ArticleBMC genomic data2024
Development and verification of a 10K liquid chip for Hainan black goat based on genotyping by pinpoint sequencing of liquid captured targets.
Article in BMC genomic data, 2024. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 8 papers.
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Who cites it
8 citing papers in PubMed.
- Genetic Variants in the ATF6 Gene and Their Relationship with Milk-Quality Traits in Yaks.Animals : an open access journal from MDPI · 2025Article
- Comparative Analysis of Fecal Microbiota and Metabolomic Profiles in Male and Female Leizhou Goats Offered a 10% Crude Protein Diet Among Four Energy Levels.Animals : an open access journal from MDPI · 2025Article
- Development and Application of a 40 K Liquid Capture Chip for Beef Cattle.Animals : an open access journal from MDPI · 2025Article
- Design and verification of a 25 K multiple-SNP liquid-capture chip by target sequencing for dairy goat.BMC genomics · 2025Article
- Development of a 101.6K liquid-phased probe for GWAS and genomic selection in pine wilt disease-resistance breeding in Masson pine.The plant genome · 2025Article
- Heat Stress Impairs Endometrial Function During Implantation by Regulating Autophagy in Hainan Black Goat.Animals : an open access journal from MDPI · 2024Article
- Article
- Study on Single Nucleotide Polymorphism ofFoods (Basel, Switzerland) · 2024Article
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Authors and funding
12 authors.
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Abstract
backgroundChina has thousands years of goat breeding and abundant goat genetic resources. Additionally, the Hainan black goat is one of the high-quality local goat breeds in China. In order to conserve the germplasm resources of the Hainan black goat, facilitate its genetic improvement and further protect the genetic diversity of goats, it is urgent to develop a single nucleotide polymorphism (SNP) chip for Hainan black goat.
resultsIn this study, we aimed to design a 10K liquid chip for Hainan black goat based on genotyping by pinpoint sequencing of liquid captured targets (cGPS). A total of 45,588 candidate SNP sites were obtained, 10,677 of which representative SNP sites were selected to design probes, which finally covered 9,993 intervals and formed a 10K cGPS liquid chip for Hainan black goat. To verify the 10K cGPS liquid chip, some southern Chinese goat breeds and a sheep breed with similar phenotype to the Hainan black goat were selected. A total of 104 samples were used to verify the clustering ability of the 10K cGPS liquid chip for Hainan black goat. The results showed that the detection rate of sites was 97.34% -99.93%. 84.5% of SNP sites were polymorphic. The heterozygosity rate was 3.08%-36.80%. The depth of more than 99.4% sites was above 10X. The repetition rate was 99.66%-99.82%. The average consistency between cGPS liquid chip results and resequencing results was 85.58%. In addition, the phylogenetic tree clustering analysis verified that the SNP sites on the chip had better clustering ability.
conclusionThese results indicate that we have successfully realized the development and verification of the 10K cGPS liquid chip for Hainan black goat, which provides a useful tool for the genome analysis of Hainan black goat. Moreover, the 10K cGPS liquid chip is conducive to the research and protection of Hainan black goat germplasm resources and lays a solid foundation for its subsequent breeding work.
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