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

## TL;DR

This study examines a rare CSN1S101 allele in Chinese goats and finds it is linked to traits like body length and litter size, especially in Laoshan dairy goats.

## Contribution

The study introduces a cost-effective method to genotype the CSN1S101 allele and identifies its associations with economically important traits in goats.

## Key findings

- The '1' allele of CSN1S101 is more common than the '0' allele across 11 Chinese goat breeds.
- CSN1S101 genotypes are significantly associated with body length and litter size in Laoshan dairy goats.
- The '0' allele of CSN1S101 occurs at low frequency, indicating limited genetic diversity at this locus.

## Abstract

The casein alpha s1 (CSN1S1) gene is a critical milk protein locus in goats, characterized by extensive genetic polymorphism. The CSN1S101 allele is a key ‘null’ variant. However, its distribution across diverse breeds and large populations remains unclear. Furthermore, its associations with economic traits have not been fully elucidated. In this study, a cost-effective genotyping approach was employed to screen 2319 goats from 11 Chinese breeds for the CSN1S101 allele. Our results show that the “1” allele predominates across all populations, whereas the “0” allele occurs at a low frequency, indicating limited genetic diversity at this locus. Association analysis revealed that CSN1S101 genotypes are significantly correlated with body length, third-parity litter size, and average litter size, specifically in Laoshan dairy goats. This study provides important evidence for the association of CSN1S101 genetic variation within goat populations.

The casein alpha s1 (CSN1S1) 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 CSN1S1 variants have been reported. Among them, the CSN1S101 allele has been described as a key “null” variant that may influence goat milk production traits through its effect on CSN1S1 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 CSN1S101 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 CSN1S101 genotypes and body length, third parity, and average kidding number in Laoshan dairy goats (p < 0.05). In addition, the low-frequency distribution of the CSN1S1 “0” allele was further confirmed. Overall, this study provides population-based association evidence supporting the consideration of CSN1S101 genetic variation in goat breeding programs.