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Shibutani S, Endo M, Mizukami K, Hosoi E, Sakai Y, Taniguchi M, Harada H, Momozawa Y, Iwata H. Development of a high-throughput screening method for the detection of 188 pathogenic variants and its application in Mishima cattle. Anim Genet 2023; 54:416-417. [PMID: 36785519 DOI: 10.1111/age.13301] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/26/2022] [Revised: 01/24/2023] [Accepted: 01/24/2023] [Indexed: 02/15/2023]
Affiliation(s)
- Shusaku Shibutani
- Laboratory of Veterinary Hygiene, Joint Faculty of Veterinary Medicine, Yamaguchi University, Yamaguchi, Japan
| | - Mikiko Endo
- Laboratory for Genotyping Development, RIKEN Center for Integrative Medical Sciences, Yokohama, Japan
| | - Keijiro Mizukami
- Laboratory for Genotyping Development, RIKEN Center for Integrative Medical Sciences, Yokohama, Japan
| | - Eiji Hosoi
- Graduate School of Sciences and Technology for Innovation, Yamaguchi University, Yamaguchi, Japan
| | - Yusuke Sakai
- Laboratory of Veterinary Pathology, Joint Faculty of Veterinary Medicine, Yamaguchi University, Yamaguchi, Japan
| | - Masayasu Taniguchi
- Laboratory of Veterinary Theriogenology, Joint Faculty of Veterinary Medicine, Yamaguchi University, Yamaguchi, Japan
| | - Hisashi Harada
- Yamaguchi Prefecture Northern Livestock Hygiene Service Center, Yamaguchi, Japan
| | - Yukihide Momozawa
- Laboratory for Genotyping Development, RIKEN Center for Integrative Medical Sciences, Yokohama, Japan
| | - Hiroyuki Iwata
- Laboratory of Veterinary Hygiene, Joint Faculty of Veterinary Medicine, Yamaguchi University, Yamaguchi, Japan
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Liu Z, Sun H, Lai W, Hu M, Zhang Y, Bai C, Liu J, Ren H, Li F, Yan S. Genome-wide re-sequencing reveals population structure and genetic diversity of Bohai Black cattle. Anim Genet 2021; 53:133-136. [PMID: 34783059 DOI: 10.1111/age.13155] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 11/01/2021] [Indexed: 11/29/2022]
Abstract
Bohai Black (BHB) cattle, one of eight representative indigenous breeds in China, is well known for its high resistance to disease, endurance under unfavorable feeding conditions and excellent meat quality. Over recent, the number of BHB cattle has decreased sharply. To investigate the population structure and genetic diversity of this breed, the whole-genome data of 35 individuals from a conservation farm were obtained using the Illumina 150 bp paired-end platform. The results of the genetic structure and diversity analyses showed that BHB cattle had mixed Bos taurus and Bos indicus ancestry, close phylogenic relationships with Jiaxian Red and Luxi cattle and abundant genetic diversity. The bulls tested here could be divided into six families. This study presents a comprehensive evaluation of the genetic structure and diversity of the BHB cattle, and lays the theoretical basis for conservation and utilization of the valuable germplasm resource.
