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

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

DNA methylation and hydroxymethylation in early rabbit embryo: Consequence of in vitro culture.

During the first developmental stages, the embryo’s genome is transcriptionally silent and developmental changes are under control of maternally inherited factors (RNA and proteins). Embryonic genome activation (EGA) takes place at later stages (8-16 cell stage in rabbit) and involves epigenetic modifications. CpG methylation is depleted at the early stages and reinstated at the blastocyst stage. DNA methylation at CpG dinucleotides is an important epigenetic mark for embryonic development. Recent findings have shown that demethylation is achieved by oxidation of the methylated DNA into hydroxymethylated DNA. However, the role of hydroxymethylation can probably not be restricted to an intermediate product in DNA demethylation. Indeed, hydroxymethylation seems involved in gene activation and maintenance of pluripotency, and could therefore be important for EGA. Several studies have suggested that in vitro conditions can have a negative impact on epigenetic reprogramming. Thus, 5-methylcytosine (5MeC) and 5-hydroxymethylcytosine (5hMeC) appeared as interesting candidates to investigate the impact of culture media on methylation and hydroxymethylation in rabbit embryos. We used rabbit as a model because the metabolism and timing of EGA in this species is closer to human embryos. The 2 chosen culture media that are commonly used for artificial reproduction technologies (ART) are 1 single-step medium (global), which allows development from zygote to blastocyst, and 1 sequential medium (G1+/G2+), which needs to be changed at the time of EGA. Embryos were fixed at different developmental cell stages: 2-, 4-, 8-, and 16-cell stages. To quantify the level of methylated and hydroxymethylated DNA in the nuclei, we implemented an immunofluorescence-based detection protocol. Finally, the methylated and hydroxymethylated DNA were quantified using an appropriate procedure developed in the host laboratory. Our result shows that the dynamics of 5MeC and 5hMeC are different between the 2 culture media. In the sequential 1, methylation increases between 4-cell and 8-cell stages, while there is no significant change in hydroxymethylation between 2-cell and 16-cell stages. In the single-step 1, hydroxymethylation decreases until the 8-cell stage and increases afterward, while no change is observed in methylation between 4-cell and 8-cell stages. To draw solid conclusions, it is advisable to reproduce the experiment with other applicable species, such as bovine embryos, ahead of further steps to demonstrate on human embryos. Our results will be helpful for the advancement of ART, which is challenged by abnormal embryonic development and unsuccessful pregnancy

Impact of integrated land management technology adoption on rural livelihoods in the Goyrie watershed, Southern Ethiopia: Endogenous switching regression modeling estimation

Integrated land management (ILM) technology adoption is crucial for enhancing yield production and households’ income, which are indispensable to sustainable development objectives. This research analyzes the impact of ILM technology adoptions on rural livelihoods by focusing on yield production and net farm income in the Goyrie watershed, southern Ethiopia. Deploying random sampling techniques, cross-sectional data was collected from 291 households’. Quantitative data was analyzed using percent, mean, standard deviation and independent t-test, while qualitative data was presented in a narrative forms. The Full Information Maximum Likelihood (FIML) methods and Endogenous Switching Regression Modeling (ESRM) were utilized to estimate the impact of ILM technology adoptions on yield production and net farm income. The result exhibited that the average treatment effect for technology adopters increased their yield production by 4.71% and net farm income by 2.81%. Under counterfactual scenarios, the average treatment effect on untreated control groups would increase yield production and net farm income by 5.73% and 3.71%, respectively, if they preferred to adopt the technology. The study found that adoption of ILM technologies significantly and positively impacts yield production and net farm income in Goyrie watershed. Thus, we suggest that agricultural experts and academics should assist early adopters to scale up and encourage the non-adopters to adopt combined technologies through training and enhancing extension services. Educational status, land size, livestock and membership had positive impacts on yield production and income, suggesting that policies that encourage livelihood asset indicators can enable households to boost their yield production and income

