY NUMBER VARIATION OF BOS TAURUS, BOS INDICUS AND THEIR AFRICAN HYBRIDS 4 2.1. Abstract 5 2.2. Introduction 6 2.3. Materials and Methods 8 2.4. Results ３０ 2.5. Discussion ４４ CHAPTER 3. POPULATION DIFFERENTIATED COPY NUMBER VARIATION BETWEEN EURASIAN WILD BOAR AND DOMESTICATED PIG POPULATIONS ５２ 3.1. Abstract ５３ 3.2. Introduction ５４ 3.3. Materials and Methods ５７ 3.4. Results ８０ 3.5. Discussion １１１ CHAPTER 4. CHROMOSOME-LEVEL GENOME ASSEMBLY OF KOREAN NATIVE CATTLE AND PANGENOME GRAPH OF 14 BOS TAURUS ASSEMBLIES １１７ 4.1. Abstract １１８ 4.2. Background & Summary １１９ 4.3. Materials and Methods １２１ 4.4. Data Records １４０ 4.5. Technical Validation １４０ 4.6. Usage Notes １４４ CHAPTER 5. GENERAL DISCUSSION １４７ REFERENCES １４９ 국문초록 １６9박

Veterinary Microbiology & Parasitology

Numerous pathogens affect animal health and wellbeing and production efficiency. These pathogens also have a considerable impact on social economics, food safety and security, and human health. Infectious diseases that originate from both domesticated animals and wildlife represent one of the greatest threats to human health. Recent studies show that domesticated species harbor approximately 84 times more zoonotic viruses than wild species. Eight of the top 10 mammalian species with the highest number of zoonotic viruses are domestic, such as pigs, cattle, and horses. Many animal parasites are also zoonotic, constituting an additional burden on human health. Furthermore, the rapid emergence and spread of drug-resistant pathogen strains pose new threats to animal and human health. Climate changes will undoubtedly alter the interactions between animals and between animals and humans, which will have a huge impact on the transmission rate of existing pathogens and the emergence of new pathogens or the reemergence of old pathogens. In this special collection, interactions of all major pathogen types, including viruses, bacteria, mites and flies, protozoans, and helminths, and their hosts, such as wild and companion animals and livestock species, are discussed. Further, anthelmintic activities of natural products are evaluated. The relevance and utility of cutting-edge tools, such as immunology, genomics and genetics, microbiome studies and metabolomics, and molecular epidemiology, in dissecting host-pathogen interactions are also discussed. This special collection provides a broad knowledge base that encourages dialogue across a wide distribution of the research community in veterinary microbiology and parasitology

