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Yoshinobu Uemoto

Section

Graduate School of Agricultural Science

Job title

Professor

Degree

博士（農学）（東北大学）
修士（農学）（東北大学）

researchmap

https://researchmap.jp/uemoto318

J-GLOBAL ID

201301097219723924

Research History 4

2017/04 - Present

東北大学大学院農学研究科
2008/04 - 2017/03

National Livestock Breeding Center, Incorporated Administrative Agency
2011/05 - 2013/03

エディンバラ大学ロスリン研究所
2005/04 - 2008/03

Ministry of Agriculture, Forestry and Fisheries

Committee Memberships 3

BMC Genomics, Associate Editor

2021/01 - Present
Animal Science Journal, Associate Editor

2020/04 - Present
BMC Genetics, Associate Editor

2013/09 - 2020/12

Professional Memberships 4

東北畜産学会

2020/04 - Present
THE JAPANESE SOCIETY OF SWINE SCIENCE

2008/04 - Present
JAPANESE SOCIETY OF ANIMAL BREEDING AND GENETICS

2008/04 - Present
JAPANESE SOCIETY OF ANIMAL SCIENCE

2008/04 - Present

Research Interests 6

生物統計学
統計遺伝学
GWAS
QTL解析
量的遺伝学
動物遺伝育種学

Research Areas 1

Life sciences / Animal production science /

Awards 7

日本畜産学会賞（第118号）

2024/09　日本畜産学会　持続可能な畜産を目指した家畜育種の応用に関する研究
第9回伊藤記念財団賞

2024/06　伊藤記念財団　肉用家畜における高密度SNP情報の肉質改良への応用に関する研究
2023年度日本畜産学会優秀論文賞（第97号）

2023/09　日本畜産学会　Estimation of genetic parameters for farrowing traits in purebred Landrace and Large White pigs. Animal Science Journal, 90(1): 23-28
Animal Highlighted Article - November 2021 & 2021 Editor’s Choice Article Collection in Animal.

2021/12　Estimation of genetic parameter for feed efficiency and resilience traits in three pig breeds.
2021年度日本畜産学会優秀論文賞（第80号）

2021/03　日本畜産学会　Genome-wide association study for carcass traits, fatty acid composition, chemical composition, sugar, and the effect of their candidate genes in Japanese Black cattle. Animal Science Journal (2017) 88:33-44.
2017年度日本畜産学会優秀論文賞（第52号）

2017/03　日本畜産学会　Genome Wide association study for fatty acid composition in Japanese Black cattle. Animal Science Journal. 84(10):675-82. 2013.
日本畜産学会奨励賞（第89号）

2011/03　日本畜産学会　ブタ系統造成集団における産肉、肉質形質のQTL解析に関する研究

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Papers 103

Development of prediction equations for immunoglobulin A, immunoglobulin G, and immunoglobulin M concentrations in mature milk from Holstein cows using milk infrared spectral data. International-journal Peer-reviewed

Yuri Satake, Teppei Katsura, Tao Zhuang, Megumi Urakawa, Yugo Mineshima, Toshimi Baba, Gaku Yoshida, Haruki Kitazawa, Hitoshi Shirakawa, Takehiko Nakamura, Tomonori Nochi, Yoshifumi Sakai, Masahiro Satoh, Satoshi Haga, Hisashi Aso, Yoshinobu Uemoto

Journal of dairy science　108　(7)　7354-7369　2025/07

DOI： 10.3168/jds.2024-25991 　

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Immunoglobulins in ruminant mammary secretions play a central role in active immune protection of the mammary gland against infections. Ig are present in both colostrum and milk from cows, and interest in routinely quantifying the Ig content in milk for herd management and genetic improvement of disease resistance is increasing. Therefore, the objective of this study was to develop a prediction equation for Ig (IgA, IgG, and IgM) concentrations in milk from Holstein cows using milk Fourier-transform infrared (FTIR) spectral data and to evaluate the practical feasibility of the predicted Ig concentration in milk. First, we developed prediction equations for Ig concentrations in milk using 1,633 milk samples comprising both Ig concentrations in milk and milk FTIR spectral data. We then evaluated the predictive accuracy of the developed equations using 3 different factors: derivative preprocessing, spectral wavenumber ranges, and regression models. Our results demonstrated that the prediction equations based on the partial least squares regression and 4 machine learning regression models exhibited the highest predictive accuracy for all traits under the conditions of nonderivative preprocessing and spectral wavenumber range related to milk quality traits. Their predictive accuracies were moderate, with the R2 ranging from 0.41 to 0.42, 0.50 to 0.52, and 0.38 to 0.39 for IgA, IgG, and IgM, respectively. Second, we evaluated the practical applicability of the predicted Ig concentration by comparing the trends of both the observed and predicted Ig concentrations with respect to several environmental effects. A linear model was applied using the observed and predicted Ig concentrations, and the LSM of the levels for each environmental effect (lactation stage, SCS, parity, and milk yield) was estimated. Our results showed that the estimated environmental effects of the observed and predicted values showed similar trends for all traits. These results indicate that it is possible to estimate environmental effects using the predicted values obtained via the prediction equation with moderate accuracy. Although the predictive accuracy obtained here may be effective for estimating effects at the herd level, further improvement in predictive accuracy is necessary for estimating effects at the cow level.
Dynamics of Blood Taurine Concentration and its Correlation with Nutritional and Physiological Status during the Fattening Period of Japanese Black Cattle Peer-reviewed

Shuntaro Takai, Huseong Lee, Minji Kim, Shinichiro Torii, Nishihara Koki, Joonpyo Oh, Tatsunori Masaki, Kentaro Ikuta, Eiji Iwamoto, Kota Masuda, Yoshinobu Uemoto, Fuminori Terada, Satoshi Haga, Sanggun Roh

Journal of Animal Science　102　skae347　2024/11/13
Publisher: Oxford University Press (OUP)
DOI： 10.1093/jas/skae347 　

ISSN： 0021-8812

eISSN： 1525-3163

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Abstract Taurine, biosynthesized from methionine or cysteine in the liver, plays a crucial regulatory role in bile acid conjugation, antioxidant effects, and glucose and cholesterol metabolism. This may influence the metabolic changes associated with fat accumulation in beef cattle. However, the physiological role of taurine in this species has not been fully elucidated. In this study, we explored the physiological role of taurine in Japanese Black steers (Bos taurus) in different phases during the fattening period. To examine the correlation among plasma taurine concentrations, various physiological parameters, and genes related to taurine synthesis in the liver, we used biopsied liver tissues, blood samples, and rumen fluids collected from 21 steers at three different stages, i.e., early (T1; 13 months of age), middle (T2; 20 months of age), and late (T3; 28 months of age) phases. Additionally, to investigate the regulatory mechanisms underlying the expression profile of taurine synthesis genes, primary bovine hepatocytes obtained from 4-week-old Holstein calves were treated with palmitate, oleate, acetate, propionate, or β-hydroxybutyrate (BHBA). Plasma taurine and cholesterol concentrations significantly (P &lt; 0.001) increased in the T2 phase, which is potentially attributable to increased energy intake and assimilation induced by increased intake of concentrated feed. Cysteine sulfinic acid decarboxylase (CSAD) expression significantly increased (P &lt; 0.01) in T2 than in other phases. The expression levels of cysteine dioxygenase type 1 (CDO1) and cholesterol 7 alpha-hydroxylase (CYP7A1) were significantly higher (P &lt; 0.001) in T2 than in T3; moreover, the CDO1/glutamate-cysteine ligase catalytic subunit (GCLC) ratio was higher (P &lt; 0.05) in T2 than in T1. Plasma taurine concentrations were positively correlated with plasma methionine (r = 0.51; P &lt; 0.05) and total cholesterol (r = 0.56; P &lt; 0.05) concentrations at T2. Relative CDO1 mRNA expression was upregulated in cultured bovine hepatocytes treated with oleate and propionate, whereas it was downregulated upon acetate treatment. These findings indicate that the increase in plasma taurine concentrations in the T2 phase is associated with changes in lipid and methionine metabolism in Japanese Black steers.
Elevated levels of cyclophilin A secreted in milk during bovine mastitis Peer-reviewed

Satoru Takanashi, Kozue Yoshimura, Yuma Endo, Megumi Urakawa, Hidetoshi Sato, Tao Zhuang, Tomohito Hayashi, Yoshio Kiku, Yuya Nagasawa, Haruki Kitazawa, Michael T. Rose, Yoshinobu Uemoto, Kouichi Watanabe, Tomonori Nochi, Hisashi Aso

Journal of Dairy Science　2024/10
Publisher: American Dairy Science Association
DOI： 10.3168/jds.2024-24715 　

ISSN： 0022-0302
Incorporating body measurement traits to increase genetic gain of feed efficiency and carcass traits in Japanese Black steers. International-journal Peer-reviewed

Nodoka Kemmotsu, Masayuki Takeda, Atsushi Ogino, Toshio Watanabe, Kazuhito Kurogi, Masahiro Satoh, Yoshinobu Uemoto

Journal of animal science　2024/06/29

DOI： 10.1093/jas/skae176 　

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The objective of the present study was to comprehensively evaluate whether body measurement traits, including BW and body size, could be used as indicators of genetic selection for feed efficiency and carcass traits in Japanese Black steers. First, we estimated the genetic parameters for body measurements, feed efficiency, and carcass traits. Second, we estimated the correlated responses in feed efficiency and carcass traits when selection was applied to one or multiple body measurement traits. In total, 4,578 Japanese Black steers with phenotypic values of residual feed intake (RFI) and residual BW gain (RG) as feed efficiency traits and carcass weight (CWT) and beef marbling standard (BMS) as carcass traits were used. Eleven body measurement traits were measured at the start and finish of the fattening periods (BMT1 and BMT2, respectively), and their growth during the fattening period (BMT3) was used for genetic analyses. The results of genetic parameters showed that the heritability estimates were low to moderate (0.10-0.66), and the genetic correlations among body measurement traits were also estimated to be positively moderate to high in each measuring point (0.23-0.99). The genetic correlations of body measurement traits with RFI and BMS were estimated to be low (-0.14-0.30 and -0.17-0.35, respectively), but those with CWT were positively low to high (0.12-0.97). The genetic correlation estimates between BMT3 and RG were moderate to high (0.38-0.78). Second, correlated responses were estimated under positive selection for body measurement traits. Positive selection for BMT2 and BMT3 increased CWT and RG; however, positive selection for body measurement traits resulted in no change in RFI and BMS. Favorable directions of genetic gains, which were positive for RG, CWT, and BMS and negative for RFI, were obtained by selection indices, including multiple traits in BMT1. Our results suggest that using only one body measurement trait as an indicator of genetic selection for RFI is difficult. However, body measurement traits can be indirect indicators of improved RG. Our results also suggest that genetic improvement of both RFI and RG without reducing CWT and BMS could be achieved using selection indices that account for a balance of body conformation using multiple body measurement traits in Japanese Black cattle.
Estimation of genetic parameters for bull conception rate and its genetic correlations with semen production traits in Japanese Black bulls Peer-reviewed

Y. Uemoto, R. Nagai, M. Kinukawa, T. Watanabe, A. Ogino, K. Kurogi, M. Satoh

Animal　18　(5)　2024/05

DOI： 10.1016/j.animal.2024.101137 　

ISSN： 1751-7311

eISSN： 1751-732X
Assessing the impact of three feeding stages on rumen bacterial community and physiological characteristics of Japanese Black cattle International-journal Peer-reviewed

Huseong Lee, Minji Kim, Tatsunori Masaki, Kentaro Ikuta, Eiji Iwamoto, Koki Nishihara, Itoko Nonaka, Akane Ashihara, Youlchang Baek, Sungdae Lee, Yoshinobu Uemoto, Satoshi Haga, Fuminori Terada, Sanggun Roh

