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12. Phylogenomics and Spatiotemporal Dynamics of Bovine Leukemia Virus Focusing on Asian Native Cattle: Insights Into the Early Origin and Global Dissemination

Author

Nishikaku, Kohei, primary, Yonezawa, Takahiro, additional, Nishibori, Masahide, additional, Harada, Masashi, additional, Kawaguchi, Fuki, additional, Sasazaki, Shinji, additional, Torii, Yasushi, additional, Imakawa, Kazuhiko, additional, Kawai, Kuniko, additional, Liu, Jianquan, additional, Mannen, Hideyuki, additional, and Kobayashi, Tomoko, additional

Published
2022
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32. Detection of candidate polymorphisms around the QTL for fat area ratio to rib eye area on BTA7 using whole‐genome resequencing in Japanese Black cattle

Author

Sasazaki, Shinji, primary, Kawaguchi, Fuki, additional, Nakajima, Ayaka, additional, Yamamoto, Raito, additional, Akiyama, Takayuki, additional, Kohama, Namiko, additional, Yoshida, Emi, additional, Kobayashi, Eiji, additional, Honda, Takeshi, additional, Oyama, Kenji, additional, and Mannen, Hideyuki, additional

Published
2020
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34. Zebu Cattle Are an Exclusive Legacy of the South Asia Neolithic

Author

Chen, Shanyuan, Lin, Bang-Zhong, Baig, Mumtaz, Mitra, Bikash, Lopes, Ricardo J., Santos, António M., Magee, David A., Azevedo, Marisa, Tarroso, Pedro, Sasazaki, Shinji, Ostrowski, Stephane, Mahgoub, Osman, Chaudhuri, Tapas K., Zhang, Ya-ping, Costa, Vânia, Royo, Luis J., Goyache, Félix, Luikart, Gordon, Boivin, Nicole, Fuller, Dorian Q., Mannen, Hideyuki, Bradley, Daniel G., and Beja-Pereira, Albano

Published
2010

35. Low mitochondrial DNA diversity of Japanese Polled and Kuchinoshima feral cattle

Author

Mannen, Hideyuki, Yonesaka, Riku, Noda, Aoi, Shimogiri, Takeshi, Oshima, Ichiro, Katahira, Kiyomi, Kanemaki, Misao, Kunieda, Tetsuo, Inayoshi, Yousuke, Mukai, Fumio, and Sasazaki, Shinji

Subjects
Japanese Polled, mtDNA, education, Kuchinoshima feral cattle, genetic diversity, small population size
Abstract

This study aims to estimate the mitochondrial genetic diversity and structure of Japanese Polled and Kuchinoshima feral cattle, which are maintained in small populations. We determined the mitochondrial DMA (mtDNA) displacement loop (D-loop) sequences for both cattle populations and analyzed these in conjunction with previously published data from Northeast Asian cattle populations. Our findings showed that Japanese native cattle have a predominant, Asian-specific mtDNA haplogroup T4 with high frequencies (0.43-0.81). This excluded Kuchinoshima cattle (32 animals), which had only one mtDNA haplotype belonging to the haplogroup T3. Japanese Polled showed relatively lower mtDNA diversity in the average sequence divergence (0.0020) than other Wagyu breeds (0.0036-0.0047). Japanese Polled have been maintained in a limited area of Yamaguchi, and the population size is now less than 200. Therefore, low mtDNA diversity in the Japanese Polled could be explained by the decreasing population size in the last three decades. We found low mtDNA diversity in both Japanese Polled and Kuchinoshima cattle. The genetic information obtained in this study will be useful for maintaining these populations and for understanding the origin of Japanese native cattle.

