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Sasaki S, Watanabe T, Ibi T, Hasegawa K, Sakamoto Y, Moriwaki S, Kurogi K, Ogino A, Yasumori T, Wakaguri H, Muraki E, Miki Y, Yoshida Y, Inoue Y, Tabuchi I, Iwao K, Arishima T, Kawashima K, Watanabe M, Sugano S, Sugimoto Y, Suzuki Y. Identification of deleterious recessive haplotypes and candidate deleterious recessive mutations in Japanese Black cattle. Sci Rep 2021; 11:6687. [PMID: 33758295 PMCID: PMC7988166 DOI: 10.1038/s41598-021-86225-y] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/24/2020] [Accepted: 03/05/2021] [Indexed: 02/01/2023] Open
Abstract
Intensive use of a few elite sires has increased the risk of the manifestation of deleterious recessive traits in cattle. Substantial genotyping data gathered using single-nucleotide polymorphism (SNP) arrays have identified the haplotypes with homozygous deficiency, which may compromise survival. We developed Japanese Black cattle haplotypes (JBHs) using SNP array data (4843 individuals) and identified deleterious recessive haplotypes using exome sequencing of 517 sires. We identified seven JBHs with homozygous deficiency. JBH_10 and JBH_17 were associated with the resuming of estrus after artificial insemination, indicating that these haplotypes carried deleterious mutations affecting embryonic survival. The exome data of 517 Japanese Black sires revealed that AC_000165.1:g.85341291C>G of IARS in JBH_8_2, AC_000174.1:g.74743512G>T of CDC45 in JBH_17, and a copy variation region (CNVR_27) of CLDN16 in JBH_1_1 and JBH_1_2 were the candidate mutations. A novel variant AC_000174.1:g.74743512G>T of CDC45 in JBH_17 was located in a splicing donor site at a distance of 5 bp, affecting pre-mRNA splicing. Mating between heterozygotes of JBH_17 indicated that homozygotes carrying the risk allele died around the blastocyst stage. Analysis of frequency of the CDC45 risk allele revealed that its carriers were widespread throughout the tested Japanese Black cattle population. Our approach can effectively manage the inheritance of recessive risk alleles in a breeding population.
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Affiliation(s)
- Shinji Sasaki
- grid.267625.20000 0001 0685 5104Faculty of Agriculture, University of the Ryukyus, 1 Senbaru, Nishihara, Nakagami-gun, Okinawa, 903-0213 Japan ,grid.258333.c0000 0001 1167 1801United Graduate School of Agricultural Sciences, Kagoshima University, 1-21-24 Korimoto, Kagoshima, 890-0065 Japan
| | - Toshio Watanabe
- Maebashi Institute of Animal Science, Livestock Improvement Association of Japan, Inc., Maebashi, 371-0121 Japan
| | - Takayuki Ibi
- grid.261356.50000 0001 1302 4472Graduate School of Environmental and Life Science, Okayama University, Tsushima-naka, Okayama, 700-8530 Japan
| | - Kiyotoshi Hasegawa
- Shimane Prefecture Livestock Technology Center, Koshi, Izumo, Shimane 693-0031 Japan
| | - Yoichi Sakamoto
- Shimane Prefecture Livestock Technology Center, Koshi, Izumo, Shimane 693-0031 Japan
| | - Shunsuke Moriwaki
- Shimane Prefecture Livestock Technology Center, Koshi, Izumo, Shimane 693-0031 Japan
| | - Kazuhito Kurogi
- Maebashi Institute of Animal Science, Livestock Improvement Association of Japan, Inc., Maebashi, 371-0121 Japan
| | - Atsushi Ogino
- Maebashi Institute of Animal Science, Livestock Improvement Association of Japan, Inc., Maebashi, 371-0121 Japan
| | - Takanori Yasumori
- Maebashi Institute of Animal Science, Livestock Improvement Association of Japan, Inc., Maebashi, 371-0121 Japan
| | - Hiroyuki Wakaguri
- grid.26999.3d0000 0001 2151 536XDepartment of Medical Genome Sciences, and Department of Computational Biology, Graduate School of Frontier Sciences, The University of Tokyo, Chiba, 277-8562 Japan
| | - Eiji Muraki
