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Guo Y, Cui Y, Sun M, Zhu X, Zhang Y, Lu J, Li C, Lv J, Guo M, Liu X, Chen Z, Du X, Huo X. Establishment and Application of a Novel Genetic Detection Panel for SNPs in Mongolian Gerbils. Genes (Basel) 2024; 15:817. [PMID: 38927752 PMCID: PMC11202554 DOI: 10.3390/genes15060817] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2024] [Revised: 06/13/2024] [Accepted: 06/17/2024] [Indexed: 06/28/2024] Open
Abstract
The Mongolian gerbil is a distinctive experimental animal in China, as its genetic qualities possess significant value in the field of medical biology research. Here, we aimed to establish an economical and efficient panel for genetic quality detection in Mongolian gerbils using single-nucleotide polymorphism (SNP) markers. To search for SNPs, we conducted whole-genome sequencing (WGS) in 40 Mongolian gerbils from outbred populations. Reliable screening criteria were established to preliminarily select SNPs with a wide genome distribution and high levels of polymorphism. Subsequently, a multiple-target regional capture detection system based on second-generation sequencing was developed for SNP genotyping. Based on the results of WGS, 219 SNPs were preliminarily selected, and they were established and optimized in a multiple-amplification system that included 206 SNP loci by genotyping three outbred populations. PopGen.32 analysis revealed that the average effective allele number, Shannon index, observed heterozygosity, expected heterozygosity, average heterozygosity, polymorphism information content, and other population genetic parameters of the Capital Medical University (CMU) gerbils were the highest, followed by those of Zhejiang gerbils and Dalian gerbils. Through scientific screening and optimization, we successfully established a novel, robust, and cost-effective genetic detection system for Mongolian gerbils by utilizing SNP markers for the first time.
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Affiliation(s)
- Yafang Guo
- School of Basic Medical Sciences, Capital Medical University, Beijing 100069, China
- Laboratory for Clinical Medicine, Capital Medical University, Beijing 100069, China
- Beijing Key Laboratory of Cancer Invasion and Metastasis Research, Beijing 100069, China
| | - Yutong Cui
- School of Basic Medical Sciences, Capital Medical University, Beijing 100069, China
| | - Minghe Sun
- School of Basic Medical Sciences, Capital Medical University, Beijing 100069, China
- Laboratory for Clinical Medicine, Capital Medical University, Beijing 100069, China
- Beijing Key Laboratory of Cancer Invasion and Metastasis Research, Beijing 100069, China
| | - Xiao Zhu
- School of Basic Medical Sciences, Capital Medical University, Beijing 100069, China
- Laboratory for Clinical Medicine, Capital Medical University, Beijing 100069, China
- Beijing Key Laboratory of Cancer Invasion and Metastasis Research, Beijing 100069, China
| | - Yilang Zhang
- School of Basic Medical Sciences, Capital Medical University, Beijing 100069, China
- Laboratory for Clinical Medicine, Capital Medical University, Beijing 100069, China
- Beijing Key Laboratory of Cancer Invasion and Metastasis Research, Beijing 100069, China
| | - Jing Lu
- School of Basic Medical Sciences, Capital Medical University, Beijing 100069, China
- Laboratory for Clinical Medicine, Capital Medical University, Beijing 100069, China
- Beijing Key Laboratory of Cancer Invasion and Metastasis Research, Beijing 100069, China
| | - Changlong Li
- School of Basic Medical Sciences, Capital Medical University, Beijing 100069, China
- Laboratory for Clinical Medicine, Capital Medical University, Beijing 100069, China
- Beijing Key Laboratory of Cancer Invasion and Metastasis Research, Beijing 100069, China
| | - Jianyi Lv
- School of Basic Medical Sciences, Capital Medical University, Beijing 100069, China
- Laboratory for Clinical Medicine, Capital Medical University, Beijing 100069, China
- Beijing Key Laboratory of Cancer Invasion and Metastasis Research, Beijing 100069, China
| | - Meng Guo
- School of Basic Medical Sciences, Capital Medical University, Beijing 100069, China
- Laboratory for Clinical Medicine, Capital Medical University, Beijing 100069, China
- Beijing Key Laboratory of Cancer Invasion and Metastasis Research, Beijing 100069, China
| | - Xin Liu
- School of Basic Medical Sciences, Capital Medical University, Beijing 100069, China
- Laboratory for Clinical Medicine, Capital Medical University, Beijing 100069, China
- Beijing Key Laboratory of Cancer Invasion and Metastasis Research, Beijing 100069, China
| | - Zhenwen Chen
- School of Basic Medical Sciences, Capital Medical University, Beijing 100069, China
- Laboratory for Clinical Medicine, Capital Medical University, Beijing 100069, China
- Beijing Key Laboratory of Cancer Invasion and Metastasis Research, Beijing 100069, China
| | - Xiaoyan Du
- School of Basic Medical Sciences, Capital Medical University, Beijing 100069, China
- Laboratory for Clinical Medicine, Capital Medical University, Beijing 100069, China
| | - Xueyun Huo
- School of Basic Medical Sciences, Capital Medical University, Beijing 100069, China
