Estimation of Genetic Parameters by Single-Trait and Multi-Trait Models for Carcass Traits in Hanwoo Cattle

Hanwoo breed is preferred in South Korea because of the high standards in marbling and the palatability of its meat. Numerous studies have been conducted and are ongoing to increase the meat production and quality in this beef population. The aim of this study was to estimate and compare genetic parameters for carcass traits using BLUPF90 software. Four models were constructed, single trait pedigree model (STPM), single-trait genomic model (STGM), multi-trait pedigree model (MTPM), and multi-trait genomic model (MTGM), using the pedigree, phenotype, and genomic information of 7991 Hanwoo cattle. Four carcass traits were evaluated: Back fat thickness (BFT), carcass weight (CWT), eye muscle area (EMA), and marbling score (MS). Heritability estimates of 0.40 and 0.41 for BFT, 0.33 and 0.34 for CWT, 0.36 and 0.37 for EMA, and 0.35 and 0.38 for MS were obtained for the single-trait pedigree model and the multi-trait pedigree model, respectively, in Hanwoo. Further, the genomic model showed more improved results compared to the pedigree model, with heritability of 0.39 (CWT), 0.39 (EMA), and 0.46 (MS), except for 0.39 (BFT), which may be due to random events. Utilization of genomic information in the form of single nucleotide polymorphisms (SNPs) has allowed more capturing of the variance from the traits improving the variance components