Scientific Reports　14　(1)　4923-4923　2024/02/28
Publisher: Springer Science and Business Media LLC
DOI： 10.1038/s41598-024-55539-y 　

eISSN： 2045-2322

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Abstract In Japan, Japanese Black cattle, known for their exceptional meat quality owing to their abundant intramuscular fat, undergo a unique three-stage feeding system with varying concentrate ratios. There is limited research on physiological and rumen microbial changes in Japanese Black cattle during these stages. Therefore, this study aimed to examine Japanese Black steers in these three stages: early (T1, 12–14 months), middle (T2, 15–22 months), and late (T3, 23–30 months). The rumen bacteria of 21 cattle per phase was analyzed using 16S rRNA gene sequencing. Rumen bacterial diversity was significantly higher in T1, with a distinct distribution, than in T2 and T3. Specific phyla and genera were exclusive to each stage, reflecting the shifts in feed composition. Certain genera dominated each stage: T1 had Flexilinea, Streptococcus, Butyrivibrio, Selenomonas, and Kandleria; T2 had Bifidobacterium, Shuttleworthia, and Sharpea; and T3 had Acetitomaculum, Mycoplasma, Atopobium, and Howardella. Correlation analysis revealed significant associations between certain microbial populations and physiological parameters. These findings indicate that changes in energy content and feed composition are associated with physiological and ruminal alterations. This study may guide strategies to improve rumen health and productivity in Japanese Black cattle by modifying diets to specific fattening stages.
Exploring indicators of genetic selection using the sniffer method to reduce methane emissions from Holstein cows. International-journal Peer-reviewed

Yoshinobu Uemoto, Tomohisa Tomaru, Masahiro Masuda, Kota Uchisawa, Kenji Hashiba, Yuki Nishikawa, Kohei Suzuki, Takatoshi Kojima, Tomoyuki Suzuki, Fuminori Terada

Animal bioscience　37　(2)　173-183　2024/02

DOI： 10.5713/ab.23.0120 　

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OBJECTIVE: This study aimed to evaluate whether the methane (CH4) to carbon dioxide (CO2) ratio (CH4/CO2) and methane-related traits obtained by the sniffer method can be used as indicators for genetic selection of Holstein cows with lower CH4 emissions. METHODS: The sniffer method was used to simultaneously measure the concentrations of CH4 and CO2 during milking in each milking box of the automatic milking system to obtain CH4/CO2. Methane-related traits, which included CH4 emissions, CH4 per energy-corrected milk, methane conversion factor (MCF), and residual CH4, were calculated. First, we investigated the impact of the model with and without body weight (BW) on the lactation stage and parity for predicting methane-related traits using a first on-farm dataset (Farm 1; 400 records for 74 Holstein cows). Second, we estimated the genetic parameters for CH4/CO2 and methane-related traits using a second on-farm dataset (Farm 2; 520 records for 182 Holstein cows). Third, we compared the repeatability and environmental effects on these traits in both farm datasets. RESULTS: The data from Farm 1 revealed that MCF can be reliably evaluated during the lactation stage and parity, even when BW is excluded from the model. Farm 2 data revealed low heritability and moderate repeatability for CH4/CO2 (0.12 and 0.46, respectively) and MCF (0.13 and 0.38, respectively). In addition, the estimated genetic correlation of milk yield with CH4/CO2 was low (0.07) and that with MCF was moderate (-0.53). The on-farm data indicated that CH4/CO2 and MCF could be evaluated consistently during the lactation stage and parity with moderate repeatability on both farms. CONCLUSION: This study demonstrated the on-farm applicability of the sniffer method for selecting cows with low CH4 emissions.
Effect of residual methane emission on physiological characteristics and carcass performance in Japanese Black cattle Peer-reviewed

Minji Kim, Tatsunori Masaki, Kohei Oikawa, Akane Ashihara, Kentaro Ikuta, Eiji Iwamoto, Huseong Lee, Satoshi Haga, Yoshinobu Uemoto, Sanggun Roh, Fuminori Terada, Itoko Nonaka

Animal Science Journal　95　(1)　2024/01
Publisher: Wiley
DOI： 10.1111/asj.13954 　

ISSN： 1344-3941

eISSN： 1740-0929

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Abstract This study investigated the physiological characteristics and carcass performance associated with residual methane emissions (RME), and the effects of bull differences on CH₄‐related traits in Japanese Black cattle. Enteric methane (CH₄) emissions from 156 Japanese Black cattle (111 heifers and 45 steers) were measured during early fattening using the sniffer method. Various physiological parameters were investigated to clarify the physiological traits between the high, middle, and low RME groups. CH₄‐related traits were examined to determine whether bull differences affected progeny CH₄ emissions. Ruminal butyrate and NH₃ concentrations were significantly higher in the high‐RME group than in the low‐RME group, whereas the propionate content was significantly higher in the low‐RME group. Blood urea nitrogen, β‐hydroxybutyric acid, and insulin concentrations were significantly higher, and blood amino acids were lower in the high‐RME group than in the other groups. No significant differences were observed in the carcass traits and beef fat composition between RME groups. CH₄‐related traits were significantly different among bull herds. Our results show that CH₄‐related traits are heritable, wherein bull differences affect progeny CH₄ production capability, and that the above‐mentioned rumen fermentations and blood metabolites could be used to evaluate enteric methanogenesis in Japanese Black cattle.
Metabolomics and Transcriptomics Analyses of Curcumin Alleviation of Ochratoxin A-Induced Hepatotoxicity. International-journal Peer-reviewed

Peng Hui, Xianrui Zheng, Jiao Dong, Fan Lu, Chao Xu, Huan Qu, Xiaoyang Zhu, Yoshinobu Uemoto, Xiaoyang Lv, Zongjun Yin, Wei Sun, Wenbin Bao, Haifei Wang

International journal of molecular sciences　25　(1)　2023/12/21

DOI： 10.3390/ijms25010168 　

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Ochratoxin A (OTA) is one of the mycotoxins that poses a serious threat to human and animal health. Curcumin (CUR) is a major bioactive component of turmeric that provides multiple health benefits. CUR can reduce the toxicities induced by mycotoxins, but the underlying molecular mechanisms remain largely unknown. To explore the effects of CUR on OTA toxicity and identify the key regulators and metabolites involved in the biological processes, we performed metabolomic and transcriptomic analyses of livers from OTA-exposed mice. We found that CUR can alleviate the toxic effects of OTA on body growth and liver functions. In addition, CUR supplementation significantly affects the expressions of 1584 genes and 97 metabolites. Integrated analyses of transcriptomic and metabolomic data showed that the pathways including Arachidonic acid metabolism, Purine metabolism, and Cholesterol metabolism were significantly enriched. Pantothenic acid (PA) was identified as a key metabolite, the exogenous supplementation of which was observed to significantly alleviate the OTA-induced accumulation of reactive oxygen species and cell apoptosis. Further mechanistical analyses revealed that PA can downregulate the expression level of proapoptotic protein BAX, enhance the expression level of apoptosis inhibitory protein BCL2, and decrease the level of phosphorylated extracellular signal-regulated kinase 1/2 (pERK1/2). This study demonstrated that CUR can alleviate the adverse effects of OTA by influencing the transcriptomic and metabolomic profiles of livers, which may contribute to the application of CUR in food and feed products for the prevention of OTA toxicity.
Genetic aspects of immunoglobulins and cyclophilin A in milk as potential indicators of mastitis resistance in Holstein cows Peer-reviewed

Yoshinobu Uemoto, Teppei Katsura, Yuma Endo, Koutaro Tanaka, Tao Zhuang, Megumi Urakawa, Toshimi Baba, Gaku Yoshida, Haifei Wang, Haruki Kitazawa, Hitoshi Shirakawa, Takehiko Nakamura, Tomonori Nochi, Hisashi Aso

Journal of Dairy Science　2023/10
Publisher: American Dairy Science Association
DOI： 10.3168/jds.2022-23075 　

ISSN： 0022-0302
気象観測記録による豚舎外気温の推定とその精度 Peer-reviewed

佐藤正寛, 日下和樹, 小川伸一郎, 上本吉伸

日本畜産学会報　94　(3)　277-282　2023/08/25

DOI： 10.2508/chikusan.94.277 　

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複数の気象観測所における気温データから豚舎外気温を推定するための適切な方法を考案することを目的とした。選定した９地点の気象庁気象観測所における気温データ（日平均気温、日最高気温、日最低気温）をマスクし、その周辺の近隣１～８観測所における気温データを用いて、逆距離加重法によってマスクした気温データを推定した。また、日最高気温と日最低気温から日較差を推定した。その結果、日平均気温および日最高気温は、近隣の３つの観測所から推定することで精度の高い推定値を得られることが明らかとなった。１年を通した推定値の経時的変化では、平均誤差の絶対値および二乗平均平方根誤差はいずれの気温も６月から10月にかけて小さく、相関数は９月を中心に高くなる傾向にあった。以上の結果から、本研究に用いた気温における推定精度は日平均気温または日最高気温が高く、特に暑熱の影響を考慮する場合には有効であると考えられた
Physiological roles and regulation of hepatic angiopoietin-like protein 3 in Japanese Black cattle (Bos taurus) during the fattening period. International-journal Peer-reviewed

Rika Shikida, Minji Kim, Makoto Futohashi, Koki Nishihara, Huseong Lee, Yutaka Suzuki, Yeolchang Baek, Tatsunori Masaki, Kentaro Ikuta, Eiji Iwamoto, Yoshinobu Uemoto, Satoshi Haga, Fuminori Terada, Sanggun Roh

Journal of animal science　2023/06/15

DOI： 10.1093/jas/skad198 　

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Angiopoietin-like protein 3 (ANGPTL3) is expressed predominantly in the liver and plays a major role in regulating the circulating triglyceride and lipoprotein fraction concentrations by inhibiting lipoprotein lipase (LPL) activity. Given these physiological roles, ANGPTL3 may play an important role in metabolic changes related to fat accumulation during the fattening period in Japanese Black. This study aimed to reveal the physiological roles of hepatic ANGPTL3 in Japanese Black steers (Bos taurus) during the fattening period and investigate the regulatory effects of hepatic ANGPTL3. To investigate the gene expression and protein localization of ANGPTL3, 18 tissue samples were collected from tree male Holstein bull calves aged 7 weeks. Biopsied liver tissues and blood samples were collected from 21 Japanese Black steers during the early (T1; 13 months of age), middle (T2; 20 months), and late fattening phases (T3; 28 months). Relative mRNA expression, blood metabolite concentrations, hormone concentrations, growth, and carcass traits were analyzed. To identify the regulatory factors of hepatic ANGPTL3, primary bovine hepatocytes collected by 2 Holstein calves aged 7 weeks were incubated with insulin, palmitate, oleate, propionate, acetate, or beta-hydroxybutyric acid (BHBA). The ANGPTL3 gene was most highly expressed in the liver, with minor expression in the renal cortex, lungs, reticulum, and jejunum in Holstein bull calves. In Japanese Black steers, relative ANGPTL3 mRNA expressions were less as fattening progressed, and blood triglyceride, total cholesterol, and non-esterified fatty acid (NEFA) concentrations increased. Relative ANGPTL8 and Liver X receptor alpha (LXRα) mRNA expressions decreased in late and middle fattening phases, respectively. Furthermore, relative ANGTPL3 mRNA expression was positively correlated with ANGPTL8 (r = 0.650; P < 0.01) and ANGPTL4 (r = 0.540; P < 0.05) in T3 and T1, respectively, and LXRα showed no correlation with ANGPTL3. Relative ANGTPL3 mRNA expression was negatively correlated with total cholesterol (r = -0.434; P < 0.05) and triglyceride (r = -0.645; P < 0.01) concentrations in T3 and T1, respectively; There was no significant correlation between ANGTPL3 and carcass traits. Relative ANGTPL3 mRNA expression in cultured bovine hepatocytes was downregulated in oleate treatment. Together, these findings suggest that ANGPTL3 downregulation in late fattening phases is associated with the changes in lipid metabolism.
黒毛和種雌牛の採卵性形質と体型審査形質との遺伝的関連性 Peer-reviewed

造田篤, 香川梨乃, 大日方塁, 浦川真実, 大野喜雄, 小川伸一郎, 上本吉伸, 佐藤正寛

日本畜産学会報　94　(2)　185-191　2023/05/25

DOI： 10.2508/chikusan.94.185 　

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黒毛和種雌牛における採卵性形質と体型審査形質の遺伝相関を推定し、採卵性形質に関する育種価の多形質モデル評価における体型審査形質の有用性について検討した。2008年から2018年に雌牛1,532頭から収集された19,155回分の総回収卵数および高品質胚数の記録ならびに2014年以降に審査された雌牛372頭に関する体型審査記録を分析に用いた。遺伝率および遺伝相関の推定には単形質および２形質アニマルモデルREML法を用いた。体尺測定項目および審査形質のうち体積項目では中程度以上の、種牛性に関わる項目では低い遺伝率が推定された。いくつかの体型審査形質では、採卵性形質との間に好ましい遺伝相関が推定されたが標準誤差は大きかった。多形質モデル評価に関する数値シミュレーションから、採卵性形質の遺伝的改良には、遺伝率が中程度以上かつ採卵性形質との遺伝相関の絶対値が大きい補助形質が有効であると推察された。
A potent allele marker related to low bull conception rate in Japanese Black bulls. International-journal Peer-reviewed

