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Wang Z, Zhou B, Zhang T, Yan X, Yu Y, Li J, Mei B, Wang Z, Zhang Y, Wang R, Lv Q, Liu Z, Zhao Y, Du C, Su R. Assessing Genetic Diversity and Estimating the Inbreeding Effect on Economic Traits of Inner Mongolia White Cashmere Goats Through Pedigree Analysis. Front Vet Sci 2021; 8:665872. [PMID: 34239910 PMCID: PMC8258104 DOI: 10.3389/fvets.2021.665872] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2021] [Accepted: 05/10/2021] [Indexed: 11/13/2022] Open
Abstract
Objective: The purpose of this study was to discover the population structure and genetic diversity of Inner Mongolia White Cashmere goats (IMCGs) and demonstrate the effect of inbreeding on the live body weight (LBW), cashmere yield (CY), fiber length (FL), and fiber diameter (FD) of IMCGs. Materials and Methods: All data were collected from pedigree information and production performance records of IMCGs from 1983 to 2019. The population structure and genetic diversity were analyzed by Endog 4.8 software. Inbreeding coefficients were obtained by the pedigree package in R. Then, a linear regression model was used to analyze how inbreeding influences economic traits in IMCGs. Four levels of inbreeding coefficients (Fi) were classified in this study, including Fi = 0, 0< Fi ≤ 6.25, 6.25< Fi ≤ 12.5 and Fi≥12.5. Variance analysis was performed to determine whether inbreeding levels had a significant effect on economic traits in IMCGs. Results: The proportions of rams and dams in IMCGs for breeding were relatively small, with values of 0.8 and 20.5%, respectively. The proportion of inbred animals in the entire population was high, with values up to 68.6%; however, the average inbreeding coefficient and relatedness coefficient were 4.50 and 8.48%, respectively. To date, the population has experienced 12 generations. The average generation interval obtained in the present study was 4.11 ± 0.01 years. The ram-to-son pathway was lowest (3.97 years), and the ewe-to-daughter pathway was highest (4.24 years). It was discovered that the LBW, CY, and FL increased by 3.88 kg, 208.7 g, and 1.151 cm, respectively, with every 1% increase in the inbreeding coefficient, and the FD decreased by 0.819 μm with every 1% increase in the inbreeding coefficient. Additionally, multiple comparison analysis indicated that when the inbreeding coefficient was higher than 6.25%, the LBW showed an obvious decreasing trend. The threshold value of inbreeding depression in the CY is 12.5%. However, inbreeding depression has not been observed in the FL and FD. Conclusion: Pedigree completeness needs to be further strengthened. The degree of inbreeding in this flock should be properly controlled when designing breeding programs.
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Affiliation(s)
- Zhiying Wang
- College of Animal Science, Inner Mongolia Agricultural University, Hohhot, China
| | - Bohan Zhou
- College of Animal Science, Inner Mongolia Agricultural University, Hohhot, China
| | - Tao Zhang
- College of Animal Science, Inner Mongolia Agricultural University, Hohhot, China.,Inner Mongolia Bigvet Co., Ltd., Hohhot, China
| | - Xiaochun Yan
- College of Animal Science, Inner Mongolia Agricultural University, Hohhot, China
| | - Yongsheng Yu
- College of Animal Science, Inner Mongolia Agricultural University, Hohhot, China
| | - Jinquan Li
- Key Laboratory of Mutton Sheep Genetics and Breeding, Ministry of Agriculture, Hohhot, China.,Key Laboratory of Animal Genetics, Breeding and Reproduction in Inner Mongolia Autonomous Region, Hohhot, China.,Engineering Research Center for Goat Genetics and Breeding, Inner Mongolia Agriculture University, Hohhot, China
| | - Bujun Mei
- Department of Agriculture, Hetao College, Hetao University, Bayannaoer, China
| | - Zhixin Wang
- College of Animal Science, Inner Mongolia Agricultural University, Hohhot, China
| | - Yanjun Zhang
- College of Animal Science, Inner Mongolia Agricultural University, Hohhot, China
| | - Ruijun Wang
- College of Animal Science, Inner Mongolia Agricultural University, Hohhot, China
| | - Qi Lv
- College of Animal Science, Inner Mongolia Agricultural University, Hohhot, China
| | - Zhihong Liu
- Inner Mongolia Bigvet Co., Ltd., Hohhot, China
| | | | - Chen Du
