Growth curve analysis in different generations of Boer x Central Highland goats using alternative estimation models.

Growth curve analysis can help to optimize the management, determine nutritional requirements, predict the weight of animals at a specific age, and to select highly productive animals. Therefore, this study aimed to find the best-fitted nonlinear functions to provide a specific shape of the growth curve from birth to yearling age in different generations of Boer x Central Highland goats. Gompertz, Logistic, Brody, Von Bertalanffy, Monomolecular, Negative exponential, and Richards models were evaluated to quantify their ability to describe the biological growth curve. Root mean square error (RMSE), Bayesian information criterion (BIC), adjusted coefficient of determination (AdjR2), and Akaike's information criterion (AIC) were used to evaluate the goodness of fit and flexibility of the models. Data were analyzed using the nonlinear regression procedure of SAS. High AdjR2 and lower AIC, BIC, and RMSE values are indicators of best-fitted model. The best-fitting model for the first filial generation (F1), second filial generation (F2), and male goats' growth data was Brody function, whereas the Richards model, followed by Brody, best described the growth of third filial generation (F3) and female goats. The values of parameter A (asymptotic weight) for F1, F2, F3, female, and male goats based on the Brody model were 30.5±1.32, 28.2±1.38, 24.4±1.04, 27.8±0.94, and 29.8±1.32 kg for F1, F2, F3, female, and male goats, respectively. As per the best-fitted growth function, the asymptotic weight tended to reduce when the filial generation increased. The asymptotic weight for male goats was higher than for female goats. F1 had a slightly small value of parameter K, followed by F2 and F3. Both males and females had similar maturity rates. Based on the Brody function, the correlation between maturation rate and mature weight was high (-0.98, P<0.001). The correlation estimates for A-B and B-K were 0.27 and -0.15, respectively. Brody was best fitted for most goat categories, although Richards, followed by Brody, was best fitted for female and F3 goats. Besides, Brody could be better than Richards due to the ease of interpretation, convergence, and applicability for a small sample size. Therefore, the Brody function can predict the mature body weight, maturation rate, and growth rate of Boer x Central Highland goats and be used to formulate breeding and management strategies for profitable goat farming.

Estimation of crossbreeding and genetic parameters for reproductive traits of Boer x Central Highland goats in Ethiopia.

Additive genetic and non-additive parameters for reproductive traits of Boer x Central Highland goats were estimated. Pedigree and performance records comprised of Central Highland and their crosses with Boer goats were collected from 2009 to 2018 in the Sirinka Agricultural Research Center sheep and goat breeding station. Least-squares means for genotypes were obtained using a general linear model procedure in SAS. To estimate crossbreeding parameters, breed additive, heterotic, and recombination effects were fitted as fixed covariates instead of genotypes. Variance, heritability, and repeatability estimates were estimated through the AI-REML algorithm using WOMBAT software. Genotype did not significantly (P>0.05) influence most of the reproductive traits studied except for gestation length. The additive effect for litter size at birth (LSB), total litter birth weight (LBW), total litter weaning weight (LWW), litter size at weaning (LSW), and gestation length (GL) was estimated to be -0.004 kid, 0.08 kg, -3.18 kg, -0.54 kid, and 3.69 days, respectively. The contribution of heterosis to LSB, LWW, and GL of crossbred goats was negative, while the estimates for LBW and LSW were positive. However, Boer goats' heterosis effect and direct additive contribution to reproductive traits were insignificant (P>0.05) except for LSW. The recombination effect was negligible and not significant (P>0.05) for all traits examined. The direct heritability estimate for LSB, LWB, LWW, LSW, and GL were 0.050, 0.098, 0.086, 0.018, and 0.00, respectively. The repeatability estimates for LSB, LWB, LWW, LSW, and GL were 0.149, 0.116, 0.099, 0.086, and 0.061, respectively. The result indicates that improvement in reproductive traits would not be expected by crossing Boer with Central Highland goats. In addition, heritability estimates indicate that the improvement of reproductive traits through selection will be small, and the repeatability estimates indicate that multiple records have to be used to make a decision of culling or selection.