The Genetic Architecture of Carcass and Meat Quality Traits in Beef Cattle

This thesis explores the genetic variation of carcass and meat quality traits in beef cattle. Estimation of genetic parameters including heritability, genetic and phenotypic correlations is the first step in the genetic evaluation process to understand the nature of quantitative traits. Subsequently, the estimated parameters are required for the establishing of a selection program in livestock. Alongside with performance data, pedigree information is essential to estimate the relationship between animals more accurately in the conventional breeding program. In beef cattle, carcass traits cannot be recorded on selection candidates and therefore time-consuming progeny tests are often used to gain selection accuracy. However, the discovery of genomic information has enabled to select high merit individuals at an early age without scarifying the selection candidate. Furthermore, the availability of high-density SNP panels and whole genome sequence data has improved the selection accuracy of high merit individuals. Therefore, the general aim of this thesis was to understand the genetic variability of carcass and meat quality traits using pedigree and genomic information in beef cattle. The first experiment of this thesis explored the genetic variation of carcass and meat quality traits in Hanwoo beef cattle using pedigree information. The phenotypic data were collected from 469,002 Hanwoo beef cattle raised at 3646 farms in the Republic of South Korea. The studied carcass traits were carcass weight, eye muscle area, back fat thickness, body weight, and meat index. In addition, the studied meat quality traits included marbling score, meat colour, fat colours and meat texture. Carcass traits, including carcass weight, eye muscle area, back fat thickness and marbling score showed high genetic variation and moderate to high heritability in the Hanwoo beef cattle population. However, the study also revealed that carcass weight and eye muscle area traits showed low and negative (unfavourable) genetic associations with meat texture, meat and fat color traits. Low heritabilities were observed for meat and fat colour traits, however, the observed moderate and positive genetic correlations among meat texture, meat and fat colour traits suggests that these traits can be jointly improved in a breeding program of beef cattle. In this study, the genetic and phenotypic correlations between carcass and meat quality traits were low in general, indicating that these traits are independent and require careful application in selection schemes. In conclusion, the estimates of genetic parameters in this study could be useful for designing breeding programs to improve various carcass and meat quality traits in Hanwoo cattle. The second experiment was designed to examine the drawback of the data obtained from slaughterhouses that were used in the first experiment. Therefore, the second experiment assesses bias due to sorting of animals based on body weight for the genetic evaluation of carcass traits using simulation data. Various sources of bias in genetic evaluation including parental selection, sequential selection, culling of animals before records, and misclassification or manipulation of contemporary groups have been discussed widely in the literature. We hypothesized that the sorting of animals into different contemporary groups based on their yearling weight had an impact on the genetic evaluation of this trait and other correlated traits. The experiment aimed to observe the impact of sorting animals into different contemporary groups based on an early measured trait and then examine the effect on the genetic evaluation of subsequent measured traits. Our result showed that when animals are sorted based on yearling weight leads to biased estimated breeding values in genetic evaluation of carcass traits. The magnitude of the bias in the estimated breeding values that was observed in the current study varied with heritability, and genetic and residual correlations between the simulated traits. The current result demonstrated that the detected sorting biases were stronger when higher genetic and residual correlations were allocated to the simulated traits. However, the observed sorting bias in the univariate model was accounted for by multi-trait evaluation methods. In addition, a slight decrease of bias in estimated breeding values was observed when carcass weight was fitted as a linear covariate in the model for the genetic evaluation of subcutaneous fat depths at the 12th/13th rib (CRIB) trait. Overall, the current simulation study provides insights into how the genetic architecture of studied traits affects the genetic evaluation of animals. The third experiment explored the genetic architecture underlying genetic variability of meat quality traits through the analysis of a genome-wide association study (GWAS) in Hanwoo beef cattle. Genome-wide association studies using common SNP chips have revealed many quantitative trait loci for various production traits such as growth, efficiency, carcass and meat quality traits; however, GWAS using whole genome sequence data are scarce in beef cattle. The current GWAS was conducted using whole-genome sequence data from 2110 Hanwoo beef cattle recorded for marbling score, meat texture, meat and fat color traits. The study identified several chromosomal regions on various chromosomes that contained 107 significant SNPs associated with meat quality traits. 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 studied traits, and their potential influence on the given trait was discussed. The fourth and fifth experiments examined factors that influence the genomic prediction accuracy in beef cattle. Prediction of the breeding values based on information on DNA of the animals is changing breeding strategies and saving time and costs in a breeding program of beef production. The fourth experiment mainly focused on the impact of the relationship between reference and test population was examined on the accuracy of genomic prediction using distantly versus closely related animals in the reference and test populations. The result showed that when the animals in the reference and test populations were closely related, the prediction accuracy was higher than when the animals were related distantly. The fifth experiment assessed the effect of SNP densities including 50K, 777K (HD), whole genome sequence (WGS)) and preselected SNP on the accuracy of genomic prediction. The results showed that similar prediction accuracies were observed across all SNP densities. Small sample size in genomic prediction is a limiting factor to capitalize the benefit of using WGS data since the effect of causal mutations on quantitative traits cannot be accurately estimated. Additionally, high-density markers and WGS data may not help to improve the prediction accuracy in a breed with small effective population size such as Hanwoo beef cattle used in the current study. Depending on the SNP selection methods, zero to 5% improvement of genomic prediction accuracy was gained due to the inclusion of SNPs that were significantly associated with the studied traits, as detected in the GWAS previously. Similarly, different magnitudes of bias were observed in the genomic breeding values depending on the SNP selection methods used in the study. Potential reasons for the observed bias due to the inclusion of preselected SNPs have been discussed and found in other relevant literatures. Overall, the study shows that marbling score and meat texture traits had higher genomic prediction accuracy in all scenarios, suggesting that genomic selection for these traits may contribute well to the genetic improvement of meat quality in Hanwoo beef cattle