- Beijing Key Laboratory of Cancer Invasion and Metastasis Research, Beijing 100069, China
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Wang T, Liu Z, Shi X, Zhang Z, Li Y, Huang B, Ren W, Wang X, Wang C, Chai W. An investigation of genetic diversity in three Dezhou donkey original breeding farms. Sci Rep 2023; 13:11203. [PMID: 37433834 DOI: 10.1038/s41598-023-38219-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2023] [Accepted: 07/05/2023] [Indexed: 07/13/2023] Open
Abstract
Dezhou donkey is one of the excellent large donkey breeds in China. In our study, eight microsatellite markers were used to genotype from each of three populations of Chinese Dezhou donkeys: 67 individuals in Liaocheng (pop1), 103 individuals in Binzhou 1 (pop2), and 102 individuals in Binzhou 2 (pop3), in order to study the genetic diversity of these populations. A total of 213 alleles were detected, and the PIC results showed that eight loci were all highly polymorphic. The means of Ho and He of pop2 were the highest, which were 0.646 and 0.717, respectively. The PCoA analysis demonstrated that the samples from three conservation farms were mixed together. The phylogenetic tree showed that pop 2 and pop 3 were closely related. The phylogenetic tree results clustered that 272 donkeys were divided into six groups. AMOVA analysis showed that the genetic variation was mainly concentrated within the population and the genetic differentiation among the populations was low. Fst values between populations also indicated that genetic differentiation between populations was too small to be considered. This indicated a low probability of inbreeding within the population. And this also showed that the conservation and breeding of Dezhou donkeys in recent years have achieved excellent results. The investigation of genetic diversity in three Dezhou donkey original breeding farms can provide reference data for the selection and breeding of excellent breeds of Dezhou donkey.
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Affiliation(s)
- Tianqi Wang
- Liaocheng Research Institute of Donkey High-Efficiency Breeding and Ecological Feeding, Agricultural Science and Engineering School, Liaocheng University, Liaocheng, 252059, China
| | - Ziwen Liu
- Liaocheng Research Institute of Donkey High-Efficiency Breeding and Ecological Feeding, Agricultural Science and Engineering School, Liaocheng University, Liaocheng, 252059, China
| | - Xiaoyuan Shi
- Liaocheng Research Institute of Donkey High-Efficiency Breeding and Ecological Feeding, Agricultural Science and Engineering School, Liaocheng University, Liaocheng, 252059, China
| | - Zhenwei Zhang
- Liaocheng Research Institute of Donkey High-Efficiency Breeding and Ecological Feeding, Agricultural Science and Engineering School, Liaocheng University, Liaocheng, 252059, China
| | - Yuhua Li
- Liaocheng Research Institute of Donkey High-Efficiency Breeding and Ecological Feeding, Agricultural Science and Engineering School, Liaocheng University, Liaocheng, 252059, China
| | - Bingjian Huang
- Liaocheng Research Institute of Donkey High-Efficiency Breeding and Ecological Feeding, Agricultural Science and Engineering School, Liaocheng University, Liaocheng, 252059, China
| | - Wei Ren
- Liaocheng Research Institute of Donkey High-Efficiency Breeding and Ecological Feeding, Agricultural Science and Engineering School, Liaocheng University, Liaocheng, 252059, China
| | - Xinrui Wang
- Liaocheng Research Institute of Donkey High-Efficiency Breeding and Ecological Feeding, Agricultural Science and Engineering School, Liaocheng University, Liaocheng, 252059, China
| | - Changfa Wang
- Liaocheng Research Institute of Donkey High-Efficiency Breeding and Ecological Feeding, Agricultural Science and Engineering School, Liaocheng University, Liaocheng, 252059, China.
| | - Wenqiong Chai
- Liaocheng Research Institute of Donkey High-Efficiency Breeding and Ecological Feeding, Agricultural Science and Engineering School, Liaocheng University, Liaocheng, 252059, China.
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Development of Microsatellite Marker System to Determine the Genetic Diversity of Experimental Chicken, Duck, Goose, and Pigeon Populations. BIOMED RESEARCH INTERNATIONAL 2021; 2021:8851888. [PMID: 33511214 PMCID: PMC7822670 DOI: 10.1155/2021/8851888] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/10/2020] [Revised: 12/09/2020] [Accepted: 01/05/2021] [Indexed: 12/28/2022]
Abstract
Poultries including chickens, ducks, geese, and pigeons are widely used in the biological and medical research in many aspects. The genetic quality of experimental poultries directly affects the results of the research. In this study, following electrophoresis analysis and short tandem repeat (STR) scanning, we screened out the microsatellite loci for determining the genetic characteristics of Chinese experimental chickens, ducks, geese, and pigeons. The panels of loci selected in our research provide a good choice for genetic monitoring of the population genetic diversity of Chinese native experimental chickens, ducks, geese, and ducks.
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