M Kinukawa, M Ito, Y Uemoto, A Ogino, S Haruta, K Kurogi, T Watanabe, S Sasaki, Y Naniwa, K Uchiyama, K Togashi

Animal : an international journal of animal bioscience　17　(5)　100804-100804　2023/05

DOI： 10.1016/j.animal.2023.100804 　

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Over the years, there has been considerable variation in the bull conception rate (BCR) of Japanese Black cattle; moreover, several Japanese Black bulls with a low BCR of ≤10% have been identified. However, the alleles responsible for the low BCR are not determined yet. Therefore, in this study, we aimed to identify single-nucleotide polymorphisms (SNPs) for predicting low BCR. To this end, the genome of Japanese Black bulls was comprehensively examined by a genome-wide association study with whole-exome sequencing (WES), and the effect of the identified marker regions on BCR was determined. The WES analysis of six sub-fertile bulls with a BCR of ≤10% and 73 normal bulls with a BCR of ≥40% identified a homozygous genotype for low BCR in Bos taurus autosome 5 in the region between 116.2 and 117.9 Mb. The g.116408653G > A SNP in this region had the most significant effect on the BCR (P-value = 1.0 × 10-23), and the GG (55.4 ± 11.2%) and AG (54.4 ± 9.4%) genotypes in the SNP had a higher phenotype than the AA (9.5 ± 6.1%) genotype for the BCR. The mixed model analysis revealed that g.116408653G > A was related to approximately 43% of the total genetic variance. In conclusion, the AA genotype of g.116408653G > A is a useful index for identifying sub-fertile Japanese Black bulls. Some positive and negative effects of SNP on the BCR were presumed to identify the causative mutations, which can help evaluate bull fertility.
Metabolomic and Proteomic Profiling of Porcine Intestinal Epithelial Cells Infected with Porcine Epidemic Diarrhea Virus. International-journal Peer-reviewed

Haifei Wang, Peng Hui, Yoshinobu Uemoto, Yueyun Ding, Zongjun Yin, Wenbin Bao

International journal of molecular sciences　24　(6)　2023/03/07

DOI： 10.3390/ijms24065071 　

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Porcine epidemic diarrhea virus (PEDV) infection results in severe epidemic diarrhea and the death of suckling pigs. Although new knowledge about the pathogenesis of PEDV has been improved, alterations in metabolic processes and the functional regulators involved in PEDV infection with host cells remain largely unknow. To identify cellular metabolites and proteins related to PEDV pathogenesis, we synergistically investigated the metabolome and proteome profiles of PEDV-infected porcine intestinal epithelial cells by liquid chromatography tandem mass spectrometry and isobaric tags for relative and absolute quantification techniques. We identified 522 differential metabolites in positive and negative ion modes and 295 differentially expressed proteins after PEDV infection. Pathways of cysteine and methionine metabolism, glycine, serine and threonine metabolism, and mineral absorption were significantly enriched by differential metabolites and differentially expressed proteins. The betaine-homocysteine S-methyltransferase (BHMT) was indicated as a potential regulator involved in these metabolic processes. We then knocked down the BHMT gene and observed that down-expression of BHMT obviously decreased copy numbers of PEDV and virus titers (p < 0.01). Our findings provide new insights into the metabolic and proteomic profiles in PEDV-infected host cells and contribute to our further understanding of PEDV pathogenesis.
Characteristics of Physiological Parameters of Japanese Black Calves Relate to Carcass Weight Peer-reviewed

Shotaro Arakawa, Minji Kim, Tatsuya Aonuma, Michihiro Takagi, Satoshi Watanabe, Huseong Lee, Koki Nishihara, Satoshi Haga, Yoshinobu Uemoto, Sanggun Roh

Animals　13　(3)　487-487　2023/01/31
Publisher: MDPI AG
DOI： 10.3390/ani13030487 　

eISSN： 2076-2615

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This study aimed to identify the growth performance and blood factors associated with carcass weight in Japanese Black calves based on 675 performance tests and field carcass records. We measured the body weight, withers height, and chest girth at the start of fattening age (approximately 8–10 months) and analyzed eight blood factors, including vitamins and metabolites. Single- and two-trait animal models were used to estimate the heritability and genetic correlations. The heritability estimates for growth performance were moderate to high (ranging from 0.48 to 0.74), and those for blood metabolites were low to moderate (ranging from 0.19 to 0.51). Estimates for genetic correlations of carcass or body weight with body weight, withers height, and chest girth were high (ranging from 0.42 to 0.80). The body weight and withers height at 8 months of age are possibly closely related to the final carcass weight. The blood metabolites associated with body weight were vitamin E in steers (castrated males) and β-carotene in heifers. Our findings indicate that body measurements and blood metabolites measured during the growing period could be used to determine the nutritional and physiological status of cattle as well as predict carcass weight.
Genome-wide detection of changes in allelic frequency in Landrace pigs selected for resistance to mycoplasma pneumonia of swine. International-journal Peer-reviewed

Yoshinobu Uemoto, Kasumi Ichinoseki, Toshimi Matsumoto, Nozomi Oka, Hironori Takamori, Hiroshi Kadowaki, Chihiro Shibata, Eisaku Suzuki, Toshihiro Okamura, Hisashi Aso, Haruki Kitazawa, Masahiro Satoh, Hirohide Uenishi, Keiichi Suzuki

Animal science journal = Nihon chikusan Gakkaiho　94　(1)　e13827　2023/01

DOI： 10.1111/asj.13827 　

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Closed-pig line breeding could change the genetic structure at a genome-wide scale because of the selection in a pig breeding population. We investigated the changes in population structure among generations at a genome-wide scale and the selected loci across the genome by comparing the observed and expected allele frequency changes in mycoplasma pneumonia of swine (MPS)-selected pigs. Eight hundred and seventy-four Landrace pigs, selected for MPS resistance without reducing average daily gain over five generations, had 37,299 single nucleotide polymorphisms (SNPs) and were used for genomic analyses. Regarding population structure, individuals in the first generation were the most widely distributed and then converged into a specific group, as they were selected over five generations. For allele frequency changes, 96 and 14 SNPs had higher allele frequency changes than the 99.9% and 99.99% thresholds of the expected changes, respectively. These SNPs were evenly spread across the genome, and a few of these selected regions overlapped with previously detected quantitative trait loci for MPS and immune-related traits. Our results indicated that the considerable changes in allele frequency were identified in many regions across the genome by closed-pig line breeding based on estimated breeding value.
Physiological responses and adaptations to high methane production in Japanese Black cattle Peer-reviewed

Minji Kim, Tatsunori Masaki, Kentaro Ikuta, Eiji Iwamoto, Koki Nishihara, Makoto Hirai, Yoshinobu Uemoto, Fuminori Terada, Sanggun Roh

Scientific Reports　12　(1)　11154　2022/12
Publisher: Springer Science and Business Media LLC
DOI： 10.1038/s41598-022-15146-1 　

eISSN： 2045-2322

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Abstract In this study, using enteric methane emissions, we investigated the metabolic characteristics of Japanese Black cattle. Their methane emissions were measured at early (age 13 months), middle (20 months), and late fattening phases (28 months). Cattle with the highest and lowest methane emissions were selected based on the residual methane emission values, and their liver transcriptome, blood metabolites, hormones, and rumen fermentation characteristics were analyzed. Blood β-hydroxybutyric acid and insulin levels were high, whereas blood amino acid levels were low in cattle with high methane emissions. Further, propionate and butyrate levels differed depending on the enteric methane emissions. Hepatic genes, such as SERPINI2, SLC7A5, ATP6, and RRAD, which were related to amino acid transport and glucose metabolism, were upregulated or downregulated during the late fattening phase. The above mentioned metabolites and liver transcriptomes could be used to evaluate enteric methanogenesis in Japanese Black cattle.
Genomic dissection of repeatability considering additive and non-additive genetic effects for semen production traits in beef and dairy bulls. International-journal Peer-reviewed

Rintaro Nagai, Masashi Kinukawa, Toshio Watanabe, Atsushi Ogino, Kazuhito Kurogi, Kazunori Adachi, Masahiro Satoh, Yoshinobu Uemoto

Journal of animal science　skac241　2022/07/21

DOI： 10.1093/jas/skac241 　

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The low heritability and moderate repeatability of semen production traits in beef and dairy bulls suggest that non-additive genetic effects, such as dominance and epistatic effects, play an important role in semen production and should therefore be considered in genetic improvement programs. In this study, the repeatability of semen production traits in Japanese Black bulls (JB) as beef bulls and Holstein bulls (HOL) as dairy bulls was evaluated by considering additive and non-additive genetic effects using the Illumina BovineSNP50 BeadChip. We also evaluated the advantage of using more complete models that include non-additive genetic effects by comparing the rank of genotyped animals and the phenotype prediction ability of each model. In total, 65,463 records for 615 genotyped JB and 48,653 records for 845 genotyped HOL were used to estimate additive and non-additive (dominance and epistatic) variance components for semen volume (VOL), sperm concentration (CON), sperm motility (MOT), MOT after freeze-thawing (aMOT), and sperm number (NUM). In the model including both additive and non-additive genetic effects, the broad-sense heritability (0.17-0.43) was more than twice as high as the narrow-sense heritability (0.04-0.11) for all traits and breeds, and the differences between the broad-sense heritability and repeatability were very small for VOL, NUM, and CON in both breeds. A large proportion of permanent environmental variance was explained by epistatic variance. The epistatic variance as a proportion of total phenotypic variance was 0.07-0.33 for all traits and breeds. In addition, heterozygosity showed significant positive relationships with NUM, MOT, and aMOT in JB and NUM in HOL, when the heterozygosity rate was included as a covariate. In a comparison of models, the inclusion of non-additive genetic effects resulted in a re-ranking of the top genotyped bulls for the additive effects. Adjusting for non-additive genetic effects could be expected to produce a more accurate breeding value, even if the models have similar fitting. However, including non-additive genetic effects did not improve the ability of any model to predict phenotypic values for any trait or breed compared with the predictive ability of a model that includes only additive effects. Consequently, although non-additive genetic effects, especially epistatic effects, play an important role in semen production traits, they do not improve prediction accuracy in beef and dairy bulls.
An attempt of using public ambient temperature data in swine genetic evaluation for litter-size traits at birth in japan Peer-reviewed

Hitomi Hara, Shinichiro Ogawa, Chika Ohnishi, Kazuo Ishii, Yoshinobu Uemoto, Masahiro Satoh

ANIMAL PRODUCTION SCIENCE　2022/05

DOI： 10.1071/AN21463 　

ISSN： 1836-0939

eISSN： 1836-5787
Genome-wide transcriptional profiling and functional analysis reveal miR-330-MAPK15 axis involving in cellular responses to deoxynivalenol exposure. International-journal Peer-reviewed

Haifei Wang, Yajing Zhou, Chao Xu, Yue Cao, Yeyi Xiao, Demin Cai, Yoshinobu Uemoto, Shenglong Wu, Wenbin Bao

Chemosphere　134199　2022/03/09

DOI： 10.1016/j.chemosphere.2022.134199 　

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Deoxynivalenol (DON) is one of the mycotoxins that is toxic to agricultural environment, which poses high risks to human and farm animal health. Noncoding RNAs have been shown to be crucial regulators of toxicological processes and as promising biomarkers for toxicity monitoring and prevention of mycotoxin contamination. Herein, we characterized genome-wide transcriptional profiling of porcine intestinal epithelial cells upon DON exposure and illustrated a subset of miRNAs and lncRNAs involved in the cellular processes by targeting genes associated with stress responses. A total of 110 differential expression miRNAs and 143 differential expression lncRNAs were identified between the DON exposure and control cell samples. Interactive network analysis showed that miR-330 was one hub noncoding RNA, expression of which was significantly increased upon DON exposure. Functional enrichment analysis indicated that the genes involved in the networks were mainly enriched in the terms of plasma membrane bounded cell projection assembly, mRNA processing, and regulation of mitochondrion organization. Further functional analysis revealed that high expression of miR-330 inhibits the reactive oxygen species production, cell apoptosis, and autophagic flux in cells upon DON exposure. Luciferase assay further indicated that miR-330 could directly target MAPK15. Knockdown of MAPK15 resulted in decreased reactive oxygen species level and cell apoptosis induced by DON, indicating the existence of miR-330-MAPK15 regulatory axis in regulating DON toxicity. Our work shed novel insights into the mode of action of DON at cellular level and indicated the potential of miR-330 as a biomarker for toxicity monitoring of DON contamination, which contributes to the development of effective biomonitoring and prevention strategies to reduce the toxicological effects of DON.
Changes in the liver transcriptome and physiological parameters of Japanese Black steers during the fattening period. International-journal Peer-reviewed

