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Genetic diversity and population structure in five Inner Mongolia cashmere goat populations using whole-genome genotyping |
Tao Zhang1,2 
, Zhiying Wang1,3,4
, Yaming Li1,3,4
, Bohan Zhou1,3,4
, Yifan Liu1,3,4
, Jinquan Li3,4
, Ruijun Wang1,3,4
, Qi Lv1,3,4
, Chun Li5
, Yanjun Zhang1,3,4,*
, Rui Su1,3,4,*
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1College of Animal Science, Inner Mongolia Agricultural University, Hohhot, Inner Mongolia Autonomous Region, 010018, China
2Grassland Research Institute, Chinese Academy of Agricultural Sciences, Hohhot, Inner Mongolia Autonomous Region, 010018, China
3Inner Mongolia Key Laboratory of Sheep and Goat Genetics Breeding and Reproduction, Hohhot, Inner Mongolia Autonomous Region, 010018, China
4Key Laboratory Of Mutton Sheep and Goat Genetics And Breeding, Ministry of Agriculture And Rural Affairs, Hohhot, Inner Mongolia Autonomous Region, 010018, China
5College of Animal Science and Technology, Inner Mongolia Minzu University, Tongliao, Inner Mongolia Autonomous Region, 028000, China |
Correspondence:
Yanjun Zhang, Tel: +86-13190601108, Fax: +86-0471-430-9178, Email: imauzyj@163.com
Rui Su, Tel: +86-15947510736, Fax: +86-0471-430-9178, Email: suruiyu@126.com
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Received: 17 October 2023 • Revised: 3 December 2023 • Accepted: 26 January 2024 |
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| Abstract |
Objective
As a charismatic species, cashmere goats have rich genetic resources. In the Inner Mongolia Autonomous Region, there are three cashmere goat varieties named and approved by the state. These goats are renowned for their high cashmere production and superior cashmere quality. Therefore, it is vitally important to protect their genetic resources as they will serve as breeding material for developing new varieties in the future.
Methods
Three breeds including Inner Mongolia cashmere goats (IMCG), Hanshan White cashmere goats (HS), and Ujimqin white cashmere goats (WZMQ) were studied. IMCG were of three types: Aerbas (AEBS), Erlangshan (ELS), and Alashan (ALS). Nine DNA samples were collected for each population, and they were genomically re-sequenced to obtain high-depth data. The genetic diversity parameters of each population were estimated to determine selection intensity. Principal component analysis, phylogenetic tree construction and genetic differentiation parameter estimation were performed to determine genetic relationships among populations.
Results
Samples from the 45 individuals from the five goat populations were sequenced, and 30,601,671 raw single nucleotide polymorphisms (SNPs) obtained. Then, variant calling was conducted using the reference genome, and 17,214,526 SNPs were retained after quality control. Individual sequencing depth of individuals ranged from 21.13× to 46.18×, with an average of 28.5×. In the AEBS, locus polymorphism (79.28) and expected heterozygosity (0.2554) proportions were the lowest, and the homologous consistency ratio (0.1021) and average inbreeding coefficient (0.1348) were the highest, indicating that this population had strong selection intensity. Conversely, ALS and WZMQ selection intensity was relatively low. Genetic distance between HS and the other four populations was relatively high, and genetic exchange existed among the other four populations.
Conclusion
The Inner Mongolia cashmere goat (AEBS type) population has a relatively high selection intensity and a low genetic diversity. The IMCG (ALS type) and WZMQ populations had relatively low selection intensity and high genetic diversity. The genetic distance between HS and the other four populations was relatively high, with a moderate degree of differentiation. Overall, these genetic variations provide a solid foundation for resource identification of Inner Mongolia Autonomous Region cashmere goats in the future. |
| Keywords:
Cashmere Goat; Genetic Diversity; Inner Mongolia Autonomous Region; Population Structure |
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