Rapid Bioethical Assessment for Mycobacterium tuberculosis and Host Genetic Study in Amhara Regional State, Ethiopia: Towards a Context-Specific Ethical Approach.

Background: Rapid Ethical Assessment (REA) is a rapid qualitative study anticipated to understand the ethical sphere of the research setting prior to recruiting study subjects. This study assessed the communities' knowledge about tuberculosis (TB) and research, understand the social arrangements advisable for recruiting research participant and appraised the information provision and consent process. Methods: The study was conducted in Amhara region, Ethiopia from 5th-30th January 2021. Google-based survey, face-to-face in-depth interview and focus group discussion were carried out to collect the data from researchers, data collectors, health professionals, TB program officers. A structured questionnaire was administered to assess the knowledge of TB patients and healthy controls about TB, research, gene, (co)evolution and consent process. Results: Over 71% of researchers were not satisfied with the current consent process, and 82.7% of researchers agreed that the best interest of the research participants was not adequately addressed in the current research practices in ANRS. TB patients and healthy controls misunderstood research and its goals. Participants advised the researchers to approach the community with the assistance of health extension workers (HEW) or religious/local leaders. Combined use of verbal and written based information provision at individual participant level is the preferred way for information provision. Conclusions: The adherence of researchers to standard information provision and consent process was very low. Healthy controls and TB patients have low level of knowledge and awareness about research, ethics and genomic research-related common terms. Hence, public education is required to strengthen the research ethics in the region.

Morpho-biometric characterization of indigenous chicken ecotypes in north-western Ethiopia.

Morphological characterization of Animal Genetic Resources is the first step to documenting diversity and designing breed specific breeding programs. The current study characterized the morpho-biometric variation of indigenous chicken ecotypes prevailing in northwestern Ethiopia. A multi-stage purposive, stratified, and random sampling method was employed to select the study areas and chickens. A total of 1200 adult chickens were sampled and characterized for 12 qualitative and 11 quantitative traits. Univariate and multivariate data analysis methods were employed to analyze the data using SAS and R statistical software. Red plumage colour (33.2%), white and red earlobe colour (73.8%) and yellow shank colour (57.0%) were the most predominant colour trait categories. Sex, agro-ecology, location, and the interaction of sex and location had a highly significant (p<0.001) effect on all body measurements. Shank traits were found to have the highest discriminating power in both sexes. The overall classification rates for the female and male sample populations were 57.47% and 69.97%, respectively. The squared Mahalanobis distances between sites were significant (p<0.001) for both sexes. The longest distance was obtained between North Achefer and Banja (19.25) and between North Achefer and Dembecha (16.80) in female and male chickens, respectively. In female chickens, canonical variates 1 (CAN 1) and 2 (CAN 2) explained 82% of total variation and distinctly separated the sample populations of North Achefer and Jawi from others. In male chickens, 90% of the total variance is explained by CAN1, CAN2, and CAN3, which distinctly separate the sample populations of the North Achefer, Sinan, and Jawi, among others. Using cluster analysis, the indigenous chickens found in the study area could be classified into four ecotypes: ecotype 1 (Banja, Dembecha, and Aneded), ecotype 2 (North Achefer), ecotype 3 (Sinan), and ecotype 4 (Jawi).

Quantifying morphometric and adaptive characteristics of indigenous cattle genetic resources in northwest Ethiopia.

Ethiopia is the gateway of livestock genetic resources to Africa and has a wide range of altitude. It is endowed with huge diverse cattle genetic resources. The aim of this research was to determine the morphometric and potentioally adaptive characteristics of cattle populations. Multi-stage purposive and random sampling methods were employed to select the study areas, households and animals. A total of 1200 adult cattle were sampled and characterized for 14 qualitative and eight morphometric variables. The comparison of marginal means, chi-square tests, canonical discriminant analysis, and clustering analysis were employed using SAS and SPSS statistical software. The sex of the animal, location and agro-ecology were fitted as fixed effects in the model and had highly significant (p<0.001) effects for most body measurements. The chi-square test values of all categorical variables were significantly different (p<0.001) and potentioally adaptive characteristics such as coat colour type, navel flap, and tail length had higher association (> 0.45) values. White with red, light red, black and dark red were the most predominant coat colour types of cattle. The maximum hit rates were recorded in Enebsie and Sinan cattle. From five extracted canonical variate, (can1 and can2) accounted 75.4% and 78.8% in the female and male cattle populations, respectively. The canonical class has separated cattle populations of Sinan from Banja at can1 and Mecha from Sinan populations at can2. The square Mahalanobis distances between sites were significant (p<0.001) and the largest distance was found between Banja and Sinan locations. Cluster analysis result classified the study populations into four major cattle groups. The cumulative analysis results showed that the cattle populations of the study area can be categorized into four breed types as Jawi Sanga, Gojjam Zenga, Banja cattle, and Sinan cattle. However, this morphology based grouping need to be confirmed by molecular data.

