ゲノムワイドな一塩基多型マーカーを用いた 黒毛和種集団における遺伝的特性把握の試み
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| Published in | 動物遺伝育種研究 Vol. 50; no. 1; pp. 3 - 9 |
|---|---|
| Main Authors | , , , , , , |
| Format | Journal Article |
| Language | English |
| Published |
日本動物遺伝育種学会
2022
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| Online Access | Get full text |
| ISSN | 1345-9961 1884-3883 |
| DOI | 10.5924/abgri.50.3 |
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| Author | 造田, 葵 祝前, 博明 小川, 伸一郎 谷口, 幸雄 杉本, 喜憲 松田, 洋和 渡邊, 敏夫 |
|---|---|
| Author_xml | – sequence: 1 fullname: 造田, 葵 organization: 京都大学大学院農学研究科、京都市左京区、606-8502 – sequence: 1 fullname: 小川, 伸一郎 organization: 現所属：東北大学大学院農学研究科、仙台市青葉区、980-8572 – sequence: 1 fullname: 杉本, 喜憲 organization: 公益社団法人 畜産技術協会 動物遺伝研究所、文京区湯島、371-0121 – sequence: 1 fullname: 松田, 洋和 organization: 現所属：公益社団法人 全国和牛登録協会、京都市中京区、604-0845 – sequence: 1 fullname: 渡邊, 敏夫 organization: 現所属：一般社団法人 家畜改良事業団、前橋市金丸町、371-0121 – sequence: 1 fullname: 谷口, 幸雄 organization: 京都大学大学院農学研究科、京都市左京区、606-8502 – sequence: 1 fullname: 祝前, 博明 organization: 現所属：新潟大学佐渡自然共生科学センター里山領域、佐渡市新穂潟上、952-0103 |
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| Copyright | 2022 日本動物遺伝育種学会 |
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| DOI | 10.5924/abgri.50.3 |
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| EndPage | 9 |
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| References | Doekes HP, Veerkamp RF, Bijma P, Hiemstra SJ, Windig JJ.2018. Trends in genome-wide and region-specificgenetic diversity in the Dutch-Flemish Holstein-Friesian breeding program from 1986 to 2015. GeneticsSelection Evolution, 50: 15. Goddard ME. 2009. Genomic selection: prediction ofaccuracy and maximization of long term response.Genetica, 136: 245–257. Ogawa S, Matsuda H, Taniguchi Y, Watanabe T, NishimuraS, Sugimoto Y, Iwaisaki H. 2014. Effects of singlenucleotide polymorphism marker density on degree ofgenetic variance explained and genomic evaluation forcarcass traits in Japanese Black beef cattle. BMCGenetics, 15: 15. Doublet A-C, Croiseau P, Fritz S, Michenet A, Hozé C,Danchin-Burge C, Laloë D, Restoux G. 2019. Theimpact of genomic selection on genetic diversity andgenetic gain in three French dairy cattle breeds.Genetics Selection Evolution, 51: 52. Sasaki Y, Miyake T, Gaillard C, Oguni T, Matsumoto M, ItoM, Kurahara T, Sasae Y, Fujinaka K, Ohtagaki S,Dougo, T. 2006. Comparison of genetic gains per yearfor carcass traits among breeding programs in theJapanese Brown and the Japanese Black cattle. Journalof Animal Science, 84: 317–323. Daetwyler HD, Villanueva B, Woolliams JA. 2008.Accuracy of predicting the genetic risk of disease usinga genome-wide approach. PLoS One, 3: e3395. Forutan M, Mahuari SA, Baes C, Melzer N, Schenkel FS,Sargolzaei M. 2018. Inbreeding and runs ofhomozygosity before and after genomic selection inNorth American Holstein cattle. BMC Genomics, 19:98. Namikawa K. 1992. WAGYU: JAPANESE BEEF CATTLE- Historical Breeding Processes of Japanese Beef Cattleand Preservation of genetic resources as economic farmanimals. Wagyu Registry Association, Kyoto Japan. Nomura T, Hayashi H, Sasaki Y. 1987. The breedingstructure and genetic analysis of the Japanese Black cattle in the Chugoku district. The Japanese Journal ofZootechnical Science, 58: 21–27. (in Japanese) Nomura T, Sasaki Y. 1986. Breeding structure based onmovements of sires between prefectures and on geneticcontribution of prefectural sub population to theJapanese Black cattle. The Japanese Journal ofZootechnical Science. 