Animal Bioscience

Asian Australasian Association of Animal Production Societies (아세아태평양축산학회)
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Genetic diversity and population structure in five Inner Mongolia cashmere goat populations using whole-genome genotyping

  • Tao Zhang (College of Animal Science, Inner Mongolia Agricultural University) ;
  • Zhiying Wang (College of Animal Science, Inner Mongolia Agricultural University) ;
  • Yaming Li (College of Animal Science, Inner Mongolia Agricultural University) ;
  • Bohan Zhou (College of Animal Science, Inner Mongolia Agricultural University) ;
  • Yifan Liu (College of Animal Science, Inner Mongolia Agricultural University) ;
  • Jinquan Li (Inner Mongolia Key Laboratory of Sheep and Goat Genetics Breeding and Reproduction) ;
  • Ruijun Wang (College of Animal Science, Inner Mongolia Agricultural University) ;
  • Qi Lv (College of Animal Science, Inner Mongolia Agricultural University) ;
  • Chun Li (College of Animal Science and Technology, Inner Mongolia Minzu University) ;
  • Yanjun Zhang (College of Animal Science, Inner Mongolia Agricultural University) ;
  • Rui Su (College of Animal Science, Inner Mongolia Agricultural University)
  • Received : 2023.10.17
  • Accepted : 2024.01.26
  • Published : 2024.07.01
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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

Acknowledgement

Thanks are due to Libing He for assistance with the experiments and to Oljibilig Chen for valuable discussion.

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