Minji Kim, Tatsunori Masaki, Kentaro Ikuta, Eiji Iwamoto, Yoshinobu Uemoto, Fuminori Terada, Sanggun Roh

Scientific reports　12　(1)　4029-4029　2022/03/07

DOI： 10.1038/s41598-022-08057-8 　

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We investigated the physiological changes during the fattening period and production characteristics in Japanese Black steers bred and raised using the typical feeding system in Japan. Here, 21 Japanese Black steers aged 12 months were used, with experimental period divided into early (12-14 months of age), middle (15-22 months), and late fattening phases (23-30 months). The liver transcriptome, blood metabolites, hormones, and rumen fermentation characteristics were analyzed. Blood triglyceride and non-esterified fatty acid concentrations increased, whereas blood ketone levels decreased, with fattening phases. Blood insulin increased with fattening phases and was positively correlated with carcass weight and marbling in late fattening phases. Rumen fermentation characteristics showed high propionate levels and low butyrate levels in late fattening phases, likely due to increased energy intake. Genes related to glucose metabolism, such as SESN3, INSR, LEPR, and FOXO3, were down-regulated in late fattening phases. Genes related to lipid metabolism, such as FABP4, were up-regulated, whereas FADS1 and FADS2 were down-regulated. These findings suggest that the physiological changes resulted from changes in the energy content and composition of diets. Liver metabolism changed with changes in fat metabolism. Insulin was strongly associated with physiological changes and productivity in Japanese Black cattle.
Genome-wide detection of non-additive quantitative trait loci for semen production traits in beef and dairy bulls. International-journal Peer-reviewed

R Nagai, M Kinukawa, T Watanabe, A Ogino, K Kurogi, K Adachi, M Satoh, Y Uemoto

Animal : an international journal of animal bioscience　16　(3)　100472　2022/02/23

DOI： 10.1016/j.animal.2022.100472 　

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Semen production traits are important aspects of bull fertility, because semen quantity leads to direct profits for artificial insemination centres, and semen quality is associated with the probability of achieving a pregnancy. Most genome-wide association studies (GWASs) for semen production traits have assumed that each quantitative trait locus (QTL) has an additive effect. However, GWASs that account for non-additive effects are also important in fitness traits, such as bull fertility. Here, we performed a GWAS using models that accounted for additive and non-additive effects to evaluate the importance of non-additive effects on five semen production traits in beef and dairy bulls. A total of 65 463 records for 615 Japanese Black bulls (JB) and 50 734 records for 873 Holstein bulls (HOL), which were previously genotyped using the Illumina BovineSNP50 BeadChip, were used to estimate genetic parameters and perform GWAS. The heritability estimates were low (ranged from 0.11 to 0.23), and the repeatability estimates were low to moderate (ranged from 0.28 to 0.45) in both breeds. The estimated repeatability was approximately twice as high as the estimated heritability for all traits. In this study, only one significant region with an additive effect was detected in each breed, but multiple significant regions with non-additive effects were detected for each breed. In particular, the region at approximately 64 Mbp on Bos taurus autosome 17 had the highest significant non-additive effect on four semen production traits in HOL. The rs41843851 single nucleotide polymorphism (SNP) in the region had a much lower P-value for the non-additive effect (P-value = 1.1 × 10-31) than for the additive effect (P-value = 1.1 × 10-8) in sperm motility. The AA and AB genotypes on the SNP had a higher phenotype than the BB genotype in HOL, and there was no bull with the BB genotype in JB. Our results showed that non-additive QTLs affect semen production traits, and a novel QTL accounting for non-additive effects could be detected by GWAS. This study provides new insights into non-additive QTLs that affect fitness traits, such as semen production traits in beef and dairy bulls.
Ultra‐rapid real‐time polymerase chain reaction assay for genotyping of the NT5E gene in Japanese black beef using a mobile PCR device, PCR 1100 Peer-reviewed

Tomohiko Komatsu, Masataka Komatsu, Hiroaki Nakajima, Yoshinobu Uemoto

Animal Science Journal　93　(1)　e13763　2022/01
Publisher: Wiley
DOI： 10.1111/asj.13763 　

ISSN： 1344-3941

eISSN： 1740-0929
Estimates of genetic parameters for adenosine triphosphate‐related compounds at different aging periods and NT5E genotypes in Japanese Black beef Peer-reviewed

Tomohiko Komatsu, Tsuyoshi Toita, Yoshinobu Uemoto

Animal Science Journal　93　(1)　e13748　2022/01
Publisher: Wiley
DOI： 10.1111/asj.13748 　

ISSN： 1344-3941

eISSN： 1740-0929
Genetic relationship between superovulatory response traits and carcass traits in Japanese Black cattle. International-journal Peer-reviewed

Atsushi Zoda, Rino Kagawa, Rui Obinata, Manami Urakawa, Yoshio Oono, Shinichiro Ogawa, Yoshinobu Uemoto, Masahiro Satoh

Animal science journal = Nihon chikusan Gakkaiho　93　(1)　e13731　2022/01

DOI： 10.1111/asj.13731 　

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We estimated the genetic correlations between superovulatory response traits and carcass traits in Japanese Black cattle. As regards the superovulatory response traits in cows, we analyzed the phenotypic records of the total number of embryos and oocytes (TNE) and the number of good embryos (NGE) collected from 1532 donors between 2008 and 2018. As regards the carcass traits in fattened animals, we analyzed the phenotypic records for cold carcass weight, rib eye area, rib thickness, subcutaneous fat thickness, estimated yield percent, and marbling score for 1448 progenies derived from 596 donors and slaughtered between 2004 and 2020. Variance components were estimated using single-trait and two-trait animal models and the restricted maximum likelihood approach. The estimated genetic correlations with the carcass traits ranged from -0.05 to 0.04 for TNE and from -0.14 to 0.04 for NGE, and their standard errors ranged from 0.10 to 0.14. These results imply that the genetic relationship between the superovulatory response traits in Japanese Black donor cows and the carcass traits in their fattened progenies was weak to negligible. Therefore, we concluded that selecting donors with superior genetic ability for superovulatory responses would not have antagonistic effects on carcass performance in their fattened progenies.
Genetic relationships of feed efficiency and growth traits with carcass traits in Japanese Shorthorn cattle. International-journal Peer-reviewed

Chiharu Shinoda, Jumpei Yasuda, Kousuke Yamagata, Keiichi Suzuki, Masahiro Satoh, Sanggun Roh, Yoshinobu Uemoto

Animal science journal = Nihon chikusan Gakkaiho　93　(1)　e13691　2022/01

DOI： 10.1111/asj.13691 　

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In this study, we examined genetic parameters for feed efficiency, growth, and carcass traits in Japanese Shorthorn cattle, based on 714 performance tests and 15,790 field carcass records. Feed efficiency traits, including residual feed intake (RFI) and residual body weight gain (RG), were calculated. Single-trait and two-trait animal models were used to estimate heritability and genetic correlations. Heritability estimates for feed efficiency traits were found to be low to moderate (ranging from 0.03 to 0.36); notably, heritability was moderate for RG and low for RFI. Estimates for genetic correlations between feed efficiency traits and average daily gain (DG) were favorably moderate to high (absolute values of 0.43-0.85), and those with daily feed intake were low (absolute values of 0.00-0.32). We also estimated a high genetic correlation between RG and DG. The backfat thickness (BF) of bull calves showed favorable or no genetic correlation estimates with feed efficiency and growth traits, whereas RG and BF showed favorable or no genetic correlation estimates with carcass traits. Our findings indicate that genetic improvements in both feed utilization ability and carcass traits could be achieved by utilizing RG and BF in Japanese Shorthorn cattle.
Genome-wide association studies for production, respiratory disease, and immune-related traits in Landrace pigs Peer-reviewed

Yoshinobu Uemoto, Kasumi Ichinoseki, Toshimi Matsumoto, Nozomi Oka, Hironori Takamori, Hiroshi Kadowaki, Chihiro Kojima-Shibata, Eisaku Suzuki, Toshihiro Okamura, Hisashi Aso, Haruki Kitazawa, Masahiro Satoh, Hirohide Uenishi, Keiichi Suzuki

Scientific Reports　11　(1)　15823　2021/12
Publisher: Springer Science and Business Media LLC
DOI： 10.1038/s41598-021-95339-2 　

eISSN： 2045-2322

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<title>Abstract</title>Identification of a quantitative trait locus (QTL) related to a chronic respiratory disease such as Mycoplasmal pneumonia of swine (MPS) and immune-related traits is important for the genetic improvement of disease resistance in pigs. The objective of this study was to detect a novel QTL for a total of 22 production, respiratory disease, and immune-related traits in Landrace pigs. A total of 874 Landrace purebred pigs, which were selected based on MPS resistance, were genotyped using the Illumina PorcineSNP60 BeadChip. We performed single nucleotide polymorphism (SNP)-based and haplotype-based genome-wide association studies (GWAS) to detect a novel QTL and to evaluate the possibility of a pleiotropic QTL for these traits. SNP-based GWAS detected a total of six significant regions in backfat thickness, ratio of granular leucocytes to lymphatic cells, plasma concentration of cortisol at different ages, and complement alternative pathway activity in serum. The significant region detected by haplotype-based GWAS was overlapped across the region detected by SNP-based GWAS. Most of these detected QTL regions were novel regions with some candidate genes located in them. With regard to a pleiotropic QTL among traits, only three of these detected QTL regions overlapped among traits, and many detected regions independently affected the traits.
Exploring the size of reference population for expected accuracy of genomic prediction using simulated and real data in Japanese Black cattle. International-journal Peer-reviewed

Masayuki Takeda, Keiichi Inoue, Hidemi Oyama, Katsuo Uchiyama, Kanako Yoshinari, Nanae Sasago, Takatoshi Kojima, Masashi Kashima, Hiromi Suzuki, Takehiro Kamata, Masahiro Kumagai, Wataru Takasugi, Tatsuya Aonuma, Yuusuke Soma, Sachi Konno, Takaaki Saito, Mana Ishida, Eiji Muraki, Yoshinobu Inoue, Megumi Takayama, Shota Nariai, Ryoya Hideshima, Ryoichi Nakamura, Sayuri Nishikawa, Hiroshi Kobayashi, Eri Shibata, Koji Yamamoto, Kenichi Yoshimura, Hironori Matsuda, Tetsuro Inoue, Atsumi Fujita, Shohei Terayama, Kazuya Inoue, Sayuri Morita, Ryotaro Nakashima, Ryohei Suezawa, Takeshi Hanamure, Atsushi Zoda, Yoshinobu Uemoto

BMC genomics　22　(1)　799　2021/11/06

DOI： 10.1186/s12864-021-08121-z 　

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BACKGROUND: Size of reference population is a crucial factor affecting the accuracy of prediction of the genomic estimated breeding value (GEBV). There are few studies in beef cattle that have compared accuracies achieved using real data to that achieved with simulated data and deterministic predictions. Thus, extent to which traits of interest affect accuracy of genomic prediction in Japanese Black cattle remains obscure. This study aimed to explore the size of reference population for expected accuracy of genomic prediction for simulated and carcass traits in Japanese Black cattle using a large amount of samples. RESULTS: A simulation analysis showed that heritability and size of reference population substantially impacted the accuracy of GEBV, whereas the number of quantitative trait loci did not. The estimated numbers of independent chromosome segments (Me) and the related weighting factor (w) derived from simulation results and a maximum likelihood (ML) approach were 1900-3900 and 1, respectively. The expected accuracy for trait with heritability of 0.1-0.5 fitted well with empirical values when the reference population comprised > 5000 animals. The heritability for carcass traits was estimated to be 0.29-0.41 and the accuracy of GEBVs was relatively consistent with simulation results. When the reference population comprised 7000-11,000 animals, the accuracy of GEBV for carcass traits can range 0.73-0.79, which is comparable to estimated breeding value obtained in the progeny test. CONCLUSION: Our simulation analysis demonstrated that the expected accuracy of GEBV for a polygenic trait with low-to-moderate heritability could be practical in Japanese Black cattle population. For carcass traits, a total of 7000-11,000 animals can be a sufficient size of reference population for genomic prediction.
Estimation of genetic parameter for feed efficiency and resilience traits in three pig breeds. International-journal Peer-reviewed

