Genetic diversity and population structure in five Inner Mongolia cashmere goat populations using whole-genome genotyping
文献类型: 外文期刊
第一作者: Zhang, Tao
作者: Zhang, Tao;Wang, Zhiying;Li, Yaming;Zhou, Bohan;Liu, Yifan;Wang, Ruijun;Lv, Qi;Zhang, Yanjun;Su, Rui;Zhang, Tao;Wang, Zhiying;Li, Yaming;Zhou, Bohan;Liu, Yifan;Li, Jinquan;Wang, Ruijun;Lv, Qi;Zhang, Yanjun;Su, Rui;Wang, Zhiying;Li, Yaming;Zhou, Bohan;Liu, Yifan;Li, Jinquan;Wang, Ruijun;Lv, Qi;Zhang, Yanjun;Su, Rui;Li, Chun
作者机构: Inner Mongolia Agr Univ, Coll Anim Sci, Hohhot 010018, Inner Mongolia, Peoples R China;Chinese Acad Agr Sci, Grassland Res Inst, Hohhot 010018, Inner Mongolia, Peoples R China;Inner Mongolia Key Lab Sheep & Goat Genet Breeding, Hohhot 010018, Inner Mongolia, Peoples R China;Minist Agr & Rural Affairs, Key Lab Mutton Sheep & Goat Genet & Breeding, Hohhot 010018, Inner Mongolia, Peoples R China;Inner Mongolia Minzu Univ, Coll Anim Sci & Technol, Tongliao 028000, Inner Mongolia, Peoples R China
关键词: Cashmere Goat; Genetic Diversity; Inner Mongolia Autonomous Region; Population Structure
期刊名称:ANIMAL BIOSCIENCE ( 2023影响因子:2.4; 五年影响因子:2.4 )
ISSN: 2765-0189
年卷期: 2024 年 37 卷 7 期
收录情况: SCI
摘要: 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 21.13x to 46.18x, with an average of 28.5x. 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.
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