Stories and Challenges of Genome Wide Association Studies in Livestock - A Review.

Undoubtedly livestock is one of the major contributors to the economy of any country. The economic value of livestock includes meat, dairy products, fiber, fertilizer etc. Understanding and identifying the associations of quantitative trait loci (QTL) with the economically important traits is believed to substantially benefit the livestock industry. The past two decades have seen a flurry of interest in mapping the QTL associated with traits of economic importance on the genome. With the availability of single nucleotide polymorphism chip of various densities it is possible to identify regions, QTL and genes on the genome that explain the association and its effect on the phenotype under consideration. Remarkable advancement has been seen in genome wide association studies (GWAS) since its inception till the present day. In this review we describe the progress and challenges of GWAS in various livestock species.

Genetic analysis of ultrasound and carcass measurement traits in a regional hanwoo steer population.

Ultrasound measurements of backfat thickness (UBF), longissimus muscle area (ULMA) and marbling score (UMS) and carcass measurements of carcass weight (CW), backfat thickness (BF), longissimus muscle area (LMA), and marbling score (MS) on 7,044 Hanwoo steers were analyzed to estimate genetic parameters. Data from Hanwoo steers that were raised, finished in Hoengseong-gun, Gangwon-do (province) and shipped to slaughter houses during the period from October 2010 to April 2013 were evaluated. Ultrasound measurements were taken at approximately three months before slaughter by an experienced operator using a B-mode real-time ultrasound device (HS-2000, FHK Co. Ltd., Tokyo, Japan) with a 3.5 MHz linear probe. Ultrasound scanning was on the left side between 13th rib and the first lumbar vertebrae. All slaughtering processes and carcass evaluations were performed in accordance with the guidelines of beef grading system of Korea. To estimate genetic parameters, multiple trait animal models were applied. Fixed effects included in the models were: the effects of farm, contemporary group effects (year-season at the time of ultrasound scanning in the models for UBF, ULMA, and UMS, and year-season at slaughter in the models for CW, BF, LMA, and MS), the effects of ultrasound technicians as class variables and the effects of the age in days at ultrasound scanning or at slaughtering as linear covariates, respectively for ultrasound and carcass measures. Heritability estimates obtained from our analyses were 0.37 for UBF, 0.13 for ULMA, 0.27 for UMS, 0.44 for CW, 0.33 for BF, 0.36 for LMA and 0.54 MS, respectively. Genetic correlations were strongly positive between corresponding traits of ultrasound and carcass measures. Genetic correlation coefficient between UBF and BF estimate was 0.938, between ULMA and LMA was 0.767 and between UMS and MS was 0.925. These results suggest that ultrasound measurement traits are genetically similar to carcass measurement traits.

National trend of the treatment for chronic venous diseases in Korea between 2010 and 2020.

Purpose: Limited data are available on the nationwide trend of treatments for chronic venous disease (CVD). The aim of the present study was to identify the nationwide trends of CVD treatments in Korea. Methods: A serial, cross-sectional study was conducted with the use of time trends to analyze patients with CVD between 2010 and 2020. The trends in the number of patients and procedures were analyzed including sclerotherapy, open surgery, and endovenous thermal ablation (ETA). Health Insurance Review and Assessment Service data were used to analyze the trends. For the statistical analysis, MedCalc Statistical software was used. P < 0.05 was considered statistically significant. Results: A total of 1,867,307 patients with CVD were managed in Korea between 2010 and 2020. The annual number of patients with CVD increased from 143,108 in 2010 to 219,319 in 2020 (risk ratio [RR], 1.53; P < 0.001). The percentage of patients with CVD who had venous ulcer gradually decreased from 3.1% in 2010 to 1.7% in 2020 (RR, 0.86; P < 0.001). The number of conventional surgeries including stripping and local resection of varicose veins decreased from 32,384 in 2010 to 21,792 in 2020 (RR, 0.67; P < 0.001). The number of ETAs performed increased, from 290 in 2011 to 12,126 procedures in 2020 (RR, 41.81; P < 0.001). Conclusion: The total number of patients with CVD increased during the last 11 years. The number of conventional open surgery and sclerotherapy procedures decreased. On the contrary, the number of ETAs significantly increased in Korea.