C Homma, K Hirose, T Ito, M Kamikawa, S Toma, S Nikaido, M Satoh, Y Uemoto

Animal : an international journal of animal bioscience　15　(11)　100384　2021/11

DOI： 10.1016/j.animal.2021.100384 　

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Recently, automatic feeders have become popular for collecting daily feed intake data in the pig industry, making it possible to evaluate genetic effects on feed efficiency and resilience traits, expressed as day-to-day fluctuations in feeding records. This study aimed to understand the influence of genetic factors on feed efficiency traits, including residual intake and BW gain (RIG), and resilience traits, as well as to compare the differences in genetic parameter estimates among three purebred pig breeds. A total of 6 103 pigs from three breeds (Large White: 1 193 pigs, Landrace: 3 010 pigs, and Duroc: 1 900 pigs) were raised in a specific pathogen-free environment. The growth and feed intake records during the testing period were obtained using automatic feeders, and the average daily gain (ADG) and average feed intake (AFI) were calculated. Feed conversion ratio (FCR), residual feed intake (RFI), residual gain, and RIG were calculated as feed efficiency traits, and the log-transformed variance of deviation for the daily feed intake (LnVar_FI), daily occupation time (LnVar_OC), and the daily number of visits to the feeder (LnVar_VT) was calculated as resilience traits. After estimating the genetic parameters for each breed, a meta-analysis was performed to obtain the weighted mean of heritability estimates (hm2) and genetic correlation estimates (GCm) for the three breeds. The hm2 were moderate and ranged from 0.31 to 0.39 for feed efficiency traits and 0.31 to 0.40 for resilience traits, and there were no significant differences in heritability estimates among the three breeds except for AFI, RFI, and RIG. For feed efficiency traits, the FCR and RIG showed favourably moderate GCm with AFI (0.29 and -0.33, respectively) and ADG (-0.39 and 0.31, respectively). For resilience traits, the LnVar_FI and LnVar_VT showed favourably low to moderate GCm with FCR (0.33 and 0.28, respectively) and RIG (-0.37 and 0.28, respectively), and there were no genetic relationships of LnVar_OC with FCR and RIG (the absolute value of GCm was 0.01). There was no significant difference in the genetic correlation estimates among the three breeds for feed efficiency and resilience traits. Our results suggest that feed efficiency and resilience traits were heritable, and resilience traits showed favourable or no genetic correlation with feed efficiency traits. In addition, the influence of genetic factors on feed efficiency and resilience traits could be the same among breeds.
Maternal effect on body measurement and meat production traits in purebred Duroc pigs. International-journal Peer-reviewed

Shinichiro Ogawa, Natsumi Yazaki, Chika Ohnishi, Kazuo Ishii, Yoshinobu Uemoto, Masahiro Satoh

Journal of animal breeding and genetics = Zeitschrift fur Tierzuchtung und Zuchtungsbiologie　138　(2)　237-245　2021/03

DOI： 10.1111/jbg.12505 　

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We investigated maternal effect on nine body measurement traits (body height, body length, front width (FW), chest width (CW), hind width (HW), chest depth, chest girth (CHG), front cannon circumference (FCC) and rear cannon circumference (RCC)) measured at the end of performance testing and five meat production traits (ages at the start and end of performance testing (D30 and D105), average daily gain (ADG), backfat thickness and loin muscle area) in purebred Duroc pigs. Genetic parameters for each trait were estimated by using six single-trait models with and without common litter environmental effect, maternal genetic effect and direct-maternal genetic correlation. The value of Akaike's information criterion was lowest with the model including direct additive genetic and common litter environmental effects for 10 traits. The estimated proportion of common litter environmental variance to phenotypic variance was approximately ≥0.1 for D30, D105, ADG, FW, CW, HW, CHG, FCC and RCC. Using a model without common litter environmental effect would overestimate the direct heritability of most traits. Standard errors of estimated genetic parameters tended to be larger in models including maternal genetic effect. The results indicate that a compromise could be made for accurate genetic parameter estimation for body measurement traits, as well as meat production traits, in pigs by considering common litter environmental effect.
比の形質を一定にして構成形質を増加させる選抜における遺伝的改良量：乳脂率の選抜による一例 Peer-reviewed

矢崎夏実, 上本吉伸, 小川伸一郎, 佐藤正寛

日本畜産学会報　92　(1)　35-39　2021/02
Comparison of selection responses based on feed conversion ratio and its component traits in pigs Peer-reviewed

矢崎夏実, 上本吉伸, 小川伸一郎, 佐藤正寛

日本畜産学会報　92　(3)　279-284　2021

ISSN： 1346-907X
Evaluation of inbreeding and genetic diversity in Japanese Shorthorn cattle by pedigree analysis. International-journal Peer-reviewed

Yoshinobu Uemoto, Keiichi Suzuki, Jumpei Yasuda, Sanggun Roh, Masahiro Satoh

Animal science journal = Nihon chikusan Gakkaiho　92　(1)　e13643　2021

DOI： 10.1111/asj.13643 　

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The Japanese Shorthorn is a Japanese Wagyu breed maintained at a small population size. We assessed the degree of inbreeding and genetic diversity among Japanese Shorthorn cattle using pedigree analysis. We analyzed the pedigree records of registered Japanese Shorthorn born between 1980 and 2018, after evaluating the pedigree completeness. The average of the actual inbreeding coefficients increased at the same rates annually from approximately 1.5% in 1980 to 4.2% in 2018 and was higher than the expected inbreeding coefficients over time. The effective population size based on the individual coancestry rate largely decreased from 127.8 in 1980 to 82.6 in 1999, and then remained almost constant at approximately 90. Three effective numbers of ancestors decreased over time until 1995, then remained almost constant. In particular, the effective number of founder genomes (Nge ) decreased from 43.8 in 1980 to 11.9 in 2018. The index of genetic diversity based on Nge decreased from 0.99 in 1980 to 0.96 in 2018 due to genetic drift in non-founder generations. Changes in inbreeding and genetic diversity parameters were similar between Japanese Shorthorn and other Japanese Wagyu breeds, but the magnitude of the changes was lower in the Japanese Shorthorn.
Genetic analysis for sow stayability at different parities in purebred Landrace and Large White pigs Peer-reviewed

Shinichiro Ogawa, Makoto Kimata, Kazuo Ishii, Yoshinobu Uemoto, Masahiro Satoh

Animal Science Journal　92　(1)　e13599　2021/01
Publisher: Wiley
DOI： 10.1111/asj.13599 　

ISSN： 1344-3941

eISSN： 1740-0929
Effectiveness of body measurement traits for improving production traits in Duroc pigs Peer-reviewed

YAZAKI Natsumi, OGAWA Shinichiro, OHNISHI Chika, ISHII Kazuo, UEMOTO Yoshinobu, SATOH Masahiro

Nihon Chikusan Gakkaiho　91　(1)　9-16　2020
Publisher: Japanese Society of Animal Science
DOI： 10.2508/chikusan.91.9 　

ISSN： 1346-907X

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<p>Genetic parameters for 13 body measurement traits (body length, body height, front width, chest width, hind width, chest depth, chest girth, front and rear cannon circumferences, front and rear pastern postures, body mass index, and body density) and six production traits (age at start and end of test, average daily gain (DG), backfat thickness (BF), loin muscle area (LMA), and intramuscular fat content (IMF)) were estimated in Duroc pigs. Data on 2,835 individual pigs were collected from 2009 through 2017. Heritability estimates for body measurement traits ranged from moderate to high. The largest absolute values of estimated genetic correlations between each production traits (DG, BF, LMA, and IMF) and body measurement traits were chest girth (0.42), chest girth (0.68), front pastern postures (－0.28), and chest width (0.38), respectively. Our results suggest that these body measurement traits can be used as indicator traits for improving production traits. We also recommend taking leg conformation traits into consideration due to the estimated negative genetic correlations between cannon circumference and BF, front pastern posture and LMA, and the positive genetic correlation between front pastern posture and DG.</p>
Genetic relationship between litter size traits at birth and body measurement and production traits in purebred Duroc pigs. International-journal Peer-reviewed

Shinichiro Ogawa, Chika Ohnishi, Kazuo Ishii, Yoshinobu Uemoto, Masahiro Satoh

Animal science journal = Nihon chikusan Gakkaiho　91　(1)　e13497　2020/01

DOI： 10.1111/asj.13497 　

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Heritabilities of litter size traits at birth (total number born (TNB), number born alive (NBA), and number still born (NSB)) and their genetic correlations with body measurement (body height, body length, front width (FW), chest width (CW), hind width, chest depth, chest girth, front cannon circumference, and rear cannon circumference) and production traits (ages at the start and end of performance testing (D30 and D105), average daily gain (ADG), backfat thickness, and loin muscle area) in purebred Duroc pigs were estimated. Records of performance testing for 2,835 animals and farrowing records of 1,168 litters from 437 dams were used. Genetic parameters were estimated using single-trait and two-trait animal models. Permanent environment effect was considered for litter size traits and common litter environmental effect was considered for body measurement and production traits. The estimated heritability was 0.10 ± 0.06 for TNB, 0.16 ± 0.06 for NBA, and 0.08 ± 0.05 for NSB. Positive genetic correlation of NBA was estimated with D30, D105, and ADG (0.51, 0.11, and 0.39). The estimated genetic correlation of NBA was 0.47 ± 0.17 with FW and 0.55 ± 0.18 with CW, implying that FW and CW could be promising indicator traits for efficiently improving NBA.
Comparison of two models to estimate genetic parameters for number of born alive in pigs Peer-reviewed

Ayane Konta, Shinichiro Ogawa, Makoto Kimata, Kazuo Ishii, Yoshinobu Uemoto, Masahiro Satoh

ANIMAL SCIENCE JOURNAL　91　(1)　e13417　2020/01

DOI： 10.1111/asj.13417 　

ISSN： 1344-3941

eISSN： 1740-0929
Effect of genotyped bulls with different numbers of phenotyped progenies on quantitative trait loci detection and genomic evaluation in a simulated cattle population Peer-reviewed

Masayuki Takeda, Yoshinobu Uemoto, Masahiro Satoh

ANIMAL SCIENCE JOURNAL　91　(1)　e13432　2020/01

DOI： 10.1111/asj.13432 　

ISSN： 1344-3941

eISSN： 1740-0929
Genetic and genomic analyses for predicted methane-related traits in Japanese Black steers Peer-reviewed

Yoshinobu Uemoto, Masayuki Takeda, Atushi Ogino, Kazuhito Kurogi, Shinichro Ogawa, Masahiro Satoh, Fuminori Terada

ANIMAL SCIENCE JOURNAL　91　(1)　e13383　2020/01

DOI： 10.1111/asj.13383 　

ISSN： 1344-3941

eISSN： 1740-0929
Development of prediction equation for methane-related traits in beef cattle under high concentrate diets Peer-reviewed

Yoshinobu Uemoto, Shinichiro Ogawa, Masahiro Satoh, Hiroyuki Abe, Fuminori Terada

Animal Science Journal　91　(1)　e13341　2020/01/01

DOI： 10.1111/asj.13341 　

ISSN： 1344-3941

eISSN： 1740-0929
Genome-wide association study and genomic evaluation of feed efficiency traits in Japanese Black cattle using single-step genomic best linear unbiased prediction method International-journal Peer-reviewed

Masayuki Takeda, Yoshinobu Uemoto, Keiichi Inoue, Atushi Ogino, Takayoshi Nozaki, Kazuhito Kurogi, Takanori Yasumori, Masahiro Satoh

ANIMAL SCIENCE JOURNAL　91　(1)　e13316　2020/01

DOI： 10.1111/asj.13316 　

ISSN： 1344-3941

eISSN： 1740-0929
The NT5E gene variant strongly affects the degradation rate of inosine 5'-monophosphate under postmortem conditions in Japanese Black beef. International-journal Peer-reviewed

Komatsu T, Komatsu M, Uemoto Y

Meat science　158　107893　2019/12

DOI： 10.1016/j.meatsci.2019.107893 　

ISSN： 0309-1740

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Inosine 5'-monophosphate (IMP) contributes to the umami taste in Japanese Black beef. In a previous study, it was suggested that single nucleotide polymorphisms (SNPs) in the ecto-5'-nucleotidase (NT5E) gene affect the concentration of IMP under postmortem conditions by regulating NT5E enzymatic activity in Japanese Black beef. The present study showed that the degradation rate of IMP in Japanese Black beef was significantly different among NT5E genotypes in the middle stage of postmortem, indicating a significant difference in the concentrations of IMP and its degradation products among NT5E genotypes. In addition, no significant difference was observed among NT5E genotypes in the concentrations of IMP precursors or other taste-active compounds. These results indicate the significant effect of the interaction between the NT5E genotype and the aging period on the degradation rate of IMP in beef.
Genetic relationship of litter traits between farrowing and weaning in Landrace and Large White pigs. International-journal Peer-reviewed