포유류 유전체 내 선택압에 의한 적응 흔적 및 특성 발굴

학위논문(박사)--서울대학교 대학원 :자연과학대학 협동과정 생물정보학전공,2019. 8. 김희발.The central goal of evolutionary biology is to understand the genetic basis of evolutionary processes and adaptive traits. In this regard, the recent advances in sequencing technologies and the explosion of sequence data provide a better opportunity to reach this goal. Various genomic variations are now easily and precisely obtained for large-scale of samples. They are expanding the scope of typical genomic studies, allowing us to take into account diverse evolutionary processes. The aim of this thesis is to demonstrate the applications of such genomic variations while taking into account diverse evolutionary scenarios and time scales. As such, this thesis will fill in the gaps in the knowledge of mammalian genetic background underlying adaptive traits through genome-wide scan and comparative genome analysis. This thesis consists of five chapters and includes results of genome analysis for detecting evolutionary signatures in three mammal species; pinnipeds, primates, and cattle. The basic background, terminologies and recent example studies related to this thesis were introduced in chapter 1. Chapter 2 and 3 focused on divergence between species (macroevolution), while chapter 4 and 5 focused on polymorphism within species (microevolution). Pinnipeds are a remarkable group of marine animals with unique adaptations to semi-aquatic life. However, their genomes are poorly characterized. In chapter 2, evolutionary signatures of pinnipeds have been investigated using amino acid substitutions. Novel genome assemblies of 3 pinniped species; Phoca largha, Callorhinus ursinus, and Eumetopias jubatus have been generated. These genome assemblies have been used to detect rapidly evolving genes and substitutions unique to pinnipeds associated with their specificities. As a result, unique substitutions were found within the TECTA gene and are likely related to the adaptation to amphibious sound perception in pinnipeds. In addition, several genes (FASN, KCNA5, and IL17RA) containing substitutions specific to pinnipeds were found to be potential candidates of phenotypic convergence in all marine mammals. It indicates the weak link between molecular and phenotypic convergence, and confirms the results of previous studies. This study provides candidate targets for future studies of gene function, as well as backgrounds for convergent evolution of marine mammals. Humans have the largest brain among extant primates with specialized neuronal connections. However, how the human brain rapidly evolved compared to that of closely related primates is not fully understood. In chapter 3, a genome-wide survey has been performed to find an explanation for the rapid evolution of human brain. Based on the hypothesis that tandem repeats could play a key role in introducing genetic variations due to their unstable nature, a genome-wide survey detected 152 human-specific TRs (HSTR) that have emerged only in the human lineage. The HSTRs are associated with biological functions in brain development and synapse function, and the expression level of HSTR-associated genes in brain tissues was significantly higher in human than in other primates. These results suggest a possibility that de novo emergence of TRs might have contributed to the rapid evolution of human brain. The genetic history of cattle is complex, but contains plentiful information to comprehend mammalian evolutionary process such as domestication, and environmental adaptations. In chapter 4, the genomic influence of recent artificial selection has been examined in the case of Korean native cattle, Hanwoo. Using runs of homozygosity (ROH), an increase of inbreeding for decades has been shown, and at the same