Published
2017

36. Identification of leptin gene polymorphisms associated with carcass traits and fatty acid composition in Japanese Black cattle

Author

Kawaguchi, Fuki, Okura, Kazuki, Oyama, Kenji, Mannen, Hideyuki, and Sasazaki, Shinji

Subjects
fatty acid composition, food and beverages, lipids (amino acids, peptides, and proteins), leptin, Japanese Black cattle
Abstract

Previous studies have indicated that some leptin gene polymorphisms were associated with economically important traits in cattle breeds. However, polymorphisms in the leptin gene have not been reported thus far in Japanese Black cattle. Here, we aimed to identify the leptin gene polymorphisms which are associated with carcass traits and fatty acid composition in Japanese Black cattle. We sequenced the full‐length CDS of leptin gene for eight Japanese Black cattle. Sequence comparison revealed eight SNPs. Three of these were predicted to cause amino acid substitutions: Y7F, R25C, and A80V. Then, we genotyped these SNPs in two populations (JB1 with 560 animals and JB2 with 450 animals) and investigated the effects on the traits. Y7F in JB1 and A80V in JB2 were excluded from statistical analysis because the minor allele frequencies were low (

Published
2017

41. The Eurasian Steppe is an important goat propagation route: A phylogeographic analysis using mitochondrial DNA and Y‐chromosome sequences of Kazakhstani goats

Author

Tabata, Risa, primary, Kawaguchi, Fuki, additional, Sasazaki, Shinji, additional, Yamamoto, Yoshio, additional, Bakhtin, Meirat, additional, Kazymbet, Polat, additional, Meldevekob, Alykhan, additional, Suleimenov, Maratbek Z., additional, Nishibori, Masahide, additional, and Mannen, Hideyuki, additional

Published
2018
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42. Kazakhstani native cattle reveal highly divergent mtDNA fromBos taurusandBos indicuslineages with an absence ofBos indicusY chromosome

Author

Yamanaka, Hayate, primary, Murata, Kako, additional, Tabata, Risa, additional, Kawaguchi, Fuki, additional, Sasazaki, Shinji, additional, Yamamoto, Yoshio, additional, Bakhtin, Meirat, additional, Kazymbet, Polat, additional, Meldevekob, Alykhan, additional, Suleimenov, Maratbek Z., additional, Nishibori, Masahide, additional, and Mannen, Hideyuki, additional

Published
2018
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44. Association between fatty acid compositions and genotypes of FABP4 and LXR-alpha in Japanese Black cattle

Author

Oyama Kenji, Taniguchi Masaaki, Sasazaki Shinji, Ohsaki Hideki, Tanaka Atsuko, Hinenoya Tomoko, Hoashi Shogo, Mukai Fumio, and Mannen Hideyuki

Subjects
Genetics, QH426-470
Abstract

Abstract Background Fatty acid composition has become an important trait in the beef industry in terms of beef flavor and decreasing the circulating concentration of LDL cholesterol. In this study, we examined the association between polymorphisms of six genes, adipocytes-type fatty acid binding protein (FABP4), liver X receptor α (LXRα), cytochrome b5 (Cyt b5), long-chain acyl-CoA synthetase (ACSL) 1, ACSL4 and diacylglycerol acyltransferase 2 (DGAT2) and fatty acid composition. Results Sequence comparisons revealed 14 single nucleotide polymorphisms in six genes. Four of them, I74V and V110M in FABP4 and G51E and V133I in LXRα, were nonsynonymous substitutions. The associations between the genotypes and fatty acid compositions were analyzed by using 234 Japanese Black cattle. The genotypes of FABP4 I74V and LXRα V133I were significantly associated with palmitoleic acids (C16:1, P = 0.0086) and linoleic acid (C18:2, P = 0.0121) content in intramuscular fat, respectively. Conclusion Our findings suggest that the two polymorphisms of FABP4 I74V and LXRα V133I might be genetic factors in part associated with palmitoleic acid (FABP4 I74V) and linoleic acid (LXRα V133I) composition in intramuscular fat of Japanese Black cattle, respectively. Especially, FABP4 I74V had highly significant effect (P < 0.01) on C16:1 proportion, indicating that the I/I homozygote exhibited 0.5% higher percentage than V/V homozygote.