Shinichiro Ogawa, Ayane Konta, Makoto Kimata, Kazuo Ishii, Yoshinobu Uemoto, Masahiro Satoh

Animal science journal = Nihon chikusan Gakkaiho　90　(12)　1510-1516　2019/12

DOI： 10.1111/asj.13304 　

ISSN： 1344-3941

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We estimated genetic parameters in Landrace and Large White pig populations for litter traits at farrowing (total number born, number born alive, number stillborn, total litter weight at birth (LWB), and mean litter weight at birth) and those at weaning (litter size at weaning (LSW), total litter weight at weaning (LWW), mean litter weight at weaning (MWW), and survival rate from farrowing to weaning). We analyzed 65,579 records at farrowing and 6,306 at weaning for Landrace, and 52,557 and 5,360, respectively, for Large White. Single-trait and two-trait repeatability animal models were exploited to estimate heritability and genetic correlation respectively. Heritability estimates of LSW were 0.09 for Landrace and 0.08 for Large White. Genetic correlations of LSW with MWW were -0.43 for Landrace and -0.24 for Large White. Genetic correlations of LSW with LWW and LWB ranged from 0.5 to 0.6. The genetic correlation of MWW with LWW was positive, but that with LWB was negligible. The results indicate that utilizing LWW or LWB could improve LSW efficiently, despite the antagonistic genetic correlation between LSW and MWW.
Genetic parameter estimation for number born alive at different parities in Landrace and Large White pigs. Peer-reviewed

Ogawa S, Konta A, Kimata M, Ishii K, Uemoto Y, Satoh M

Animal science journal = Nihon chikusan Gakkaiho　90　(9)　1111-1119　2019/09

DOI： 10.1111/asj.13252 　

ISSN： 1344-3941
Addition of Wakame seaweed (Undaria pinnatifida) stalk to animal feed enhances immune response and improves intestinal microflora in pigs. International-journal Peer-reviewed

Tomoyuki Shimazu, Liushiqi Borjigin, Kazuo Katoh, Sang-Gun Roh, Haruki Kitazawa, Keietsu Abe, Yoshihito Suda, Hayato Saito, Hiroshi Kunii, Ken Nihei, Yoshinobu Uemoto, Hisashi Aso, Keiichi Suzuki

Animal science journal = Nihon chikusan Gakkaiho　90　(9)　1248-1260　2019/09

DOI： 10.1111/asj.13274 　

ISSN： 1344-3941

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This study was conducted to evaluate the effects of supplementation of Wakame seaweed stalks on the immunity and intestinal microflora of pigs. Three separate experiments were performed: Relatively young (start at 20-30 kg; Experiments 1 and 2) and fattening period (70 kg; Experiment 3). All pigs (including the control group) were fed the same commercial feed, free from antibiotic additives, but in the feed for the treatment groups, 1% seaweed powder was added. There were no group differences observed in daily weight gain and feed intake in Experiments 1 and 2 between groups; however, daily weight gain was significantly higher in the treatment group compared to the control group in Experiment 3. The percentage of peripheral blood natural killer cells of the treatment group was significantly higher than that of the control group in all experiments. Although addition of seaweed changed the gene expression of cytokine and toll-like receptors of the small intestinal Peyer's patches slightly, seaweed seems to alter intestinal microflora preferentially, for instance, there was an increase in Lactobacillus and a decrease of Escherichia coli observed. These results suggest that Wakame seaweed can be used as supplement for pig feed to improve the gut health and immunity of pigs.
Correlations between mitochondrial respiration activity and residual feed intake after divergent genetic selection for high- and low- oxygen consumption in mice. Peer-reviewed

Darhan H, Zoda A, Kikusato M, Toyomizu M, Katoh K, Roh SG, Ogawa S, Uemoto Y, Satoh M, Suzuki K

Animal science journal = Nihon chikusan Gakkaiho　90　(7)　818-826　2019/07
Publisher: Wiley
DOI： 10.1111/asj.13210 　

ISSN： 1344-3941

eISSN： 1740-0929
Estimation of genetic parameters for farrowing traits in purebred Landrace and Large White pigs Peer-reviewed

Ogawa Shinichiro, Konta Ayane, Kimata Makoto, Ishii Kazuo, Uemoto Yoshinobu, Satoh Masahiro

ANIMAL SCIENCE JOURNAL　90　(1)　23-28　2019/01

DOI： 10.1111/asj.13120 　

ISSN： 1344-3941
A study on the potential for improving number born alive using teat number in pig female breeds Peer-reviewed

今田彩音, 小川伸一郎, 木全誠, 石井和雄, 上本吉伸, 佐藤正寛

日本畜産学会報　90　(3)　207-212　2019

DOI： 10.2508/chikusan.90.207 　

ISSN： 1346-907X
Pool-based genome-wide association study identified novel candidate regions on BTA9 and 14 for oleic acid percentage in Japanese Black cattle Peer-reviewed

Fuki Kawaguchi, Hiroto Kigoshi, Ayaka Nakajima, Yuta Matsumoto, Yoshinobu Uemoto, Moriyuki Fukushima, Emi Yoshida, Eiji Iwamoto, Takayuki Akiyama, Namiko Kohama, Eiji Kobayashi, Takeshi Honda, Kenji Oyama, Hideyuki Mannen, Shinji Sasazaki

Animal Science Journal　89　(8)　1060-1066　2018/08
Publisher: Wiley
DOI： 10.1111/asj.13035 　

ISSN： 1344-3941
Genome-wide association studies identified variants for taurine concentration in Japanese Black beef. International-journal Peer-reviewed

Nanae Sasago, Masayuki Takeda, Tsuyoshi Ohtake, Tsuyoshi Abe, Hironori Sakuma, Takatoshi Kojima, Shinji Sasaki, Yoshinobu Uemoto

Animal science journal = Nihon chikusan Gakkaiho　89　(8)　1051-1059　2018/08

DOI： 10.1111/asj.13030 　

ISSN： 1344-3941

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We performed genome-wide association studies (GWAS) using the BovineSNP50 array to detect significant single nucleotide polymorphisms (SNPs) that may affect the concentration of 22 free amino acids and three peptides in Japanese Black beef cattle. A total of 574 Japanese Black cattle and 40,657 SNPs from the array were used for this study. Genome-wide significant SNPs were detected for β-alanine (three SNPs on chromosomes 22 and 29) and taurine (26 SNPs on chromosome 22). Importantly, the top two SNPs for taurine were highly significant (p = 6.2 × 10-21 ), and the frequency of the increase-concentration allele (Q) for taurine was found to be 0.73. The Q allele frequency of this population was similar to that of the other unrelated Japanese Black cattle, but different from that of the other breeds. In addition, the significant SNPs were not associated with carcass traits or fatty acid compositions. Interestingly, the top three of the four most significant SNPs for taurine were located near solute carrier family 6, member 6 (SLC6A6), which is a membrane transporter for taurine. We also found two associated variants in the 5'-upstream region of SLC6A6; however, they were less significantly associated than the SNPs from the BovineSNP50 array.
A genome-wide association study for fat-related traits computed by image analysis in Japanese Black cattle Peer-reviewed

Ayaka Nakajima, Fuki Kawaguchi, Yoshinobu Uemoto, Moriyuki Fukushima, Emi Yoshida, Eiji Iwamoto, Takayuki Akiyama, Namiko Kohama, Eiji Kobayashi, Takeshi Honda, Kenji Oyama, Hideyuki Mannen, Shinji Sasazaki

Animal Science Journal　89　(5)　743-751　2018/05
Publisher: Wiley
DOI： 10.1111/asj.12987 　

ISSN： 1344-3941
Evaluation of feed efficiency traits for genetic improvement in Japanese black cattle Peer-reviewed

Masayuki Takeda, Yoshinobu Uemoto, Keiichi Inoue, Atsushi Ogino, Takayoshi Nozaki, Kazuhito Kurogi, Takanori Yasumori, Masahiro Satoh

Journal of Animal Science　96　(3)　797-805　2018/04/03
Publisher: American Society of Animal Science
DOI： 10.1093/jas/skx054 　

ISSN： 1525-3163 0021-8812
Effect of two non-synonymous ecto-5 '-nucleotidase variants on the genetic architecture of inosine 5 '-monophosphate (IMP) and its degradation products in Japanese Black beef Peer-reviewed

Yoshinobu Uemoto, Tsuyoshi Ohtake, Nanae Sasago, Masayuki Takeda, Tsuyoshi Abe, Hironori Sakuma, Takatoshi Kojima, Shinji Sasaki

BMC GENOMICS　18　(1)　874　2017/11

DOI： 10.1186/s12864-017-4275-4 　

ISSN： 1471-2164
Genome-wide association studies reveal additional related loci for fatty acid composition in a Duroc pig multigenerational population Peer-reviewed

Shuji Sato, Yoshinobu Uemoto, Takashi Kikuchi, Sachiko Egawa, Kimiko Kohira, Tomomi Saito, Hironori Sakuma, Satoshi Miyashita, Shinji Arata, Keiichi Suzuki

ANIMAL SCIENCE JOURNAL　88　(10)　1482-1490　2017/10

DOI： 10.1111/asj.12793 　

ISSN： 1344-3941

eISSN： 1740-0929
Genomic evaluation using SNP- and haplotype-based genomic relationship matrices in a closed line of Duroc pigs Peer-reviewed

Yoshinobu Uemoto, Shuji Sato, Takashi Kikuchi, Sachiko Egawa, Kimiko Kohira, Hironori Sakuma, Satoshi Miyashita, Shinji Arata, Takatoshi Kojima, Keiichi Suzuki

ANIMAL SCIENCE JOURNAL　88　(10)　1465-1474　2017/10

DOI： 10.1111/asj.12805 　

ISSN： 1344-3941

eISSN： 1740-0929
Effect of genotyped cows in the reference population on the genomic evaluation of Holstein cattle Peer-reviewed

Y. Uemoto, T. Osawa, J. Saburi

ANIMAL　11　(3)　382-393　2017/03

DOI： 10.1017/S1751731116001762 　

ISSN： 1751-7311

eISSN： 1751-732X
Estimates of genetic parameters for chemical traits of meat quality in Japanese black cattle Peer-reviewed

Hironori Sakuma, Kaoru Saito, Kimiko Kohira, Fumie Ohhashi, Noriaki Shoji, Yoshinobu Uemoto

ANIMAL SCIENCE JOURNAL　88　(2)　203-212　2017/02

DOI： 10.1111/asj.12622 　

ISSN： 1344-3941

eISSN： 1740-0929
Genome-wide association study for carcass traits, fatty acid composition, chemical composition, sugar, and the effects of related candidate genes in Japanese Black cattle Peer-reviewed

Nanae Sasago, Tsuyoshi Abe, Hironori Sakuma, Takatoshi Kojima, Yoshinobu Uemoto

ANIMAL SCIENCE JOURNAL　88　(1)　33-44　2017/01

DOI： 10.1111/asj.12595 　

ISSN： 1344-3941

eISSN： 1740-0929
Effect of candidate gene polymorphisms on reproductive traits in a Large White pig population Peer-reviewed

Shuji Sato, Takashi Kikuchi, Yoshinobu Uemoto, Satoshi Mikawa, Keiichi Suzuki

ANIMAL SCIENCE JOURNAL　87　(12)　1455-1463　2016/12

DOI： 10.1111/asj.12580 　

ISSN： 1344-3941

eISSN： 1740-0929
Polymorphisms associated with four reproductive traits have no adverse effects on meat traits in Japanese Black cattle Peer-reviewed

S. Sasaki, Y. Uemoto, N. Sasago, T. Abe, S. Nishimura, Y. Sugimoto

ANIMAL GENETICS　47　(3)　386-387　2016/06

DOI： 10.1111/age.12414 　

ISSN： 0268-9146

eISSN： 1365-2052
SNP- and haplotype-based genome-wide association studies for growth, carcass, and meat quality traits in a Duroc multigenerational population Peer-reviewed

Shuji Sato, Yoshinobu Uemoto, Takashi Kikuchi, Sachiko Egawa, Kimiko Kohira, Tomomi Saito, Hironori Sakuma, Satoshi Miyashita, Shinji Arata, Takatoshi Kojima, Keiichi Suzuki