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Affiliation(s)
- Z Liu
- College of Animal Science, Jilin University, Changchun, 130062, China
| | - H Sun
- College of Animal Science, Jilin University, Changchun, 130062, China
| | - W Lai
- College of Animal Science, Jilin University, Changchun, 130062, China
| | - M Hu
- College of Animal Science, Jilin University, Changchun, 130062, China
| | - Y Zhang
- College of Animal Science, Jilin University, Changchun, 130062, China
| | - C Bai
- College of Animal Science, Jilin University, Changchun, 130062, China
| | - J Liu
- Shandong Binzhou Animal Science & Veterinary Medicine Academy, Binzhou, 256600, China
| | - H Ren
- Key Laboratory of Zoonosis Research, Ministry of Education, Institute of Zoonosis, Jilin University, Changchun, 130062, China
| | - F Li
- Shandong Binzhou Animal Science & Veterinary Medicine Academy, Binzhou, 256600, China
| | - S Yan
- College of Animal Science, Jilin University, Changchun, 130062, China
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Chen Q, Shen J, Hanif Q, Chen N, Huang Y, Dang R, Lan X, Chen H, Lei C. Whole genome analyses revealed genomic difference between European taurine and East Asian taurine. J Anim Breed Genet 2020; 138:56-68. [PMID: 32770713 DOI: 10.1111/jbg.12501] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2020] [Revised: 06/29/2020] [Accepted: 07/10/2020] [Indexed: 12/19/2022]
Abstract
European taurine and East Asian taurine are two main clades in Bos taurus, but their genomic differences are not clearly elucidated. Here, we sequenced 16 Mongolian cattle genomes and compared them to the 92 genomes of 10 representative breeds worldwide. We found the highest LD level in Mishima cattle and the fastest LD decay in European taurine. Phylogenetic analysis revealed that Mongolian, Hanwoo and Mishima cattle were clustered into East Asian taurine. From selective sweep, gene annotation, functional enrichment and differential expression analysis, we identified selective signals including genes and/or pathways related to rapid growth and large body size in European taurine, and superior meat quality in East Asian taurine. Our findings will help us understand the evolutionary history and formation process of the breeds and provide theoretical materials regarding the genetic mechanism underlying breed characteristics and molecular breeding programmes of the taurine clades in the future.
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Affiliation(s)
- Qiuming Chen
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, Yangling, China
| | - Jiafei Shen
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, Yangling, China
| | - Quratulain Hanif
- National Institute for Biotechnology and Genetic Engineering, Pakistan Institute of Engineering and Applied Sciences, Faisalabad, Pakistan.,Pakistan Institute of Engineering and Applied Sciences, Nilore, Islamabad, Pakistan
| | - Ningbo Chen
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, Yangling, China
| | - Yongzhen Huang
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, Yangling, China
| | - Ruihua Dang
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, Yangling, China
| | - Xianyong Lan
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, Yangling, China
| | - Hong Chen
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, Yangling, China
| | - Chuzhao Lei
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, Yangling, China
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Interspecific comparison of allometry between body weight and chest girth in domestic bovids. Sci Rep 2017; 7:4817. [PMID: 28684855 PMCID: PMC5500593 DOI: 10.1038/s41598-017-04976-z] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2016] [Accepted: 05/23/2017] [Indexed: 11/08/2022] Open
Abstract
The sizes of body parts often co-vary through exponential scaling, known as allometry. The evolution of allometry is central to the generation of morphological diversity. To make inferences regarding the evolved responses in allometry to natural and artificial selection, we compared allometric parameters (slope and intercept) among seven species and breeds of domestic bovids using cross-sectional ontogenetic data and attempted to interpret the differences in these parameters. The allometric slopes were not different among some species, whereas those between breeds within species were, indicating that the slopes were typically invariant but could be changed under strong, specific selection. With the exception of yak, the differences in the intercept independent of the slopes (the alternative intercept) among species might better correspond to their divergence times than the differences in allometric slope, and the remarkably higher alternative intercept found in yaks can be explained by their unique morphological evolution. These findings provide evidence that differences in the alternative intercept can retain traces of the phylogenetic changes derived from differentiation and evolution.