Enteromorpha polysaccharide and yeast glycoprotein mixture improves growth, antioxidant activity, serum lipid profile and regulates lipid metabolism in broiler chickens.

This study aimed to analyze the growth performance, antioxidant activity, serum lipid profile, meat quality, and lipid metabolism of broiler chickens fed mixtures containing Enteromorpha polysaccharide (EP) and yeast glycoprotein (YG). A total of 400 one-day-old broiler chickens were randomly divided into 4 treatment groups of 10 replicates with 10 birds each replicate. The dietary treatments consisted of the control group (fed basal diet), and diets supplemented with Enteromorpha polysaccharide (EP; 400 mg/kg), yeast glycoprotein (YG;400 mg/kg), and EP+YG (200 mg/kg EP + 200 mg/kg YG). Compared with the control group, EP+YG supplementation enhanced growth performance and significantly reduced (P < 0.05) serum total triglyceride (TG), cholesterol (CHOL), and low-density lipoprotein LDL levels, and increased high-density lipoprotein (HDL) levels. Besides, birds fed EP+YG supplemented diet exhibited higher (P < 0.05) serum catalase (CAT), total antioxidant capacity, superoxide dismutase (SOD), and lower malonaldehyde (MDA) activities, and upregulated expressions of related genes, such as nuclear factor-erythroid factor 2-related factor 2 (NRF2), SOD1, and glutathione peroxidase 4 (GPX4) in the liver and intestinal tissues than the control group. Interestingly, higher (P < 0.05) serum SOD and lower MDA contents were observed in the EP+YG group than in either EP or YG group, suggesting a synergetic effect. Breast meat from EP+YG supplemented group had significantly higher redness value (a*), and lower pH24, total saturated fatty acid profiles, C14:0, C16:0, C18:0 fatty acid, atherogenic index, and thrombogenicity index than meat from the control group (P < 0.05). Furthermore, the mRNA expressions of fatty acid synthesis genes were downregulated (P < 0.05), whereas lipid ß-oxidation-related genes were upregulated (P < 0.05) in the liver of the EP+YG supplemented group than in the control group. Overall, our data suggest that dietary EP+YG inclusion may have a synergistic effect, and therefore improve growth performance, regulate serum biochemical indexes, enhance antioxidant activity, and modulate lipid metabolism in broilers, indicating that it is a potential feed additive for chickens.

Structural indices of indigenous goats reared under traditional management systems in East Gojjam Zone, Amhara Region, Ethiopia.

In phenotypic characterization of animal genetic resources, structural indices are essential components to understand the breed structure and body proportions. They are the ethnological characteristics as well as functional traits of animals providing information about the type, aptitude, and production purpose of animals. This study intends to provide information on the structural indices of indigenous goats reared under the smallholder management systems in selected districts of East Gojjam Zone, Amhara region, Ethiopia. Data on body weight and nine morphometric measurements were collected from 706 goats (589 does and 117 bucks) selected using their dentition (≥ One Pair of Permanent Incisor), physiological status (lactating females and intact males), and health condition (healthy). Nineteen structural indices were calculated from morphometric measurements and analyzed using the general linear model (GLM) procedure of the statistical analysis system (SAS, 9.0). Data were analyzed for does and bucks separately. Location had a significant (p < 0.05) influence on pelvic index, transversal and longitudinal pelvic indices, dactyl thoracic index, and relative cannon thickness index of bucks. Except for height slope, pelvic index, baron and crevat, body ratio, areal index, over increase index, weight-1, and weight-2, all other structural indices calculated for does were significantly (p < 0.05) influenced by location. Strong correlations were observed between the structural indices calculated from the linear body measurements. The study revealed that goats in the study area are longilinear and light animals that have dairy biotype. However, further studies are needed to classify the goat types for their production purposes.