Need for individual-based evaluation to determine the association between humidifier disinfectants and health injuries.

BACKGROUND: Injuries caused by humidifier disinfectants (HDs) can no longer be grouped under the concept of HD lung injury. Focusing on individual cases, we were able to evaluate the relevance not only of diseases for which epidemiological correlation is recognized but also all diseases and symptoms that the victims complain of. METHODS: In-depth interviews and reassessment of 113 HD-exposed patients who had not been acknowledged as victims by the government were conducted, and their medical records were reviewed. Based on these processes, an assessment questionnaire for the injuries related to HDs was completed and the involvement of HDs was assessed either as "strong association," "association," or "no association." RESULTS: In this study, of the 113 patients included who claimed damages, 78 (69.0%) had HD-related injuries. Among the cases of 22 patients who applied for injury acknowledgment due to upper respiratory inflammation that was not included among the acknowledged diseases, 17 (77.3%) were judged to be HD-related injuries (strong association vs. association: 10 [45.5%] vs. 7 [31.8%]). When the cases of 12 rhinitis patients were reassessed, 9 were HD-related injuries (strong association vs. association: 4 [33.3%] vs. 5 [41.7%]). When the cases of 18 asthma patients unacknowledged as a victim were reassessed, 17 (94.4%) were humidifier-related injuries (strong association vs. association: 12 [66.6%] vs. 5 [27.8%]). Among 4 interstitial lung disease patients unacknowledged as a victim, 2 (50.0%) were HD-related injuries. CONCLUSIONS: HD-related health injuries should be assessed through both individual interviews and detailed chart reviews for more accurate injury acknowledgment. In the future, efforts should go beyond existing methods based on the adherence to acknowledgment criteria to directly listen to the victims.

Erratum: Need for individual-based evaluation to determine the association between humidifier disinfectants and health injuries.

[This corrects the article e21 in vol. 33.].

Mental health impact on a humidifier disinfectant disaster victim: a case report.

In Korea, the cause of lung disease of unknown origin was identified as humidifier disinfectants in November 2011. In February 2017, the 'Special Act on Remedy for Damage Caused by Humidifier Disinfectants' was promulgated. Even though emotional and mental injuries caused by humidifier disinfectants have been reported, the focus of the special act has been on physical injury only, and criteria for recognizing mental health impact have not been considered. This case considers emotional and mental injury caused by humidifier disinfectants. After a humidifier disinfectant was used from January 2005 to April 2006, the patient's son aged 20 months was hospitalized with respiratory symptoms, and he died within two weeks. Also, the patient was hospitalized for a month with the same symptoms, and then she led a normal life with no symptoms. After both mother and son were diagnosed with definite (level 1) humidifier disinfectant lung injury (HDLI) in 2017, she took to drinking alcohol because of extreme guilt over her son's death. In March 2018 she died from acute liver failure due to alcohol use disorder. The patient's death was caused by continuous alcoholism, due to emotional and mental trauma caused by her son's death after HDLI was revealed as the cause. The government did not acknowledge her death was due to humidifier disinfectants, but the company that sold the humidifier disinfectants recognized her as a victim and compensated the family of the victim. There are still lots of psychological responses among humidifier disinfectant disaster victims. Mental health impact on humidifier disinfectant victims should be considered more carefully, and institutional improvements should be made into establish psychological interventions and measures.

Problems with diagnostic criteria for humidifier disinfectant lung injury (HDLI): two cases of radiologically improved HDLI.

BACKGROUND: In Korea, to investigate the casual relationship between humidifier disinfectant and lung disease, four rounds of investigation and judgment were conducted. During this investigation, two adults who performed lung biopsy were recognized for their relevance between humidifier disinfectants and lung disease. At first, we did not think of the relationship to humidifier disinfectant because chest computed tomography (CT) finding of 2 cases were improved. However, they performed lung biopsy and it showed typical humidifier disinfectant lung injury (HDLI) pathologic findings, they could be recognized as HDLI. We report these cases here. CASE PRESENTATION: We selected 2 cases from the fourth-round investigation at Kangbuk Samsung Hospital. Patient of case 1 used humidifier disinfectants since September 2010. The patient was admitted 6 months later to the intensive care unit (ICU) due to severe dyspnea. Pathology following a lung biopsy revealed typical HDLI finding which was determined to be due to humidifier disinfectant exposure. Patient of case 2 used humidifier disinfectant from 2001 to 2008 for about 3 months each winter. The patient's cough and sputum production symptoms began in December of 2007. The patient was admitted to the respiratory medicine department due to worsening dyspnea. Pathology following a lung biopsy revealed typical HDLI finding. This was determined to have been caused by humidifier disinfectant exposure. CONCLUSIONS: Because the typical radiologic findings associated with HDLI can improve over time, it is necessary to consider the revision of current diagnostic criteria that the presence of radiologic findings is important.