time, it has been demonstrated that inbreeding has been of little influence on body weight trait. In chapter 5, admixture between two cattle populations; Bos taurus, and Bos indicus has been examined in Indigenous African cattle populations., Several evidences based on single nucleotide polymorphism (SNP) support that adaptive admixture is at the root of the success of African cattles rapid dispersion across African continent. The findings in this thesis demonstrated applications of various genomic variations under diverse evolutionary scenarios and time scales, and thus may contribute to the understanding of evolutionary processes in mammals.진화 생물학의 핵심 목표는 진화 과정과 적응 형질의 유전적 기초를 이해하는 것이다. 이와 관련하여 최근 시퀀싱 기술의 진보와 서열 데이터의 폭발적 증가는 이러한 목표를 달성 할 수 있는 더 좋은 기회를 제공하고 있다. 실제로 시퀀싱 기술의 발달로 대규모 시료에 대하여 좀 더 쉽고 정확하게 다양한 유전변이를 얻을 수 있게 되었으며, 이 덕분에 일반적인 유전체 연구의 범위가 확장되었고 다양한 진화 과정을 고려할 수도 있게 되었다. 이에 이 논문의 목적은 다양한 진화과정 하에서 여러 유전변이의 유용성을 보여주고, 전장 유전체 및 비교 유전체 분석을 통해 포유류 적응 형질의 유전적 배경을 밝히는 것이다. 이 논문은 세 가지 포유 동물 종(기각류, 영장류, 소)의 유전체 분석 결과를 포함한 5 개의 장으로 구성되어있다. 제 1장에서는 이 논문과 관련된 배경 지식과 최근의 연구 사례를 소개하고 있다. 전반부 (제 2, 3장)는 종간 비교분석에 중점을 두었고, 후반부(제4, 5장)는 종내의 다형성에 초점을 두고 있다. 기각류는 반 수생 환경에 적응한 특징적인 해양 동물이다. 그러나 그 유전체는 특성이 잘 알려져 있지 않다. 제2 장에서는 아미노산 치환 정보를 이용하여 기각류의 진화 및 적응 흔적을 조사하였다. 구체적으로 기각류3 종의 새로운 유전체를 이용하여 기각류의 생활환경과 관련된 양성선택 유전자 및 아미노산 치환 흔적을 발굴하였다. 특히 TECTA 유전자 내의 고유한 아미노산 치환 흔적은 기각류의 청각과 밀접한 관련이 있을 것으로 예상된다. 또한, 이전 연구결과와 같이 해양 포유류에서 표현형의 수렴진화와 직접적으로 연관되어 있는 서열 수렴은 흔하지 않다는 것을 확인하였다. 예를 들어, FASN, KCNA5 및 IL17RA는 기각류에 특이적인 아미노산 치환을 포함하지만 모든 해양 포유 동물에서 공통적으로 표현형 수렴진화 (두꺼운 지방조직, 저산소 적응 및 병원체에 대한 면역 반응)가 일어났을 것으로 예상된다. 이러한 연구 결과들은 해양 포유류의 수렴 진화 특성에 대한 지식을 제공함과 동시에 유전자 기능 연구에 대한 후보 표적을 제공할 것으로 기대된다. 인간은 현존하는 영장류 중에서 가장 큰 두뇌를 가지고 있다. 그러나 인간의 뇌가 어떻게 영장류 중에서 특히 빠르게 진화했는지 는 완전히 밝혀지지 않았다. 제 3 장에서는 인간 두뇌의 급속한 진화에 대한 가설을 찾기 위해 유전체 분석을 수행하였다. 반복서열이 그 불안정한 성질 때문에 급속한 유전적 변이를 일으키는 데 핵심적인 역할을 할 수 있다는 가설에 근거하여, 유전체 비교분석에서 인간 특이적인 152 개의 반복서열을 검출하였다. 특이하게도, 이러한 반복서열들은 뇌 발달 및 시냅스 기능과 관련이 있었으며, 뇌 조직에서 해당 반복서열과 관련된 유전자의 발현 수준은 다른 영장류보다 인간에서 유의하게 높았다. 이러한 결과는 반복서열이 인간 두뇌의 급속한 진화에 기여하였을 수도 있다는 하나의 가능성을 제시한다. 소의 유전적 역사는 복잡하지만 가축화 및 환경 적응과 같은 포유 동물의 진화 과정을 이해할 수 있는 풍부한 정보를 담고있다. 제 4 장에서는 한국 토종 소품종인 한우의 유전체 선발이 한우 집단에 미친 유전적 영향을 조사 하였다. Runs of humozygosity를 이용하여, 최근에 일어난 근친 교배의 증가를 보여 주었고 동시에, 근교약세가 체중에 영향을 미칠 만큼 크지 않았다는 것을 유전정보를 통해 보여주었다. 제 5 장에서는 소의 두 아종 (Bos taurus, Bos indicus)사이의 유전적 혼합을 아프리카 토착 소의 단일 염기 다형성 자료를 통해 분석하였다. 이를 통해 아프리카 소의 환경에 대한 빠른 적응의 원인은 유전적 혼합에 있다는 여러 증거를 제시하였다. 이 논문은 다양한 진화과정 하에서 다양한 유전변이의 적용사례를 보여주고, 또한 이를 통해 포유 동물의 다양한 진화 과정을 이해하는 데에 기여할 수 있을 것으로 기대된다.ABSTRACT I CONTENTS V LIST OF TABLES VII LIST OF FIGURES IX GENERAL INTRODUCTION XIV CHAPTER 1. LITERATURE REVIEW 1 1.1 GENOMIC VARIATIONS 2 1.2 SIGNATURES OF POSITIVE SELECTION 7 1.3 SIGNATURES OF INTROGRESSION 13 CHAPTER 2. DECIPHERING THE EVOLUTIONARY SIGNATURES OF PINNIPEDS USING NOVEL GENOME SEQUENCES: THE FIRST GENOMES OF PHOCA LARGHA, CALLORHINUS URSINUS, AND EUMETOPIAS JUBATUS 17 2.1 ABSTRACT 18 2.2 INTRODUCTION 19 2.3 MATERIALS AND METHODS 23 2.4 RESULTS 37 2.5 DISCUSSION 66 CHAPTER 3. DE NOVO EMERGENCE AND POTENTIAL FUNCTION OF HUMAN-SPECIFIC TANDEM REPEATS IN BRAIN-RELATED LOCI 70 3.1 ABSTRACT 71 3.2 INTRODUCTION 72 3.3 MATERIALS AND METHODS 75 3.4 RESULTS 89 3.5 DISCUSSION 109 CHAPTER 4. ARTIFICIAL SELECTION INCREASED BODY WEIGHT BUT INDUCED INCREASE OF RUNS OF HOMOZYGOSITY IN HANWOO CATTLE 114 4.1 ABSTRACT 115 4.2 INTRODUCTION 116 4.3 MATERIALS AND METHODS 121 4.4 RESULTS 128 4.5 DISCUSSION 150 CHAPTER 5. THE MOSAIC GENOME ARCHITECTURE OF INDIGENOUS AFRICAN CATTLE AS A UNIQUE GENETIC RESOURCE FOR ADAPTATION TO LOCAL ENVIRONMENTS 154 5.1 ABSTRACT 155 5.2 INTRODUCTION 157 5.3 MATERIALS AND METHODS 161 5.4 RESULTS 174 5.5 DISCUSSION 199 GENERAL DISCUSSION 204 REFERENCES 207 요약(국문초록) 234Docto