Phenotypic and genetic parameter estimates for early growth, growth rate and growth efficiency-related traits of Fogera cattle in Ethiopia.

BACKGROUND: Understanding the phenotypic and genetic parameter estimates of growth traits is important for an effective livestock genetic improvement programme. OBJECTIVES: In this study, we evaluated the phenotypic performances and estimated genetic parameters for birthweight (BWT), weaning weight (WWT), pre-weaning average daily gain (PADG), pre-weaning Kleiber ratio (PKR), pre-weaning growth efficiency (PGE) and pre-weaning relative growth rate (PRGR) of Fogera cattle in Ethiopia. METHODS: Growth data collected from 2000 to 2018 in Andassa Livestock Research Center were used for the study. General linear model of SAS 9.1 was used to estimate the least squares mean (LSM) ± standard error (SE) for phenotypic performances, and AI-REML of Wombat software combined with a series of five single-trait animal models to estimate phenotypic variance and its direct, maternal and residual components. Calf sex, calf birth season and calf birth year were the fixed effects considered. RESULTS: The overall LSM ± SE BWT, WWT, PADG, PKR, PGE and PRGR were 21.28 ± 0.05 kg, 97.99 ± 0.67 kg, 320.29 ± 2.79 g, 10.10 ± 0.04, 3.51 ± 0.35 and 1.95 ± 0.00, respectively. All the fixed effects considered significantly (p < 0.001) affected all the traits. The direct heritability estimates for BWT, WWT, PADG, PKR, PGE and PRGR were 0.21 ± 0.07, 0.26 ± 0.01, 0.55 ± 0.19, 0.53 ± 0.18, 0.33 ± 0.00 and 0.50 ± 0.00, respectively. The genetic correlations among the traits ranged from negative (-0.20 ± 0.04; BWT-PKR) to positive (0.99 ± 0.00; BW-PGE, BW-GR, WWT-PGE, WWT-PGR, ADG-PGR, PKR-PGR, PKR-PGE and PGE-PGR). Similarly, the phenotypic correlations ranged from -0.03 ± 0.20 to 0.99 ± 0.01; BWT-PGE, BWT-PRGR, WWT-PGE, WWT-PRGR, PKR-PGE, PKR-PRGR and PGE-PRGR). CONCLUSION: The positive and larger phenotypic and genetic correlations between most of the traits implied that selection based on one trait could improve the other traits. However, the negative phenotypic and genetic correlation between BWT-PKRA implies that selection of Fogera calves based on either of the traits has an adverse effect on the other. Therefore, caution should be taken when designing the selection criteria for growth improvement.

Estimation of genetic parameters for growth traits and Kleiber ratios in Boer x Central Highland goat.

Accurate performance evaluation and genetic parameters estimation are the prerequisites for any successful genetic improvement program. This study was conducted to estimate genetic parameters for growth and Kleiber ratio traits in Boer x Central Highland goats. On-station data collected from 2009 to 2018 were utilized for the study. A general linear model procedure of the Statistical Analysis System (SAS, version 9.0) was used to analyze fixed effects, and genetic parameters were estimated using the WOMBAT software fitted animal model. The log-likelihood ratio test was used for selecting the best fitted model. Based on best fitted models, the total heritability (h2t) estimate for birth weight (BWT), weaning weight (WWT), six-month weight (SMWT), nine-month weight (NMWT), and yearling weight (YWT) were 0.38, 0.12, 0.05, 0.30, and 0.28, respectively. The total heritability (h2t) estimates for weight gain from birth to weaning (ADG1), 3 to 6 months (ADG2), 6 to 9 months (ADG3), and 9 to 12 months of age (ADG4) were 0.09, 0.08, 0.16, and 0.14, respectively. The heritability estimates for Kleiber ratios in different growth phases were found to be low (0.09 to 0.18) based on the selected models. Even with this figure, including the Kleiber ratio in the selection criteria would be imperative to improve the feed efficiency of crossbred goats. The direct genetic correlation estimates among growth traits range from 0.60 ± 0.14 to 0.97 ± 0.12. Except for NMWT, ADG4, and Kleiber ratio from 9 months to yearling age, the maternal effect had a significant influence on all considered traits. However, the contribution of the maternal genetic effect was more important for early growth traits. Thus, considering both the direct additive genetic effect and the maternal genetic effect is imperative for accurate genetic evaluation and for high selection response. The moderate heritability estimates for most of the growth traits implies the possibility of selection in conjunction with crossbreeding for a better genetic response. The positive and high genetic correlation estimates among growth traits confirm the possibility of a selection of goats at an early age.

