Development and Validation of a 5K Liquid Chip for Identifying Cashmere Goat Populations in Inner Mongolia Autonomous Region

(1) Background: Cashmere goats, as one of the characteristic species, are rich in genetic resources. Protecting and rationally utilizing these genetic resources is of great significance for the genetic improvement of cashmere goats. (2) Methods: In this study, tissue samples were collected from <i>Inner Mongolia white cashmere goats</i>, which included the Arbas type (<i>ARBS</i>); Erlangshan type (<i>ELS</i>); Alashan type (<i>ALS</i>), <i>Hanshan white cashmere goats</i> (<i>HS</i>), and <i>Ujimqin white cashmere goats</i> (<i>WZMQ</i>). Genomic DNA was extracted and subjected to high-depth genome resequencing. GenoBait technology was used for probe design and site optimization, followed by the synthesis of a low-density liquid phase chip. Finally, a total of 281 individuals from five cashmere goat populations in the Inner Mongolia Autonomous Region were randomly selected to verify the chip. (3) Results: The results showed that a total of 5002 SNP sites were finally screened and retained for the synthesis of the low-density liquid chip for identifying cashmere goats in Inner Mongolia Autonomous Region. Principal component analysis and phylogenetic tree construction indicated that the <i>ARBS</i>, <i>ELS</i>, and <i>ALS</i> populations were clustered into one category. (4) Conclusions: This chip can accurately identify the three breeds: <i>Inner Mongolia white cashmere goats</i>, <i>Hanshan white cashmere goats</i>, and <i>Ujimqin white cashmere goats</i>.