Comparison of accuracy of breeding value for cow from three methods in Hanwoo (Korean cattle) population

In Korea, Korea Proven Bulls (KPN) program has been well-developed. Breeding and evaluation of cows are also an essential factor to increase earnings and genetic gain. This study aimed to evaluate the accuracy of cow breeding value by using three methods (pedigree index [PI], pedigree-based best linear unbiased prediction [PBLUP], and genomic-BLUP [GBLUP]). The reference population (n = 16,971) was used to estimate breeding values for 481 females as a test population. The accuracy of GBLUP was 0.63, 0.66, 0.62 and 0.63 for carcass weight (CWT), eye muscle area (EMA), back-fat thickness (BFT), and marbling score (MS), respectively. As for the PBLUP method, accuracy of prediction was 0.43 for CWT, 0.45 for EMA, 0.43 for MS, and 0.44 for BFT. Accuracy of PI method was the lowest (0.28 to 0.29 for carcass traits). The increase by approximate 20% in accuracy of GBLUP method than other methods could be because genomic information may explain Mendelian sampling error that pedigree information cannot detect. Bias can cause reducing accuracy of estimated breeding value (EBV) for selected animals. Regression coefficient between true breeding value (TBV) and GBLUP EBV, PBLUP EBV, and PI EBV were 0.78, 0.625, and 0.35, respectively for CWT. This showed that genomic EBV (GEBV) is less biased than PBLUP and PI EBV in this study. In addition, number of effective chromosome segments (Me) statistic that indicates the independent loci is one of the important factors affecting the accuracy of BLUP. The correlation between Me and the accuracy of GBLUP is related to the genetic relationship between reference and test population. The correlations between Me and accuracy were −0.74 in CWT, −0.75 in EMA, −0.73 in MS, and −0.75 in BF, which were strongly negative. These results proved that the estimation of genetic ability using genomic data is the most effective, and the smaller the Me, the higher the accuracy of EBV

Functional Partitioning of Genomic Variance and Genome-Wide Association Study for Carcass Traits in Korean Hanwoo Cattle Using Imputed Sequence Level SNP Data

Quantitative traits are usually controlled by numerous genomic variants with small individual effects, and variances associated with those traits are explained in a continuous manner. However, the relative contributions of genomic regions to observed genetic variations have not been well explored using sequence level single nucleotide polymorphism (SNP) information. Here, imputed sequence level SNP data (11,278,153 SNPs) of 2109 Hanwoo steers (Korean native cattle) were partitioned according to functional annotation, chromosome, and minor allele frequency (MAF). Genomic relationship matrices (GRMs) were constructed for each classified region and fitted in the model both separately and together for carcass weight (CWT), eye muscle area (EMA), backfat thickness (BFT), and marbling score (MS) traits. A genome-wide association study (GWAS) was performed to identify significantly associated variants in genic and exon regions using a linear mixed model, and the genetic contribution of each exonic SNP was determined using a Bayesian mixture model. Considering all SNPs together, the heritability estimates for CWT, EMA, BFT, and MS were 0.57 ± 0.05, 0.46 ± 0.05, 0.45 ± 0.05, and 0.49 ± 0.05, respectively, which reflected substantial genomic contributions. Joint analysis revealed that the variance explained by each chromosome was proportional to its physical length with weak linear relationships for all traits. Moreover, genomic variances explained by functional category and MAF class differed greatly among the traits studied in joint analysis. For example, exon regions had larger contributions for BFT (0.13 ± 0.08) and MS (0.22 ± 0.08), whereas intron and intergenic regions explained most of the total genomic variances for CWT and EMA (0.22 ± 0.09–0.32 ± 0.11). Considering different functional classes of exon regions and the per SNP contribution revealed the largest proportion of genetic variance was attributable to synonymous variants. GWAS detected 206 and 27 SNPs in genic and exon regions, respectively, on BTA4, BTA6, and BTA14 that were significantly associated with CWT and EMA. These SNPs were harbored by 31 candidate genes, among which TOX, FAM184B, PPARGC1A, PRKDC, LCORL, and COL1A2 were noteworthy. BayesR analysis found that most SNPs (>93%) had very small effects and the 4.02–6.92% that had larger effects (10-4 × σA2, 10-3 × σA2, and 10-2 × σA2) explained most of the total genetic variance, confirming polygenic components of the traits studied