차세대 염기서열 및 단일염기다형성 데이터를 이용한 포유류의 유전체 변이와 유효집단크기 해독

학위논문 (박사)-- 서울대학교 대학원 : 농생명공학부, 2014. 8. 김희발.This doctoral dissertation consists of five studies related to mammalian genetic variation and effective population size using SNP data or NGS data. Effective population size is essential to measure data size, quality and genetic diversity of animal population. I thus investigated economic trait-associated genetic variation of domesticated animal using SNP data. In addition, I examined copy number variation related to domestication process of cattle using NGS data. In chapter 1, I introduced the basic background and necessity of the series of worked in this doctoral dissertation. The effective population size (Ne) is important to assess the genetic diversity of animal populations. In chapter 2, I characterized more accurate linkage disequilibrium in a sample of 96 dairy cattle producing milk in Korea and estimated Ne that is approximately 122. And I inferred historical Ne and I can knew that a rapid increase Ne over the past 10 generations, and increased slowly thereafter. These results can be rationalized using current knowledge of the history of the dairy cattle breeds producing milk in Korea. In chapter 3, I investigated the common minke whale (Balaenoptera acutorostrata) genome using next generation sequencing. After then, I estimated historical effective population size in the minke whale based on coalescent model to know when minke whale population size decreases rapidly. As a result, I guessed that minke whale population diversity downsized to approximately 3.1%. And strong predicted time of minke whale declination during Holocene is approximately between 194 and 902 years ago. These whole-genome sequencing offers a chance to better understand the population history of the largest aquatic mammals on earth. After knowing population characteristic, I investigated genetic variant related to economic traits of domesticated animal. In chapter 4, I identified SNPs related to horse racing performance. Thoroughbred, a relatively recent horse breed, is best known for its use in horse racing. Although myostatin (MSTN) variants have been reported to be highly associated with horse racing performance, the trait is more likely to be polygenic in nature. I conducted a two-stage genome-wide association study to search for genetic variants associated with the EBV. I identified 28 significant SNPs related to 17 genes. Among these, six genes have a function related to myogenesis and five genes are involved in muscle maintenance. To my knowledge, these genes are newly reported for the genetic association with racing performance of Thoroughbreds. It complements a recent horse GWAS of racing performance that identified other SNPs and genes as the most significant variants. These results will help to expand my knowledge of the polygenic nature of racing performance in Thoroughbreds. In chapter 5, I identified SNPs related to milk production of dairy cattle. Holsteins are known as the world's highest-milk producing dairy cattle. I inferred each EBVs using recent ridge regression BLUP. After then, I conducted multivariate genome-wide association study to search for genetic variants associated with the EBVs for milk production traits using SNP data. I identified 128 significant SNPs related to 47 genes. These genes were related to cellular component localization, protein localization, intracellular signaling cascade and microtubule. These genes are newly reported for the genetic association with milk production of Holstein. It complements a recent Holstein GWAS that identified other SNPs and genes as the most significant variants. These results will help to expand my knowledge of the polygenic nature of milk production in Holstein. Finally, I detected cattle copy number variations related to domestication process, as another genetic source except SNP. Copy number variation (CNV), a source of genetic diversity in mammals, has been shown to underlie biological functions related to production traits. Notwithstanding, there have been few studies conducted on CNVs using next generation sequencing at the population level. I used NGS data containing ten Holsteins, a dairy cattle, and 22 Hanwoo, a beef cattle. The sequence data for each of the 32 animals varied from 13.58-fold to almost 20-fold coverage. I detected a total of 6,811 deleted CNVs across the analyzed individuals (average length = 2,732.2 bp) corresponding to 0.74% of the cattle genome (18.6 Mbp of variable sequence). By examining the overlap between CNV deletion regions and genes, I selected 30 genes with the highest deletion scores. These genes were found to be related to the nervous system, more specifically with nervous transmission, neuron motion, and neurogenesis. I regarded these genes as having been effected by the domestication process. Further analysis of the CNV genotyping information revealed 94 putative selected CNVs and 954 breed-specific CNVs. This study provides useful information for assessing the impact of CNVs on cattle traits using NGS data at the population level.Abstract i Contents iv List of Tables vii List of Figures ix Abbreviation xv General Introduction 1 Chapter 1. Literature Review 8 1.1 Effective Population Size 9 1.2 Genome-wide Association Study 19 1.3 Copy Number Variation Using Next Generation Sequencing 27 Chapter 2. Accurate estimation of effective population size in the Korean dairy cattle based on linkage disequilibrium corrected by genomic relationship matrix 34 2.1 Abstract 35 2.2 Introduction 36 2.3 Materials and Methods 38 2.4 Results 48 2.5 Discussion 60 Chapter 3. Estimation of historical effective population size in the Minke whale based on coalescent model 65 3.1 Abstract 66 3.2 Introduction 67 3.3 Materials and Methods 68 3.4 Results 75 3.5 Discussion 80 Chapter 4. Multiple genes related to muscle identified through a joint analysis of a two-stage genome-wide association study for racing performance of 1,156 Thoroughbreds 82 4.1 Abstract 83 4.2 Introduction 84 4.3 Materials and Methods 86 4.4 Results 91 4.5 Discussion 116 Chapter 5. Multivariate GWAS of milk production traits using genomic estimated breeding value 122 5.1 Abstract 123 5.2 Introduction 124 5.3 Materials & Methods 127 5.4 Results 133 5.5 Discussion 149 Chapter 6. Deleted copy number variation of Hanwoo and Holstein using next generation sequencing at the population level 153 6.1 Abstract 154 6.2 Introduction 155 6.3 Materials & Methods 158 6.4 Results 169 6.5 Discussion 207 General Discussion 223 Reference 225 국문초록 250 감사의 글 253Docto