57: 372–378. (in Japanese) Browning BL, Browning SR. 2007. Rapid and accuratehaplotype phasing and missing-data inference forwhole-genome association studies by use of localizedhaplotype clustering. American Journal of Human Genetics, 81: 1084–1097. Chen CY, Misztal I, Aguilar I, Legarra A, Muir WM. 2011.Effect of different genomic relationship matrices onaccuracy and scale. Journal of Animal Science, 89:2673–2679. Nishimaki T, Ibi T, Tanabe Y, Miyazaki Y, Kobayashi N,Matsuhashi T, Akiyama T, Yoshida E, Imai K, MatsuiM, Uemura K, Watanabe N, Fujita T, Saito Y, KomatsuT, Yamada T, Mannen H, Sasazaki S, Kunieda T. 2013.The assessment of genetic diversity within and amongthe eight subpopulations of Japanese Black cattle using52 microsatellite markers. Animal Science Journal, 84:585–591. Hirano T, Watanabe T, Nishimura S, Takasuga A, HanzawaK, Sugimoto Y. 2013. SNP discovery and evaluationwith whole genome re-sequencing using pooled DNA inJapanese Black cattle. Nihon Chikusan Gakkaiho, 84:319–325. (in Japanese) Engelsma KA, Veerkamp RF, Calus MPL, Bijma P, WindigJJ. 2012. Pedigree- and marker-based methods in theestimation of genetic diversity in small groups ofHolstein cattle. Journal of Animal Breeding andGenetics, 129: 195–205. Eynard SE, Windig JJ, Hiemstra SJ, Calus MPL. 2016.Whole-genome sequence data uncover loss of geneticdiversity due to selection. Genetics Selection Evolution,48: 33. de Roos APW, Hayes BJ, Spelman RJ, Goddard ME. 2008.Linkage disequilibrium and persistence of phase inHolstein-Friesian, Jersey and Angus cattle. Genetics,179: 1503–1512. Pérez-Enciso M. 2014. Genomic relationships computedfrom either next-generation sequence or array SNP data.Journal of Animal Breeding and Genetics, 131: 85–96. Honda T, Nomura T, Yamaguchi Y, Mukai F. 2004.Monitoring of genetic diversity in the Japanese Blackcattle population by the use of pedigree information.Journal of Animal Breeding and Genetics, 121: 242–252. Wagyu Registry Association. 2007. Breeding andImprovement of Wagyu. 2nd ed. Wagyu RegistryAssociation. Kyoto, Japan. (in Japanese) Ashida I, Iwaisaki H. 1998. A numerical technique forREML estimation of variance components usingaverage information algorithm and its computingproperty. Animal Science and Technology (Japan), 69:631–636. Sonesson AK, Wooliams JA, Meuwissen THE. 2012.Genomic selection requires genomic control ofinbreeding. Genetics Selection Evolution, 44: 27. Takayanagi S, Moriya K, Nomura T, Dohgo T, Sasaki Y.1996. Population structure of Japanese Black cattle inHyogo prefecture. Nihon Chikusan Gakkaiho, 67: 286– 290. (in Japanese) Yang J, Benyamin B, McEvoy BP, Gordon S, Henders AK,Nyholt DR, Madden PA, Heath AC, Martin NG,Montgomery GW, Goddard ME, Visscher PM. 2010.Common SNPs explain a large proportion of theheritability for human height. Nature Genetics, 42: 565–569. Nomura T, Honda T, Mukai F. 2001. Inbreeding andeffective population size of Japanese Black cattle.Journal of Animal Science, 79: 366–370. Ogawa S, Matsuda H, Taniguchi Y, Watanabe T, Kitamura Y,Tabuchi I, Sugimoto Y, Iwaisaki H. 2016. Genomicprediction for carcass traits in Japanese Black cattleusing single nucleotide polymorphism markers ofdifferent densities. Animal Production Science, 57:1631–1636. Honda T, Nomura T, Fukushima