Multivariate genome-wide association studies on tenderness of Berkshire and Duroc pig breeds.

Genome-wide association studies (GWAS) have been steadily used for identification of genomic links to disease and various economical traits. Of those traits, a tenderness of pork is one of the most important factors in quality evaluation of consumers. In this study, we use two pig breed populations; Berkshire is known for its excellent meat quality and Duroc which is known for its high intramuscular fat content in meat. Multivariate genome-wide association studies (MV-GWAS) was executed to compare SNPs of two pigs to find out what genetic variants occur the tenderness of pork. Through MV-GWAS, we have identified candidate genes and the association of biological pathways involved in the tenderness of pork. From these direct and indirect associations, we displayed the usefulness of simple statistical models and their potential contribution to improving the meat quality of pork. We identified a candidate gene related to the tenderness in only Berkshire. Furthermore, several of the biological pathways involved in tenderness in both Berkshire and Duroc were found. The candidate genes identified in this study will be helpful to use them in breeding programs for improving pork quality.

Deciphering signature of selection affecting beef quality traits in Angus cattle.

Artificial selection towards a desired phenotype/trait has modified the genomes of livestock dramatically that generated breeds that greatly differ in morphology, production and environmental adaptation traits. Angus cattle are among the famous cattle breeds developed for superior beef quality. This paper aimed at exploring genomic regions under selection in Angus cattle that are associated with meat quality traits and other associated phenotypes. The whole genome of 10 Angus cattle was compared with 11 Hanwoo (A-H) and 9 Jersey (A-J) cattle breeds using a cross-population composite likelihood ratio (XP-CLR) statistical method. The top 1% of the empirical distribution was taken as significant and annotated using UMD3.1. As a result, 255 and 210 genes were revealed under selection from A-H and A-J comparisons, respectively. The WebGestalt gene ontology analysis resulted in sixteen (A-H) and five (A-J) significantly enriched KEGG pathways. Several pathways associated with meat quality traits (insulin signaling, type II diabetes mellitus pathway, focal adhesion pathway, and ECM-receptor interaction), and feeding efficiency (olfactory transduction, tight junction, and metabolic pathways) were enriched. Genes affecting beef quality traits (e.g., FABP3, FTO, DGAT2, ACS, ACAA2, CPE, TNNI1), stature and body size (e.g., PLAG1, LYN, CHCHD7, RPS20), fertility and dystocia (e.g., ESR1, RPS20, PPP2R1A, GHRL, PLAG1), feeding efficiency (e.g., PIK3CD, DNAJC28, DNAJC3, GHRL, PLAG1), coat color (e.g., MC1-R) and genetic disorders (e.g., ITGB6, PLAG1) were found to be under positive selection in Angus cattle. The study identified genes and pathways that are related to meat quality traits and other phenotypes of Angus cattle. The findings in this study, after validation using additional or independent dataset, will provide useful information for the study of Angus cattle in particular and beef cattle in general.

Analysis of cross-population differentiation between Thoroughbred and Jeju horses.