MYOSTATIN GENE SEQUENCE AND ITS MORPHOMETRIC IMPLICATIONS IN HELMETED GUINEA FOWL BREEDS

Various methods and tools have been utilized to establish genetic variability in poultry production which remains a platform for genetic improvement of poultry species. Although, myostatin gene sequences of some poultry species have been fully sequenced on various exons, that of guinea fowl is yet to gain the needed attention making the guinea fowl database incomplete. The genetic enhancement of guinea fowls would increase the production potentials of the species as well as providing data on their genetic differences, which is critical for strategic breeding plans and genetic improvement. The study aimed to explore the polymorphisms of the gene encoding for myostatin in helmeted guinea fowl using Single Nucleotide Polymorphisms. Ten matured guinea fowls were randomly selected for DNA assay. A 640bp fragment of myostatin gene was amplified using genomic DNA extracted from the blood. Production traits of sixty birds of three plumages were measured using standard procedures. Blood samples were taken by wing venepuncture and the samples were subjected to DNA amplification and electrophoresis to determine genetic polymorphisms of the myostatin gene on several sites. Morphometric data were analyzed using descriptive statistics and oneway ANOVA. Body weight ranged from 1.35 to 2.67kg while head lengths were 4.00cm, 4.80cm, and 5.00cm for white, pearl, and exotic guinea fowls, respectively. Morphologically, exotic guinea fowl was superior in all production traits than their counterparts except for neck length. Averagely, pearl guinea fowls showed better performance than white guinea fowls. Nucleotide diversity among the guinea fowl sequence was 0.02887, which is quite low. This suggests that guinea fowl sequences are quite closely related, due to indiscriminate interbreeding among domestic guinea fowl that reduced nucleotide diversity. The study, therefore, recommends sequencing of the whole genome of helmeted guinea fowl, which is yet to be established. This will allow the improvement of the birds and the genetic database. Keywords: Myostatin, Polymorphism, Sequence, Morphometric, Helmeted Guinea Fowl

The application of omics in ruminant production: a review in the tropical and sub-tropical animal production context

The demand for animal products (e.g. dairy and beef) in tropical regions is expected to increase in parallel with the public demand for sustainable practices, due to factors such as population growth and climate change. The necessity to increase animal production output must be achieved with better management and production technologies. For this to happen, novel research methodologies, animal selection and postgenomic tools play a pivotal role. Indeed, improving breeder selection programs, the quality of meat and dairy products as well as animal health will contribute to higher sustainability and productivity. This would surely benefit regions where resource quality and quantity are increasingly unstable, and research is still very incipient, which is the case of many regions in the tropics. The purpose of this review is to demonstrate how omics-based approaches play a major role in animal science, particularly concerning ruminant production systems and research associated to the tropics and developing countriesinfo:eu-repo/semantics/acceptedVersio

Molecular characterization of Ethiopian indigenous goat populations: Genetic diversity and structure, demographic dynamics and assessment of the kisspeptin gene polymorphism

Ethiopia lies within the earliest geographic center for the dispersal of livestock into the African continent. It therefore comprises a unique repository of livestock genetic diversity in the continent. However, information relating to the origin and divergence of domestic goats in the North-East African region, and Ethiopia in particular, remains unknown despite the availability of genomic tools to assess the same. Here, the complete mitochondrial DNA D-loop region of 309 individuals representing 13 Ethiopian indigenous populations of goats was sequenced to investigate the maternal historical demographic dynamics of Ethiopian indigenous goats. Similarly, genotype data were generated from 14 populations by the 50K Caprine SNP CHIP array to investigate the genetic diversity and structure of Ethiopian indigenous goats. The Chinese Cashmere, Cashmere-Ibex hybrid and the wild Swiss Alpine Ibex populations were also included as outgroup for comparison. In addition, analysis of polymorphism of the KISS1 gene and its association with litter size, and haplotype and patterns of linkage disequilibrium (LD) analysis were conducted in exon regions of the kisspeptin gene of Gondar and Woyto-Guji goat populations. A total of 173 and 242 Sanger sequences were employed for further analysis of exon1 (1210 bp) and exon2 (325 bp) regions of the kisspeptin gene, respectively. Sequencing of the mtDNA, 174 variable sites that generated 231 haplotypes were observed in the D-loop region of mtDNA sequences and these haplotypes defined two haplogroups lacking a phylogeographic structure but with a high genetic diversity. In a combined analysis of reference haplotypes representing the six globally defined Caprine haplogroups revealed out two haplogroups to be A and G, with the former being the most predominant. The lack of phylogeographic structure and a weak population differentiation (overall FST = 0.0245) suggest extensive gene flow amongst indigenous Ethiopian goats. In the genome wide survey, high genetic diversity (HE ≥ 0.35) but low level of genetic differentiation among the populations is revealed. The 14 populations were grouped into six clusters and none of them was specific to one population or geographic region. Interestingly, population phylogenetic analysis did not support the classification of Ethiopian goats based on their agro-ecological location, associated production system and phenotypic family as suggested previously, but differentiated the Kaffa goat from the rest of 13 Ethiopian goat populations. Based on the admixture and phylogenetic network analyses, the 14 Ethiopian goat populations can be re-grouped into seven goat types. On the other hand, polymorphism analysis of the KISS1 gene revealed five complete substitutions and 15 polymorphic sites in both exon regions. The overall average HE was 0.18863±0.21 for exon1 and 0.03155±0.01 for exon2. Among detected polymorphic sites only four SNPs contributed 18%-31% multiple birth. Similarly, a total of 29 and three haplotypes were detected in exon1 and exon2, respectively. The overall haplotype diversity was 0.8703 for exon1 and 0.0703 for exon2. Lowest (0.083 for Woyto-Guji and 0.081 for Gondar goats) and modest (0.656 for Woyto-Guji and 0.635 for Gondar goats) average estimates of R2 and |D’| were obtained in LD decay analysis in exon1, respectively, and most of the R2 and |D’| values suffer floor and ceiling effects. The neutrality tests showed significant and negative values of FS for Woyto-Guji (FS = -8.098) and for Gondar goats (FS = -12.08); whereas, the Tajima’s D test was positive and non-significant. Overall, there was high goat population dynamics that caused to have highest level of population admixture

