Population Genomics Reveals Elevated Inbreeding and Accumulation of Deleterious Mutations in White Raccoon Dogs
The formation of animal breeds usually begins with a small subsample from their ancestral population. Deleterious mutations accumulate in the population under genetic drift, inbreeding, and artificial selection during the development and maintenance of traits desired by humans. White raccoon dogs ar...
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2025-01-01
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| author | Yinping Tian Yu Lin Yue Ma Jiayi Li Sunil Kumar Sahu Jiale Fan Chen Lin Zhiang Li Minhui Shi Fengping He Lianduo Bai Yuan Fu Zhangwen Deng Huabing Guo Haimeng Li Qiye Li Yanchun Xu Tianming Lan Zhijun Hou Yanling Xia Shuhui Yang |
| author_facet | Yinping Tian Yu Lin Yue Ma Jiayi Li Sunil Kumar Sahu Jiale Fan Chen Lin Zhiang Li Minhui Shi Fengping He Lianduo Bai Yuan Fu Zhangwen Deng Huabing Guo Haimeng Li Qiye Li Yanchun Xu Tianming Lan Zhijun Hou Yanling Xia Shuhui Yang |
| author_sort | Yinping Tian |
| collection | DOAJ |
| description | The formation of animal breeds usually begins with a small subsample from their ancestral population. Deleterious mutations accumulate in the population under genetic drift, inbreeding, and artificial selection during the development and maintenance of traits desired by humans. White raccoon dogs are among the most popular breeds of farmed raccoon dogs, but white raccoon dogs are more susceptible to disease and have a lower reproductive ability. However, the accumulation of deleterious mutations in this white breed is largely unknown. By analyzing and comparing whole-genome sequencing data from 20 white raccoon dogs and 38 normal raccoon dogs, we detected an increased occurrence of loss-of-function (LoF) mutations in white raccoon dogs compared with normal raccoon dogs. With the finding of a significantly higher dosage of homozygous missense mutations in the white raccoon dog genome, we detected a greater fitness cost in white raccoon dogs. Although a much higher FROH level for ROH fragments longer than 1 Mb has been reported in white raccoon dogs, we did not detect a genetic signal of genetic purging in white raccoon dogs. This study provides valuable genomic resources and new insights into the accumulation of mutation loads in farmed raccoon dogs. |
| format | Article |
| id | doaj-art-3fe2390e3849462089c448b7bae5d14e |
| institution | Kabale University |
| issn | 2079-7737 |
| language | English |
| publishDate | 2025-01-01 |
| publisher | MDPI AG |
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| series | Biology |
| spelling | doaj-art-3fe2390e3849462089c448b7bae5d14e2025-01-24T13:23:21ZengMDPI AGBiology2079-77372025-01-011413010.3390/biology14010030Population Genomics Reveals Elevated Inbreeding and Accumulation of Deleterious Mutations in White Raccoon DogsYinping Tian0Yu Lin1Yue Ma2Jiayi Li3Sunil Kumar Sahu4Jiale Fan5Chen Lin6Zhiang Li7Minhui Shi8Fengping He9Lianduo Bai10Yuan Fu11Zhangwen Deng12Huabing Guo13Haimeng Li14Qiye Li15Yanchun Xu16Tianming Lan17Zhijun Hou18Yanling Xia19Shuhui Yang20College of Wildlife and Protected Area, Northeast Forestry University, Harbin 150040, ChinaCollege of Wildlife and Protected Area, Northeast Forestry University, Harbin 150040, ChinaCollege of Wildlife and Protected Area, Northeast Forestry University, Harbin 150040, ChinaCollege of Wildlife and Protected Area, Northeast Forestry University, Harbin 150040, ChinaBGI Research, Wuhan 430074, ChinaCollege of Wildlife and Protected Area, Northeast Forestry University, Harbin 150040, ChinaCollege of Wildlife and Protected Area, Northeast Forestry University, Harbin 150040, ChinaCollege of Life Science, Northeast Forestry University, Harbin 150040, ChinaState Key Laboratory of Agricultural Genomics, BGI-Shenzhen, Shenzhen 518083, ChinaCollege of