Genome-Wide Association Study of Meat Quality Traits in Hanwoo Beef Cattle Using Imputed Whole-Genome Sequence Data

The discovery of single nucleotide polymorphisms (SNP) and the subsequent genotyping of large numbers of animals have enabled large-scale analyses to begin to understand the biological processes that underpin variation in animal populations. In beef cattle, genome-wide association studies using genotype arrays have revealed many quantitative trait loci (QTL) for various production traits such as growth, efficiency and meat quality. Most studies regarding meat quality have focused on marbling, which is a key trait associated with meat eating quality. However, other important traits like meat color, texture and fat color have not commonly been studied. Developments in genome sequencing technologies provide new opportunities to identify regions associated with these traits more precisely. The objective of this study was to estimate variance components and identify significant variants underpinning variation in meat quality traits using imputed whole genome sequence data. Phenotypic and genomic data from 2,110 Hanwoo cattle were used. The estimated heritabilities for the studied traits were 0.01, 0.16, 0.31, and 0.49 for fat color, meat color, meat texture and marbling score, respectively. Marbling score and meat texture were highly correlated. The genome-wide association study revealed 107 significant SNPs located on 14 selected chromosomes (one QTL region per selected chromosome). Four QTL regions were identified on BTA2, 12, 16, and 24 for marbling score and two QTL regions were found for meat texture trait on BTA12 and 29. Similarly, three QTL regions were identified for meat color on BTA2, 14 and 24 and five QTL regions for fat color on BTA7, 10, 12, 16, and 21. Candidate genes were identified for all traits, and their potential influence on the given trait was discussed. The significant SNP will be an important inclusion into commercial genotyping arrays to select new breeding animals more accurately

Systematic environmental influences and variances due to direct and maternal effects and trends for yearling weight in cattle

Pedigree yearling records from 1021 local Tuli calves born at Matopos Research Station were analyzed for non genetic factors, genetic parameers and trends on the yearling weight. It was found that sre year of brth, sex of calf age of dam had sgnfcant effect (p < 0.01) on a growthtrait. The inconsistency of literature estimates indicated the importance o estmation of environmental factors that affect yearling weight within specific experimental herds and environment. Model incorporating both direct and maternal additive genetic effect, covariance and correlations of direct-maternal and permanent environmental maternal effects was adopted for thestudy Directand maternal heritabity estmates of 0.18 ± 0.001 and 0.04 ± 0001 were observed, respectvely. Direct-maternal genetic correlaton was low andposive, 0.07± 0.012. The regression of average direct breeding values on year was almost zero and the regression of average maternal breeding values on year 0.03 kg/yr. Correction of environmental effects was necessary to increase accuracy for selection of yearling weight in local Tuli cattle. Maternal genetic effects should be included in a model of covariance components estimation at 12 months of age.Keywords: Non genetic, Direct, Maternal trends, Yearling weight, Growth traits, Tuli cattl

Population genetic features of calving interval of the Limousin beef cattle breed in Hungary

Variance, covariance components, heritability, breeding values (BV) and genetic trends in calving interval (CI) of the Limousin population in Hungary were evaluated. A total of 3,008 CI data of 779 cows from three herds in 1996–2016 were processed. For influencing effects GLM method, for population genetic parameters and BV estimation BLUP animal model, for trend analyses linear regression was applied. The average CI obtained was 378.8 ± 3.1 days. The variance distribution components of the phenotype were as follow: age of cow at calving 34.30%, season of calving 26.09%, year of calving 23.00%, sire 7.45%, herd 3.23%, sex of calf 0.33% and type of calving 0.30%. The heritability of CI proved to be low (h 2 d = 0.04 ± 0.02 and 0.03 ± 0.02; h 2 m = 0.01 ± 0.02). The repeatability was low ( R = 0.03 ± 0.02). Based on the phenotypic trend calculation, the CI of cows decreased by an average of 0.60 days per year ( R 2 = 0.19; P < 0.05). In case of genetic trend calculation, the average BV of sires in CI increased 0.07 and 0.17 days per year ( R 2 = 0.23 and 0.27; P < 0.05)

