The novel SNPs of leptin gene and their associations with growth traits in Chinese Nanjiang Yellow goat

• Six novel SNPs were detected in the caprine LEP gene.
• Our study confirmed the association between LEP SNPs and growth traits in NJ goats.
• Obvious linkage disequilibrium block was revealed in cultured goat breeds.

The leptin (LEP) gene encodes a protein that greatly affects the regulation of body weight, energy balance, and food intake in mammals. The objective of the present work was to identify genetic variants of the caprine LEP gene in 411 individuals from five Chinese goat breeds. Six novel single nucleotide polymorphisms (SNPs) (g.117 T > C, g.1642G > A, g.2883G > A, g.3053 T > C, g.3190G > A, and g.3314 T > C) were detected using DNA sequencing. A chi-squared (χ2) test showed that all of the LEP SNPs were in Hardy–Weinberg equilibrium in the studied population (P > 0.05). Six common haplotypes were identified in the five goat populations, with frequencies ranging from 0.083 to 0.244. The r2 linkage disequilibrium plot of the LEP SNPs indicated linkage disequilibrium only in the cultured breeds (NJ and JY). Statistical analysis revealed that all of the six SNPs of the LEP gene were associated with growth traits. The individuals with the GG genotype at g.1642G > A and g.3190G > A loci showed higher birth weight (2.38 ± 0.03, 2.43 ± 0.05) and weight at 2 months of age (10.59 ± 0.16, 10.71 ± 0.26) than the A-bearing genotypes (AA or GA, P < 0.05). Our findings indicate that polymorphisms of the caprine LEP gene might be important genetic factors influencing growth traits, and these genetic markers may be useful for future marker-assisted selection programs in goat breeding and production.