Effects of integrated land management technology adoptions on soil properties, evidence from the Goyrie watershed, Southern Ethiopia

Since 2008, integrated land management technology (ILMT) adoptions have been applied to minimize soil depletion and improve soil properties in the Ethiopian highlands, including the study watershed. However, the effect of combined technologies on soil properties was not investigated through standard laboratory procedures in the Goyrie watershed. Thus, the purpose of this study was to evaluate the effects of ILMTs on selected soil properties in the Goyrie Watershed of southern Ethiopia. A total of 27 composite soil samples (three replications, three farmlands per management category, and three slope positions) were randomly collected from the top soils at a depth of 0–20 cm. A one-way analysis of variance (ANOVA) was used to examine mean soil property variation between treated and non-treated farmlands and slope positions, while a two-way ANOVA was used to examine the interaction effects. The result showed that farmlands treated with soil bunds and desho grasses had significantly higher mean clay content (50%), total porosity (59.6%), soil pH (6.7%), soil organic carbon (SOC) (2,49%), soil organic matter (SOM) (4.29%), total nitrogen (TN) (.23%), available phosphorus (Av. P) (7.83%), cation exchange capacity (40.11%), and exchangeable basic captions compared to farmland treated with only single technologies and without conserved farmlands. Non-treated farmlands had higher sand (32.84%) and bulk density (1.38%) contents. Whereas lower landscape sites had higher mean value of clay (29%), K+ (.49%), Ca2+ (8.93%), and Mg2+ (2.23%) content than the middle and upper slope sites. Clay content, soil pH, SOC and SOM contents were statistically and significantly influenced by the interaction effects of management technologies and slope gradient. Overall, the three PCAs’ contributed to 71.52% of the total variance. Adoption of soil bunds with multipurpose fodder species is a promising approach for improving soil properties and should be applied to the non-treated farmlands of the Goyrie Watershed

Finding the marble - The polygenic architecture of intramuscular fat

Intramuscular fat (IMF) is one of the most important traits in the meat industry. It has been positively correlated with tenderness, juiciness and an overall improved eating experience. It also attracts premium pricing and a much clearer market signal than any other production trait. In this short review, we summarize what is known about the genetic architecture of IMF in Korean Hanwoo cattle. There is a lot of discordancy and limited validation across the many IMF studies, which we suggest is driven to a large extent by the highly polygenic nature of the trait, with individual studies capturing different facets of the trait but never the full picture. A true handle on the functional genetics of marbling will require larger projects and concerted effort between researchers, industry and government. The payoff however has potential to be very high as IMF is the main determinant of profitability in the Hanwoo industry

Assessment of 'one-step' versus 'sequential' embryo culture conditions through embryonic genome methylation and hydroxymethylation changes (vol 31, pg 2471, 2016)

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