Genetic, management, and nutritional factors affecting intramuscular fat deposition in beef cattle — A review

Intramuscular fat (IMF) content in skeletal muscle including the longissimus dorsi muscle (LM), also known as marbling fat, is one of the most important factors determining beef quality in several countries including Korea, Japan, Australia, and the United States. Genetics and breed, management, and nutrition affect IMF deposition. Japanese Black cattle breed has the highest IMF content in the world, and Korean cattle (also called Hanwoo) the second highest. Here, we review results of research on genetic factors (breed and sex differences and heritability) that affect IMF deposition. Cattle management factors are also important for IMF deposition. Castration of bulls increases IMF deposition in most cattle breeds. The effects of several management factors, including weaning age, castration, slaughter weight and age, and environmental conditions on IMF deposition are also reviewed. Nutritional factors, including fat metabolism, digestion and absorption of feed, glucose/starch availability, and vitamin A, D, and C levels are important for IMF deposition. Manipulating IMF deposition through developmental programming via metabolic imprinting is a recently proposed nutritional method to change potential IMF deposition during the fetal and neonatal periods in rodents and domestic animals. Application of fetal nutritional programming to increase IMF deposition of progeny in later life is reviewed. The coordination of several factors affects IMF deposition. Thus, a combination of several strategies may be needed to manipulate IMF deposition, depending on the consumer’s beef preference. In particular, stage-specific feeding programs with concentrate-based diets developed by Japan and Korea are described in this article