The association between long working hours and marital status change: middle-aged and educated Korean in 2014-2015.

BACKGROUND: We investigated the association between long workhours and marital status change from married to divorced or separated status that might have bad health effects. METHODS: A total of 40,654 participants with married status in 2014 were followed up in 2015. Weekly workhours were categorized into four groups: ≤ 40, 41-52, 53-60, and > 60 hours per week. Univariate and multivariate logistic regression analyses were performed to determine the relationship between groups of workhours and marital status change after adjusting for age, total monthly household income, working type, and depression with sex stratification. RESULTS: The study populations consisted of 8,346 (20.5%) females and 32,308 (79.5%) males. Odd ratios (ORs) of marital status change for females working for more than 60 hours per week was 4.26 (95% confidence interval [CI]: 1.25-14.5), when working less than or equal to 40 hours per week was used as reference in the crude model. ORs of working more than 60 hours per week was 4.57 (95% CI: 1.02-20.5) in female workers when considering age, total household earning per month, working type of daytime, and depression in a dose-response manner. However, for male workers, long workhours were not significantly related to change of marriage status. CONCLUSIONS: Long workhours for more than 60 hours per week had significantly higher risk of divorce or separation in females, but not in males. Further follow-up studies are needed to evaluate long term effects of long workhours on divorce risk.

Relationship between working hours and probability to take alopecia medicine among Korean male workers: a 4-year follow-up study.

BACKGROUND: Many studies have reported the negative effects of long working hours on various health problems. However, whether hair loss is associated with working hours has been rarely investigated so far. The main purpose of this study is to explore the relationship between long working hours and the development of alopecia among Korean male workers. METHODS: A total of 13,391 male workers not to take alopecia medicine in 2013 were followed up to see if they have alopecia medicine after 4 years, and that was used to confirm the alopecia development. Weekly working hours were categorized into three groups: reference working hours (RWH; < 40 hours/week), long working hours (LWH, 40-52 hours/week), and much longer working hours (MLWH; > 52 hours/week). Multiple logistic regression analyses were conducted to investigate the relationship between long working hours and the development of alopecia after adjusting age, marital status, education, monthly household income, smoking, and work schedule within strata of the covariates. RESULTS: Long working hours was significantly related to the development of alopecia. The adjusted odds ratios (ORs) for the development of alopecia were 1.57 (95% confidence interval [CI]: 1.21-2.05) for LWH group and 1.74 (95% CI: 1.23-2.47) for MLWH group relative to RWH group. CONCLUSIONS: Our findings suggest that unintentional development of alopecia is another potential health consequence of long working hours among Korean male workers. Preventive interventions to promote appropriate and reasonable working hours are required in our society.

Copy number variations in Hanwoo and Yanbian cattle genomes using the massively parallel sequencing data.

Hanwoo is an indigenous Korean beef cattle breed, and it shared an ancestor with Yanbian cattle that are found in the Northeast provinces in China until the last century. During recent decades, those cattle breeds experienced different selection pressures. Here, we present genome-wide copy number variations (CNVs) by comparing Hanwoo and Yanbian cattle sequencing data. We used ~3.12 and ~3.07 billion sequence reads from Hanwoo and Yanbian cattle, respectively. A total of 901 putative CNV regions (CNVRs) were identified throughout the genome, representing 5,513,340bp. This is a smaller number than has been reported in previous studies, indicating that Hanwoo are genetically close to Yanbian cattle. Of the CNVRs, 53.2% and 46.8% were found to be gains and losses in Hanwoo. Potential functional roles of each CNVR were assessed by annotating all CNVRs and gene ontology (GO) enrichment analysis. We found that 278 CNVRs overlapped with cattle gene-sets (genic-CNVRs) that could be promising candidates to account for economically important traits in cattle. The enrichment analysis indicated that genes were significantly over-represented in GO terms, including developmental process, multicellular organismal process, reproduction, and response to stimulus. These results provide a valuable genomic resource for determining how CNVs are associated with cattle traits.