- Reproductive Medicine Center, Affiliated Hospital of Inner Mongolia Medical University, Hohhot, China
| | - Rui Su
- College of Animal Science, Inner Mongolia Agricultural University, Hohhot, China
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Li X, Su R, Wan W, Zhang W, Jiang H, Qiao X, Fan Y, Zhang Y, Wang R, Liu Z, Wang Z, Liu B, Ma Y, Zhang H, Zhao Q, Zhong T, Di R, Jiang Y, Chen W, Wang W, Dong Y, Li J. Identification of selection signals by large-scale whole-genome resequencing of cashmere goats. Sci Rep 2017; 7:15142. [PMID: 29123196 PMCID: PMC5680388 DOI: 10.1038/s41598-017-15516-0] [Citation(s) in RCA: 34] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2017] [Accepted: 10/27/2017] [Indexed: 01/14/2023] Open
Abstract
Inner Mongolia and Liaoning cashmere goats are two outstanding Chinese multipurpose breeds that adapt well to the semi-arid temperate grassland. These two breeds are characterized by their soft cashmere fibers, thus making them great models to identify genomic regions that are associated with cashmere fiber traits. Whole-genome sequencing of 70 cashmere goats produced more than 5.52 million single-nucleotide polymorphisms and 710,600 short insertions and deletions. Further analysis of these genetic variants showed some population-specific molecular markers for the two cashmere goat breeds that are otherwise phenotypically similar. By analyzing FST and θπ outlier values, we identified 135 genomic regions that were associated with cashmere fiber traits within the cashmere goat populations. These selected genomic regions contained genes, which are potential involved in the production of cashmere fiber, such as FGF5, SGK3, IGFBP7, OXTR, and ROCK1. Gene ontology enrichment analysis of identified short insertions and deletions also showed enrichment in keratinocyte differentiation and epidermal cell differentiation. These findings demonstrate that this genomic resource will facilitate the breeding of cashmere goat and other Capra species in future.
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Affiliation(s)
- Xiaokai Li
- College of Animal Science, Inner Mongolia Agricultural University, Hohhot, Inner Mongolia, 010018, China
| | - Rui Su
- College of Animal Science, Inner Mongolia Agricultural University, Hohhot, Inner Mongolia, 010018, China.,Key Laboratory of Animal Genetics, Breeding and Reproduction - Inner Mongolia Autonomous Region, Inner Mongolia Agricultural University, Hohhot, Inner Mongolia, 010018, China.,Key Laboratory of Mutton Sheep Genetics and Breeding, Ministry of Agriculture, Inner Mongolia Agricultural University, Hohhot, Inner Mongolia, 010018, China.,Engineering Research Center for Goat Genetics and Breeding - Inner Mongolia Autonomous Region, Inner Mongolia Agricultural University, Hohhot, Inner Mongolia, 010018, China.,State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, Yunnan, 650223, China
| | - Wenting Wan
- Center for Ecological and Environmental Sciences, Key Laboratory for Space Bioscience & Biotechnology, Northwestern Polytechnical University, Xi'an, Shaanxi, 710072, China
| | - Wenguang Zhang
- College of Animal Science, Inner Mongolia Agricultural University, Hohhot, Inner Mongolia, 010018, China
| | - Huaizhi Jiang
- College of Animal Science and Technology, Jilin Agricultural University, Changchun, Jilin, 130118, China
| | - Xian Qiao
- College of Animal Science, Inner Mongolia Agricultural University, Hohhot, Inner Mongolia, 010018, China
| | - Yixing Fan
- College of Animal Science, Inner Mongolia Agricultural University, Hohhot, Inner Mongolia, 010018, China
| | - Yanjun Zhang
- College of Animal Science, Inner Mongolia Agricultural University, Hohhot, Inner Mongolia, 010018, China.,Key Laboratory of Animal Genetics, Breeding and Reproduction - Inner Mongolia Autonomous Region, Inner Mongolia Agricultural University, Hohhot, Inner Mongolia, 010018, China.,Key Laboratory of Mutton Sheep Genetics and Breeding, Ministry of Agriculture, Inner Mongolia Agricultural University, Hohhot, Inner Mongolia, 010018, China.,Engineering Research Center for Goat Genetics and Breeding - Inner Mongolia Autonomous Region, Inner Mongolia Agricultural University, Hohhot, Inner Mongolia, 010018, China
| | - Ruijun Wang
