Background: Finding molecular markers linked to quantitative trait loci is the first step in marker-assisted selection (MAS). Microsatellites are excellent molecular markers because of their large numbers, even distribution in the genome, and high polymorphism. In this study, the polymerisation effect of four microsatellites (OarAE101, BM1329, BM143, and LSCV043) on litter size was analysed using microsatellite markers and pedigrees.

Results: The results indicate that the polymerisation effect of four microsatellite loci significantly affected the litter size. E₅E₁₀F₂F₆G₁G₅H₆H₁₁ and E₃E₈F₅F₇G₁G₅H₃H₉ had the highest and lowest litter sizes in the F2 generation, respectively. The polymerisation effect value (v) of the E₅E₁₀ genotype was 3.18% higher than that of the E₂E₇ genotype. The v of genotype F₂F₆ was 14.47% higher than that of the F₅F₇ genotype. The v of genotype G₁G₅ was 58.99% higher than that of the G₂G₇ genotype. The v of the H₆H₁₁ genotype was 5.60% to 49.74% higher than those of the H₄H₁₀ and H₁H₇ genotypes. The v of the H₃H₉ genotype was 17.22% higher than that of the H₁H₇ genotype.

Conclusions: The results of the present study are vital to improving the reproductive performance in goat breeds MAS.