OBJECTIVE: This study was intended to identify genes positively selected in Thoroughbred horses (THBs) that potentially contribute to their running performances. METHODS: The genomes of THB and Jeju horses (JH, Korean native horse) were compared to identify genes positively selected in THB. We performed cross-population extended haplotype homozygosity (XP-EHH) and cross-population composite likelihood ratio test (XP-CLR) statistical methods for our analysis using whole genome resequencing data of 14 THB and 6 JH. RESULTS: We identified 98 (XP-EHH) and 200 (XP-CLR) genes that are under positive selection in THB. Gene enrichment analysis identified 72 gene ontology biological process (GO BP) terms. The genes and GO BP terms explained some of THB's characteristics such as immunity, energy metabolism and eye size and function related to running performances. GO BP terms that play key roles in several cell signaling mechanisms, which affected ocular size and visual functions were identified. GO BP term Eye photoreceptor cell differentiation is among the terms annotated presumed to affect eye size. CONCLUSION: Our analysis revealed some positively selected candidate genes in THB related to their racing performances. The genes detected are related to the immunity, ocular size and function, and energy metabolism.

Exploring evidence of positive selection signatures in cattle breeds selected for different traits.

Since domestication, the genome landscape of cattle has been changing due to natural and artificial selection forces resulting in several general and specialized cattle breeds of the world. Identifying genomic regions affected due to these forces in livestock gives an insight into the history of selection for economically important traits and genetic adaptation to specific environments of the populations under consideration. This study explores the genes/genomic regions under selection in relation to the phenotypes of Holstein, Hanwoo, and N'Dama cattle breeds using Tajima's D, XP-CLR, and XP-EHH population statistical methods. The whole genomes of 10 Holstein (South Korea), 11 Hanwoo (South Korea), and 10 N'Dama (West Africa-Guinea) cattle breeds re-sequenced to ~11x coverage and retained 37 million SNPs were used for the study. Selection signature analysis revealed 441, 512, and 461 genes under selection from Holstein, Hanwoo, and N'Dama cattle breeds, respectively. Among all these, seven genes including ARFGAP3, SNORA70, and other RNA genes were common between the breeds. From each of the gene lists, significant functional annotation cluster terms including milk protein and thyroid hormone signaling pathway (Holstein), histone acetyltransferase activity (Hanwoo), and renin secretion (N'Dama) were enriched. Genes that are related to the phenotypes of the respective breeds were also identified. Moreover, significant breed-specific missense variants were identified in CSN3, PAPPA2 (Holstein), C1orf116 (Hanwoo), and COMMD1 (N'Dama) genes. The genes identified from this study provide an insight into the biological mechanisms and pathways that are important in cattle breeds selected for different traits of economic significance.

Whole genome detection of signature of positive selection in African cattle reveals selection for thermotolerance.

As African indigenous cattle evolved in a hot tropical climate, they have developed an inherent thermotolerance; survival mechanisms include a light-colored and shiny coat, increased sweating, and cellular and molecular mechanisms to cope with high environmental temperature. Here, we report the positive selection signature of genes in African cattle breeds which contribute for their heat tolerance mechanisms. We compared the genomes of five indigenous African cattle breeds with the genomes of four commercial cattle breeds using cross-population composite likelihood ratio (XP-CLR) and cross-population extended haplotype homozygosity (XP-EHH) statistical methods. We identified 296 (XP-EHH) and 327 (XP-CLR) positively selected genes. Gene ontology analysis resulted in 41 biological process terms and six Kyoto Encyclopedia of Genes and Genomes pathways. Several genes and pathways were found to be involved in oxidative stress response, osmotic stress response, heat shock response, hair and skin properties, sweat gland development and sweating, feed intake and metabolism, and reproduction functions. The genes and pathways identified directly or indirectly contribute to the superior heat tolerance mechanisms in African cattle populations. The result will improve our understanding of the biological mechanisms of heat tolerance in African cattle breeds and opens an avenue for further study.

The genome landscape of indigenous African cattle.

BACKGROUND: The history of African indigenous cattle and their adaptation to environmental and human selection pressure is at the root of their remarkable diversity. Characterization of this diversity is an essential step towards understanding the genomic basis of productivity and adaptation to survival under African farming systems. RESULTS: We analyze patterns of African cattle genetic variation by sequencing 48 genomes from five indigenous populations and comparing them to the genomes of 53 commercial taurine breeds. We find the highest genetic diversity among African zebu and sanga cattle. Our search for genomic regions under selection reveals signatures of selection for environmental adaptive traits. In particular, we identify signatures of selection including genes and/or pathways controlling anemia and feeding behavior in the trypanotolerant N'Dama, coat color and horn development in Ankole, and heat tolerance and tick resistance across African cattle especially in zebu breeds. CONCLUSIONS: Our findings unravel at the genome-wide level, the unique adaptive diversity of African cattle while emphasizing the opportunities for sustainable improvement of livestock productivity on the continent.