M, Mukai F. 2001. Geneticdiversity of a closed population of Japanese Black cattlein Hyogo prefecture. Animal Science Journal, 72: 378–385. VanRaden PM. 2008. Efficient methods to compute genomicpredictions. Journal of Dairy Science, 91: 4414–4423. Hill WG, Robertson A. 1968. Linkage disequilibrium infinite populations. Theoretical and Applied Genetics, 38: 226–231. Watanabe T. 2016. Genomic breeding value evaluation foreconomically important traits of Japanese Black cattle.The Journal of Animal Genetics, 44: 3–10. (in Japanese) Moore KL, Vilela C, Kaseja K, Mrode R, Coffey M. 2019.Forensic use of the genomic relationship matrix tovalidate and discover livestock pedigrees. Journal ofAnimal Science, 97: 35–42. Sasaki S, Watanabe T, Ibi T, Hasegawa K, Sakamoto Y,Moriwaki S, Kurogi K, Ogino A, Yasumori T, WakaguriH, Muraki E, Miki Y, Yoshida Y, Inoue Y, Tabuchi I,Iwao K, Arishima T, Kawashima K, Watanabe M,Sugano S, Sugimoto Y, Suzuki Y. 2021. Identification ofdeleterious recessive haplotypes and candidatedeleterious recessive mutations in Japanese Black cattle.Scientific Reports, 11: 6687. Komiya R, Ogawa S, Aonuma T, Satoh M. 2022.Performance of using opposing homozygotes forpaternity testing in Japanese Black cattle. Journal ofAnimal Breeding and Genetics, 139: 113–124. Thomasen JR, Sørensen AC, Su G, Madsen P, Lund MS,Guldbrandtsen B. 2013. The admixed populationstructure in Danish Jersey dairy cattle challengesaccurate genomic predictions. Journal of AnimalScience, 91: 3105–3112. de Cara MAR, Fernández J, Toro MA, Villanueva B. 2011.Using genome-wide information to minimize the lossof diversity in conservation programmes. Journal ofAnimal Breeding and Genetics, 128: 456–464. Meuwissen THE, Luan T, Woolliams JA. 2011. The unifiedapproach to the use of genomic and pedigreeinformation in genomic evaluations revisited. Journal ofAnimal Breeding and Genetics, 128: 429–439. Mukai F, Tuji S, Fukazawa K, Ohtagaki S, Nambu Y. 1989.History and population structure of a closed strain ofJapanese Black cattle. Journal of Animal Breeding andGenetics, 106: 254–264. |
| References_xml | – reference: Sonesson AK, Wooliams JA, Meuwissen THE. 2012.Genomic selection requires genomic control ofinbreeding. Genetics Selection Evolution, 44: 27. – reference: Doublet A-C, Croiseau P, Fritz S, Michenet A, Hozé C,Danchin-Burge C, Laloë D, Restoux G. 2019. Theimpact of genomic selection on genetic diversity andgenetic gain in three French dairy cattle breeds.Genetics Selection Evolution, 51: 52. – reference: Chen CY, Misztal I, Aguilar I, Legarra A, Muir WM. 2011.Effect of different genomic relationship matrices onaccuracy and scale. Journal of Animal Science, 89:2673–2679. – reference: Nomura T, Hayashi H, Sasaki Y. 1987. The breedingstructure and genetic analysis of the Japanese Black cattle in the Chugoku district. The Japanese Journal ofZootechnical Science, 58: 21–27. (in Japanese) – reference: Nomura T, Honda T, Mukai F. 2001. Inbreeding andeffective population size of Japanese Black cattle.Journal of Animal Science, 79: 366–370. – reference: Honda T, Nomura T, Yamaguchi Y, Mukai F. 2004.Monitoring of genetic diversity in the Japanese Blackcattle population by the use of pedigree information.Journal of Animal Breeding and Genetics, 121: 242–252. – reference: Thomasen JR, Sørensen AC, Su G, Madsen P, Lund MS,Guldbrandtsen B. 2013. The admixed populationstructure in Danish Jersey