- Hida Beef Cattle Research Department, Gifu Prefectural Livestock Research Institute, Makigadou, Kiomi, Takayama, Gifu 506-0101 Japan
| | - Youko Miki
- Hyogo Prefectural Technology Center for Agriculture, Forest and Fisher, Hokubu Agricultural Technology Institute, Asago, Hyogo 669-5254 Japan
| | - Yuichi Yoshida
- Hyogo Prefectural Technology Center for Agriculture, Forest and Fisher, Hokubu Agricultural Technology Institute, Asago, Hyogo 669-5254 Japan
| | - Yoshinobu Inoue
- Tottori Prefecture Livestock Research Center, Tohaku-gun, Kotoura-cho 689-2503 Japan
| | - Ichiro Tabuchi
- Tottori Prefecture Livestock Research Center, Tohaku-gun, Kotoura-cho 689-2503 Japan
| | - Ken Iwao
- Tottori Prefecture Livestock Research Center, Tohaku-gun, Kotoura-cho 689-2503 Japan
| | - Taichi Arishima
- Cattle Breeding Development Institute of Kagoshima Prefecture, Osumi, So, Kagoshima 899-8212 Japan
| | - Keisuke Kawashima
- Cattle Breeding Development Institute of Kagoshima Prefecture, Osumi, So, Kagoshima 899-8212 Japan
| | - Manabu Watanabe
- grid.26999.3d0000 0001 2151 536XDepartment of Medical Genome Sciences, and Department of Computational Biology, Graduate School of Frontier Sciences, The University of Tokyo, Chiba, 277-8562 Japan
| | - Sumio Sugano
- grid.26999.3d0000 0001 2151 536XDepartment of Medical Genome Sciences, and Department of Computational Biology, Graduate School of Frontier Sciences, The University of Tokyo, Chiba, 277-8562 Japan
| | - Yoshikazu Sugimoto
- Shirakawa Institute of Animal Genetics, Japan Livestock Technology Association, Yushima, Bunkyouku, Tokyo 113-0034 Japan
| | - Yutaka Suzuki
- grid.26999.3d0000 0001 2151 536XDepartment of Medical Genome Sciences, and Department of Computational Biology, Graduate School of Frontier Sciences, The University of Tokyo, Chiba, 277-8562 Japan
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Kasarda R, Moravčíková N, Vostrý L, Krupová Z, Krupa E, Lehocká K, Olšanská B, Trakovická A, Nádaský R, Polák P, Židek R, Belej Ľ, Golian J. Fine-scale analysis of six beef cattle breeds revealed patterns of their genomic diversity. ITALIAN JOURNAL OF ANIMAL SCIENCE 2020. [DOI: 10.1080/1828051x.2020.1852894] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/22/2022]
Affiliation(s)
- Radovan Kasarda
- Katedra genetiky a plemenárskej biológie, Slovak University of Agriculture in Nitra, Nitra, Slovak Republic
| | - Nina Moravčíková
- Katedra genetiky a plemenárskej biológie, Slovak University of Agriculture in Nitra, Nitra, Slovak Republic
| | - Luboš Vostrý
- Katedra genetiky a šlechtění, Czech University of Life Sciences Prague, Praha, Czech Republic
- Institute of Animal Science, Praha-Uhříněves, Czech Republic
| | - Zuzana Krupová
- Institute of Animal Science, Praha-Uhříněves, Czech Republic
| | - Emil Krupa
- Institute of Animal Science, Praha-Uhříněves, Czech Republic
| | - Kristína Lehocká
- Katedra genetiky a plemenárskej biológie, Slovak University of Agriculture in Nitra, Nitra, Slovak Republic
| | - Barbora Olšanská
- Katedra genetiky a plemenárskej biológie, Slovak University of Agriculture in Nitra, Nitra, Slovak Republic
| | - Anna Trakovická
- Katedra genetiky a plemenárskej biológie, Slovak University of Agriculture in Nitra, Nitra, Slovak Republic
| | - Rudolf Nádaský
- Agricultural cooperation Špačince, Špačince, Slovak Republic
| | - Peter Polák
- Beef Breeders Association, Ivanka pri Nitre, Slovak Republic
| | - Radoslav Židek
- Katedra hygieny a bezpečnosti potravín, Slovak University of Agriculture in Nitra, Nitra, Slovak Republic
| | - Ľubomír Belej
- Katedra hygieny a bezpečnosti potravín, Slovak University of Agriculture in Nitra, Nitra, Slovak Republic
| | - Jozef Golian
- Katedra hygieny a bezpečnosti potravín, Slovak University of Agriculture in Nitra, Nitra, Slovak Republic
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