Development and verification of a 10K liquid chip for Hainan black goat based on genotyping by pinpoint sequencing of liquid captured targets.

Publisher: BioMed Central Country of Publication: England NLM ID: 101775394 Publication Model: Electronic Cited Medium: Internet ISSN: 2730-6844 (Electronic) Linking ISSN: 27306844 NLM ISO Abbreviation: BMC Genom Data Subsets: MEDLINE

Original Publication: London : BioMed Central, [2021]-

Goats*/genetics ; Polymorphism, Single Nucleotide*/genetics ; Oligonucleotide Array Sequence Analysis*/methods; Animals ; China ; Genotyping Techniques/methods ; Genotype ; Sequence Analysis, DNA/methods ; Breeding/methods

Background: China 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.
Results: In 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.
Conclusion: These 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.
(© 2024. The Author(s).)

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No. YSPTZX202153 This work was financially supported by Academician Innovation Platform Project of Hainan Province; No. YSPTZX202013 This work was financially supported by Academician Innovation Platform Project of Hainan Province; CARS-38 This work was financially supported by China Agriculture Research System of MOF and MARA; ZY2022HN09 This work was financially supported by Special Funding Projects for Local Science and Technology Development Guided by the Central Committee; ZDYF2021XDNY174 This work was financially supported by Hainan Province key research and development project

Keywords: Genotyping; Hainan black goat; Liquid chip; Targeted sequencing

Date Created: 20240507 Date Completed: 20240508 Latest Revision: 20240509

20240509

PMC11075337

10.1186/s12863-024-01228-8

38714950