Published
2008
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45. An assessment of population structure in eight breeds of cattle using a whole genome SNP panel

Author

Gao Chuan, Gill Clare A, Neto Emmanuel, Crews Denny, Coppieters Wouter, Aerts Jan, Matukumalli Lakshmi K, Murdoch Brenda M, Schnabel Robert D, McKay Stephanie D, Mannen Hideyuki, Wang Zhiquan, Van Tassell Curt P, Williams John L, Taylor Jeremy F, and Moore Stephen S

Subjects
Genetics, QH426-470
Abstract

Abstract Background Analyses of population structure and breed diversity have provided insight into the origin and evolution of cattle. Previously, these studies have used a low density of microsatellite markers, however, with the large number of single nucleotide polymorphism markers that are now available, it is possible to perform genome wide population genetic analyses in cattle. In this study, we used a high-density panel of SNP markers to examine population structure and diversity among eight cattle breeds sampled from Bos indicus and Bos taurus. Results Two thousand six hundred and forty one single nucleotide polymorphisms (SNPs) spanning all of the bovine autosomal genome were genotyped in Angus, Brahman, Charolais, Dutch Black and White Dairy, Holstein, Japanese Black, Limousin and Nelore cattle. Population structure was examined using the linkage model in the program STRUCTURE and Fst estimates were used to construct a neighbor-joining tree to represent the phylogenetic relationship among these breeds. Conclusion The whole-genome SNP panel identified several levels of population substructure in the set of examined cattle breeds. The greatest level of genetic differentiation was detected between the Bos taurus and Bos indicus breeds. When the Bos indicus breeds were excluded from the analysis, genetic differences among beef versus dairy and European versus Asian breeds were detected among the Bos taurus breeds. Exploration of the number of SNP loci required to differentiate between breeds showed that for 100 SNP loci, individuals could only be correctly clustered into breeds 50% of the time, thus a large number of SNP markers are required to replace the 30 microsatellite markers that are currently commonly used in genetic diversity studies.

Published
2008
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46. Whole genome linkage disequilibrium maps in cattle

Author

Mannen Hideyuki, Gao Chuan, Gill Clare A, Neto Emmanuel, Crews Denny, Coppieters Wouter, Aerts Jan, Matukumalli Lakshmi K, Murdoch Brenda M, Schnabel Robert D, McKay Stephanie D, Stothard Paul, Wang Zhiquan, Van Tassell Curt P, Williams John L, Taylor Jeremy F, and Moore Stephen S

Subjects
Genetics, QH426-470
Abstract

Abstract Background Bovine whole genome linkage disequilibrium maps were constructed for eight breeds of cattle. These data provide fundamental information concerning bovine genome organization which will allow the design of studies to associate genetic variation with economically important traits and also provides background information concerning the extent of long range linkage disequilibrium in cattle. Results Linkage disequilibrium was assessed using r2 among all pairs of syntenic markers within eight breeds of cattle from the Bos taurus and Bos indicus subspecies. Bos taurus breeds included Angus, Charolais, Dutch Black and White Dairy, Holstein, Japanese Black and Limousin while Bos indicus breeds included Brahman and Nelore. Approximately 2670 markers spanning the entire bovine autosomal genome were used to estimate pairwise r2 values. We found that the extent of linkage disequilibrium is no more than 0.5 Mb in these eight breeds of cattle. Conclusion Linkage disequilibrium in cattle has previously been reported to extend several tens of centimorgans. Our results, based on a much larger sample of marker loci and across eight breeds of cattle indicate that in cattle linkage disequilibrium persists over much more limited distances. Our findings suggest that 30,000–50,000 loci will be needed to conduct whole genome association studies in cattle.

Published
2007
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48. Pool-based genome-wide association study identified novel candidate regions on BTA9 and 14 for oleic acid percentage in Japanese Black cattle

Author

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

Published
2018
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49. A genome-wide association study for fat-related traits computed by image analysis in Japanese Black cattle

Author

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

Published
2018
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