Whole genome scan reveals the genetic signature of African Ankole cattle breed and potential for higher quality beef.

BACKGROUND: Africa is home to numerous cattle breeds whose diversity has been shaped by subtle combinations of human and natural selection. African Sanga cattle are an intermediate type of cattle resulting from interbreeding between Bos taurus and Bos indicus subspecies. Recently, research has asserted the potential of Sanga breeds for commercial beef production with better meat quality as compared to Bos indicus breeds. Here, we identified meat quality related gene regions that are positively selected in Ankole (Sanga) cattle breeds as compared to indicus (Boran, Ogaden, and Kenana) breeds using cross-population (XP-EHH and XP-CLR) statistical methods. RESULTS: We identified 238 (XP-EHH) and 213 (XP-CLR) positively selected genes, of which 97 were detected from both statistics. Among the genes obtained, we primarily reported those involved in different biological process and pathways associated with meat quality traits. Genes (CAPZB, COL9A2, PDGFRA, MAP3K5, ZNF410, and PKM2) involved in muscle structure and metabolism affect meat tenderness. Genes (PLA2G2A, PARK2, ZNF410, MAP2K3, PLCD3, PLCD1, and ROCK1) related to intramuscular fat (IMF) are involved in adipose metabolism and adipogenesis. MB and SLC48A1 affect meat color. In addition, we identified genes (TIMP2, PKM2, PRKG1, MAP3K5, and ATP8A1) related to feeding efficiency. Among the enriched Gene Ontology Biological Process (GO BP) terms, actin cytoskeleton organization, actin filament-based process, and protein ubiquitination are associated with meat tenderness whereas cellular component organization, negative regulation of actin filament depolymerization and negative regulation of protein complex disassembly are involved in adipocyte regulation. The MAPK pathway is responsible for cell proliferation and plays an important role in hyperplastic growth, which has a positive effect on meat tenderness. CONCLUSION: Results revealed several candidate genes positively selected in Ankole cattle in relation to meat quality characteristics. The genes identified are involved in muscle structure and metabolism, and adipose metabolism and adipogenesis. These genes help in the understanding of the biological mechanisms controlling beef quality characteristics in African Ankole cattle. These results provide a basis for further research on the genomic characteristics of Ankole and other Sanga cattle breeds for quality beef.

Detecting Positive Selection of Korean Native Goat Populations Using Next-Generation Sequencing.

Goats (Capra hircus) are one of the oldest species of domesticated animals. Native Korean goats are a particularly interesting group, as they are indigenous to the area and were raised in the Korean peninsula almost 2,000 years ago. Although they have a small body size and produce low volumes of milk and meat, they are quite resistant to lumbar paralysis. Our study aimed to reveal the distinct genetic features and patterns of selection in native Korean goats by comparing the genomes of native Korean goat and crossbred goat populations. We sequenced the whole genome of 15 native Korean goats and 11 crossbred goats using next-generation sequencing (Illumina platform) to compare the genomes of the two populations. We found decreased nucleotide diversity in the native Korean goats compared to the crossbred goats. Genetic structural analysis demonstrated that the native Korean goat and crossbred goat populations shared a common ancestry, but were clearly distinct. Finally, to reveal the native Korean goat's selective sweep region, selective sweep signals were identified in the native Korean goat genome using cross-population extended haplotype homozygosity (XP-EHH) and a cross-population composite likelihood ratio test (XP-CLR). As a result, we were able to identify candidate genes for recent selection, such as the CCR3 gene, which is related to lumbar paralysis resistance. Combined with future studies and recent goat genome information, this study will contribute to a thorough understanding of the native Korean goat genome.

The Prediction of the Expected Current Selection Coefficient of Single Nucleotide Polymorphism Associated with Holstein Milk Yield, Fat and Protein Contents.