소전장유전체에서 적응적 흔적 발굴

학위논문 (박사)-- 서울대학교 대학원 : 농업생명과학대학 농생명공학부, 2018. 2. Heebal Kim.Cattle are one of the most common and numerous domestic ungulates. The genomes of domes¬ticated cattle breeds harbor the history of domestication and breed for¬mation due to the combined effect of natural and artificial selection forces. Deciphering the footprints of these selection forces in the genome of cattle breeds is of great interest from the perspective of evolutionary biology seeking to understand the key adaptive features that have generated enormous morphological and production phenotypic variations currently observed within and between populations. Recently, professionals from molecular popu¬lation and evolu¬tionary genetics have shown growing interest in distinguishing neutral molecular vari¬ations from variations that are subject to selection, particularly positive selection, in the genomes of multiple organisms including cattle. The building of the bovine reference genome and the accumulation of single nucleotide polymorphism (SNP) data from geo¬graphically and biologically diverse cattle breeds – due to the emergence of low cost and high throughput Next Generation Sequencing (NGS) technologies – has created unprecedented opportunities and facilitated efforts to uncover and understand this variation. In this doctoral dissertation, the whole genome NGS SNP data from African, NDama, Ankole, Holstein, Hanwoo, and Angus cattle breeds were used to elucidate the footprints of natural and artificial selection forces that have contributed to the major phenotypes of the respective breeds. The cross-population extended haplotype homozygosity (XP-EHH) and cross-population composite likelihood ratio (XP-CLR) statistical methods were used to search for the genes/gene regions affected due to selection. The reference genome of cattle (UMD3.1) was used to annotate genes in outlier regions under selection from these analyses. I used the Database for Annotation, Visualization, and Integrated Discovery (DAVID) gene ontology and annotation tool for gene enrichment analysis to understand the biological functions and pathways of genes iden¬tified under selection. In Chapter 1, I introduced the variations in cattle breeds with special emphasis to African cattle breeds, the principles behind signature of positive selection, and the objectives and methods of identification of signature of positive selection. In addition, previously reported results of studies on selection signatures from genetically diverse cattle breeds were reviewed. In Chapter 2, the genome of African cattle breeds was compared with the genome of Commercial Asian-European taurine cattle breeds to reveal genomic regions under selection in African cattle in relation to tropical environment adaptation traits. African cattle breeds have evolved in a hot tropical climate for millennia, which helped them to develop an inherent superior thermotolerance ability. The study revealed several genes/gene regions under selection that are overrepresented in different biological process (BP) terms and pathways in a gene enrichment analysis. In relation to heat stress response, angiogenesis and regeneration BP terms were enriched. Moreover, several selected genes were involved in anatomical structures, and physi¬ological and/or molecular functions that are associated with heat tolerance mecha¬nisms. These genes are involved in oxidative stress response, osmotic stress response, heat shock response, hair and skin properties, sweat gland devel¬opment and sweating, feed intake and metabolism, and reproduction functions. Therefore, the genes and BP terms identified here directly and/or indirectly con¬tribute to the superior heat tolerance mechanisms of African cattle populations. The high tropical temperature where these cattle breeds have evolved for millennia could be a selec¬tive pressure for the develop¬ment of these thermotolerance mechanisms. In Chapter 3, the genomes of Holstein, Hanwoo, and NDama cattle breeds were explored in order to decipher genomic regions affected due to divergent selection for milk traits, meat production and quality traits, and environ¬mental adaptation traits, respectively. Artificial and natural selection for a particular trait in cattle have signif¬icantly modified the cattle genome. Due to this, several cattle breeds have been developed with a mosaic of morphological, productivity, and environmental adapta¬tion characteristics. Holstein cattle are evolved as dairy cattle and Hanwoo cattle are evolved as beef cattle under artificial selection, whereas NDama cattle are evolved as a general-purpose breed – a breed that does not artificially selected for a particular purpose under natural selection. Identifying genomic regions affected due to artificial and natural selection forces in cattle would give an insight into the history of selection for economically important traits and genetic adaptation to specific environments of populations under consideration. From this study, genes/gene regions that are related to milk traits (e.g., CSN3, PAPPA2, and ADIPOQ), meat production and quality traits (e.g., NCOA2, and PITPN3), and environmental adaptation traits (e.g., SLC40A1, STOM, and COMMD1) were found under positive selection from the genomes of Holstein, Hanwoo and NDama cattle breeds, respectively. Moreover, significant functional annotation cluster terms including milk protein and thyroid hormone signaling pathway, histone acetyl-trans¬ferase activity, and renin secretion were enriched from gene lists identified under selec¬tion in Holstein, Hanwoo, and NDama cattle breeds, respectively. In Chapter 4, the genome of Ankole cattle (African