dairy cattle challengesaccurate genomic predictions. Journal of AnimalScience, 91: 3105–3112. – reference: Pérez-Enciso M. 2014. Genomic relationships computedfrom either next-generation sequence or array SNP data.Journal of Animal Breeding and Genetics, 131: 85–96. – reference: Doekes HP, Veerkamp RF, Bijma P, Hiemstra SJ, Windig JJ.2018. Trends in genome-wide and region-specificgenetic diversity in the Dutch-Flemish Holstein-Friesian breeding program from 1986 to 2015. GeneticsSelection Evolution, 50: 15. – reference: Eynard SE, Windig JJ, Hiemstra SJ, Calus MPL. 2016.Whole-genome sequence data uncover loss of geneticdiversity due to selection. Genetics Selection Evolution,48: 33. – reference: Mukai F, Tuji S, Fukazawa K, Ohtagaki S, Nambu Y. 1989.History and population structure of a closed strain ofJapanese Black cattle. Journal of Animal Breeding andGenetics, 106: 254–264. – reference: Ogawa S, Matsuda H, Taniguchi Y, Watanabe T, Kitamura Y,Tabuchi I, Sugimoto Y, Iwaisaki H. 2016. Genomicprediction for carcass traits in Japanese Black cattleusing single nucleotide polymorphism markers ofdifferent densities. Animal Production Science, 57:1631–1636. – reference: Wagyu Registry Association. 2007. Breeding andImprovement of Wagyu. 2nd ed. Wagyu RegistryAssociation. Kyoto, Japan. (in Japanese) – reference: Moore KL, Vilela C, Kaseja K, Mrode R, Coffey M. 2019.Forensic use of the genomic relationship matrix tovalidate and discover livestock pedigrees. Journal ofAnimal Science, 97: 35–42. – reference: Sasaki S, Watanabe T, Ibi T, Hasegawa K, Sakamoto Y,Moriwaki S, Kurogi K, Ogino A, Yasumori T, WakaguriH, Muraki E, Miki Y, Yoshida Y, Inoue Y, Tabuchi I,Iwao K, Arishima T, Kawashima K, Watanabe M,Sugano S, Sugimoto Y, Suzuki Y. 2021. Identification ofdeleterious recessive haplotypes and candidatedeleterious recessive mutations in Japanese Black cattle.Scientific Reports, 11: 6687. – reference: Sasaki Y, Miyake T, Gaillard C, Oguni T, Matsumoto M, ItoM, Kurahara T, Sasae Y, Fujinaka K, Ohtagaki S,Dougo, T. 2006. Comparison of genetic gains per yearfor carcass traits among breeding programs in theJapanese Brown and the Japanese Black cattle. Journalof Animal Science, 84: 317–323. – reference: Goddard ME. 2009. Genomic selection: prediction ofaccuracy and maximization of long term response.Genetica, 136: 245–257. – reference: Engelsma KA, Veerkamp RF, Calus MPL, Bijma P, WindigJJ. 2012. Pedigree- and marker-based methods in theestimation of genetic diversity in small groups ofHolstein cattle. Journal of Animal Breeding andGenetics, 129: 195–205. – reference: Takayanagi S, Moriya K, Nomura T, Dohgo T, Sasaki Y.1996. Population structure of Japanese Black cattle inHyogo prefecture. Nihon Chikusan Gakkaiho, 67: 286– 290. (in Japanese) – reference: Hirano T, Watanabe T, Nishimura S, Takasuga A, HanzawaK, Sugimoto Y. 2013. SNP discovery and evaluationwith whole genome re-sequencing using pooled DNA inJapanese Black cattle. Nihon Chikusan Gakkaiho, 84:319–325. (in Japanese) – reference: Meuwissen THE, Luan T, Woolliams JA. 2011. The unifiedapproach to the use of genomic and pedigreeinformation in genomic evaluations revisited. Journal ofAnimal Breeding and Genetics, 128: 429–439. – reference: Hill WG, Robertson A. 1968. Linkage disequilibrium infinite populations. Theoretical and Applied Genetics, 38: 226–231. – reference: Komiya R, Ogawa S, Aonuma T, Satoh M. 2022.Performance