Whole-Genome Resequencing Analysis of Hanwoo and Yanbian Cattle to Identify Genome-Wide SNPs and Signatures of Selection.

Over the last 30 years, Hanwoo has been selectively bred to improve economically important traits. Hanwoo is currently the representative Korean native beef cattle breed, and it is believed that it shared an ancestor with a Chinese breed, Yanbian cattle, until the last century. However, these two breeds have experienced different selection pressures during recent decades. Here, we whole-genome sequenced 10 animals each of Hanwoo and Yanbian cattle (20 total) using the Illumina HiSeq 2000 sequencer. A total of approximately 3.12 and 3.07 billion sequence reads were mapped to the bovine reference sequence assembly (UMD 3.1) at an average of approximately 10.71- and 10.53-fold coverage for Hanwoo and Yanbian cattle, respectively. A total of 17,936,399 single nucleotide polymorphisms (SNPs) were yielded, of which 22.3% were found to be novel. By annotating the SNPs, we further retrieved numerous nonsynonymous SNPs that may be associated with traits of interest in cattle. Furthermore, we performed whole-genome screening to detect signatures of selection throughout the genome. We located several promising selective sweeps that are potentially responsible for economically important traits in cattle; the PPP1R12A gene is an example of a gene that potentially affects intramuscular fat content. These discoveries provide valuable genomic information regarding potential genomic markers that could predict traits of interest for breeding programs of these cattle breeds.

Hanwoo cattle: origin, domestication, breeding strategies and genomic selection.

Hanwoo (Korean cattle) is the native, taurine type of cattle breed of Korea and its history as a draft animal dates back to 5000 Years. In earlier times Hanwoo was used extensively for farming, transportation. Over the period of time, Hanwoo has changed to be meat type cattle. Full-scale production of Hanwoo as meat-type cattle has occurred since 1960s with the rapid growth of the Korean economy. Hanwoo is one of the most economically important species in Korea as it is a significant source of nutrition to the Korean people. Hanwoo beef is the most cherished food of Korea. One of the main goals of researchers is to increase the meat quality, quantity and taste of the beef. In this review we describe the origin, domestication of Hanwoo cattle and breeding program initiated from 1980's. Moreover the advent of technological advancement had provided us a platform to perform genome wide selection on economic traits and its implementation into traditional breeding programs.

Mutations in calpastatin and µ-calpain are associated with meat tenderness, flavor and juiciness in Hanwoo (Korean cattle): molecular modeling of the effects of substitutions in the calpastatin/µ-calpain complex.

The objective of this study was to evaluate the effects of seven single nucleotide polymorphisms (SNPs) in Calpain 1 and Calpastatin genes previously associated with meat tenderness attributes in other cattle breeds in Korean Hanwoo cattle. The Hanwoo resource population was used to study association of 7 SNPs with beef tenderness, flavor, juiciness, intramuscular fat and shear force. In this association study, CAST:c.182A>G (+0.14, P=0.04) and CAST:c.1985G>C (-0.12, P=0.02) had significant effects on juiciness, but no effects on other traits. In contrast, CAPN1:c.1589G>A was associated with meat tenderness (P=0.01) and juiciness (P=0.04). The CAPN1:c.1589G>A (Val530Ile) SNP marker displayed significant effect on the meat tenderness score which is strongly supported by molecular modeling of the CAPN1:c.1589G>A (Val530Ile) variant that inhibits CAST protein from binding more strongly than the wild-type protein, which may explain its effect on meat tenderness.

Whole-genome analyses of Korean native and Holstein cattle breeds by massively parallel sequencing.