- College of Animal Science, Inner Mongolia Agricultural University, Hohhot, Inner Mongolia, 010018, China.,Key Laboratory of Animal Genetics, Breeding and Reproduction - Inner Mongolia Autonomous Region, Inner Mongolia Agricultural University, Hohhot, Inner Mongolia, 010018, China.,Key Laboratory of Mutton Sheep Genetics and Breeding, Ministry of Agriculture, Inner Mongolia Agricultural University, Hohhot, Inner Mongolia, 010018, China.,Engineering Research Center for Goat Genetics and Breeding - Inner Mongolia Autonomous Region, Inner Mongolia Agricultural University, Hohhot, Inner Mongolia, 010018, China
| | - Zhihong Liu
- College of Animal Science, Inner Mongolia Agricultural University, Hohhot, Inner Mongolia, 010018, China.,Key Laboratory of Animal Genetics, Breeding and Reproduction - Inner Mongolia Autonomous Region, Inner Mongolia Agricultural University, Hohhot, Inner Mongolia, 010018, China.,Key Laboratory of Mutton Sheep Genetics and Breeding, Ministry of Agriculture, Inner Mongolia Agricultural University, Hohhot, Inner Mongolia, 010018, China.,Engineering Research Center for Goat Genetics and Breeding - Inner Mongolia Autonomous Region, Inner Mongolia Agricultural University, Hohhot, Inner Mongolia, 010018, China
| | - Zhiying Wang
- College of Animal Science, Inner Mongolia Agricultural University, Hohhot, Inner Mongolia, 010018, China.,Key Laboratory of Animal Genetics, Breeding and Reproduction - Inner Mongolia Autonomous Region, Inner Mongolia Agricultural University, Hohhot, Inner Mongolia, 010018, China.,Key Laboratory of Mutton Sheep Genetics and Breeding, Ministry of Agriculture, Inner Mongolia Agricultural University, Hohhot, Inner Mongolia, 010018, China.,Engineering Research Center for Goat Genetics and Breeding - Inner Mongolia Autonomous Region, Inner Mongolia Agricultural University, Hohhot, Inner Mongolia, 010018, China
| | - Bin Liu
- Institute of Animal Husbandry, Academy of Agriculture and Stockbreeding Sciences, Hohhot, Inner Mongolia, 010030, China
| | - Yuehui Ma
- The Key Laboratory for Farm Animal Genetic Resources and Utilization of Ministry of Agriculture of China, Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing, 100193, China
| | - Hongping Zhang
- Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, College of Animal Science and Technology, Sichuan Agricultural University, Chengdu, 611130, China
| | - Qianjun Zhao
- The Key Laboratory for Farm Animal Genetic Resources and Utilization of Ministry of Agriculture of China, Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing, 100193, China
| | - Tao Zhong
- Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, College of Animal Science and Technology, Sichuan Agricultural University, Chengdu, 611130, China
| | - Ran Di
- The Key Laboratory for Farm Animal Genetic Resources and Utilization of Ministry of Agriculture of China, Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing, 100193, China
| | - Yu Jiang
- College of Animal Science and Technology, Northwest A&F University, Yangling, 712100, China
| | - Wei Chen
- College of Biological Big Data, Yunnan Agriculture University, Kunming, Yunnan, 650504, China.,Yunnan Research Institute for Local Plateau Agriculture and Industry, Kunming, Yunnan, 650201, China
| | - Wen Wang
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, Yunnan, 650223, China.
| | - Yang Dong
- College of Biological Big Data, Yunnan Agriculture University, Kunming, Yunnan, 650504, China. .,BGI-Shenzhen, Shenzhen, Guangdong, 518083, China. .,Yunnan Research Institute for Local Plateau Agriculture and Industry, Kunming, Yunnan, 650201, China.
| | - Jinquan Li
- College of Animal Science, Inner Mongolia Agricultural University, Hohhot, Inner Mongolia, 010018, China. .,Key Laboratory of Animal Genetics, Breeding and Reproduction - Inner Mongolia Autonomous Region, Inner Mongolia Agricultural University, Hohhot, Inner Mongolia, 010018, China. .,Key Laboratory of Mutton Sheep Genetics and Breeding, Ministry of Agriculture, Inner Mongolia Agricultural University, Hohhot, Inner Mongolia, 010018, China. .,Engineering Research Center for Goat Genetics and Breeding - Inner Mongolia Autonomous Region, Inner Mongolia Agricultural University, Hohhot, Inner Mongolia, 010018, China.
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