Veterinary Medicine, Yunnan Agricultural University, Kunming 650201, ChinaCollege of Wildlife and Protected Area, Northeast Forestry University, Harbin 150040, ChinaCollege of Wildlife and Protected Area, Northeast Forestry University, Harbin 150040, ChinaGuangxi Zhuang Autonomous Region Forest Inventory and Planning Institute, Nanning 530011, ChinaForest Inventory and Planning Institute of Jilin Province, Changchun 130022, ChinaCollege of Wildlife and Protected Area, Northeast Forestry University, Harbin 150040, ChinaCollege of Life Science, Northeast Forestry University, Harbin 150040, ChinaCollege of Wildlife and Protected Area, Northeast Forestry University, Harbin 150040, ChinaCollege of Wildlife and Protected Area, Northeast Forestry University, Harbin 150040, ChinaCollege of Wildlife and Protected Area, Northeast Forestry University, Harbin 150040, ChinaCollege of Wildlife and Protected Area, Northeast Forestry University, Harbin 150040, ChinaCollege of Wildlife and Protected Area, Northeast Forestry University, Harbin 150040, ChinaThe formation of animal breeds usually begins with a small subsample from their ancestral population. Deleterious mutations accumulate in the population under genetic drift, inbreeding, and artificial selection during the development and maintenance of traits desired by humans. White raccoon dogs are among the most popular breeds of farmed raccoon dogs, but white raccoon dogs are more susceptible to disease and have a lower reproductive ability. However, the accumulation of deleterious mutations in this white breed is largely unknown. By analyzing and comparing whole-genome sequencing data from 20 white raccoon dogs and 38 normal raccoon dogs, we detected an increased occurrence of loss-of-function (LoF) mutations in white raccoon dogs compared with normal raccoon dogs. With the finding of a significantly higher dosage of homozygous missense mutations in the white raccoon dog genome, we detected a greater fitness cost in white raccoon dogs. Although a much higher FROH level for ROH fragments longer than 1 Mb has been reported in white raccoon dogs, we did not detect a genetic signal of genetic purging in white raccoon dogs. This study provides valuable genomic resources and new insights into the accumulation of mutation loads in farmed raccoon dogs.https://www.mdpi.com/2079-7737/14/1/30inbreedingmutational loadgenetic purgingdeleterious mutationROHpopulation genomics |
| spellingShingle | Yinping Tian Yu Lin Yue Ma Jiayi Li Sunil Kumar Sahu Jiale Fan Chen Lin Zhiang Li Minhui Shi Fengping He Lianduo Bai Yuan Fu Zhangwen Deng Huabing Guo Haimeng Li Qiye Li Yanchun Xu Tianming Lan Zhijun Hou Yanling Xia Shuhui Yang Population Genomics Reveals Elevated Inbreeding and Accumulation of Deleterious Mutations in White Raccoon Dogs Biology inbreeding mutational load genetic purging deleterious mutation ROH population genomics |
| title | Population Genomics Reveals Elevated Inbreeding and Accumulation of Deleterious Mutations in White Raccoon Dogs |
| title_full | Population Genomics Reveals Elevated Inbreeding and Accumulation of Deleterious Mutations in White Raccoon Dogs |
| title_fullStr | Population Genomics Reveals Elevated Inbreeding and Accumulation of Deleterious Mutations in White Raccoon Dogs |
| title_full_unstemmed | Population Genomics Reveals Elevated Inbreeding and Accumulation of Deleterious Mutations in White Raccoon Dogs |
| title_short | Population Genomics Reveals Elevated Inbreeding and Accumulation of Deleterious Mutations in White Raccoon Dogs |
| title_sort | population genomics reveals elevated inbreeding and accumulation of deleterious mutations in white raccoon dogs |
| topic | inbreeding mutational load genetic purging deleterious mutation ROH population genomics |
| url | https://www.mdpi.com/2079-7737/14/1/30 |
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