Investigation of a Rare CSN1S101 Allele in Goats Using Allele-Specific PCR and Mathematical Expectation Analysis

The <i>casein alpha s1</i> (<i>CSN1S1</i>) gene plays an important role in milk protein synthesis and has been associated with milk quality and calcium-related physiological processes in mammals. To date, 19 <i>CSN1S1</i> variants have been reported. Among them, the <i>CSN1S1</i>⁰¹ allele has been described as a key "null" variant that may influence goat milk production traits through its effect on <i>CSN1S1</i> gene expression. However, the association between this allele and economically important traits in goats remains poorly understood. Therefore, the present study aimed to investigate the <i>CSN1S1</i>⁰¹ allele in goats using economical and rapid approaches, including mathematical expectation (ME) analysis and allele-specific PCR (AS-PCR), and to evaluate its association with economic traits in Chinese goat breeds. A total of 2319 goats from 11 breeds were analyzed. Compared with the "0" allele, the "1" allele showed a higher frequency across all populations and exhibited low genetic diversity. Significant associations were detected between <i>CSN1S1</i>⁰¹ genotypes and body length, third parity, and average kidding number in Laoshan dairy goats (<i>p</i> < 0.05). In addition, the low-frequency distribution of the <i>CSN1S1</i> "0" allele was further confirmed. Overall, this study provides population-based association evidence supporting the consideration of <i>CSN1S1</i>⁰¹ genetic variation in goat breeding programs.