Milk-related traits (milk yield, fat and protein) have been crucial to selection of Holstein. It is essential to find the current selection trends of Holstein. Despite this, uncovering the current trends of selection have been ignored in previous studies. We suggest a new formula to detect the current selection trends based on single nucleotide polymorphisms (SNP). This suggestion is based on the best linear unbiased prediction (BLUP) and the Fisher's fundamental theorem of natural selection both of which are trait-dependent. Fisher's theorem links the additive genetic variance to the selection coefficient. For Holstein milk production traits, we estimated the additive genetic variance using SNP effect from BLUP and selection coefficients based on genetic variance to search highly selective SNPs. Through these processes, we identified significantly selective SNPs. The number of genes containing highly selective SNPs with p-value <0.01 (nearly top 1% SNPs) in all traits and p-value <0.001 (nearly top 0.1%) in any traits was 14. They are phosphodiesterase 4B (PDE4B), serine/threonine kinase 40 (STK40), collagen, type XI, alpha 1 (COL11A1), ephrin-A1 (EFNA1), netrin 4 (NTN4), neuron specific gene family member 1 (NSG1), estrogen receptor 1 (ESR1), neurexin 3 (NRXN3), spectrin, beta, non-erythrocytic 1 (SPTBN1), ADP-ribosylation factor interacting protein 1 (ARFIP1), mutL homolog 1 (MLH1), transmembrane channel-like 7 (TMC7), carboxypeptidase X, member 2 (CPXM2) and ADAM metallopeptidase domain 12 (ADAM12). These genes may be important for future artificial selection trends. Also, we found that the SNP effect predicted from BLUP was the key factor to determine the expected current selection coefficient of SNP. Under Hardy-Weinberg equilibrium of SNP markers in current generation, the selection coefficient is equivalent to 2*SNP effect.

Genome-wide Association Study (GWAS) and Its Application for Improving the Genomic Estimated Breeding Values (GEBV) of the Berkshire Pork Quality Traits.

The missing heritability has been a major problem in the analysis of best linear unbiased prediction (BLUP). We introduced the traditional genome-wide association study (GWAS) into the BLUP to improve the heritability estimation. We analyzed eight pork quality traits of the Berkshire breeds using GWAS and BLUP. GWAS detects the putative quantitative trait loci regions given traits. The single nucleotide polymorphisms (SNPs) were obtained using GWAS results with p value <0.01. BLUP analyzed with significant SNPs was much more accurate than that with total genotyped SNPs in terms of narrow-sense heritability. It implies that genomic estimated breeding values (GEBVs) of pork quality traits can be calculated by BLUP via GWAS. The GWAS model was the linear regression using PLINK and BLUP model was the G-BLUP and SNP-GBLUP. The SNP-GBLUP uses SNP-SNP relationship matrix. The BLUP analysis using preprocessing of GWAS can be one of the possible alternatives of solving the missing heritability problem and it can provide alternative BLUP method which can find more accurate GEBVs.

Evaluation of growth performance of abergele goats under traditional management systems in Sekota District, Ethiopia.

The study was conducted at Abergele in the semi arid parts of Sekota district to evaluate growth performance of Abergele goats managed under traditional management systems. Data on growth and growth rates were collected from 724 kids for two years. The least squares mean birth, three months, six months and yearling weight of kids obtained were 1.91 +/- 0.04, 6.84 +/- 0.19, 9.13 +/- 0.31 and 16.42 +/- 1.20 kg, respectively. Parity of doe and birth type of kid significantly affected birth weight and three months weight while sex of kid and season of birth of kid affected birth, three months, six months and yearling weight consistently. Kids from first parity does were lighter at birth, three months and six months of age than kids from higher parity does. Twin born kids were lower in weight at birth and three months of ages than their single born counterparts. Female kids and kids born during the dry season had lower weight at all ages considered. The least squares mean pre-weaning and post-weaning growth rates obtained were 53.4 +/- 2.30 and 29.3 +/- 4.32 g day(-1), respectively. Parity of doe, type of birth and season birth of kid affected pre-weaning growth rate. Kids from first parity does, twin born kids and kids born during the dry season had lower growth rate. The significant effect of fixed factors needs to be considered in an effort to improve productivity of goats in the study areas.