A main goal of cattle genomics is to identify DNA differences that account for variations in economically important traits. In this study, we performed whole-genome analyses of three important cattle breeds in Korea--Hanwoo, Jeju Heugu, and Korean Holstein--using the Illumina HiSeq 2000 sequencing platform. We achieved 25.5-, 29.6-, and 29.5-fold coverage of the Hanwoo, Jeju Heugu, and Korean Holstein genomes, respectively, and identified a total of 10.4 million single nucleotide polymorphisms (SNPs), of which 54.12% were found to be novel. We also detected 1,063,267 insertions-deletions (InDels) across the genomes (78.92% novel). Annotations of the datasets identified a total of 31,503 nonsynonymous SNPs and 859 frameshift InDels that could affect phenotypic variations in traits of interest. Furthermore, genome-wide copy number variation regions (CNVRs) were detected by comparing the Hanwoo, Jeju Heugu, and previously published Chikso genomes against that of Korean Holstein. A total of 992, 284, and 1881 CNVRs, respectively, were detected throughout the genome. Moreover, 53, 65, 45, and 82 putative regions of homozygosity (ROH) were identified in Hanwoo, Jeju Heugu, Chikso, and Korean Holstein respectively. The results of this study provide a valuable foundation for further investigations to dissect the molecular mechanisms underlying variation in economically important traits in cattle and to develop genetic markers for use in cattle breeding.

Comparative Transcriptome Analysis of Adipose Tissues Reveals that ECM-Receptor Interaction Is Involved in the Depot-Specific Adipogenesis in Cattle.

Adipocytes mainly function as energy storage and endocrine cells. Adipose tissues showed the biological and genetic difference based on their depots. The difference of adipocytes between depots might be influenced by the inherent genetic programing for adipogenesis. We used RNA-seq technique to investigate the transcriptomes in 3 adipose tissues of omental (O), subcutaneous (S) and intramuscular (I) fats in cattle. Sequence reads were obtained from Illumina HiSeq2000 and mapped to the bovine genome using Tophat2. Differentially expressed genes (DEG) between adipose tissues were detected by EdgeR. We identified 5797, 2156, and 5455 DEGs in the comparison between OI, OS, and IS respectively and also found 5657 DEGs in the comparison between the intramuscular and the combined omental and subcutaneous fats (C) (FDR<0.01). Depot specifically up- and down- regulated DEGs were 853 in S, 48 in I, and 979 in O. The numbers of DEGs and functional annotation studies suggested that I had the different genetic profile compared to other two adipose tissues. In I, DEGs involved in the developmental process (eg. EGR2, FAS, and KLF7) were up-regulated and those in the immune system process were down-regulated. Many DEGs from the adipose tissues were enriched in the various GO terms of developmental process and KEGG pathway analysis showed that the ECM-receptor interaction was one of commonly enriched pathways in all of the 3 adipose tissues and also functioned as a sub-pathway of other enriched pathways. However, genes involved in the ECM-receptor interaction were differentially regulated depending on the depots. Collagens, main ECM constituents, were significantly up-regulated in S and integrins, transmembrane receptors, were up-regulated in I. Different laminins were up-regulated in the different depots. This comparative transcriptome analysis of three adipose tissues suggested that the interactions between ECM components and transmembrane receptors of fat cells depend on the depot specific adipogenesis.

Differential expression of genes associated with lipid metabolism in longissimus dorsi of Korean bulls and steers.

The objective of this study was to compare expression of genes associated with lipid deposition and removal between bulls and steers in the longissimus dorsi muscle (LM) tissue of Korean cattle. Castration increased the expression of lipid uptake lipoprotein lipase, fatty acid translocase, and fatty acid transport protein 1 in LM. Castration increased lipogenic gene expression of both acetyl-CoA carboxylase and fatty acid synthase. In contrast, castration downregulated lipolytic gene expression of both adipose triglyceride lipase (ATGL) and monoglyceride lipase. Steers showed higher expression levels of insulin signaling phospho-v-akt murine thymoma viral oncogene homolog 1 than bulls but lower protein levels of nuclear Forkhead box O 1 (FoxO1) than bulls, suggesting that increased insulin signaling following castration decreases nuclear FoxO1 levels, leading to downregulation of ATGL gene expression. These findings suggest that castration contributes to increases in lipid uptake and lipogenesis and a decrease in lipolysis, resulting in improved marbling.