BMC GENETICS　17　60　2016/04

DOI： 10.1186/s12863-016-0368-3 　

ISSN： 1471-2156
Impact of QTL minor allele frequency on genomic evaluation using real genotype data and simulated phenotypes in Japanese Black cattle Peer-reviewed

Yoshinobu Uemoto, Shinji Sasaki, Takatoshi Kojima, Yoshikazu Sugimoto, Toshio Watanabe

BMC GENETICS　16　134　2015/11

DOI： 10.1186/s12863-015-0287-8 　

ISSN： 1471-2156
Accuracy of high-density genotype imputation in Japanese Black cattle Peer-reviewed

Y. Uemoto, S. Sasaki, Y. Sugimoto, T. Watanabe

ANIMAL GENETICS　46　(4)　388-394　2015/08

DOI： 10.1111/age.12314 　

ISSN： 0268-9146

eISSN： 1365-2052
The g.841G > C SNP of FASN gene is associated with fatty acid composition in beef cattle Peer-reviewed

Kiri Hayakawa, Takayuki Sakamoto, Atsushi Ishii, Keita Yamaji, Yoshinobu Uemoto, Nanae Sasago, Eiji Kobayashi, Naohiko Kobayashi, Tamako Matsuhashi, Shin Maruyama, Hirokazu Matsumoto, Kenji Oyama, Hideyuki Mannen, Shinji Sasazaki

ANIMAL SCIENCE JOURNAL　86　(8)　737-746　2015/08

DOI： 10.1111/asj.12357 　

ISSN： 1344-3941

eISSN： 1740-0929
Effect of VRTN gene polymorphisms on Duroc pig production and carcass traits, and their genetic relationships Peer-reviewed

Hikaru Nakano, Shuji Sato, Yoshinobu Uemoto, Takashi Kikuchi, Tomoya Shibata, Hiroshi Kadowaki, Eiji Kobayashi, Keiichi Suzuki

ANIMAL SCIENCE JOURNAL　86　(2)　125-131　2015/02

DOI： 10.1111/asj.12260 　

ISSN： 1344-3941

eISSN： 1740-0929
Evaluation of quantitative trait loci affecting intramuscular fat and reproductive traits in pigs using marker-assisted introgression Peer-reviewed

S. Sato, C. Ohnishi, T. Kikuchi, K. Kohira, S. Egawa, S. Terai, T. Nakamura, S. Arata, A. Komatsuda, Y. Uemoto

ANIMAL GENETICS　45　(6)　799-807　2014/12

DOI： 10.1111/age.12203 　

ISSN： 0268-9146

eISSN： 1365-2052
Association between Motilin Receptor Gene Haplotypes and Growth Traits in Japanese Hinai-dori Crossbred Chickens Peer-reviewed

Hideaki Takahashi, Kazuhiro Rikimaru, Megumi Komatsu, Yoshinobu Uemoto, Keiichi Suzuki

ASIAN-AUSTRALASIAN JOURNAL OF ANIMAL SCIENCES　27　(3)　316-323　2014/03

DOI： 10.5713/ajas.2013.13500 　

ISSN： 1011-2367

eISSN： 1976-5517
Fine mapping of the chicken congenital loco locus on chromosome 12 Peer-reviewed

Y. Okumura, T. Ohtake, Y. Uemoto, S. Sato, S. Sato, E. Kobayashi

ANIMAL GENETICS　44　(6)　778-781　2013/12

DOI： 10.1111/age.12065 　

ISSN： 0268-9146

eISSN： 1365-2052
Genome-wide association study for fatty acid composition in Japanese Black cattle Peer-reviewed

Atsushi Ishii, Keita Yamaji, Yoshinobu Uemoto, Nanae Sasago, Eiji Kobayashi, Naohiko Kobayashi, Tamako Matsuhashi, Shin Maruyama, Hirokazu Matsumoto, Shinji Sasazaki, Hideyuki Mannen

ANIMAL SCIENCE JOURNAL　84　(10)　675-682　2013/10

DOI： 10.1111/asj.12063 　

ISSN： 1344-3941
Effect of a Single-Nucleotide Polymorphism in the Cholecystokinin Type A Receptor Gene on Growth Traits in the Hinai-dori Chicken Breed Peer-reviewed

Kazuhiro Rikimaru, Hisato Takeda, Yoshinobu Uemoto, Megumi Komatsu, Daiki Takahashi, Keiichi Suzuki, Hideaki Takahashi

JOURNAL OF POULTRY SCIENCE　50　(3)　206-211　2013/07

DOI： 10.2141/jpsa.0120130 　

ISSN： 1346-7395
Genetic Variation of the MC1R Gene that Controls Black Plumage Color in Different Breeds Peer-reviewed

OKUMURA YUMI, OTAKE TSUYOSHI, SATO SHIN'ICHI, NIINOMI TATSUYA, UEMOTO YOSHINOBU, KOBAYASHI EIJI

日本家禽学会誌　50　J1-J9　2013/04

ISSN： 0029-0254
SCD(stearoyl‐CoA desaturase)遺伝子情報を利用したデュロック豚選抜モデルにおけるオレイン酸割合の選抜反応に関する基礎的検討 Peer-reviewed

及川卓郎, 上本吉伸, 小林英治, 鈴木啓一

日本暖地畜産学会報　56　(1)　55-60　2013/03
Publisher: Warm Regional Society of Animal Science, Japan
DOI： 10.11461/jwaras.56.55 　

ISSN： 2185-081X

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Selection responses by deterministic simulation were compared among selection models which had different source of information: SCD (stearoyl-CoA desaturase) genotypes, phenotypic values of an individual and relatives. Selection response per a generation or per unit of a time (half a year) was computed with a framework of selection index. A target trait of the simulated selection was oleic acid (C18:1) percentage of outer layer of subcutaneous fat, and parameter of a gene was assumed to be that of SCD gene. The highest selection response was obtained in a combined selection model of phenotypes of half sib and progeny. The second highest response was in a combined model with phenotypes and genotypes of parents and half sibs of them. Compared among genotypic selection models, a model with information from individual and half sib of them had higher response at earlier generation of the selection, however, it decreased after fourth generation. Whereas, in terms of selection response per unit of time, the model with progeny information had lower response due to longer generation interval. Due to moderate heritability of the oleic acid percentage, selection models with genotypic information had no advantage over the models with only phenotypic information.
Effects of SCD, FASN, SREBP-1 and GH gene polymorphisms on fatty acid composition of subcutaneous fat in the carcass of Japanese Shorthorn Peer-reviewed

SATO YOICHI, SASAGO NANAE, UEMOTO YOSHINOBU, HASEBE HIROYUKI, ABE TSUYOSHI, YASUDA JUMPEI, KOBAYASHI EIJI, KUMAGAI MITSUHIRO, SUZUKI KEIICHI

日本畜産学会報　84　(1)　27-33　2013/02
Publisher: Zootechnical Science Society of Japan
DOI： 10.2508/chikusan.84.27 　

ISSN： 1346-907X

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In recent years, fatty acid composition has attracted attention as a new trait for evaluation of beef quality. Although there are a lot of information given, mainly in marbling in Japanese Shorthorn red meat, there are few reports on fatty acid composition. Therefore, the effect each genotype polymorphism SCD, FASN, SREBP-1 and GH is given to the fatty acid ratio and carcass traits in 279 Japanese Shorthorn head were analyzed using mixed-inheritance animal model. Heritability of fatty acid ratio was 0.39-0.51, C18:2 had the lowest which was similar to the report on Japanese Black Cattle. Both FASN and SCD were effective in C14:0 and C14:1, FASN was effective in C16:1 and C18:1, SCD was effective in C18:0, C18:2, SFA and MUFA. On the other hand, effect of GH was not observed. SREBP-1 polymorphism could not be confirmed. It was suggested that the genetic influence on fatty acid composition was strong, and genotype information of FASN and SCD were useful as markers in Japanese Shorthorn.
The power of regional heritability analysis for rare and common variant detection: simulations and application to eye biometrical traits. Peer-reviewed

Uemoto Y, Pong-Wong R, Navarro P, Vitart V, Hayward C, Wilson JF, Rudan I, Campbell H, Hastie ND, Wright AF, Haley CS

Frontiers in genetics　4　232　2013

DOI： 10.3389/fgene.2013.00232 　
A genome-wide scan for quantitative trait loci affecting respiratory disease and immune capacity in Landrace pigs Peer-reviewed

T. Okamura, W. Onodera, T. Tayama, H. Kadowaki, C. Kojima-Shibata, E. Suzuki, Y. Uemoto, S. Mikawa, T. Hayashi, T. Awata, N. Fujishima-Kanaya, A. Mikawa, H. Uenishi, K. Suzuki

ANIMAL GENETICS　43　(6)　721-729　2012/12

DOI： 10.1111/j.1365-2052.2012.02359.x 　

ISSN： 0268-9146

eISSN： 1365-2052
Practical capability of a DNA pool-based genome-wide association study using BovineSNP50 array in a cattle population Peer-reviewed

Yoshinobu Uemoto, Nanae Sasago, Tsuyoshi Abe, Hideki Okada, Hitomi Maruoka, Hiroaki Nakajima, Noriaki Shoji, Shin Maruyama, Naohiko Kobayashi, Hideyuki Mannen, Eiji Kobayashi

ANIMAL SCIENCE JOURNAL　83　(11)　719-726　2012/11

DOI： 10.1111/j.1740-0929.2012.01022.x 　

ISSN： 1344-3941
Association between cholecystokinin type A receptor haplotypes and growth traits in Japanese Hinai-dori crossbred chickens Peer-reviewed

Kazuhiro Rikimaru, Megumi Komatsu, Keiichi Suzuki, Yoshinobu Uemoto, Hisato Takeda, Hideaki Takahashi

MOLECULAR BIOLOGY REPORTS　39　(4)　4479-4484　2012/04

DOI： 10.1007/s11033-011-1237-9 　

ISSN： 0301-4851
Fine mapping of porcine SSC14 QTL and SCD gene effects on fatty acid composition and melting point of fat in a Duroc purebred population Peer-reviewed

Y. Uemoto, H. Nakano, T. Kikuchi, S. Sato, M. Ishida, T. Shibata, H. Kadowaki, E. Kobayashi, K. Suzuki

ANIMAL GENETICS　43　(2)　225-228　2012/04

DOI： 10.1111/j.1365-2052.2011.02236.x 　

ISSN： 0268-9146
Genome-wide mapping for fatty acid composition and melting point of fat in a purebred Duroc pig population Peer-reviewed

Y. Uemoto, Y. Soma, S. Sato, M. Ishida, T. Shibata, H. Kadowaki, E. Kobayashi, K. Suzuki

ANIMAL GENETICS　43　(1)　27-34　2012/02

DOI： 10.1111/j.1365-2052.2011.02218.x 　

ISSN： 0268-9146

eISSN： 1365-2052
Polymorphism of insulin-like growth factor 1 gene is associated with breast muscle yields in chickens Peer-reviewed

Shinichi Sato, Tsuyoshi Ohtake, Yoshinobu Uemoto, Yumi Okumura, Eiji Kobayashi

ANIMAL SCIENCE JOURNAL　83　(1)　1-6　2012

DOI： 10.1111/j.1740-0929.2011.00917.x 　

ISSN： 1344-3941

eISSN： 1740-0929
Effects of porcine leptin receptor gene polymorphisms on backfat thickness, fat area ratios by image analysis, and serum leptin concentrations in a Duroc purebred population Peer-reviewed

Yoshinobu Uemoto, Takashi Kikuchi, Hikaru Nakano, Shuji Sato, Tomoya Shibata, Hiroshi Kadowaki, Kazuo Katoh, Eiji Kobayashi, Keiichi Suzuki

ANIMAL SCIENCE JOURNAL　83　(5)　375-385　2012

DOI： 10.1111/j.1740-0929.2011.00963.x 　

ISSN： 1344-3941

eISSN： 1740-0929
Mapping QTL for fat area ratios and serum leptin concentrations in a Duroc purebred population Peer-reviewed

Yoshinobu Uemoto, Yusuke Soma, Shuji Sato, Tomoya Shibata, Hiroshi Kadowaki, Kazuo Katoh, Eiji Kobayashi, Keiichi Suzuki

ANIMAL SCIENCE JOURNAL　83　(3)　187-193　2012

DOI： 10.1111/j.1740-0929.2011.00951.x 　

ISSN： 1344-3941

eISSN： 1740-0929
The Effect of SLC45A2 Gene Polymorphisms on Goshiki Plumage Color Trait in Aizu-Jidori Chickens Peer-reviewed