Sanga cattle) was explored in order to identify genes and genomic regions under positive selection in relation to meat quality traits. African Sanga cattle are an intermediate type of cattle resulting from interbreeding between B. taurus and B. indicus sub-species. Recently, experi¬mental evidence on the po¬tential of African Sanga cattle breeds for superior beef quality traits over their indicine coun¬terparts has emerged. In this study, the whole genome SNP data of Ankole (Sanga cattle) was compared with the genome of indicine cattle breeds using XP-EHH and XP-CLR statistical methods. As a result, several genes including those affecting beef quality traits such as tenderness, intramuscular fat (IMF) content, and meat color were found under posi¬tive selection. The genes identified are involved in BP terms and KEGG pathways that affect muscle structure and metabolism, adipose metabolism, and adipogenesis – which in turn affects meat quality traits. This study asserted that Ankole cattle have the potential for higher meat production and quality traits under the prevailing tropical environmental conditions. These results provide a basis for further re-search on the genomic characteristics of Ankole and other Sanga cattle breeds for better quality beef in tropical Africa. In Chapter 5, the genetic blueprint behind the superior beef quality characteristics and other associated phenotypes of Angus cattle were elucidated. Angus cattle have been inten¬sively selected for superior beef quality characteristics for decades. Anno¬tating genomic re¬gions under selection in the genomes of Angus cattle resulted in several genes including those associated with beef quality traits and coat color. In addition, putative genes that po-tentially cause genetic disorders in Angus cattle were identified. The results from this study will help to further improve Angus cattle beef quality, and take a precaution on the associated genetic disorders which ultimately reduce production and productivity. In conclusion, from these studies, a catalog of genes were identified under positive selection from African, NDama, Ankole, Holstein, Hanwoo, and Angus cattle breeds in relation to the major economic and adaptation traits of the respective breeds to which they have been selected for. The findings in this dissertation will help us to better understand the adaptive events that have generated the enormous phenotypic variation observed between cattle breeds prevailing today. Molecular markers that contribute to local environmental adaptations (e.g., thermotolerance mechanisms - markers that are difficult to identify with other laboratory experimental methods) were revealed in addition to those affecting production traits such as milk production and quality, beef production and quality, reproduction and other associated traits. The markers identified in these studies help to understand the genetic merit of the breeds and can be used in genomic selection and breeding programs to further improve the respective breeds.CHAPTER 1 . GENERAL INTRODUCTION 1 1.1 The Genetic Resource of Cattle 2 1.2 Positive Selection Signature 5 1.2.1 Definition and principles of positive selection 5 1.2.2 Methods to identify signature of positive selection in livestock genomes 8 1.3 Signature of selection in the cattle genome 12 CHAPTER 2 . WHOLE GENOME DETECTION OF SIGNATURE OF POSITIVE SELECTION IN AFRICAN CATTLE REVEALS SELECTION FOR THERMOTOLERANCE 15 2.1 Abstract 16 2.2 Introduction 17 2.3 Materials and Methods 19 2.3.1 Data description and whole genome re-sequencing 19 2.3.2 Population structure 20 2.3.3 Detection of signals of positive selection 21 2.3.4 Characterization of candidate genes under selection 22 2.4 Result and Discussion 23 2.4.1 Population structure and description 23 2.4.2 Positive selection signature in African cattle populations 25 2.5 Conclusion 54 CHAPTER 3 . EXPLORING EVIDENCE OF POSITIVE SELECTION SIGNATURES IN CATTLE BREEDS SELECTED FOR DIFFERENT TRAITS 55 3.1 Abstract 56 3.2 Introduction 57 3.3 Materials and Methods 59 3.3.1 Sample preparation and whole genome re-sequencing 59 3.3.2 Population stratification 60 3.3.3 Detection of selection signature 61 3.3.4 Characterization of genes and candidate association analysis 63 3.4 Result and Discussion 64 3.4.1 Data description 64 3.4.2 Structure and principal component analysis 64 3.4.3 Positive selection signature 65 3.5 Conclusion 86 CHAPTER 4 . WHOLE GENOME SCAN IN AFRICAN ANKOLE CATTLE BREED REVEALS GENETIC SIGNATURE FOR QUALITY BEEF 87 4.1 Abstract 88 4.2 Introduction 89 4.3 Materials and Methods 91 4.3.1 Ethics statement 91 4.3.2 Sample preparation and whole genome re-sequencing 92 4.3.3 Phylogenetic construction 93 4.3.4 Detection of positive selection signals 94 4.3.5 Characterization of candidate genes under selection 95 4.4 Results and Discussion 96 4.4.1 Data description 96 4.4.2 Phylogenetic tree 96 4.4.3 Positive selective signature in Ankole cattle population 98 4.4.4 Implication of the results of this study on Ankole population 125 4.4.5 Limitations of the present study 126 4.5 Conclusion 126 CHAPTER 5 . DECIPHERING SIGNATURE OF SELECTION AFFECTING BEEF QUALITY TRAITS IN ANGUS CATTLE 127 5.1 Abstract 128 5.2 Introduction 129 5.3 Materials and Methods 131 5.3.1 Data preparation and description 131 5.3.2 Phylogenetic tree and population structure 132 5.3.3 Signature of positive selection 133 5.3.4 Characterizing genes under selection 134 5.4 Result and Discussion 135 5.4.1 Data description 135 5.4.2 Phylogenetic tree and structure analysis 135 5.4.3 Signature of positive selection 137 5.5 Conclusion 163 GENERAL DISCUSSION 164 REFERENCES 169 국문초록 194Docto