Investigating the relative influence of genetic drift and natural selection in shaping patterns of population structure in Delphinids (Delphinus delphis; Tursiops spp.)

Speciation models relying on geographic barriers to limit gene flow gather widespread consensus, but are insufficient to explain diversification in highly mobile marine organisms. Adaptation to different environments has been suggested as an alternative driver for differentiation, particularly in cetaceans. In this study, patterns of population structure at neutral and functional markers were investigated for both common (Delphinus delphis) and bottlenose dolphin (Tursiops spp.), chosen due to high levels of morphological and ecological variation within each genus. Candidate functional markers were selected by investigating signals of positive selection in both mammals and cetaceans. No population structure was found in the European common dolphin for neutral microsatellite loci, in contrast to what is observed in other sympatric cetacean species. The previously described differention of the Eastern Mediterranean Sea population, probably results from a recent human-mediated bottleneck. Functional markers showed almost complete uniformity suggesting purifying selection. One non-synonymous mutation in β-casein and the DQβ1 locus were exceptions, with patterns of population differentiation possibly the result of differences in local selective pressures. Additionally, large mitogenomic sequences were used to investigate the worldwide phylogeography of several ecotypes/species within the genus Tursiops, with a recent biogeographical calibration point being used to calculate divergence times. Good node resolution with high statistical support was achieved, with good separation between most ecotypes in their own lineages. However, the results give no support for a monophiletic Tursiops. Divergence times are clustered in specific geological periods characterized by climatic fluctuations from cold to warmer periods. The Common and bottlenose dolphins exhibit contrasting patterns of population structure in an environment containing few geographical barriers. Such difference is speculated to be related with different feeding ecologies and social structures, although data on such are still limited. Although selection can be detected in the genomes of cetaceans both at the species and population level, current patterns of differentiation are thought to occur mainly due to drift

Candidate Genes and Their Expressions Involved in the Regulation of Milk and Meat Production and Quality in Goats (Capra hircus)

Despite their pivotal position as relevant sources for high-quality proteins in particularly hard environmental contexts, the domestic goat has not benefited from the advances made in genomics compared to other livestock species. Genetic analysis based on the study of candidate genes is considered an appropriate approach to elucidate the physiological mechanisms involved in the regulation of the expression of functional traits. This is especially relevant when such functional traits are linked to economic interest. The knowledge of candidate genes, their location on the goat genetic map and the specific phenotypic outcomes that may arise due to the regulation of their expression act as a catalyzer for the efficiency and accuracy of goat-breeding policies, which in turn translates into a greater competitiveness and sustainable profit for goats worldwide. To this aim, this review presents a chronological comprehensive analysis of caprine genetics and genomics through the evaluation of the available literature regarding the main candidate genes involved in meat and milk production and quality in the domestic goat. Additionally, this review aims to serve as a guide for future research, given that the assessment, determination and characterization of the genes associated with desirable phenotypes may provide information that may, in turn, enhance the implementation of goat-breeding programs in future and ensure their sustainability