OHTAKE Tsuyoshi, SATO Taeko, KOKUBUN Youichi, UEMOTO Yoshinobu, SATO Shuji, OKUMURA Yumi, KOBAYASHI Eiji

Japanese journal of poultry science　48　(2)　J58-J62　2011/10
Publisher:
ISSN： 0029-0254
Evaluation of Meat Spot Traits by Picture Image Analysis of the Eggs of Three Chicken Breeds Producing Eggs with Brown Eggshells Peer-reviewed

OKUMURA Yumi, UNO Satoru, KASHI Takahide, TAMURA Katsushi, SAKAKIBARA Toyokazu, MIYATA Toru, UEMOTO Yoshinobu, KOBAYASHI Eiji, TANIGUCHI Shin

Japanese journal of poultry science　48　(1)　J1-J5　2011/04
Publisher:
ISSN： 0029-0254
Whole-genome association study for fatty acid composition of oleic acid in Japanese Black cattle Peer-reviewed

Y. Uemoto, T. Abe, N. Tameoka, H. Hasebe, K. Inoue, H. Nakajima, N. Shoji, M. Kobayashi, E. Kobayashi

ANIMAL GENETICS　42　(2)　141-148　2011/04

DOI： 10.1111/j.1365-2052.2010.02088.x 　

ISSN： 0268-9146
Genome-wide mapping and identification of new quantitative trait loci affecting meat production, meat quality, and carcass traits within a Duroc purebred population Peer-reviewed

Y. Soma, Y. Uemoto, S. Sato, T. Shibata, H. Kadowaki, E. Kobayashi, K. Suzuki

JOURNAL OF ANIMAL SCIENCE　89　(3)　601-608　2011/03

DOI： 10.2527/jas.2010-3119 　

ISSN： 0021-8812

eISSN： 1525-3163
Haplotype analysis within quantitative trait locus affecting intramuscular fat content on porcine chromosome 7 Peer-reviewed

S. Sato, C. Ohnishi, Y. Uemoto, E. Kobayashi

CZECH JOURNAL OF ANIMAL SCIENCE　56　(12)　521-528　2011

ISSN： 1212-1819
Effects of bovine fatty acid synthase, stearoyl-coenzyme A desaturase, sterol regulatory element-binding protein 1, and growth hormone gene polymorphisms on fatty acid composition and carcass traits in Japanese Black cattle Peer-reviewed

T. Matsuhashi, S. Maruyama, Y. Uemoto, N. Kobayashi, H. Mannen, T. Abe, S. Sakaguchi, E. Kobayashi

JOURNAL OF ANIMAL SCIENCE　89　(1)　12-22　2011/01

DOI： 10.2527/jas.2010-3121 　

ISSN： 0021-8812
Ornithine decarboxylase gene is a positional candidate gene affecting growth and carcass traits in F-2 intercross chickens Peer-reviewed

Y. Uemoto, S. Sato, T. Ohtake, S. Sato, Y. Okumura, E. Kobayashi

POULTRY SCIENCE　90　(1)　35-41　2011/01

DOI： 10.3382/ps.2010-01119 　

ISSN： 0032-5791
Sequence analysis of a pea comb locus on chicken chromosome 1 Peer-reviewed

S. Sato, S. Sato, T. Otake, C. Suzuki, Y. Uemoto, J. Saburi, H. Hashimoto, E. Kobayashi

ANIMAL GENETICS　41　(6)　659-661　2010/12

DOI： 10.1111/j.1365-2052.2010.02048.x 　

ISSN： 0268-9146
The Distribution of Genotypic and Allelic Frequencies among Breeds about TVA Receptor Gene for the Subgroup A Avian Sarcoma and Leukosis Viruses Peer-reviewed

SATO Shin-ichi, OHTAKE Tsuyoshi, UEMOTO Yoshinobu, YAMAMOTO Rikiya, MIYATA Toru, SUZUKI Kohei, YAMASHITA Hideji, MITSUHASHI Tadayoshi, KOBAYASHI Eiji

Japanese journal of poultry science　47　(2)　J65-J70　2010/10
Publisher:
ISSN： 0029-0254
Polymorphism Analysis and Linkage Mapping of the Porcine CD4 Gene to SSC5 Peer-reviewed

KOBAYASHI Eiji, MATSUMOTO Toshimi, YANAI Satoshi, SATO Shuji, OHNISHI Chika, UEMOTO Yoshinobu, AWATA Takashi, SUZUKI Kei-ichi

The Japanense journal of swine science　47　(2)　55-60　2010/06
Publisher:
DOI： 10.5938/youton.47.55 　

ISSN： 0913-882X
Quantitative trait loci for leg weakness traits in a Landrace purebred population Peer-reviewed

Yoshinobu Uemoto, Shuji Sato, Chika Ohnishi, Kensuke Hirose, Kenji Kameyama, Kazuo Fukawa, Osamu Kudo, Eiji Kobayashi

ANIMAL SCIENCE JOURNAL　81　(1)　28-33　2010

DOI： 10.1111/j.1740-0929.2009.00713.x 　

ISSN： 1344-3941
Polymorphism of the ovocalyxin-32 gene and its association with egg production traits in the chicken Peer-reviewed

Y. Uemoto, C. Suzuki, S. Sato, S. Sato, T. Ohtake, O. Sasaki, H. Takahashi, E. Kobayashi

POULTRY SCIENCE　88　(12)　2512-2517　2009/12

DOI： 10.3382/ps.2009-00331 　

ISSN： 0032-5791
Detection of Quantitative Trait Loci Affecting Muscle Histochemical Properties in the F-2 Progeny of a Cross Between Japanese Black and Limousin Breed Peer-reviewed

Tsuyoshi Abe, Hiroyuki Hasebe, Tetsuo Nakagawa, Yoshinobu Uemoto, Kaoru Saito, Toshihiro Nade, Tadashi Kawamura, Eiji Kobayashi

JOURNAL OF ANIMAL AND VETERINARY ADVANCES　8　(11)　2190-2195　2009/11

ISSN： 1680-5593
The effects of single and epistatic quantitative trait loci for fatty acid composition in a Meishan x Duroc crossbred population Peer-reviewed

Y. Uemoto, S. Sato, C. Ohnishi, S. Terai, A. Komatsuda, E. Kobayashi

JOURNAL OF ANIMAL SCIENCE　87　(11)　3470-3476　2009/11

DOI： 10.2527/jas.2009-1917 　

ISSN： 0021-8812
Quantitative Trait Loci Affecting Rous Sarcoma Virus Induced Tumor Regression Trait in F2 Intercross Chickens Peer-reviewed

Y. Uemoto, J. Saburi, S. Sato, S. Odawara, T. Ohtake, R. Yamamoto, T. Miyata, K. Suzuki, H. Yamashita, C. Irina, G. Plastow, T. Mitsuhashi, E. Kobayashi

ASIAN-AUSTRALASIAN JOURNAL OF ANIMAL SCIENCES　22　(10)　1359-1365　2009/10

ISSN： 1011-2367
Genetic mapping of quantitative trait loci affecting growth and carcass traits in F-2 intercross chickens Peer-reviewed

Y. Uemoto, S. Sato, S. Odawara, H. Nokata, Y. Oyamada, Y. Taguchi, S. Yanai, O. Sasaki, H. Takahashi, K. Nirasawa, E. Kobayashi

POULTRY SCIENCE　88　(3)　477-482　2009/03

DOI： 10.3382/ps.2008-00296 　

ISSN： 0032-5791
Quantitative trait loci analysis on Sus scrofa chromosome 7 for meat production, meat quality, and carcass traits within a Duroc purebred population Peer-reviewed

Y. Uemoto, Y. Nagamine, E. Kobayashi, S. Sato, T. Tayama, Y. Suda, T. Shibata, K. Suzuki

JOURNAL OF ANIMAL SCIENCE　86　(11)　2833-2839　2008/11

DOI： 10.2527/jas.2007-0293 　

ISSN： 0021-8812

eISSN： 1525-3163
Effects of heart fatty acid-binding protein genotype on intramuscular fat content in Duroc pigs selected for meat production and meat quality traits Peer-reviewed

Yoshinobu Uemoto, Keiichi Suzuki, Eiji Kobayashi, Syushi Sato, Tomoya Shibata, Hiroshi Kadowaki, Akira Nishida

ASIAN-AUSTRALASIAN JOURNAL OF ANIMAL SCIENCES　20　(5)　622-626　2007/05

ISSN： 1011-2367
Identification of Quantitative Trait Loci for Immune Traits in Landrace Purebred Swine. Peer-reviewed

42　(2)　187-194　2006/12

ISSN： 0913-882X
PCR-RFLP Analysis of The Heart Fatty Acid-binding Protein Gene in Four Pig Breeds Peer-reviewed

KOBAYASHI Eiji, UEMOTO Yoshinobu, AKITA Tomiji, SATO Shuji, SATO Shin-ichi, HASEBE Hiroyuki, SUZUKI Keiichi

The Japanense journal of swine science　41　(3)　169-174　2004/09
Publisher: The Japanese Society of Swine Science
DOI： 10.5938/youton.41.169 　

ISSN： 0913-882X 1881-655X

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Misc. 7

生産性を損なわずメタン関連形質の改良は可能ゲノム育種は環境保全にどこまで貢献できるか Invited

上本吉伸

Dairyman　27-29　2024/08
EAAP,WAAP,インターブル共催畜産に関する国際会議についてその2 気候変動・生物多様性・地球規模の持続性と家畜生産 Invited

上本吉伸, 小櫃剛人

畜産技術　(823)　22-24　2023/12

ISSN： 0389-1348
EAAP,WAAP,インターブル共催畜産に関する国際会議についてその1 気候変動・生物多様性・地球規模の持続性と家畜生産 Invited

上本吉伸, 小櫃剛人

畜産技術　(822)　21-23　2023/11
我が国の畜産業の将来に向けた家畜育種の課題と展望～持続可能な畜産を目指したゲノム育種～ Invited

上本吉伸

公益財団法人全国競馬・畜産振興会創立30周年記念講演記念誌「JRA畜産振興事業を活用した畜産技術」　2021/10
黒毛和種の肉質形質に関する遺伝的改良の現状と展開 Invited

上本吉伸

肉牛ジャーナル　34　(2)　42-45　2021/02
高密度SNP情報を用いた家畜育種への応用 Invited

上本吉伸

畜産技術　(734)　25‐31-31　2016/07
Publisher: 畜産技術協会
ISSN： 0389-1348
Quantitative Trait Loci Analysis Using a Closed Pig Line Breeding Population Peer-reviewed

上本吉伸, 小林栄治, 鈴木啓一

日本養豚学会誌　48　(4)　147-163　2011/12
Publisher: 日本養豚学会
DOI： 10.5938/youton.48.147 　

ISSN： 0913-882X

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Books and Other Publications 1

農学生命科学を学ぶための入門生物学

鳥山, 欽哉

東北大学出版会　2020/01/31

ISBN: 9784861633430

Industrial Property Rights 1

ウシ個体における屠畜後の肉中イノシン酸含量の判定方法

上本吉伸

Property Type: Patent

Research Projects 2

腸内細菌叢と宿主DNAマーカーによる新規ブタ育種基盤の構築

上本吉伸, 北澤春樹

Offer Organization: 日本学術振興会

System: 科学研究費助成事業

Category: 基盤研究(B)

Institution: 東北大学

2022/04/01 - 2025/03/31
Utilization of gut microbiome for pig breeding in feed conversion ratio

Uemoto Yoshinobu

Offer Organization: Japan Society for the Promotion of Science

System: Grants-in-Aid for Scientific Research

Category: Grant-in-Aid for Scientific Research (C)

Institution: Tohoku University

2019/04/01 - 2022/03/31

More details Close

In this study, we evaluated the genetic effects of feed conversion ratio in purebred pigs, and showed that the estimated heritability for feed conversion ratio is moderate, suggesting that genetic improvement of feed conversion ratio is possible. Next, the relationship between gut microbiome and feed conversion ratio was investigated, suggesting that the higher the diversity of gut microbiota in a pig, the higher the feed utilization. Furthermore, we investigated the genetic influence on the diversity of the gut microbiome by estimating heritability, suggesting that the diversity of the gut microbiome is influenced by a genetic factor. These results suggest that the information of gut microbiome in pig can be utilized as a new selection index for genetic improvement of feed conversion ratio in pigs.