of using opposing homozygotes forpaternity testing in Japanese Black cattle. Journal ofAnimal Breeding and Genetics, 139: 113–124. – reference: Namikawa K. 1992. WAGYU: JAPANESE BEEF CATTLE- Historical Breeding Processes of Japanese Beef Cattleand Preservation of genetic resources as economic farmanimals. Wagyu Registry Association, Kyoto Japan. – reference: Watanabe T. 2016. Genomic breeding value evaluation foreconomically important traits of Japanese Black cattle.The Journal of Animal Genetics, 44: 3–10. (in Japanese) – reference: Yang J, Benyamin B, McEvoy BP, Gordon S, Henders AK,Nyholt DR, Madden PA, Heath AC, Martin NG,Montgomery GW, Goddard ME, Visscher PM. 2010.Common SNPs explain a large proportion of theheritability for human height. Nature Genetics, 42: 565–569. – reference: Forutan M, Mahuari SA, Baes C, Melzer N, Schenkel FS,Sargolzaei M. 2018. Inbreeding and runs ofhomozygosity before and after genomic selection inNorth American Holstein cattle. BMC Genomics, 19:98. – reference: Nishimaki T, Ibi T, Tanabe Y, Miyazaki Y, Kobayashi N,Matsuhashi T, Akiyama T, Yoshida E, Imai K, MatsuiM, Uemura K, Watanabe N, Fujita T, Saito Y, KomatsuT, Yamada T, Mannen H, Sasazaki S, Kunieda T. 2013.The assessment of genetic diversity within and amongthe eight subpopulations of Japanese Black cattle using52 microsatellite markers. Animal Science Journal, 84:585–591. – reference: Daetwyler HD, Villanueva B, Woolliams JA. 2008.Accuracy of predicting the genetic risk of disease usinga genome-wide approach. PLoS One, 3: e3395. – reference: de Roos APW, Hayes BJ, Spelman RJ, Goddard ME. 2008.Linkage disequilibrium and persistence of phase inHolstein-Friesian, Jersey and Angus cattle. Genetics,179: 1503–1512. – reference: Ashida I, Iwaisaki H. 1998. A numerical technique forREML estimation of variance components usingaverage information algorithm and its computingproperty. Animal Science and Technology (Japan), 69:631–636. – reference: de Cara MAR, Fernández J, Toro MA, Villanueva B. 2011.Using genome-wide information to minimize the lossof diversity in conservation programmes. Journal ofAnimal Breeding and Genetics, 128: 456–464. – reference: Ogawa S, Matsuda H, Taniguchi Y, Watanabe T, NishimuraS, Sugimoto Y, Iwaisaki H. 2014. Effects of singlenucleotide polymorphism marker density on degree ofgenetic variance explained and genomic evaluation forcarcass traits in Japanese Black beef cattle. BMCGenetics, 15: 15. – reference: Honda T, Nomura T, Fukushima M, Mukai F. 2001. Geneticdiversity of a closed population of Japanese Black cattlein Hyogo prefecture. Animal Science Journal, 72: 378–385. – reference: Browning BL, Browning SR. 2007. Rapid and accuratehaplotype phasing and missing-data inference forwhole-genome association studies by use of localizedhaplotype clustering. American Journal of Human Genetics, 81: 1084–1097. – reference: Nomura T, Sasaki Y. 1986. Breeding structure based onmovements of sires between prefectures and on geneticcontribution of prefectural sub population to theJapanese Black cattle. The Japanese Journal ofZootechnical Science. 57: 372–378. (in Japanese) – reference: VanRaden PM. 2008. Efficient methods to compute genomicpredictions. Journal of Dairy Science, 91: 4414–4423. |
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| Title | ゲノムワイドな一塩基多型マーカーを用いた 黒毛和種集団における遺伝的特性把握の試み |
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