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Tsuda K, Kawahara-Miki R, Sano S, Imai M, Noguchi T, Inayoshi Y, Kono T. Abundant sequence divergence in the native Japanese cattle Mishima-Ushi (Bos taurus) detected using whole-genome sequencing. Genomics 2013; 102:372-8. [PMID: 23938316 DOI: 10.1016/j.ygeno.2013.08.002] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2013] [Revised: 07/06/2013] [Accepted: 08/02/2013] [Indexed: 12/30/2022]
Abstract
The native Japanese cattle Mishima-Ushi, a designated national natural treasure, are bred on a remote island, which has resulted in the conservation of their genealogy. We examined the genetic characteristics of 8 Mishima-Ushi individuals by using single nucleotide polymorphisms (SNPs), insertions, and deletions obtained by whole-genome sequencing. Mapping analysis with various criteria showed that predicted heterozygous SNPs were more prevalent than predicted homozygous SNPs in the exonic region, especially non-synonymous SNPs. From the identified 6.54 million polymorphisms, we found 400 non-synonymous SNPs in 313 genes specific to each of the 8 Mishima-Ushi individuals. Additionally, 3,170,833 polymorphisms were found between the 8 Mishima-Ushi individuals. Phylogenetic analysis confirmed that the Mishima-Ushi population diverged from another strain of Japanese cattle. This study provides a framework for further genetic studies of Mishima-Ushi and research on the function of SNP-containing genes as well as understanding the genetic relationship between the domestic and native Japanese cattle breeds.
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Affiliation(s)
- Kaoru Tsuda
- Genome Research Center, NODAI Research Institute, Tokyo University of Agriculture, 1-1-1 Sakuragaoka, Setagaya-ku, Tokyo 156-8502, Japan
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Baldursdottir BK, Kristjansson T, Hallsson JH. Diversity of the Icelandic goat breed assessed using population data. ACTA AGR SCAND A-AN 2012. [DOI: 10.1080/09064702.2012.723737] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
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Komatsu M, Itoh T, Fujimori Y, Satoh M, Miyazaki Y, Takahashi H, Shimizu K, Malau-Aduli AEO, Morita M. Genetic association between GHSR1a 5'UTR-microsatellite and nt-7(C>A) loci and growth and carcass traits in Japanese Black cattle. Anim Sci J 2011; 82:396-405. [PMID: 21615832 DOI: 10.1111/j.1740-0929.2010.00852.x] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
We carried out a genetic association study between five nucleotide polymorphisms (5'UTR microsatellite ((TG)(n)), nt-7(C>A), L24V, DelR242 and Intron 1 microsatellite) of the GHSR1a gene and growth and carcass traits in 1285 steers sired by 117 Japanese Black bulls in a progeny testing program. We report herein, a significant association between the 5'UTR microsatellite and nt-7(C>A) loci and growth and carcass traits. We also propose a translational hypothesis that the association is due to differences in the secondary structure of GHSR1b mRNA (the non-spliced type with the 5'UTR microsatellite) among the GHSR1a gene haplotypes. Furthermore, we predicted the potential increase in profitability due to increased carcass weight in cow-calf fattening enterprises through planned matings based on DNA testing of the 5'UTR microsatellite. Statistical analysis revealed that the 5'UTR microsatellite locus had a significant additive effect on carcass weight (CW) and average daily gain (ADG), but not on beef marbling score (BMS). One of the four major microsatellite alleles (19-TG allele) with an allele frequency of 0.145, had a significantly (P < 0.0007) desirable effect on CW and ADG. We concluded that the 19-TG allele could potentially be economically useful nucleotide markers for growth and carcass traits in Japanese Black cattle.
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Affiliation(s)
- Masanori Komatsu
- National Institute of Livestock and Grassland Science, Tsukuba, Japan.
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KOMATSU M, FUJIMORI Y, SATO Y, OKAMURA H, SASAKI S, ITOH T, MORITA M, NAKAMURA R, OE T, FURUTA M, YASUDA J, KOJIMA T, WATANABE T, HAYASHI T, MALAU-ADULI AE, TAKAHASHI H. Nucleotide polymorphisms and the 5′-UTR transcriptional analysis of the bovine growth hormone secretagogue receptor 1a (GHSR1a) gene. Anim Sci J 2010; 81:530-50. [DOI: 10.1111/j.1740-0929.2010.00797.x] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
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